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1994

Los Baños, Laguna, Philippines
Mailing address: P.O. Box 933, Manila 1099, Philippines
The International Rice Research Institute (IRRI) was established in 1960 by the Ford
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©International Rice Research Institute 1994
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Suggested citation:
Kirk, G J D, ed. (1994) Rice roots: nutrient and water use. Selected papers from the
International Rice Research Conference. International Rice Research Institute, P.O.
Box 933, Manila 1099, Philippines.

ISBN 971-22-0050-7
Contents

Foreword
The rice root-soil interface 1
G.J.D. KIRK, J.L. SOLIVAS, AND C.B.M. BEGG

Root growth and nitrogen uptake in rice: concepts for modeling 11
H.F.M. TEN BERGE, T.M. THIYAGARAIAN, B. MISHRA, K.S. RAO, AND R.N. DASH

Genetic variation in nitrogen uptake by rice and the effects of management
and soil fertility 29
P.C. STA. CRUZ AND G. WADA

Use of molecular markers to evaluate rice genetic variation in associative
N2 fixation, N uptake, and N use efficiency 43
P. WU, J.K. LADHA, S.R. McCOUCH, AND S.B. TENG

Rainfed lowland rice roots: soil and hydrological effects 55
PRADEEP K. SHARMA, G. PANTUWAN, K.T. INGRAM, AND S.K. DE DATTA

Rice root traits for drought resistance and their genetic variation 67
K.T. INGRAM, F.D. BUENO, O.S. NAMUCO, E.B. YAMBAO, AND C.A. BEYROUTY

Use of molecular markers to exploit rice root traits for drought tolerance 79
H.T. NGUYEN, J.D. RAY, AND LONG-XI YU
Foreword

The rice plant invests up to 60% of its energy as carbon in its root system. However,
the proportion of research effort devoted to the root system has been much smaller than
this, and consequently our understanding of the rice roots and their function in the
capture of nutrients and water lags behind our understanding of the rest of the plant.
This is particularly so for rice, compared with other cereals, because the rice plant's
ability to grow under waterlogged soil conditions arises from morphological and
physiological adaptations in its roots. These adaptations have important consequences
for nutrient and water uptake.
A greater understanding of the root system is now needed to support efforts to
increase rice yield potential and improve the productivity of resources. As part of the
1992 International Rice Research Conference, a symposium on rice roots and the
uptake of nutrients and water was held to review present knowledge and to develop
recommendations for future research. The papers included here were reviewed and
revised on the basis of the discussions during the symposium. It is hoped that they will
serve as a benchmark on the topic for some time to come.

Klaus Lampe
Director General
The rice root-soil interface
G.J.D. Kirk, J.L. Solivas, and C.B.M. Begg

Models and experimental studies of the rhizosphere of rice plants growing in an-
aerobic soil show that two major processes lead to considerable acidification (1-2 pH
units) over a wide range of root and soil conditions. One process is the generation of
H+ in the oxidation of Fe 2+ by O2 released from the roots. The other is the release of
H+ from the roots to balance the excess intake of cations over anions, N being taken
up chiefly as NH 4+. CO2 exchange between the roots and soil has a much smaller
effect. The zone of root influence extends a few millimeters from the root surface.
Substantial differences are found along the root length and over time. The acidifica-
tion and oxidation cause increased sorption of NH4+ by soil solids, thereby impeding
the movement of N to absorbing root surfaces but may also cause solubilization and
enhanced uptake of soil P. Implications for nutrient management and the develop
ment of nutrient-efficient rice germplasm are discussed.

Rice roots growing in anaerobic soil can greatly modify the soil near them. As a result,
the soil as “seen” by the root is entirely different from the bulk soil, although it is the
latter whose properties we normally measure. Some important processes influenced by
conditions in the rice rhizosphere are listed in Table 1. This paper examines the extent
and dynamics of root-induced changes and their consequences for nutrient and toxin
dynamics.
Three main processes operate. First, release of O2 from roots and its reaction with
Fe2+ , generating acidity:

4 Fe2+ + O 2 + 10 H2O = 4 Fe(OH)3 + 8H+.

Secondly, because the roots take up a considerable excess of cations over anions (N
being taken up from anaerobic soil chiefly as NH 4+ ), they release H+ into the soil to
Table 1. Effects of rice rhizosphere conditions.

Variable or process affected Example

Concentration of toxic solute Fe2+
Concentration of major nutrient NH4+ , H2 PO4 - , K +
Concentration of minor nutrient Zn2+
N2 fixation Azospirillum
Nitrification Nitrosomonas
Invasion by pathogens
Methane oxidation

maintain electrical neutrality across the root-soil interface. Thirdly, because high
pressures of CO2 arise in anaerobic soil and within the roots, the roots may either
release CO2 or take it up from the soil, with corresponding changes in soil pH.
The root-influenced zone extends just a millimeter or so into the soil, but existing
experimental methods cannot analyze the soil with resolutions much finer than a
millimeter. Because of this and because the system involves the simultaneous opera-
tion of a series of complex, linked processes, we use simulation models in addition to
experiments.

Gas transport through rice roots
Gas transport through flooded soil is very slow, and therefore rice roots must supply
O2 to respiring tissues via internal gas channels, which are called aerenchyma. Some
of this internally transported O2 is lost to the surrounding soil. There is disagreement
about the extent of this loss and about whether or not it is beneficial to the plant. Direct
measurements of loss vary from several nmol (O2 )/dm2 (root surface) per s near the root
tips as measured with cylindrical polarigraphic electrodes (Armstrong et al 1991) to
one-hundredth of this for O 2 appearing in continuously replenished, O2 -free solutions
bathing whole root systems (Bedford et al 1991). The range is in part due to differences
in leakiness between different parts of the root system and in part due to differences in
the external O2 sink. In soil, the O2 sink is enhanced by diffusion of Fe2+ toward the root
and its reaction with O2 . The net O2 loss depends on the rates of diffusion and reaction.

Model of rice rhizosphere conditions
Ahmad and Nye (1990) have measured the kinetics of iron oxidation in reduced soil,
and Kirk et al (1990) have used this information to develop a model of the coupled
diffusion and reaction of O2 , Fe 2+, and acidity in reduced soil. The kinetic measure-
ments showed that, over periods of a few days, the main reaction is between Fe2+ and
O2 with formation of Fe(OH)3 and acidity. The rates are comparable to or exceed O2
consumption by microbes. The model predicts the diffusion of O2 into the soil; the
diffusion of Fe2+ toward the oxidation zone; the rate of formation and concentration
profile of the Fe(OH)3 formed; and the diffusion by acid-base transfer of the acidity
produced in the reaction.

2 Kirk et al
1. Simulated reactant profiles in the rhizosphere after different times. Parameter values given in
Kirk (1993).

The rice root-soil interface 3
Kirk (1993) has coupled this model, converted to the cylindrical geometry of a root
and its surrounding rhizosphere, to a model of gas transport through the root. The model
allows for axial diffusion of O2 and CO2 through the root and for differences with root
length and time in cortical porosity, respiration rates in different tissues, and root wall
gas permeability. It also allows for the development of short, fine laterals along the
primary roots; by the end of the vegetative phase, these may account for the majority
of the total root length though only a small percent of root mass. Having high surface
area to volume ratios, they tend to be very O2 -leaky.
Figure 1 shows the model’s predictions for a particular depth in the soil as a root
grows through it. The O2 pressure in the root cortex is held constant and the wall
permeability decreases as the root elongates. Thus the soil at the root surface is exposed
to a declining O 2 concentration with time. The mean O2 efflux from the rod, averaged
over the 10 d of simulation, is about 0.2 nmol (O2 )/dm2 (root) per s. The model shows
that substantial amounts of Fe are transferred toward the root surface and accumulate
as Fe(OH)3 . A zone of Fe 2+ depletion arises when oxidation is intense, but is rapidly
filled in by Fe 2+ continuing to diffuse into the depletion zone after the O2 supply has
decreased. Thus Fe accumulation continues after oxidation declines.
Of interest in the present context is the very large drop in pH which persists
throughout the period simulated. This is due to the combined effects of H+ generated

2. Simulated pH profiles in the rhizosphere after 10 d. Root wall permeability and cortical O 2
concentration held constant giving mean O2 efflux from root = 0.2 nmol/dm 2 per s; H+ efflux
from root = 1 nmol/dm 2 per s. Other parameter values as in Figure 1.

4 Kirk et al
in Fe2+ oxidation and H+ released from the root to balance ion intake. The model
predicts that CO2 is lost from the root to the soil near the root tip, but taken up by the
root near the base; the resultant CO2 concentration profiles in the soil are small. There
is an important interaction between the two sources of acidity which results in their
combined effect being greater than the sum of their individual effects (Fig. 2). This is
explained as follows. pH changes are propagated through soil by the movement of
conjugate acid-base pairs: acids from regions of low pH to high and bases in the
opposite direction (Nye 1986). The most important pairs are generally H 3O+-H2O and
H2CO3 (derived from CO2)-HCO3- . The relative importance of the pair H3O+-H2O is
greater at low pH and that of H2CO3-HCO3 at high pH. Therefore the net rate of soil
acidity diffusion is minimal in the pH range in which H3O+ and HCO3- concentrations
are both low. In this pH range, a flux of acid or base through the soil results in steep
pH gradients.
The predictions in Figures 1 and 2 are for conditions around aerenchymatous
primary roots, but the model predicts similar changes in the rhizospheres of fine lateral
roots. Laterals are presumably responsible for the bulk of nutrient uptake in lowland
rice because they comprise the bulk of the total root length. (Indeed, the reason they
comprise the bulk of the root length is the slow rate of movement of N and other
nutrients to root surfaces in anaerobic soil and the consequent need for a large surface
area per unit root mass.) Thus, it is conditions in the rhizospheres of laterals that we are
most concerned with.

Experimental measurements of rice rhizosphere conditions
To test these predictions, we developed an experimental method with which to measure
reactant concentration profiles near rice root surfaces (IRRI 1991). We grew rice
seedlings in nutrient solutions with their roots contained in 7.5-cm-diameter, l-mm-
thick nylon mesh bags so that the roots formed a continuous planar layer. Each root
plane was then sandwiched between cylinders of anaerobic soil connected to water
reservoirs, and the system sealed so that the only means of O2 transfer between the
atmosphere and soil was through the roots. The plants grew healthily in this system for
more than 2 wk without showing signs of stress. At intervals, the cylinders were sliced
into 0.2-mm sections parallel to the root plane, and each section analyzed for pH, Fe(II)
extractable with 1 M NH4OAc at pH 2.8, and Fe(III) extractable with 2 M H2SO4.
Figure 3 shows profiles of pH and Fe near the root plane after 10 d of root-soil
contact. A large quantity of Fe has been transferred toward the root plane and oxidized,
producing a zone of Fe(III) accumulation; there has been a very large acidification of
the soil within 4 mm of the root plane; the pH gradient is very steep at pH levels below
6. Control experiments with soil cylinders sealed together without roots indicated that
the seals were good and that the oxidation in the cylinders with roots was indeed largely
due to root-released O2.
The total quantity of acidity generated (estimated from the pH profile using the
independently measured pH buffer power of the reduced soil while undergoing
oxidation = 0.09 mmol/g per pH unit) was of the order of 3 mmol/cylinder, and that

The rice root-soil interface 5
3. Profiles of Fe(II), Fe(III), and pH in flooded soil exposed to a planar layer of rice roots for 10
d. Plant and soil characteristics given in IRRI (1991).

generated in Fe oxidation (the quantity of Fe(III) formed multiplied by 2—see reaction
stoichiometry given earlier) was of the order of 2 mmol/cylinder. Thus, by difference,
that due to cation-anion intake imbalance is 1 mmol/cylinder. The mean flux of O2
across the root plane required to oxidize this quantity of Fe is about 0.6 nmol/dm2 (root
plane) per s.
In experiments in which we exposed cylinders of the same anaerobic soil directly
to air, greater oxidation took place, but the concentration of Fe(III) at the air-exposed
surface was much smaller. This is because in the root plane experiments, the O2
concentration maintained by the roots at their surfaces was less than that in air, and
therefore the diffusion of O 2 into the soil was smaller and the movement of Fe2+ toward
the roots greater. Movement of the soil solution due to water uptake by the roots will
enhance this effect.

Consequences for nutrient uptake
Nitrogen
The ability of the soil-root system to meet the plant’s N demand depends both on the
ability of the roots to absorb N from the soil at their surfaces and on the rate of delivery

6 Kirk et al
of N to the root surfaces. For arable crops growing in fertile aerobic soil, the dominant
form of N taken up is NO3 - and it is sufficiently mobile in the soil that root morphology
and uptake properties do not limit uptake until soil N levels become very low (Drew
1990). But for lowland rice, the situation is entirely different: the dominant form of N
taken up is NH 4+, which is far less mobile.
The rate of NH4+ transport through the soil to root surfaces depends on its
distribution between the soil solid and solution, and this is largely determined by the
concentration of anions in solution (in accordance with electroneutrality), though
modified by the concentrations of other exchangeable cations. In most flooded soils,
HCO3- is the dominant anion (in aerobic soils, it is NO 3 - ) but its concentration will
decrease as the rhizosphere pH decreases, becoming negligible below about pH 5.5.
NH4 + mobility will be correspondingly decreased. This will be offset, to some extent,
by the effect of acidity on cation sorption, tending to decrease the NH4+ concentration
in the solid relative to that in solution, but exacerbated by the depletion of exchangeable
Fe 2+.

4. Effect of Fe 2+ oxidation in the rhizosphere on the distribution of exchangeable NH4+ between
the soil solid and solution. Numbers on curves are concentrations of noncarbonate anions in
solution. Other parameter values given in IRRI (1992).

The rice root-soil interface 7
Figure 4 gives predictions of a model of these effects. In the model, cation exchange
is governed by electroneutrality in the soil solution and solid and by equations for the
preferential sorption of divalent cations over monovalent ones (IRRI 1992). For each
mole of Fe2+ oxidized, 2 moles of H+ are produced, and these react with HCO3- and the
soil solid. The increase in acidity on the soil solid causes a proportionate decrease in
pH and an equal decrease in the equivalents of cations on the solid. The set of parameter
values used for Figure 4 represent a realistic mean.
It will be seen that rhizosphere oxidation may greatly decrease the fraction of mobile
NH4+ in the soil solution, particularly at low concentrations of anions in the soil, and
thereby greatly decrease N uptake. In addition, acidification may decrease the rates of
microbially mediated processes affecting the N supply, such as mineralization of
organic N.

Phosphorus
In contrast to the effect on N uptake, rhizosphere oxidation and acidification may
enhance solubilization and uptake of P. This is important because, in many rice soils,
flooding results in a decrease in P mobility following an initial release, and rice plants
consequently depend on root-induced solubilization for the bulk of their P.
We measured concentration profiles of extractable P fractions in the soil near roots,
using the same root-plane technique. The fractions, measured sequentially, were anion
exchange resin, alkali (subdivided into inorganic and organic), acid, and residual. The
results showed a large depletion of acid-soluble and residual P in the zone of Fe
oxidation and acidification, 0-5 mm from the root plane (Fig. 5). Part of the solubilized
P appeared closer to the root plane in the alkali-soluble P pool, but the bulk was
absorbed by the roots. The quantity of P taken up by the plants during the experiment,
calculated from the increase in plant dry matter multiplied by the mean % P content,
was about 25 µmol. This was roughly matched by the net depletion of acid-soluble and
residual soil P. The quantity contained in the freely available resin pool was negligible
in comparison with plant demand.
In flooded soils, a large part of the P is often acid-soluble, being associated with
metal carbonates and hydroxides formed following soil reduction and with other
negatively charged surfaces through exchangeable cations. The alkali-soluble pool
would include that associated with Fe(OH)3 formed in the oxidation reaction and with
root-derived organic material. Evidently, the reimmobilization of acid-solubilized P
on Fe(OH)3 and root-derived organic matter did not prevent access of P to the root
surfaces.
By contrast, we found that the bulk of P taken up by rice growing in aerobic soil was
drawn from an alkali-soluble pool (Hedley et al 1994). To solubilize this P, the roots
would need an alternative mechanism. Current evidence suggests that this mechanism
involves the release of low molecular weight organic acid anions such as citrate. These
must leave the root cells in the dissociated salt form, not the acid form, because the
cytoplasmic pH (6-7) is well above the pKs of the acids in question. Therefore, from
charge-balance considerations, in anaerobic soil where N is taken up as NH4+ , export
of organic acid anions would be difficult.

8 Kirk et al
5. Profiles of extractable P fractions in flooded soil exposed to a planar layer of rice roots for
10 d. Numbers of curves are means of values in the soil bulk.

The potential for manipulating root-induced P solubilization to develop more P-
efficient rice cultivars is discussed by Kirk et al (1993).

Discussion
For reasonable rates of nutrient uptake and O2 loss from rice roots, acidification and
Fe 2+ oxidation in the rhizosphere can result in impeded N uptake but enhanced P
uptake.
These findings have interesting consequences for the relation between root traits
and nutrient uptake efficiency under different conditions. In conditions in which N is
the limiting nutrient, root porosity and wall permeability should be just sufficient to

The rice root-soil interface 9
meet the root’s respirsatory O2 requirements and perhaps to oxidize some of the toxic
products of anaerobic respiration in the soil. But in P-limited conditions, rhizosphere
oxidation and acidification would be desirable and thus a more aerenchymatous and
O2-leaky root would be wanted. Similar arguments should apply to K, which should
be immobilized like NH4+, and Zn, which should be mobilized like P.

References cited
Ahmad A R, Nye P H (1990) Coupled diffusion and oxidation of ferrous iron in soils. I. Kinetics
of oxygenation of ferrous iron in soil suspension. J. Soil Sci. 44:395-409.
Armstrong W, Justin SHFW, Beckett PM, Lythe S (1991) Root adaptation to soil waterlogging.
Aquatic Bot. 39:57-73.
Bedford B L, Bouldin D R, Beliveau B D (1991) Net oxygen and carbon dioxide balances in
solutions bathing roots of wetland plants. J. Ecol. 79:943-959.
Drew M C (1990) Root function, development, growth and mineral nutrition. Pages 35-57 in The
rhizosphere. J.M. Lynch, ed. Wiley-Interscience, Chichester.
Hedley M J, Kirk G J D, Santos M B (1994) Phosphorus efficiency and the forms of soil
phosphorus utilized by upland rice cultivars. Plant Soil 158: 53-62.
IRRI—International Rice Research Institute (1991) Program report for 1990. P.O. Box 933,
Manila, Philippines. p. 203-205.
IRRI—International Rice Research Institute (1992) Program report for 1991. P.O. Box 933,
Manila, Philippines. p. 198-199.
Kirk G J D (1993) Root ventilation, rhizosphere modification, and nutrient uptake by rice. Pages
221-232 in Systems approaches for agricultural development. F.W.T. Penning de Vries, P.S.
Teng, and K. Metselaar, eds. Kluwer Academic Publishers, Dordrecht, The Netherlands.
Kirk G J D, Ahmad A R, Nye P H (1990) Coupled diffusion and oxidation of ferrous iron in soils.
II. A model of the diffusion and reaction of Fe 2+, H+ and HCO 3- in soils and a sensitivity
analysis of the model. J. Soil Sci. 44:411-431.
Kirk G J D, Hedley M J, Bouldin D R (1993) Phosphorus efficiency in upland rice cultivars.
Pages 279-295 in Papers and reports on the management of acid soils (IBSRAM/ASIALAND).
Network Document No. 6. International Board for Soil Research and Management, Bang-
kok.
Nye P H (1986) Acid-base changes in the rhizosphere. Pages 129-153 in Advances in plant
nutrition. Vol. 2. P.B. Tinker and A. Lauchli, eds. Praeger, New York.

Notes
Authors’ address: G.J.D. Kirk, J.L.Solivas, and C.B.M. Begg, International Rice Research
Institute, P.O. Box 933, Manila, Philippines
Citation information: Kirk G J D, ed. (1994) Rice roots: nutrient and water use. International
Rice Research Institute, P.O. Box 933, Manila, Philippines.

10 Kirk et al
Root growth and nitrogen
uptake in rice: concepts
for modeling
H.F.M. ten Berge, T.M. Thiyagarajan, B. Mishra,
K.S. Rao, and R.N. Dash

Data from field experiments are used to examine the rate-limiting step in nitrogen (N)
uptake by lowland rice. For the vegetative phase over a wide range of fertilizer levels,
N uptake per ha (N c) and uptake rates per ha (dNc/dt) increased with the amount of
N applied (A). dNc /dt did not reach an upper limit. Increases in dNc /dt with A were
more than in proportion to increases in root mass (Mr). After panicle initiation (PI),
there was no consistent relation between A, dNc /dt, and Mr. The root-shoot ratio
decreased with development stages and was independent of A at any stage. Up to
PI, Mr and the rate of N absorption per unit Mr both increased with A to the extent
that fertilizer N recovery increased as A increased. An approximate calculation
showed that changes in cumulative recovery with A could be explained by differences
in Mr. Two hypotheses to explain dNc /dt during the pre-PI stage were consistent with
the experimental data: 1) the uptake rate was diffusion-limited and proportional to
the concentration of NH4+ in the root zone bulk soil solution [NH4+ ] and to root length
density (RLD), and, 2) the uptake rate was independent of [NH4+ ] and governed by
the plant internal N content through a mechanism superimposed on the effect of Mr.
Total N uptake over the season was a linear function of A. This linearity was the
result of a positive feedback between Nc and dN c/dt during vegetative growth,
followed by a negative or neutral feedback after PI.

Much work on N in rice has focused on loss processes in relation to floodwater and soil
chemistry and biology (e.g., De Datta and Patrick 1986), and detailed physicochemical
models of these processes have recently become available (Rachhpal-Singh and Kirk
1993 a,b). Also, the utilization of N by the crop once absorbed and its effects on dry
matter production are now reasonably well-understood (Yoshida 1981, Kropff et al
1993). However, the process of N uptake by the root system has received relatively
little attention. An understanding of this is essential for the development of a complete
model of the fate of N in rice production systems.
The supply of N to a single root depends on the rate of transport from the bulk soil
solution to the root surface. For lowland rice, this transport is principally by diffusion
(Makarim et al 1991). The maximum rate of diffusion is reached for “zero-sink”
conditions in which the root maintains a negligibly low concentration at its surface,
thus maximizing the concentration gradient for a given bulk concentration (de Willigen
and van Noordwijk 1987).
For an entire root system, “supply” is a more complex group of processes. Roots are
unevenly distributed and the entire root system is not necessarily equally active. Good
mathematical models exist to integrate knowledge on the various physiological,
physical, and physicochemical processes affecting uptake. Taking single root behavior
as a starting point, the uptake model of de Willigen and van Noordwijk (1987, 1991)
assesses nutrient uptake rate as a function of soil conditions (water content, bulk
nutrient concentration, and nutrient diffusivity), root length density (RLD), and
parameters specifying “crop demand” and maximum flux density over the root surface.
But parameterization of such mechanistic models is difficult. The measurement of
RLD in rice under field conditions is virtually impossible due to very fine branching
(Yoshida 1981, Drenth et al 1991) and strong spatial RLD gradients near the soil
surface. Moreover, the roles of different root fractions in uptake are unknown
(Makarim et a1 1991), and we have little information about maximum nutrient flux
densities across rice root surfaces under either controlled or field conditions, or about
the dependence of root nutrient uptake characteristics on soil and crop conditions. Also,
the concept of “demand” is not well-defined, and if the crop’s nutritional status affects
root uptake characteristics, demand turns out to directly affect supply itself.
The purpose of this study was to determine what measurable variables must be
considered to describe N uptake at different stages of lowland rice crop development,
as a first step toward a mechanistic description of the system.

Materials and methods
Three data sets were collected in experiments at three locations in India, with which
to test hypotheses on the relation between N uptake, RLD, and [NH4+].
1. The TNAU-TNRRI set (Thiyagarajan et a1 1991) was collected at the Tamil Nadu
Rice Research Institute, Aduthurai, Tamil Nadu, during the late wet season (WS)
of 1988-89. The 39-d-old seedlings of ADT39 were transplanted on 10 Dec at 20-
× 10-cm spacing, at two seedlings per hill, in a randomized block design with four
replications. Nitrogen was applied as urea at 0, 100, 200, 300, and 400 kg N/ha
in four splits: 50% basal (i.e., incorporated at transplanting), the rest in equal splits
at active tillering (26 d after transplanting [DAT]), at panicle initiation (PI) (48
DAT), and at 62 DAT. Flowering varied from 53 DAT (0 kg N treatment) to 63
DAT (400 kg N), and maturity from 89 DAT (0 kg N) to 97 DAT (400 kg N). Plant
samples were collected at 18, 25, 32, 39, 46, 53, 63, 81, 89, and 97 DAT. All
samples were split; dry weight and N content of leaves, stems plus sheaths,
panicles, and roots were determined.

12 ten Berge et al
2. The PUAT set was collected at G.B. Pant University of Agriculture and Technol-
ogy, Pantnagar, Uttar Pradesh, during the 1987 WS. Twenty-nine-d-old seedlings
of Pant Dhan 4 were transplanted on 9 Jul at 20- x 100-cm spacing, at two
seedlings per hill, in a randomized block design with four replications. Nitrogen
was applied as urea at 0, 60, 120, 180, and 240 kg N/ha in three splits: 50% basal,
25% topdressed at 27 DAT (active tillering), and 25% topdressed at 51 DAT (PI).
The 60 kg N/ha treatment received no second topdressing, but received 50% of
the total dose at 27 DAT. Flowering occurred at 72 DAT and maturity at 108 DAT.
Plant samples were collected at 25, 49, 72, and 108 DAT. Dry mass and N contents
of leaves, stems plus sheaths, grains, and roots were measured for all harvests,
except root mass which was omitted at maturity.
3. The CRRI set was collected at the Central Rice Research Institute, Cuttack,
Orissa, during the 1990 dry season (DS). Thirty-eight-d-old seedlings of IR36
were transplanted on 25 Jan at 15- x 15-cm spacing, at two seedlings per hill, in
a randomized block design with four replications. Nitrogen was applied as urea
at 0, 50, 100, and 150 kg N/ha in three splits: 50% basal, 25% at 20 DAT, and 25%
at 53 DAT (1-2 wk after PI). The crop flowered at 70 DAT and was harvested at
92 DAT. Plant samples were collected at 20, 30, 40, 50, 70, and 92 DAT and
analyzed as above. Nitrogen in plant samples was determined only at 20, 50, and
70 DAT.

Results
N uptake as a function of N application
Tables 1-3 give the results for TNAU-TNFUU, PUAT, and CRRI, respectively. The
maximum amount of N accumulated in the crop Nc (kg/ha), as a function of the amount

1. Relation between maximum total crop (leaves, stems, roots, and panicles) N uptake (N,) and
N application in the three experiments. Maximum Nc occurred on 63 DAT at TNAU-TNRRI,
on 108 DAT at PUAT, and on 70 DAT at CRRI.

Root growth and nitrogen uptake in rice: concepts for modeling 13
Table 1. Total crop (leaves, stems, roots, and panicles) N uptake and root and shoot mass on
different days after transplanting (DAT). TNAU-TNRRI, Aduthurai, 1988-89 WS.

N application level (kg N/ha)
DAT
0 100 200 300 400

Crop N uptake (kg/ha)

0 2.2 2.2 2.2 2.2 2.2
18 13.9 22.9 27.8 38.2 49.6
25 17.0 38.5 64.8 91.5 110.6
32 28.1 53.7 81.9 128.2 159.9
39 37.9 60.7 97.0 155.9 201.4
46 41.7 71.1 108.9 171.1 212.7
53 43.5 88.0 130.8 182.6 246.2
63 41.8 96.0 165.6 240.4 303.8
81 52.5 108.0 167.0 218.0 278.0

Root mass (kg/ha)

0 19 19 19 19 19
18 260 377 491 50 521
25 326 494 620 710 775
32 370 590 764 925 1,030
39 421 672 880 1,150 1,250
46 463 734 930 1,324 1,525
53 482 848 1,120 1,502 1,750
63 537 836 1,183 1,790 2,003
81 530 836 997 1,507 1,968

Shoot mass (kg/ha)

0 85 85 85 85 85
18 706 916 984 1,211 1,370
25 1,184 1,745 2,341 2,738 3,050
32 1,880 2,757 3,853 4,465 5,150
39 2,501 3,593 5,011 5,952 7,184
46 3,058 4,422 6,132 7,371 8,636
53 3,566 5,532 7,390 8,986 10,443
63 4,303 7,806 9,809 12,514 13,669
81 5,478 9,891 11,856 13,660 14,671

of N applied A (kg/ha), is shown in Figure 1 for the different sites. At TNAU-TNRRI,
the point of maximum N accumulation coincided with flowering, but at PUAT, it
occurred at harvest. (For CRRI, Nc is not known after 70 DAT, but the small difference
in Nc between 50 and 70 DAT suggests that uptake ceased at around 50 DAT.)
Nitrogen uptake in the reference treatments (A = 0) varied from 50 to 60 kg N/ha.
If these values represent the amount of soil-supplied N in the other treatments (A > 0),
the fertilizer N recovery over the season was around 55% at TNAU-TNRRI, 40-55%
at PUAT, and 60-65% at CRRI. Only at PUAT did overall N recovery decrease with
increasing A. The linearity of Nc(A) found at the other two sites is consistent with
findings of other studies. For numerous experiments in Indonesia, Van Keulen (1977)
showed that Nc(A) is usually linear up to high N application levels.

14 ten Berge et al
Table 2. Total crop (leaves, stems, roots, and panicles) N uptake and root and shoot mass on
different days after transplanting (DAT). PUAT, Pantnagar, 1987 WS.

N application level (kg N/ha)
DAT
0 60 120 180 240

Crop N uptake (kg/ha)

0 0.9 0.9 0.9 0.9 0.9
25 12.8 19.1 25.3 32.6 41.1
49 25.5 51.8 70.4 98.4 117.4
72 43.3 76.1 100.1 119.3 131.1
108a 51.7 77.7 106.1 123.7 136.3

Root mass (kg/ha)

0 13 13 13 13 13
25 317 349 414 479 520
49 638 976 1,034 1,276 1,500
72 1,016 1,434 1,566 1,806 2,041
108 ndb nd nd nd nd

Shoot mass (kg/ha)

0 32 32 32 32 32
25 853 1,187 1,481 1,797 2,043
49 2,599 4,295 5,393 6,813 7,774
72 6,502 9,570 10,887 11,722 12,485
108 4,910 6,737 7,741 9,035 9,978

a Values for 108 DAT do not include root N. b nd = not determined.

2. Relation between maximum root mass M, and N application in the three experiments.
Maximum M, occurred on 63 DAT at TNAU-TNRRI, 72 DAT at PUAT, and 50 DAT at CRRI.

Root growth and nitrogen uptake in rice: concepts for modeling 15
Table 3. Total crop (leaves, stems, roots, and panicles) N uptake and root and shoot mass on
different days after transplanting (DAT). CRRI, Cuttack, 1990 DS.

N application level (kg/ha)
DAT
0 50 100 150
I
Crop N uptake (kg/ha)

20 22.0 20.3 26.0 30.1
50 57.8 85.5 119.9 152.5
70 60.5 90.2 120.2 160.8

Root mass (kg/ha)

20 223 237 286 333
30 323 523 539 561
40 605 743 979 1,078
50 602 905 1,116 1,317
70 500 861 952 932
92 500 820 858 899

Shoot mass (kg/ha)

20 539 559 671 707
30 1,185 1,337 1,768 1,895
40 2,120 2,654 3,723 4,161
50 3,292 4,290 5,522 6,100
70 4,976 6,421 8,117 9,958
92 5,645 7,960 10,020 10,085

Root biomass and root-shoot ratio as a function of N application
The measured values of root biomass, Mr (kg/ha), are included in Tables 1-3. Mr is
given in Figure 2 as a function of A, at the time when root mass reached its maximum.
In all three experiments, root biomass generally increased linearly with A up to the
highest application levels. Maximum root biomass values of 2000 kg/ha were found
at TNAU-TNRRI and PUAT.
The root-shoot ratio at all stages was independent of A at TNAU and CRRI, but not
for young plants at PUAT (Fig. 3). Although the pattern of decreasing ratio with time
was found in all cases, values of this ratio for given development stages differed across
sites.

Discussion
We need to know what the rate-limiting step or steps in N uptake are in order to decide
what process or processes must be modeled in detail. At one extreme, the root system
might be so efficient at extracting N from the soil that the rate of uptake is essentially
independent of root and soil characteristics until the soil N concentration falls to a low
level. At the other extreme, the rate of transport of N to root surfaces might be so slow
that uptake is solely determined by the rate of transport-asgoverned by the soil
transport characteristics and the N concentration-and the root surface area or RLD.

16 ten Berge et al
3. Changes in root-shoot ratios with time at different N application levels in the three
experiments.

In between these extremes, root characteristics would have a greater or lesser effect on
uptake depending on how well the plant is able to regulate the root system’s
characteristics to match uptake with the rate of N transport through the soil. Clearly,
as the crop grows and soil N becomes depleted, the rate-controlling step may change,
and a complex model would be required to describe all eventualities. However, our
purpose here is to identify the most critical process or processes and thereby simplify
modeling as far as possible.
In the following sections, we use our experimental results to test various hypotheses
about rate-limiting steps. In the absence of detailed measurements of the changes in

Root growth and nitrogen uptake in rice: concepts for modeling 17
[NH4+] and RLD with soil depth and time (z,t), we test the hypotheses with our data
on Nc(t) and total root mass, Mr (t), by examining dNc/dt vs t, (dNc/dt)/Mr vs t, and
fertilizer N recovery. Two assumptions are made: a) that N is taken up exclusively as
NH4+; and (b) that within each experiment, RLD is proportional to M r, i.e., root length
per unit root mass is independent of N application.

Hypothesis 1: If [NH4+] is above a critical value, the uptake rate is independent of the
amount of N applied.

This hypothesis addresses the first extreme previously described. In this case, increases
in Nc with A would be due to N application extending the period over which [NH4+]
is above the critical value. To model this situation, we would only need information
on the period when [NH4+] exceeds the critical value in some part of the root zone.
We test the hypothesis by comparing rates of N uptake. Ideally, we need instanta-
neous uptake rates, but we necessarily only have average values over the time between
sampling events (sampling intervals). This is awkward because differences in time
averaged dNc/dt with A could be due to different durations of uptake at the level that
is independent of [NH4+], (dNc/dt)max , within the sampling interval, as opposed to
differences in (dNc/dt)max per se. The problem is avoided by comparing two consecu-
tive sampling intervals that are not interrupted by N application. If dNc/dt depends on
A in both such intervals, a variable duration of (dNc/dt)max is not responsible and
Hypothesis 1 can be rejected. Only the TNAU-TNRRI data set satisfies the require-
ments for such an analysis.
In the TNAU-TNRRI data, dNc/dt increases with A, both during the 0-18 and 18-
25 DAT periods (from data in Table 1). This finding is supported by other reported
data—e.g., Schnier et al (1990) for both direct seeded and transplanted rice and
Makarim et al(1991) for transplanted rice. We therefore reject Hypothesis 1.

Hypothesis 2: If [NH4+] is above a critical value, the uptake rate is proportional to RLD
but is otherwise independent of [NH4+].

This hypothesis addresses a situation in which uptake is governed by A only in so far
as it influences plant growth and RLD through the plant internal N content, A model
would then need to contain information on the relation between RLD and the plant
internal N content, on the volume of soil in which [NH4+] exceeds the critical value
at a particular time, and on RLD in these zones.
Figure 4 shows uptake rates per unit root mass, (dNc/dt)/Mr, at different times for
the period from transplanting to PI in the experiments at TNAU-TNRRI. (dNc/dt is
averaged over the sampling interval; M r is estimated for the midpoint of sampling
intervals by interpolation.) The figure shows that (dNc/dt)/Mr increased with A in
young plants but decreased with crop age. A similar pattern was found for the other data
sets. Values of (dN c/dt)/Mr of up to 13 (TNAU-TNRRI), 3 (PUAT), and 5 (CRRI) mg/
kg per d were found in young plants. These are probably not maximum values, as they
are likely to occur immediately after N application. The decrease in (dNc/dt)/Mr with

18 ten Berge et al
4. N uptake rates per unit root mass at TNAU-TNRFU. Numbers on curves are N application
levels (kg N/ha).

time is attributed to three possible causes: the decreasing [NH4+ ] as N is absorbed by
the crop or otherwise removed from the system; a decrease in the fraction of the root
system that is active or in the maximum uptake rate per unit root length as the crop ages;
and the shallow penetration of N from topdressed urea, which leaves most of the root
mass unexposed to fertilizer N.
Since Hypothesis 1 is invalid, the dependence of (dNc /dt)/Mr on A found in all three
data sets for the period from transplanting to PI must be due to differences in
instantaneous uptake rates, as opposed to differences in maximal uptake duration.
Therefore Hypothesis 2 also appears to be invalid.
But as a result of continuous root growth during the intervals between sampling
times, the exact quantity of root mass responsible for the difference in Nc measured
over a particular sampling interval is unknown. Therefore, we need to confirm that
(dNc /dt)/Mr did indeed increase with A, and we do this as follows.
We define coefficients RN and RM such that:

(1)

and

(2)

where D Nc is the change in N, over a particular sampling interval and subscript i
indicates the fertilizer treatment. The ratios RM,i and R N,i thus compare treatment i with
the next lower N level, i-1. Unlike absolute root mass, Mr, the relative root mass, RM,

Root growth and nitrogen uptake in rice: concepts for modeling 19
is fairly constant over time, so its value at the end of the sampling interval can be used
for the entire interval.
Now, if R N,i > RM,i , the root system of the crop under treatment i takes up more N
per unit root mass per time interval than under i-1. This appears to be the case for
virtually all i’s in all the data sets, until after PI (Fig. 5). For the sampling events after
PI, RN is often smaller than RM, implying that uptake did not increase in proportion to
root mass with an increment in A.
In summary, we conclude that, irrespective of the effect of N application on root
growth, uptake per unit root mass increases with N application level. This is found to
be true in all three experiments and at all A(i). We therefore reject Hypothesis 2.

Hypothesis 3: Uptake rates are linearly related to both [NH4+ ] and RLD.

This hypothesis addresses a situation in which uptake is solely limited by N transport
to root surfaces by diffusion. We use analyses of fertilizer recovery to test this
hypothesis. Fertilizer recovery depends on the rate of uptake compared with the rate
of loss processes and is expected to be closely linked to RLD and uptake rate per unit
root length.
Nc (A) is plotted for different sampling times in Figure 6. Since urea was applied in
different splits, the total amount A(t,i) applied by time t in treatment i is a cumulative
value. The leftmost points on the curves apply to treatment i=0 (no fertilizer); the next
point on each curve applies to i=l; and so forth. (The notation At(i) is used when
evaluating a response across i levels, at fixed t.)
Three types of recovery can be evaluated from these graphs. Cumulative recovery
at A in Figure 6a is the slope of the line A-E. Incremental recovery—which is also a
cumulative value—is found from the slope of the line A-B. Momentary recovery at t
applies to the sampling interval preceding t. If the beginning of the time interval (t 1) and

5. Observed ratios of N uptake at two consecutive N application levels (R N ), compared with the
corresponding ratios of root mass (RM ).

20 ten Berge et al
6. Relation between total crop (leaves, stems, roots, and panicles) N uptake (Nc ) and N
application in the three experiments at different times.

the end of the time interval (t 2) are 25 and 46 DAT in Figure 6a, respectively, the
momentary recovery for A(t 2 ,i) is It is the
extra (over the i=0 treatment) uptake in treatment i as a fraction of the latest N split
applied preceding t2 . For the first sampling event, momentary and cumulative recov-
eries are identical.
The values for each of these recoveries are given in Table 4. In the early tillering
stage (18 and 20 DAT for TNAU-TNRRI and CRRI, respectively), recoveries were in
the 0-20% range for all treatments, but part of the applied N was still in the soil. No clear
trend with A t (i) was found at this stage for any of the recovery types. Later during the
tillering stage (25 DAT at TNAU-TNRRI and PUAT), recoveries of all three types
increased slightly with At (i). Because constant recovery across i is equivalent to

Root growth and nitrogen uptake in rice: concepts for modeling 21
Table 4. Cumulative, momentary, and incremental recovery of fertilizer N observed at TNAU-
TNRRI (Aduthurai, 1988-89), PUAT (Pantnagar, 1987), and CRRl (Cuttack, 1990).

TNAU-TNRRI TNAU-TNRRI
N application (kg/ha) N application (kg/ha)
DAT
100 200 300 400 100 200 300 400

Cumulative recovery Momentary recovery
18 0.18 0.14 0.16 0.18 0.18 0.14 0.16 0.18
25 0.43 0.48 0.50 0.47 0.25 0.34 0.33 0.29
46 0.43 0.50 0.65 0.64 0.46 0.59 1.10 1.16
63 0.54 0.62 0.66 0.66 0.61 1.11 1.19 0.91
81 0.55 0.57 0.55 0.56 0.69 0.82 0.53 0.35

Incremental recovery

18 0.18 0.10 0.21 0.23
25 0.43 0.53 0.53 0.38
46 0.44 0.57 0.93 0.62
63 0.54 0.70 0.75 0.63
81 0.56 0.59 0.51 0.60

PUAT CRRl
N application (kg/ha) N application (kg/ha)
DAT DAT
60 120 180 240 50 100 150
Cumulative recovery Cumulative recovery

25 0.21 0.21 0.22 0.24 20 –0.07 0.08 0.11
49 0.44 0.50 0.54 0.51 50 0.70 0.83 0.84
72 0.55 0.47 0.42 0.37 70 0.59 0.60 0.67

Momentary recovery Momentary recovery

25 0.21 0.21 0.22 0.24 20 –0.07 0.08 0.11
49 0.67 1.08 1.18 1.06 50 2.22 2.32 2.31
72 nda 0.40 0.07 –0.07 70 0.29 –0.09 0.15

Incremental recovery Incremental recovery

25 0.21 0.21 0.24 0.28 20 -0.07 0.22 0.17
49 0.44 0.62 0.62 0.42 50 0.70 0.96 0.87
72 0.55 0.40 0.32 0.20 70 0.59 0.60 0.81

a nd = not determined since no third split was applied.

increasing absolute uptake rates, this response is consistent with the above observation
that dNc/dt increased with At (i). The generally low recoveries during the early
development stages are attributed to the limited size of the root system and possible
transplanting damage; N demand is unlikely to limit uptake because in that case
recovery would decrease with At (i).
Recoveries at PI (46, 49, and 50 DAT for TNAU-TNRRI, PUAT, and CRRI,
respectively) were generally high. Cumulative, momentary, and incremental recover-
ies all increased substantially with At (i) in each data set, except at the highest i. The

22 ten Berge et al
latter lack of response shows that Hypothesis 3 is not valid at these high application
levels. That does not contradict the earlier observation that Mr and (dNc /dt)/Mr
continued to respond to At(i) up to the highest i, but it does imply that these responses
were not strong enough to cause a sustained increase in recovery.
Momentary recoveries at PI exceeded 1.0 in all data sets, indicating that some N was
still available from the basal dressing, even after 3-4 wk. Even so, such high values
suggest that practically all N applied around early tillering had been absorbed by the
crop by PI. Incremental recoveries were near 1.0 for the two highest N application
levels in CRRI, and for i=3 in TNAU-TNRRI. The values of this variable were lower
at PUAT, but still reached 0.62 for i=2 and i=3.
Results were less consistent for the sampling intervals from PI to flowering.
Momentary recoveries were poor in all treatments at PUAT and CRRI. All recovery
types decreased from PI to flowering at PUAT, except for i=1. Moreover, recoveries
decreased here with increasing i. At CRRI, too, recoveries decreased with time. At
TNAU-TNRRI, recoveries remained fairly high and decreased only after flowering (63
DAT). Then, momentary recovery also decreased across i levels.
The decline in recovery after PI (or later in the TNAU-TNRRI case) leads us to
conclude that either Hypothesis 3 is invalid at this stage, or that the fraction of roots
active in N uptake decreases as time proceeds. For the latter to be a valid explanation,
however, we have to accept that this sencscence is more pronounced at higher i levels,
which is unlikely.
The larger root system resulting from N application makes the plant better able to
compete for N against loss processes, and hence a larger fraction of N in the root zone
is recovered. This was indeed observed during the vegetative phase, which supports
Hypothesis 3. The phenomenon of increasing recovery with A, however, may also be
caused by other mechanisms involving positive feedback between Nc and dNc /dt. In the
following section, we try to explain the observed trend in recovery vs A(i) on the basis
of observed root masses.
Assuming that the rates of N uptake and loss are both governed by first-order
processes, we obtain for the recovery fraction in treatment j as compared with that in
treatment i (Appendix 1)

(3)

Figure 7 shows cumulative recoveries during the vegetative period calculated with
Equation 3 from observed M rj/Mri and observed recovery at the lowest application
level. We conclude that cumulative recoveries at the higher A(i) levels can be
reasonably well-explained by differences in observed root mass, without invoking
other mechanisms. Therefore, Hypothesis 3 cannot be disproved on the basis of these
observations, except in the highest i of each experiment. The material presented earlier
in disproving Hypothesis 2 provides additional support for Hypothesis 3; this is
essentially independent of the recovery analysis.

Root growth and nitrogen uptake in rice: concepts for modeling 23
7. Observed cumulative fertilizer N recovery compared with recovery calculated from Eqn (3).
The first datum of each series is the observed ri=1, and is used as the starting point in Eqn (3) to
calculate recoveries at higher N application levels.

Hypothesis 4: If [NH4 +] is above a critical value, the uptake rate is regulated by a
feedback mechanism in the plant other than via RLD.

This hypothesis addresses a situation in which the uptake rate per unit root length, or
the fraction of the total root length that is active in uptake, is regulated by the plant in
accordance with its internal N content. A high crop growth rate induced by Nc is likely
to be associated with a high carbohydrate supply to the roots, which would tend to
increase N uptake through a positive feedback loop. At high growth rates, possibly the
rate of detoxification of ammoniacal N via amino acid synthesis results in another
positive feedback loop between Nc and N uptake rate.
The present experimental results do not allow differential testing of Hypotheses 3
and 4.

Root-shoot ratio
The lack of sensitivity of the root-shoot ratio to N application observed in these
experiments is unusual in crops. Numerous studies, including the early work by
Brouwer (1962a,b, 1963), have shown that higher nutrient supply results in lower root-
shoot ratio. The concept of functional equilibrium evolved from such observations, and
although the mechanisms are often questioned (Lambers 1983, van Andel et al 1983),
the occurrence of shifts in dry matter partitioning induced by nutrient supply is widely
accepted (Wilson 1988). Partitioning models describe root and shoot growth in terms
of C and N balances, applying a resistance coefficient for transport of these compounds
within the plant (Thornley 1972) or assuming an optimal allocation strategy by the
plant (Johnson and Thornley 1987). On the basis of such concepts, there is no obvious
reason why rice should behave differently from other crops. Peculiar characteristics of
the lowland rice system include the low mechanical resistance to root growth; the root’s
O2 demand being met by diffusion through internal root gas channels; the uptake of N
is as NH4+ ions; and the particular rhizosphere chemistry of anaerobic soils. Kirk et al

24 ten Berge et al
(1993) state that NH4 + uptake may be hampered by rhizosphere acidification arising
from Fe2+ oxidation and NH 4+ uptake, resulting in increased NH4+ sorption by the soil
complex. A phenomenon possibly important in view of O2 supply is the formation of
surface root mats (Kirk and Bouldin 1991), the development of which was shown to
be enhanced by NH4 + as opposed to NO 3 – nutrition (Soezima and Kawata 1969).

Linearity of uptake as a function of N application
Field studies generally show that Nc (A) is linear up to high N application levels.
Assuming that Hypothesis 3 is valid and that root length per unit root mass is
independent of A, this observation conflicts with the observation that the absolute root
mass increases with A. Under these conditions, the slope of N c (A)—i.e., cumulative
recovery—should increase with A.
The apparent contradiction arises because in most studies, Nc (A) is evaluated on a
full-season basis and the positive response of cumulative recovery to N application at
any time between crop establishment and PI is then masked by the neutral or negative
response after PI, as demonstrated in this study.

Conclusions
Hypothesis 3 seems to be the easiest starting point for the development of an uptake
model. The most important variables would be [NH4+ ] as a function of (z,t), effective
NH4+ diffusivity, and RLD. Assessing the active fraction of RLD and its dependence
on (z,t) remains problematic. This research showed no consistent relationship after PI
among uptake, application level, and root mass.
The root-shoot ratio decreased with development stage and was independent of A t (i)
at every stage. The possibility that this may be related to root O 2 supply bears further
investigation.
Root mass and the rate of N absorption per unit root mass both increased with
application At (i), resulting in high recovery levels for N.
Instantaneous N uptake rate per unit root mass is likely to be roughly proportional
to [NH4 +] up to high [NH4 + ] values. Cumulative N uptake over a finite time interval is
higher than the first-order function of At (i) during vegetative growth. An approximate
calculation shows that the response of cumulative recovery to At (i) can be explained
by differences in root mass.
Nitrogen absorption by the crop over the entire season was shown to be a linear
function of A. This linearity is the result of a positive feedback between cumulative
uptake and uptake rate during vegetative growth, followed by a negative or neutral
feedback after PI.
Nitrogen uptake in the first 3 wk after transplanting was low, but proportional to
At (i), implying that demand did not limit N uptake. Ten to twenty percent of N applied
basally was absorbed, and momentary recoveries exceeding 1.0 found for the next
sampling interval indicate that this N was still available for absorption at the time of
the first topdressing.

Root growth and nitrogen uptake in rice: concepts for modeling 25
Uptake between PI and flowering varied among sites, with low values at PUAT and
CRRI and high values at TNAU-TNRRI. The highest momentary recoveries at this
stage were found for low i at CRRI and PUAT. The generally poor recovery of this later
split cannot be entirely due to soil or management conditions, but to the crop’s N status
as well. A similar effect was observed for application at flowering in TNAU-TNRRI.
Further work is needed to explain decreases in momentary and cumulative recov-
eries as a function of time in the later stages of plant development, and the decrease in
recovery with At(i) at these later stages.

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Thornley J H M (1972) A model to describe the partitioning of photosynthate during vegetative
plant growth. Ann. Bot. 36:419-430.
Willigen P de, van Noordwijk M (1987) Roots, plant production and nutrient use efficiency. Ph
D thesis, Wageningen Agricultural University, Wageningen, The Netherlands. 282 p.
Willigen P de, van Noordwijk M (1991) Modelling nutrient uptake: from single roots to complete
root systems. Pages 277-295 in Simulation and systems analysis for rice production (SARP).
F.W.T. Penning de Vries, H.H. van Laar, and M.J. Kropff, eds. PUDOC, Wageningen, The
Netherlands.
Wilson J B (1988) A review of evidence on the control of shoot:root ratio, in relation to models.
Ann. Bot. 61:433-449.
Yoshida S (1981) Fundamentals of rice crop science. International Rice Research Institute, P.O.
Box 933, Manila, Philippines. 269 p.

Notes
Authors’ addresses: H.F.M. ten Berge, Centre for Agrobiological Research, P.O. Box 14,6700
AA Wageningen, The Netherlands; T.M. Thiyagarajan, Tamil Nadu Agricultural University,
Aduthurai, Tamil Nadu 612101, India; B. Mishra, G.B. Pant University of Agriculture and
Technology, Pantnagar, District Nainital, Uttar Pradesh 263145, India; K.S. Rao and R.N. Dash,
Central Rice Research Institute, Cuttack, Orissa 753006, India.
Citation information: Kirk G J D, ed. (1994) Rice roots: nutrient and water use. International
Rice Research Institute, P.O. Box 933, Manila, Philippines.

Root growth and nitrogen uptake in rice: concepts for modeling 27
Appendix 1
Let k1(z,t ) and k2(z,t ) be the first-order rate constants for uptake and loss, respectively
(NB k2 accounts for all losses of added fertilizer), and let c( z,t ) be [NH4+] at time t and
depth z in the active root zone. The ratio X of uptake to loss over time interval t l -t2 and
depth interval z1-z 2 is then

(A1)

Under Hypothesis 3, k1 (Id) is proportional to root mass density mr (kg/m3), specific
root length Lr (m/kg), and a coefficient D (m2 /d) accounting for diffusion from the bulk
soil solution to the root surface:

(A2)

The ratio in Equation A1 is equal to r/(l-r), where r is the recovery fraction. Writing
this ratio Xi for treatment i and X j for treatment j, we have

(A3)

Now, assuming that a) ci (z,t ) is proportional at any ( z,t ) to the applied amount A( t,i);
b) Lr is not affected by A; and c) mr (z,t ) varies across treatments by a factor Mri(t) /Mrj (t)
which is independent of t , then Equation A3 reduces to

(A4)

or

(A5)

28 ten Berge et al
Genetic variation in nitrogen
uptake by rice and the effects
of management and soil
fertility
P.C. Sta Cruz and G. Wada

Variation in nitrogen (N) uptake among rice genotype groupings (ecotype, hybrid,
inbred, modern, and traditional) and between plant types and growth types are
investigated for low to moderate fertilizer levels. Rice genotypes of varying growth
durations (GD) were evaluated in terms of N uptake and N use efficiency (NUE). Total
N in the plant at late spikelet initiation, flowering, and maturity increased with GD.
There were substantial differences in total N in the plant up to 30 d after transplant-
ing (DT), but not after maximum tillering (MT). Total N in the plant at 30 DT (NE) was
positively correlated with sink size, grain yield, and N harvest index (NHI), but not
with percent spikelet degeneration or percent filled spikelets in short- and medium-
duration genotypes. This suggests that NE is an important determinant of sink size
and grain yield in short- and medium-duration genotypes. Narrow spacing and high
basal N application shortened the duration of exponential N uptake and increased
the rate of uptake during this phase. A slow-release fertilizer and high soil fertility
increased the rate of N uptake during the middle and late growth stages. In general,
genotypes with low N uptake during the dry season at high N levels have relatively
low N uptake during the wet season at low N levels. The effects of cultural practices
and soil fertility status, shown in altered durations and rates of N absorption, were
reflected in changes in N uptake patterns.

One strategy for improving the utilization of soil and fertilizer N in rice production
systems is to exploit genotypic differences in N absorption ability. Such differences
can be sought among a) different genotype groupings: ecotypes, hybrids, inbreds, and
modem vs traditional cultivars; and b) different morphological and physiological
features: growth type, panicle type, and growth duration (GD). Genotypic differences
can also interact with cultural practices and environmental variables. This paper
examines the sources of variation in N uptake in various genotype groupings and their
interaction with cultural practices and environmental variables. The relationship
between N uptake efficiency and yield-determining parameters in various genotypes
is also considered.

Variation in N uptake among rice ecotypes,
plant types, and hybrids
Ecotypes
Variation in N uptake between indica and japonica ecotypes has been observed (Tanaca
et al 1964). Typical indicas, such as Peta and BPI76, show high N uptake at the early
growth stages, reflected by increased leaf area. N uptake increases rapidly until panicle
initiation (PI), but thereafter tends to plateau and then decline as N and other nutrient
elements are lost from the plants. By contrast, the japonica Tainan 3 has low N uptake
in the early growth stages with a gradual increase in the amount of N in the plant
sustained until maturity. The faster N uptake by the indica types in the early growth
stages results in higher total N uptake. Ehara et al (1990) found that at the seedling
stage, indica and japonica types showed no distinct differences in N uptake. Semidwarf
indicas showed an increase in leaf area at high N levels, suggesting high N uptake.
Japonica types had longer culms under high N levels (Maruyama and Tajima 1988).
Seedling growth and photosynthesis in improved indicas and japonicas are not any
more adversely affected by low N levels than those of primitive cultivars or wild
species. Cook and Evans (1983) found, however, that improved cultivars showed a
proportional increase in seedling dry weight with increasing N concentration.
Although variations in total N uptake between ecotypes do exist, generalizations
cannot be made because other variables within ecotypes, such as plant type and GD,
may dominate N uptake.

Plant types
Generally, genotypes that perform well at low N levels are tall, have a low percentage
of productive tillers, have high dry matter production, are susceptible to lodging, and
have low panicle to straw weight ratios. They grow relatively fast in the early growth
stages and cover the fields even without N addition. At high N levels, higher growth
rates in the early growth stages result in mutual shading during the middle and late
growth stages. This reduces N uptake because net photosynthesis is decreased,
resulting in fewer tillers and weaker roots. By contrast, genotypes that respond well to
high N have short stature, high panicle to straw weight ratios, high percentage of
productive tillers, and slow growth in the early growth stages. This plant type shows
little mutual shading (Tanaka et al 1964).
Current improved lowland varieties are short- to medium-maturing and intermedi-
ate in panicle number type. Although they produce many tillers and have large leaf area
indices (LAI), they are short and have erect leaves. Mutual shading is avoided by
improved leaf canopy architecture. Yoshida (1981) identified short and stiff culms,
erect leaves, and high tillering as the most important characters for lodging resistance;
increased photosynthesis as a function of LAI; and yield increment as related to number
of panicles.

30 Sta Cruz and Wada
Miyagawa (1981) reported that in indicas, total N uptake of the panicle-number type
(14-16 panicles/hill) is generally higher than that of the panicle-weight type (10-11
panicles/hill), even at different fertilizer N levels.

Hybrids
High total N uptake, dry weight, and leaf area have been observed in F1 hybrids (Blanco
and Akita 1988). This was more evident in japonica-indica crosses than in japonica-
japonica crosses. Similar results were obtained with F1 hybrids of IR varieties and lines
(Sta Cruz et al 1988). The F1 hybrids have higher N uptake compared with their inbred
parents, particularly at 3 wk after transplanting (WT). At 5 WT, differential N uptake
diminished except for the hybrid with medium GD (125 d). The medium-GD hybrids
had consistently higher N uptake until maturity. Likewise, we found that F1 hybrids
generally had higher N harvest index (NHI).

Effect of growth duration on N uptake
To determine the effect of GD on total N uptake at different growth stages, we planted
60 IR varieties and advanced lines with varying GDs at 20- × 20-cm spacing under 0
and 90 kg N/ha levels (Wada and Sta Cruz 1989).

1. Total N in the plant at flowering in relation to growth duration of different rice genotypes under
two N levels. IRRI Farm, 1987 DS.

Genetic variation in nitrogen uptake 31
2. A model for N absorption by rice plants and the occurrence of early panicle initiation in relation
to accumulated effective thermal index (Matsushima 1966, Wada 1971, Shoji and Mae 1984).

Total N uptake at critical plant growth stages was positively correlated with GD. At
zero and 90 kg N/ha fertilizer rates, the increase in GD was accompanied by a linear
increase in N uptake at flowering (Fig. 1), at the late stage of spikelet initiation (Y =
1.94 + 0.78x, r = 0.815**, 90 kg N/ha) and at maturity (Y = 2.07 + 0.069x, r = 0.789**,
90 kg N/ha). The short-duration genotypes generally had lower total N uptake than the
long-duration genotypes at flowering, late stage of spikelet initiation, and maturity.
The variation in N uptake among genotypes with different GD can be explained by
differences in the vegetative lag phase (VLP). The VLP is the difference in days
between the occurrences of panicle initiation (PI) and maximum tillering (MT). The
PI of short-duration genotypes occurred before or at the same time as MT when total
N in the plant was still low. By contrast, the PI of long-duration genotypes occurred
after MT when total N in the plant was already high (Fig. 2).

Variation in N uptake at particular growth stages
Wada and Sta Cruz (1989) evaluated differences in total N uptake of rice genotypes at
different growth stages using 10 rice genotypes with the same GD (111 d). Genotypes
with the same GD were used to correct for the possible variation in VLP duration.

32 Sta Cruz and Wada
Table 1. Differences in total N uptake of short-duration (111 d) genotypes at different growth
stages. IRRl Farm, 1986 DS.

Total N uptake (g/m 2 )a
Genotype
Active Maximum dN1 flowering dN2 Maturity dN3
tillering tillering (N2-N1) (N3) (N3-N2) (N4) (N4N3)
(N1) (N2)

IR36 1.4 bc 2.6 c 1.2 c 9.9 bc 7.3 ab 12.6 bc 2.7 a
lR2588-7-3-1 1.6 b 3.2 b 1.6 b 10.4 b 7.2 ab 13.2 b 2.8 a
lR25261-135-1-1 2.0 a 4.4 a 2.4 a 11.9 a 7.5 a 14.4 a 2.5 a
lR29658-69-2-1-2 1.5 b 2.8 bc 1.3 bc 10.0 bc 7.2 ab 12.4 c 2.4 ab
lR29692-94-2-1-3 1.4 bc 2.5 cd 1.1 cd 9.7 c 7.2 ab 12.3 c 2.6 a
IR29725-109-1-2-1 1.3 c 2.6 c 1.3 bc 9.9 c 7.3 ab 12.6 bc 2.7 a
lR31868-64-2-3-3-3 1.3 c 2.5 cd 1.2 c 9.8 c 7.3 ab 12.5 c 2.7 a
lR32419-81-2-3-3 1.2 c 2.1 e 0.9 d 9.2 d 7.1 b 11.6 c 2.4 ab
lR32429-47-3-2-2 1.3 c 2.2 de 0.9 d 9.8 c 7.6 a 12.0 c 2.2 b
lR32429-122-3-1-2 1.5 b 2.6 c 1.1 cd 10.0 bc 7.4 ab 12.4 c 2.4 ab
a In a column, means followed by a common letter are not significantly different at the 5% level by DMRT.

Table 2. Correlation coefficients for N uptake between 0 and 90 kg N/ha and between wet (WS)
and dry seasons (DS). a IRRl Farm, 1986 WS and 1987 DS.

Total N uptake
Parameter
30 DT Flowering Maturity

0 N vs 90 N
DS 0.835 0.905 0.887
WS 0.850 0.889 0.781
DS vs WS
0N 0.830 0.880 0.883
90 N 0.815 0.771 0.841
a All values are significant at the 1% level. n = 60, mean of two replications.

Variation in N uptake among genotypes was apparent during the early growth stages
(30 DT) and MT (30-35 DT). Little variation in N uptake was noted from MT to
flowering and from flowering to maturity (Table 1). This observation can be explained
by the availability of NH4 -N in the plow layer as reported by Wada et al(l989). The
NH4 -N in the plow layer decreased exponentially from 7 DT until 35 DT and remained
constant at a very low level after 35 DT (Fig. 3). During the early growth stages,
NH4-N in the plow layer was not limiting, and variation in N uptake could only have
been due to differences in N absorption abilities between the genotypes. The availabil-
ity of NH4 -N in the plow layer did limit N uptake after MT.
Sta Cruz (1990) found that there were positive correlations between 0 and 90 N
treatments and between the wet season (WS) and dry season (DS) for total N uptake
at 30 DT, flowering, and maturity (Table 2). The genotypes with low total N uptake
under low N level also had low total N uptake under high N level (Fig. 4). The same
relationship was obtained for N uptake between WS and DS (Fig. 5).

Genetic variation in nitrogen uptake 33
3. Behavior of NH4 -N in the plow layer (Wada et al 1989).

Effect of early N uptake on yield-determining parameters
Because there were significant differences in N uptake at the early growth stage, a
followup study was made using 60IR varieties and lines with varying GDs to determine
the relationship of the amount of N in the plant at the early growth stage (NE) to sink
size, grain yield, and NHI (Wada and Sta Cruz 1990).
NE was positively correlated with sink size, grain yield, and NHI, but not with
degenerated spikelets and percent unfilled spikelets in short- and medium-duration

34 Sta Cruz and Wada
4. Relationship between total N uptake at flowering under 0 and 90 kg N/ha in rice genotypes
with different growth durations. IRRI Farm, 1987 DS.

5. Relationship between total N uptake at maturity in dry-season (DS) and wet-season (WS)
croppings in rice genotypes with different growth durations. IRRI Farm, 1986 WS and 1987 DS.

Genetic variation in nitrogen uptake 35
Table 3. Correlation coefficients between N uptake at 30 DAT (NE) and yield-determining factors
in rice genotypes of different growth durations. a IRRI Farm, 1986 WS and 1987 DS.

Growth
duration Y S DEG S R NHI
(d)

1987 DS

102-104 0.551** 0.858** 0.696** –0.264 ns 0.841**
108-109 0.580** 0.723** 0.299 ns –0.449 ns 0.831**
113-116 0.600** 0.897** 0.593 ns –0.394 ns 0.938**
119-122 0.708 ns 0.920** 0.669 ns –0.529 ns 0.972**
124-127 0.660 ns 0.838** 0.936** –0.170 ns –0.040 ns
130 < 0.528 ns 0.534 ns 0.885** –0.538 ns –0.041 ns

1986 WS

104 0.7,26** 0.817** 0.339 ns –0.319 ns 0.796**
111-118 0.685 * 0.894** 0.428 ns –0.665 ns 0.894**
117-122 0.948** 0.849** 0.288 ns –0.483 ns 0.839**
125-127 0.499 ns 0.623 ns 0.725* –0.361 ns 0.532 ns
130 < 0.269 ns 0.291 ns 0.849** –0.073 ns –0.283 ns
a *, ** = significant at 5 and 1% level, respectively. ns = not statistically significant at 5% levet. Y = grain yield,
S = sink size, DEG S = degenerated spikelets, R = percent filled spikelets, and NHI = nitrogen harvest index.

genotypes (Table 3). This result suggests the importance of NE as a parameter for
increasing both sink size and yield of short- and medium-duration genotypes, without
increasing the percent unfilled spikelets and degenerated spikelets.
The NHI increased with NE in short- and medium-duration genotypes. This further
suggests the importance of NE as a parameter in increasing the yield and NUE of short-
and medium-duration genotypes.
In long-duration genotypes, NE was not correlated with sink size, grain yield, and
NHI. Although the proportion of filled spikelets was not affected by NE, degenerated
spikelets increased with NE (Table 3). This result suggests that N uptake during the
middle and late growth stages is an important yield determinant in long-duration
genotypes.

Effect of cultural practices and soil fertility
on the pattern of N uptake
Takahashi et al (1976) and Wada et al (1989) described the pattern of N absorption by
rice plants as biphasic. The amount of N in the plant increases exponentially during the
early growth stages and linearly during the middle and late growth stages. The
transition point between the two phases coincided with MT for 20- × 20-cm plant
spacing (Fig. 2). However, the uptake pattern may be altered by both native soil fertility
and cultural practices (i.e., plant spacing and the amount, type, and timing of fertilizer).
The effect is usually manifested by a shift in transition time. This shift implies a change
in the timing of MT which may alter the amount of N in the plant during the middle and
late growth stages.

36 Sta Cruz and Wada
Plant spacing and rate of basal fertilizer
Wada et al (1989) found that narrow spacing (20 × 10 cm vs 20 × 20 cm and 20 × 30
cm) and a high rate of basal N (120 vs 60 kg N/ha) shortened the duration of the
exponential phase (Figs. 6 and 7). Although the duration of N uptake was shortened,
the rate of N uptake in the exponential phase was higher. Total N uptake was higher
with narrow spacing (area basis) and with basal N (plant basis). On the other hand, the
rate of N uptake in the linear phase was not affected by narrow spacing and high basal
N. However, total N uptake was higher due to the relatively high amount of N absorbed
during the exponential phase.

Use of slow-release fertilizer
Wada et al (1989) found that the use of a slow-release fertilizer (urea coated with plastic
resin), as compared with ammonium sulfate, resulted in longer duration of the
exponential phase (Fig. 8). Although the rate of N uptake using Meister was relatively
lower than with ammonium sulfate, the lengthening of the exponential phase increased
total N uptake with Meister at MT; Meister increased the rate of N uptake during the
linear phase.

6. N absorption patterns of rice plants grown at different plant spacings (Wada et al 1989).

Genetic variation in nitrogen uptake 37
7. N absorption patterns of rice plants grown with two basal N rates (Wada et al 1989).

8. N absorption of rice plants grown with two N fertilizer sources (Wada et al 1989).

38 Sta Cruz and Wada
9. N absorption patterns of rice plants grown under two different soil fertility levels (Wada et al
1989).

Soil fertility level
N uptake patterns in two experimental sites with varying soil fertilities were compared
by Wada et al (1989). One field (Field E) had higher percentages of C and total N, a
higher C-N ratio, and higher cation exchange capacity and ammonification rate than
the other field (Field M). The rate of N uptake during the exponential phase was higher
at Field E, although duration was shorter because of the fertility level. The effect of
higher soil fertility level was apparent during the linear phase where the rate of N uptake
was higher (Fig. 9).

Conclusions
There is substantial variation in N uptake between rice ecotypes, plant types, hybrids,
and plants with different GD. Plant type (based on leaf erectness and panicle number)
and GD are the most important factors.
Nitrogen uptake during late spikelet initiation, flowering, and maturity increases
with GD. The variation in N uptake among genotypes with different GD is due to
differences in the duration of VLP. Short-duration genotypes generally have shorter
VLP than long-duration ones and consequently have lower total N uptake.
Variation in N uptake among genotypes of the same GD is apparent during the early
growth stages (30 DT). During these stages, NH 4 -N in the plow layer is likely to be
high, so N uptake is controlled by the N absorption ability of the genotype. During the
middle and late growth stages, the availability of NH4-N in the plow layer is low and
therefore may limit N uptake. Hence, differences in N uptake among rice genotypes
during the middle and late growth stages were not observed.

Genetic variation in nitrogen uptake 39
The amount of N taken up during the early growth stages is positively correlated
with sink size, yield, and NHI. Therefore, N uptake at these stages is an important
parameter for increasing yield and N utilization of short- and medium-duration
genotypes.
Generally, native soil fertility and cultural practices (such as plant spacing and type
and management of fertilizer) affect the N absorption pattern of various genotypes
differently. The effect is manifested by changes in the duration and rate of N
absorption, which in turn alter the amount of N in plants at critical growth stages,
leading to profound effects in NUE.

References cited
Blanco L C, Akita S (1988) Physiological mechanism of heterosis in seedling growth of
japonica-indica F1 rice hybrids. Jpn. J. Crop Sci. 57 (extra 1):99-100.
Cook M G, Evans L T (1983) Nutrient responses of seedlings of wild and cultivated Oryza
species. Field Crops Res. 6:205-218.
Ehara H, Tsuchiya M, Ogo T (1990) Fundamental growth response to fertilizer in rice plants.
Varietal difference in the growth rate at seedling stage. Jpn. J. Crop Sci. 59(3):426-434.
Maruyama S, Tajima K (1988) Growth response to nitrogen in Japonica and Indica rice
varieties. II. Differences in the rate of increase in culm length and leaf area due to nitrogen
fertilization. Jpn. J. Crop Sci. 57(4):692-698.
Miyagawa S (198 1) Nitrogen balance in paddy fields planted with different Indica varieties. Jpn.
J. Trop. Agric. 25:107-114.
Sta Cruz, P C (1990) Sink development in rice genotypes of different growth durations as
affected by nitrogen nutrition, plant spacing, and shading. Ph D dissertation, University of
the Philippines at Los Baños, Laguna, Philippines. 135 p.
Sta Cruz P C, Wada G, Virmani S S (1988) Nitrogen response of F1 hybrid of rice plants. Jpn.
J. Crop Sci. 57 (extra 1):247-248.
Tanaka A, Navasero S A, Garcia C V, Parao F T, Ramirez E (1964) Growth habit of the rice plant
in the tropics and its effect on nitrogen response. IRRI Technical Bulletin 3. International
Rice Research Institute, P.O. Box 933, Manila, Philippines.
Takahashi J, Wada G, Shoji S (1976) The fate of fertilizer nitrogen applied to the paddy field and
its absorption by rice plants. VI. Influence of a thermal factor on the soil ammonium nitrogen
and the absorption of nitrogen by rice plants. Proc. Crop Sci. Jpn. 45:213-219.
Wada G, Aragones D V, Aragones R C (1989) Nitrogen absorption pattern of rice plants in the
tropics. Jpn. J. Crop Sci. 58(2):225-231.
Wada G, Sta Cruz PC (1989) Varietal differences in nitrogen response of rice plants with special
reference to growth duration. Jpn. J. Crop Sci. 58(4):732-739.
Wada G, Sta Cruz P C (1990) Nitrogen response of rice varieties with reference to nitrogen
absorption at early growth stage. Jpn. J. Crop Sci. 59(3):540-547.
Yoshida S (1981) Fundamentals of rice crop science. International Rice Research Institute, P.O.
Box 933, Manila, Philippines. 269 p.

40 Sta Cruz and Wada
Notes
Authors' addresses: P.C. Sta Cruz, Agronomy, Soils, and Plant Physiology Division, PhilRice,
Maligaya, Muñoz, Nueva Ecija, Philippines; G. Wada, 8-7 Miagino 1, Chome Niyaginoko
Sendai 983 Japan.
Citation information: Kirk G J D, ed. (1994) Rice roots: nutrient and water use. International
Rice Research Institute, P.O. Box 933, Manila, Philippines.

Genetic variation in nitrogen uptake 41
Use of molecular markers
to evaluate rice genetic
variation in associative
N2 fixation, N uptake,
and N use efficiency
P. Wu, J.K. Ladha, S.R. McCouch, and S.B. Teng

Significant differences among rice varieties in associative N2 fixation, N uptake, and
N use efficiency (NUE) have been found over the last 10 yr. Three methods were
used: N balance (a measure of the plant’s ability to exploit soil N), acetylene reduc-
tion, and 15N dilution (both measures of N2 fixation). The advantages and limitations
of these methods for varietal screening are outlined below together with a summary
of our work over the past decade. It was found that IR42 consistently had high N 2
fixation and N balance and performed well in soils with low N fertility. Palawan, a
local variety, had low N2 fixation and N balance. In 15N dilution experiments in a
greenhouse and the field, IR42 and Palawan showed significant differences in
associative biological N, fixation, N uptake, and NUE. There was roughly a 20%
difference in atom % 15N excess between IR42 and Palawan. There were strong
correlations between atom % 15 N excess and the chlorophyll content of the flag leaf,
between N uptake and yield, and between NUE and yield. In a primary restriction
fragment length polymorphism (RFLP) survey comprising 11 genotypes with 4 en-
zymes and 44 probes, we found 67% polymorphism between IR42 and Palawan.
Based on the survey results, we have selected 120 polymorphic probes throughout
the 12 chromosomes for tagging genes underlying the traits identified in a parental
survey with 180 probes with 6 enzymes ( Eco RV, Sc al, Hindlll, Xba l, and Dra l). The
enzymes of X bal and Dra l performed well in detecting polymorphisms between the
test genotypes; the enzymes of Hindlll, Sc a l, and EcoRV were superior to EcoRI.

The components of rice genetic variation in N efficiency include differences in ability
to foster associative biological N, fixation (BNF) in the rhizosphere (Ladha et a1 1987,
1988; Watanabe et a1 1987), differences in N uptake efficiency (App et a1 1986), and
differences in internal N use efficiency (NUE) (Ladha et a1 1987, 1988; De Datta and
Broadbent 1988; Broadbent et al 1987). The plant and soil variables controlling
associative BNF have been described (Balandreau and Knowles 1978, Diem et a1 1978,
Asanuma et al 1979, Nishizawa et al 1983, Murty and Ladha 1987) and diallel cross
analysis has shown that the ability to foster associative BNF is heritable and is a
quantitative character (Iyama et al 1983). There is currently little information on the
heritability of N uptake and NUE in rice.
The advent of molecular marker technology makes it possible to identify the genetic
loci responsible for particular phenotypic characters, even when the products of those
genes are unknown. The availability of a well-populated molecular genetic map of rice
based on restriction fragment length polymorphism (RFLP) allows genetic evaluation
of quantitative characters associated with plant tolerance for a wide range of stress
conditions (McCouch and Tanksley 1991).
The study reported here aims to localize quantitative trait loci (QTL) governing
BNF, N uptake, and NUE in a segregating population of rice. It is a first attempt to bring
the tools of molecular genetics to bear on the complex issue of nutrition in the irrigated
rice system. We hope that such an approach will prove useful for soil microbiologists,
plant nutrition physiologists, and plant breeders alike. Studies in tomato have already
demonstrated its effectiveness (Paterson et al, 1988, Martin et al 1989), and identifica-
tion of QTLs underlying tolerance for low P stress in maize using RFLP was recently
reported (Reiter et al 1991).
In this paper, we review the state of current knowledge on the screening methods
available for measuring associative BNF, N uptake, and NUE. We also report
preliminary results of a study to evaluate genotypic variation in associative BNF, N
uptake, and NUE in rice to provide a basis for tagging the genes underlying the traits.

Review of screening methods for rice genotypic variation in
associative N2 fixation, N uptake, and NUE
Before initiating a gene tagging experiment based on RFLPs, it is necessary to develop
simple and reliable screening techniques for large-scale screening and to select
appropriate plant material.
Diverse methods have shown significant differences in BNF, N uptake, and NUE
among rice genotypes. The methods for measuring associative N2 fixation include N
balance, acetylene reduction (AR) assay, and 15N isotope techniques ( 15N dilution).

N balance method
N balance is the terminal N content of the soil minus the initial soil N content following
a given treatment. An N balance sheet gives the sum of N gains and losses. An
experiment by Ventura and Watanabe (1983) with 15N-labeled soil showed that gains
in N balance were largely due to differences in N 2 fixation.
In an N balance study with 76 rice genotypes and 8 wild rices grown in pots, App
et al (1986) found wide variation in ability to stimulate N gain (Fig. 1). Palawan, a
traditional variety, ranked low; IR42, an improved variety, ranked high among the
long-duration varieties tested. Extrapolated to a per hectare basis, N gain differences
ranged from 16 to 70 kg N/ha per crop. High positive correlation coefficients were
obtained between N gain and total N uptake, N gain and total dry matter production,

44 Wu et al
1. Differences in N gains of several rice genotypes (App et a1 1986).

and daily dry matter production. However, because N balance experiments are time-
consuming, they are not suitable for large-scale screening.

Acetylene reduction assay method
Due to its simplicity, sensitivity, and low cost, the AR assay has been the method most
frequently used in plant BNF studies. Several studies using AR assay have demon-
strated genotypic variation in associative N2 fixation in rice (Lee et al 1977; Sano et a1
1981; Barraquio et al 1986; Tirol-Padre et a1 1988; Ladha et a1 1986, 1987).
To measure a large number of field-grown plants, a short-term laboratory AR assay
involving a cut plant-soil system incubated in the dark has been developed (Barraquio
et al 1986). Using this assay, it was found that the acetylene-reducing activity (ARA)
per plant of several rice genotypes increased with rice development and was maximal
at heading (Ladha et al 1986). The coefficient of variation among replicated plants
decreased toward heading (Ladha et al 1986, 1987; Tirol-Padre et a1 1988).
Acetylene-reducing activity associated with rice genotypes and the relationship
between ARA and N harvest index (NHI = N content of grain/total N absorbed), ARA
and harvest index (HI), and ARA and N remobilization efficiency (NRE = maximum
vegetative N - final vegetative N/maximum vegetative N) were studied. The experi-
ments with 16 rice varieties or lines planted in the wet (WS) and dry seasons (DS)
demonstrated that:
significant differences in ARA/plant and ARA/g dry weight exist between long-
and short-duration varieties;
long-duration varieties had higher ARA than short-duration ones except IR50
which exhibited the highest ARA among short-duration varieties, IR42 exhibited
the highest ARA expressed on a per plant or per g dry weight basis, line IR21912-
56-3-1-2-2 ranked low in the two seasons; and

Use of molecular markers to evaluate rice genetic variation 45
NHI was significantly different between long- and short-duration varieties and
NRE differed among the short-duration varieties; no correlations between ARA
per plant and HI, NHI, and NRE were found.
Trials with 31 genotypes with different growth durations were conducted during
both WS and DS. The ability of a genotype to support ARA per plant or per unit plant
dry weight was shown more clearly by plotting ARA/plant vs ARA/g plant dry weight
at heading (Fig. 2) (Ladha, unpubl.). Genotypes with higher ARA were on the upper
side of the graph. Long-duration IR42 consistently showed the highest ARA.
Root, shoot, total plant dry weight, and N uptake positively correlated with ARA/
plant at heading (Table 1). The correlations were significant but lower between ARA
and N uptake at maturity. Acetylene-reducing activity, however, was not correlated
with grain yield or grain yield per unit of N uptake.
The ARA values in the different seasons fluctuated considerably and the wide range
of varietal growth duration made comparison difficult. To circumvent these problems,
relative ARA, based on those of genotypes exhibiting the highest ARA, was deter-
mined from the relation

2. Differences in ARA/plant and ARA/g total plant dry weight of 37 short-, medium-, and long-
duration genotypes (Ladha et al 1988).

46 Wu et al
Table 1. Correlations of plant traits with plant-associated ARA and N uptake at maturity in
37 rice genotypes of different growth durations (Ladha et ai 1988). a

r
Plant traits vs
ARA N uptake at maturity

ARA 0.425**
Root + submerged portion 0.842** 0.294
dry weight (heading)
Shoot dry weight (heading) 0.735** 0.413*
N uptake (heading) 0.735** 0.496**
Total dry weight (maturity) 0.617** 0.871**
N uptake (maturity) 0.425**
Grain yield 0.266 0.707**
Grain N 0.385* 0.822**
Grain yield/N 0.108 0.350*

a
*, ** = significant at the 5 and 1% level, respectively. ARA = acetylene reduction assay.

Although ARA has many advantages, a large plant-to-plant variation and the need
to assay the plant several times during the growth cycle limited its wide use.

15 N dilution method
The 15N dilution method has recently gained acceptance among researchers because it
is relatively simple and provides integrated values over the whole growth duration
(Chalk 1985). The importance of using the right nonfix reference plants to obtain
reliable N 2 fixation estimates and the difficulties in finding suitable ones have been
extensively reviewed (Chalk et a1 1983, Hauck and Weaver 1986, Witty 1983, Danso
1986). However, the need for a perfect match of nonfixing and fixing plants becomes
less important if the soil organic N is labeled with 15N and, on mineralization, a constant
l5N- 14 N ratio in plant available N is produced (Pareek et a1 1990, Rarivoson and Ladha

1992). Labeling and maintaining the stability of 15 N are easier in flooded soils than in
upland soils. This is because the plow sole delineates an Ap horizon where most roots
are located and which is relatively easy to homogenize.
The heterogeneity of added or natural 15N abundance in field soil and the differences
in rooting pattern between genotypes can be major sources of error in this kind of
research. Therefore, six rice genotypes of different growth durations were grown in
well-mixed soil in pots and their 15N contents in grain and straw were measured
(Watanabe et a1 1987). Differences in 15N values were small but significant. The
difference between the maximum and minimum 15N values in the grains was 22% of
the mean value (Table 2).

Selection criteria and ranking system
Broadbent et al (1987) considered several parameters in screening rice varietal
differences in NUE, including dry matter production (DM), total N uptake (Nt), uptake
of soil N (Ns), uptake of fertilizer N (Nf), grain yield (Y), weight of panicle (WP), WP/

Use of molecular markers to evaluate rice genetic variation 47
Table 2. d15 N values of grain and straw from plants grown in pots (Watanabe et al 1987).

d 15N
Variety Growth duration
(d) Grain Straw

lR18349-135-2-3-2-1 122 5.2 (8)a 5.6 (8)
Hua-chou-chi-mo-mor 101 6.0 (6) 5.8 (6)
IR50 101 6.0 (8) 5.5 (8)
IR42 150 6.1 (7) 5.5 (7)
OS4 122 6.5 (7) 6.2 (6)
Rodjolele 150 6.5 (7) 5.9 (7)
S. D. 0.38 0.50

a Values in parentheses indicate number of replications.

Table 3. Group of parameters for screening rice ARA and NUE (Ladha et al 1988).

Group Parametera Stage

1 ARA RDW-H SDW-H N-H Heading
2 TDW-M GY GN-M Maturity
3 GY/N Maturity
a RDW = root dry weight, SDW = straw dry weight, TDW = total dry weight, GY = grain yield, GN = grain nitrogen,
H = heading, M = maturity.

Nf, WP/Ns, Y/Nt, DM/Ns, WP/Nt, and DM/Nt. Significant variations in several
parameters among 24 genotypes were found. Parameters WP/Nt and Y/Nt have been
suggested as the most useful for assessing NUE. Three groups of variables were used
to rank 21 genotypes with different growth durations during the 1986 and 1987 DS
(Table 3). Rankings based on group 1 variables did not correlate significantly with
rankings based on variables of groups 2 and 3. Rankings based on groups 2 and 3
significantly and positively correlated, suggesting that a genotype with high N2
fixation may not always be high in N uptake and efficient utilization, but that a
genotype with higher N uptake may have higher utilization efficiency.

Preliminary evaluation for RFLP mapping of associative N2
fixation, N uptake, and NUE to select among genotypes for
experiments

Eleven genotypes were selected from previous field screening trials based on their
divergent BNF, N uptake, and NUE (the yield/Nt absorbed) characteristics (Watanabe
et al 1978; App et al 1986; Ladha et al 1987, 1988). These genotypes were subjected
to preliminary RFLP analysis for evaluating the frequency of polymorphism detected
among them. Four enzymes were used: EcoRV, HindIII, ScaI, and Xba I. Forty-six
mapped DNA from both a rice genomic library (RG) and an oat cDNA library (CDO)
were selected based on their distribution throughout the 12 chromosomes of rice. The
results showed that the combination of Cigalon and IR42 had the highest percentage
of polymorphism (78%), followed by IR42 and OS4 (73%), Cigalon and IR13429-150-

48 Wu et al
Table 4. Percent polymorphism of possible combinations differing in associative N 2 -flxing ability
and NUE (46 probes surveyed using 4 enzymes).a

Variety BR51-46-3-2-1-2 lR13429-150-3-2-1-2 BG367-4 IR42

Cigalon 67 69 67 78
OS4 56 58 58 73
ClCA 58 60 52 45
C66-2803 52 41 43 45
Palawan 67 43 58 67
DR33 54 65 54 45
BR40-300-2-1-E 50 54 41 37

aEnzymes used: Eco RV, Hind lll, Sca l, Xba l.

3-2-1-2-(69%), IR42 and Palawan (67%), BG367-4 and Cigalon (67%), and BR51-
46-CI and Cigalon (67%) (Table 4). Considering the good level of divergence
measuring in phenotypic values and the percentage of polymorphism detected, IR42
and Palawan were selected for further study. They are both long-duration varieties
(125-130 d). IR42 consistently demonstrated superior performance. BG367-4 and
IR13427-40-2-3-3-3-3 (100 d) were also selected as test materials. BG367-4 exhibited
higher N uptake and higher NUE than IR13427-40-2-3-3-3-3 (Broadbent et al 1987,
Ladha et al 1988).

Development of mapping population
Two sets of crosses were made: Palawan (japonica) and IR42 (indica), and IR13427-
40-2-3-3-3-3 (indica) and BG367-4 (indica). Following the evaluations of BNF, N
uptake, and NUE in the first cropping experiments, only F1 plants from Palawan and
IR42 crosses were selected to produce an F2 population of 200 plants.

Pot and field experiments
The soil used in the pot and field experiments was labeled with 15N-labeled fertilizer
as (NH4)2SO4 with 75% atom excess at the rate of 1kg 15 N/ha in February 1990. Open
pot and modified Leonard's assembly designs were employed in a pot experiment in
the greenhouse in the 1991 WS. Twelve replications for each genotype were planted
with 1.5 kg soil/pot and one plant/pot. For the Leonard's assembly experiment, water
in the jar was changed every 3 d to keep it fresh. The field experiment was conducted
simultaneously with the pot experiments in microplots (7 m x 8 m) with four
replications in a randomized block design. Forty kilograms P/ha as K2 HPO4 was
incorporated into the soil before transplanting 15-d-old seedlings. Rice-associated
BNF was measured by the 15 N dilution method.
Measurement of BNF, N uptake, NHI, NUE, leaf chlorophyll, plant biomass, and
grain yield. The percentage of N2 derived from the air (% Ndfa), Nt, NHI, NUE,
chlorophyll content of flag leaf at heading stage, plant biomass, and grain yield were
measured in first cropping in the 1991 WS. In the pot experiments, the plants were
sampled at maturity. In the field experiment, plants were sampled at maximum
tillering, heading, and maturity.

Use of molecular markers to evaluate rice genetic variation 49
Isotope 15N abundance in the samples was measured by a mass spectrometer (2HT-
03, Beijing, China). Total N uptakes of the plant shoot, root, and yield were measured
by a Perking-Elmer 2400 CHN elemental analyzer (Norwalk, Connecticut, USA,
1988). Chlorophyll content of the flag leaf was measured by a chlorophyll meter
SAPD-502 (Minolta, Japan). The chlorophyll content was calculated based on read-
ings from the SAPD-502 with 12 replications. (Formula: Y = 0.0996X - 0.152, where
Y = chlorophyll content (mg/100 cm2), X = SAPD-502 reading). Yield and dry biomass
of the shoot and the root were measured by weighing the sample after it was dried at
75 °C for 3 d.
Atom % 15N excess of selected parents. The ANOVA and Duncan's Multiple Range
Test of atom % 15N excess of plants grown in pots showed significant genotypic
variation between both pairs of parental genotypes. In the field experiment, significant
variations were found at maximum tillering and heading stages, but at maturity, only
IR42 and Palawan showed significant differences.
Considerable differences in % Ndfa between IR42 and Palawan were found in the
field and pot experiments. IR42 exhibited higher ability to stimulate associative N,
fixation. Ndfa values for IR42 as compared with those for Palawan were 22% higher
in the field experiments and 19% higher in the pot experiments.
Yield, Nt, NHI, and NUE of selected parents. IR42 and Palawan showed significant
differences in all four parameters tested (yield, Nt, NHI, and NUE) in both field and
pot experiments. Between BG367-4 and IR13427-40-2-3-3-3-3, only Nt and NUE
differed significantly.
The correlations between yield and Nt, yield and NUE, and Nt and NUE are shown
in Table 5. The results indicate that a close correlation exists between yield and Nt and
yield and NUE, but no clear correlation exists between Nt and NUE. This indicates that
Nt and NUE may be used as independent parameters for screening.

Table 5. Correlation among parameters, 1991 WS.

Correlation coefficient
Experiment a
Yield/Nt Yield/NUE Nt/NUE

Field 0.854 0.780 0.423
Pot 0.909 0.708 0.424

an = 8 in the field experiment; n = 12 in the pot experiment.

Table 6. Correlation between chlorophyll content of flag leaf at heading stage and atm % 15N
excess of straw samples.

Experiment a Correlation equationb r

Field Y = –0.017X + 0.54 -0.75
Open pot Y = – 0.009X + 0.42 -0.65
Leonard's pot Y = –0.011X + 0.42 -0.81

an = 8 for field experiment, n = 12 for open and Leonard's pot experiments. b Y = atm % 15 N excess of straw samples.

X = chlorophyll content of flag leaf (mg/100 cm 2 ).

50 Wu et al
Chlorophyll content of flag leaf. A close relationship between associative N2
fixation activity and photosynthesis has previously been established for wheat (M.I.
Chumakov, Russian Academy of Sciences, pers. commun.). When the chlorophyll
content of the flag leaf was measured in our experiments, significant variation existed
among varieties, with similar results found using an open pot and a modified Leonard’s
system. Correlations between atom % 15 N excess and chlorophyll content were found
to be negative (Table 6), suggesting that chlorophyll content and associative N2
fixation should be positively correlated. Thus, high chlorophyll content appears to be
an indication of the ability of the rice genotype to stimulate associative N2 fixation.

RFLP survey of selected genotypes
Six enzymes (Eco RI, Eco RV, Sca I, Hind III, Xba I, and Dra I) were used for identifying
polymorphic markers between test genotypes. The 120 probes (RG, CDO, and RZ)
showed 72% polymorphism between IR42 and Palawan and 62% between BG367-4
and IR13427-40-2-3-3-3-3. The degree of polymorphism detected by each of the six
enzymes is listed in Table 7. The results indicate that Dra I, Xba I, and Hind 11 are more
effective with respect to detecting polymorphisms between IR42 and Palawan than are
Sca I and Eco RV. Eco RI gave the lowest level of polymorphism.

Conclusions and perspectives
Palawan and IR42 consistently demonstrated superiority for all parameters measured
both in the pot and in the field experiments, with IR42 exhibiting a better performance
than Palawan. Accordingly, the cross of Palawan and IR42 will be the focus of future
gene tagging.
IR42 demonstrated about 20% higher Ndfa compared with Palawan. This differ-
ence is important for low-input and sustainable rice production systems needing
supplementary sources of N. The second set of experiments must confirm these
findings, however, before any conclusions are drawn.
The relationship between atom % 15N excess and the chlorophyll content of the flag
leaf indicates that the N2 fixed by associative fixation may be available as an N source
in rice systems and play an important role in photosynthesis.
NUE and Nt can be considered independent parameters and the correlation between
them and yield may have profound economic implications.

Table 7. Percent polymorphism of six enzymes between IR42 and Palawan.

Enzyme Percent polymorphism (total of 180 probes)

Eco Rl 11
Eco RV 25
Sca l 26
Hind III 31
Xba l 33
Dra l 33

Use of molecular markers to evaluate rice genetic variation 51
The Palawan/IR42 cross showed good fertility in the F1. The F2 population is
growing well and demonstrates good segregation for leaf color, height, and tiller
number, suggesting ample recombination of characters. Further study will evaluate
associative N 2 fixation, N uptake, and NUE using both the F2 and F7 populations, with
the goal of identifying the main genetic loci governing these characters. The F7
recombinant inbred (RI) lines will be derived by single seed descent and will facilitate
replication of phenotypic evaluation on identical genotypes. This RI population will
provide reliable data for the genetic analysis of physiological and biological param-
eters related to the complex N nutritional processes in rice.

References cited
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52 Wu et al
Ladha J K, Tirol-Padre A, Punzalan G C, Watanabe I (1987) Nitrogen-fixing (C 2H2 -reducing)
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Use of molecular markers to evaluate rice genetic variation 53
Notes
Authors’ addresses: P. Wu and J.K. Ladha, Soil and Water Sciences Division; S.R. McCouch,
and S.B. Teng, Plant Breeding, Genetics, and Biochemistry Division, International Rice
Research Institute, P.O. Box 933, Manila, Philippines.
Acknowledgments: It is a pleasure to acknowledge the financial support of the United Nations
Development Programme, Division of Global and International Projects. We thank Ms. Agnes
T. Padre and Genalin A. van Coppenolle for their excellent assistance.
Citation information: Kirk G J D, ed. (1994) Rice roots: nutrient and water use. International
Rice Research Institute, P.O. Box 933, Manila, Philippines.

54 Wu et al
Rainfed lowland rice roots:
soil and hydrological effects
Pradeep K. Sharma, G. Pantuwan, K.T. Ingram, and S.K. De Datta

Rice root systems differ greatly among cultivars, soil conditions, and hydraulic
regimes under rainfed lowland conditions. Unsaturated, light-textured soils should be
used for evaluating varietal differences in root systems for drought tolerance. Future
research to increase drought resistance through improved root systems must
combine germplasm improvement and soil physical management.

Rainfed rice environments are diverse and unpredictable and insufficient or excessive
water is often the major factor limiting productivity. Because root characteristics are
closely associated with drought resistance, they are particularly important under
rainfed conditions.
Root characteristics are basically genetically controlled but they are also strongly
affected by soil conditions and crop management practices (Ghildyal and Tomar 1982,
Cruz et a1 1986, Sharma et al 1987, Mambani et al 1990, Thangaraj et a1 1990). The
occurrence of drought or flood depends on the frequency and amount of rainfall, daily
evapotranspiration, and soil physical properties governing infiltration, water retention
capacity, and drainage. These factors in turn affect rice root growth. Soil nutrient
deficiencies and toxicities also affect root growth. In this paper, we focus on the effects
of soil texture, hydrology, and mechanical impedance on rice root growth.

The rice root system
The characteristics of the rice root system are described by Yoshida (1981). Root
growth, in terms of length, dry weight or volume, generally follows a sigmoidal curve
(Fig. 1). Maximum root growth is observed near flowering. Rooting depth depends on
the cultivar and the nature of the rooting medium. Roots of upland rice cultivars in light-
1. Root growth of rice (IR54) with time in a puddled and flooded clay soil (Thangaraj et al 1990).

Table 1. Depthwise root distribution of some lowland cultivars in puddled soils.

Root length (% of total)
Soil texture Cultivar Source
0-10 cm 10-20cm 20-30cm 30-40cm

Clay loam IR36 75 16 6 3 Sharma et al (1987)
Sandy loam IR36 72 16 8 4
Clay IR20 89 8 2 1 Mambani et al (1989)
Clay IR20 92 3 1 4
Clay loam IR20 93 4 3
Sandy loam IR20 88 7 4 1
Clay IR54 75 - Thangaraj et al (1990)

textured upland soils may grow as deep as 1 m or more. But roots of rice cultivars in
lowland soils rarely grow deeper than 40 cm; about 90% of the total root system is
restricted to the top 20 cm of the soil layer (Table 1).

Hydrological effects
We classify ricefield hydrology into three groups depending on topographic location
and water supply: i) pluvial, also called upper paddy, where rainfall is the only source
of water and surface water accumulation is minimal; ii) phreatic, also called middle
paddy, where rainfall, seepage, water table, and runoff provide water to the root zone
with moderate surface water accumulation; and iii) fluxial, also called the lower paddy,
where rainfall, seepage, water table, and runoff provide water to the root zone with
reliable surface water accumulation. Most rainfed lowland rice areas fall in the fluxial
and phreatic toposequence positions, and only some are in the pluvial category
(O’Toole and Chang 1978, Greenland and Bhuiyan 1982). Drought is the major

56 Sharma et al
Table 2. Influence of soil moisture condition on oxygen diffusion rate (ODR) of soil, and root
porosity, root length, and root mass of IR8 (Pradhan et al 1973).

Soil moisture ODR Root porosity Root length Root mass
treatment (10-8 g /cm2 per min) (%) (cm) (g)

Flooding, 6±1 cm 5.14 22.78 25.37 7.25
Flooding, 3±1 cm 6.32 21.06 26.62 8.12
Saturation 10.17 18.04 30.95 7.25
2 kPa 22.36 14.11 30.17 6.25
6 kPa 37.28 10.23 37.75 5.62
35 kPa 61.33 5.94 43.32 4.87
50 kPa 75.59 5.27 45.10 3.50
100 kPa 83.07 4.65 44.02 2.25

SEM ± 4.71 0.22 0.49 0.42
LSD (0.05) 9.97 0.65 1.93 1.22
LSD (0.01) 13.98 0.89 2.65 1.66

constraint to rice productivity in the pluvial and phreatic toposequence positions;
flooding is the main constraint in the fluxial toposequence position.
The rice root system is greatly. influenced by water regime. Under submerged,
anaerobic conditions, rice roots are generally short and thick with high porosity as a
result of aerenchyma formation (Pradhan et al 1973, Kar et al 1974, Maurya and
Ghildyal 1975, Ogunremi 1991). Das and Jat (1977) observed an increase in total root
length when the moisture regime changed from unsaturated to saturated. Effects of
moisture regime on some root growth parameters are shown in Table 2. Root porosity
is inversely associated with soil oxygen content. With increasing soil moisture, the flux
of oxygen through the soil to the roots decreases. In response to this, cells in the root
cortex degrade, forming aerenchyma through which oxygen is transported to respiring
tissues. As a consequence, root porosity and soil aeration near the roots are increased.
In a submerged soil, the oxygen needs of rice roots are largely met through oxygen
transport via the aerenchyma.
We transplanted three rice cultivars (KDML 105, RD9, and IR46) recommended for
cultivation in rainfed lowland areas at three locations representing two toposequence
positions: high (at the border between pluvial and phreatic) and low (fluxial, both with
loamy sand soil texture) and two soil textures: loamy sand and clay, both in the low
toposequence position. The hydraulic regimes of the three locations are shown in
Figure 2. Roots were sampled at anthesis with 20- x 20- x 50-cm metal monolith
samplers, centered over a hill. Samples were divided into soil layers, soil was washed
from the roots, and roots were dried and weighed to measure root mass density.
A strong interaction existed between the effects of rice cultivar and hydraulic
regime on root mass density (RMD). KDML 105 had greater RMD in the 0- 10 cm soil
layer at the high toposequence position (low-moisture regime) than it had at the low
toposequence position (high-moisture regime). RD9 and IR46 had greater RMD in the
10-30 cm soil layer at the low toposequence than they had at the high toposequence
position (Fig. 3). In other soil layers, RMD was not significantly different between the
two toposequence positions for any cultivar. Among cultivars, however, at the high

Rainfed lowland rice roots: soil and hydrological effects 57
2. Hydraulic regimes at three experimental sites.

toposequence position, KDML 105 produced the greatest RMD in the 0-30 cm soil
layer, but at the low toposequence position, RD9 had the greatest RMD in the 10-30
cm soil layer (Fig. 4). The differences in RMD among cultivars in other soil layers were
not significant.
RD9 and IR46 produced relatively more root mass in the 10-40 cm soil layer under
the high-moisture regime; no such differences were detected for KDML 105 in either
toposequence position (Table 3). In general, root mass decreased exponentially with
soil depth (Fig. 5). Maximum depth of root penetration was similar for all cultivars at
both toposequence positions.

Soil textural effects
Soil texture affects the root system partly through its influence on pore size distribution.
Larger pore radii in sandy soils and greater mobility of particles under the pressure of
growing roots as compared with clayey soils favor rice root growth in coarse-textured
soils (Kar et al 1979). Kar et al concluded that high content of silt and sand with a
moderate clay content (20-35%) provided the most favorable physical environment for
rice root growth.
In a field experiment at a low toposequence position, the effects of soil texture on
root growth differed among cultivars. In the 0- 10 cm soil layer, KDML 105 had greater
RMD in the loamy sand than in the clay soil. Similarly, IR46 had greater RMD in the
10-20 cm layer in the loamy sand than in the clay soil. On the other hand, RD9 had the
greater RMD in the 10-30 cm layer of the clay than in that of the loamy sand soil
(Fig. 6). Furthermore, in the clay soil, RMD did not differ significantly among cultivars
in any soil layer, but in loamy sand, RD9 had greater RMD than the other two cultivars

58 Sharma et al
3. Effect of moisture regime on root mass density of three rice cultivars at two toposequence
positions in loamy sand soil.

Table 3. Hydrological effects on percent distribution of root mass of three rice cultivars in loamy
sand soil.

Root mass (% of total)
Soil
depth KDML 105 RD9 IR46
(cm)
Higha Low b High Low High Low

0-10 77.0 77.4 84.0 66.7 84.1 79.4
10-20 20.1 19.4 15.0 26.4 13.8 16.3
20-30 2.0 2.8 0.7 6.3 1.6 3.8
30-40 0.5 0.3 0.2 0.5 0.3 0.4
40-50 0.4 0.1 0.1 0.1 0.2 0.1

a High in toposequence (low-moisture regime). b Low in toposequence (high-moisture regime).

Rainfed lowland rice roots: soil and hydrological effects 59
4. Varietal differences in root mass density of rice at two toposequence positions in loamy sand
soil.

5. Depthwise distribution of root mass of three rice cultivars in loamy sand soil at two
toposequence positions.

60 Sharma et al
in the 10-30 cm layer (Fig. 7). Therefore, soil texture must be considered when
evaluating differences in root systems among rice cultivars.

Soil mechanical impedance effects
Root growth is closely associated with soil mechanical impedance in the root zone. To
elongate, roots must exert pressure greater than the soil mechanical impedance. Soil
mechanical impedance depends greatly on bulk density and soil moisture content.
Impedance increases with bulk density and decreases with moisture content. Drought,
therefore, would increase the mechanical impedance of soil by decreasing soil
moisture content and increasing bulkdensity, especially in swelling and cracking soils.
Thangaraj et al (1990) studied the effect of mechanical impedance on the root
growth of IR54 under moisture deficit in a Maahas clay soil. Rice seedlings were grown

6. Effect of soil texture on root mass density of three rice cultivars grown at low toposequence
positions.

Rainfed lowland rice roots: soil and hydrological effects 61
7. Varietal effects on root mass density of three rice cultivars grown at low toposequence
positions in loamy sand and clay soils.

uniformly under flooded conditions until 42 days after transplanting (DT). From 42 to
61 DT, different moisture regimes were created by using a line-source sprinkler
irrigation system. The crop was reflooded uniformly after that. Soil mechanical
impedance increased from 0 to 1.0 MPa as gravimetric moisture content declined from
160 to 65%. Root length density decreased as a power function of soil mechanical
impedance (Fig. 8). Mechanical impedance as little as 0.05 MPa reduced root length
density by 60% as compared with the continuously flooded control. Mechanical
impedance greater than 0.3-0.5 MPa decreased root growth and root extension by 75%.
Although root mass and root length densities responded similarly to mechanical
impedance, effects on root length were of greater magnitude than those on root mass
density. Thus, roots became shorter and thicker in response to increased mechanical
impedance.
The effects of bulk density and mechanical impedance on root length density of
IR36 in a clay soil under flooded conditions were studied (Sharma and De Datta 1986).
Soil bulk density and mechanical impedance were modified by applying different
tillage treatments. Root length density decreased as a power function of bulk density
or mechanical impedance (Fig. 9). Similar observations were made by Mambani et al
(1989) for IR20 in soils of different texture using different tillage practices. They
concluded that mechanical impedance of 0.57 MPa was the critical limit for root
growth of rainfed lowland rice.

62 Sharma et al
8. Relation between root length density of IR54 relative to control and soil mechanical
impedance in the drying puddled lowland soil at 0-10 cm soil depth (Thangaraj et a1 1990).

Table 4. Effect of interaction between submerged soil temperature regime and bulk density
of a lateritic sandy loam soil on root growth of rice (Kar et al 1976).

Bulk density Soil temperature regime (°C) LSD
(Mg/m3)
27-15 32-20 37-25 42-30 (0.05) (0.01)

Root dry weight (g)

1.5 1.46 3.18 3.44 1.22 0.25 0.33
1.6 1.53 3.05 3.62 1.25
1.7 1.60 2.38 2.46 1.41
1.8 1.63 1.80 1.92 1.49

In flooded soils, adverse effects of increased mechanical impedance on root growth
may be compounded by anoxia (Wiersum 1957). Roots lose solutes under anaerobiosis.
Reduced osmotic potential and turgor may reduce the ability of the roots to overcome
soil resistance. Furthermore, a strong interaction exists between mechanical imped-
ance and soil temperature for their effects on rice root growth. Kar et a1 (1976) found
that root growth decreased drastically when soil temperature exceeded 37 °C and bulk
density was greater than 1.6 Mg/m 3 (Table 4). Rice roots degenerate in submerged
conditions; higher soil temperatures favor this process.

Rainfed lowland rice roots: soil and hydrological effects 63
9. Relationship between bulk density and soil strength at transplanting and root length density
of rice (IR36) at harvest in the 0-10 cm layer of a flooded clay soil (Sharma and De Datta 1988).

According to a survey of 35 rice-growing locations in South and Southeast Asia,
mechanical impedance in the surface 10 cm soil layer averaged 0.64 MPa under
flooded conditions and 1.7 MPa in puddled fields without standing water. Lower soil
horizons had impedance >2.8 MPa, high enough to inhibit root elongation (Hasegawa
et al 1985). Therefore, research on the interactive effects of bulk density, soil
mechanical impedance, soil temperature, and hydrology on rice root growth have great
implications in boosting rice production in rainfed areas of South and Southeast Asia.

Conclusions
Growing rice cultivars having extensive deep root systems that are capable of
extracting water from deep soil layers is a means of achieving more efficient use of
rainwater under drought-prone rainfed situations. The rice root system differs strongly
between cultivars, soil conditions, and hydraulic regimes. Hence, it is difficult to make
generalizations about the effects of individual variables. We found that differences
between cultivars in root growth generally decreases with a change from unsaturated
to saturated conditions and with texture from loamy sand to clay. Unsaturated, light-
textured soils rather than saturated clay soils should be used for evaluating differences
in root systems among rice cultivars. Effects of mechanical impedance on root growth,
however, appeared to be similar under saturated and unsaturated conditions; root
length and root mass densities decreased as a power function of soil mechanical

64 Sharma et al
impedance for different rice cultivars. KDML 105 appeared relatively more responsive
to hydrology and soil texture changes than RD9 and IR46. Thus, KDML 105 may be
more widely adapted to rainfed lowland situations than the other cultivars. Future
research should combine germplasm improvement and soil physical management to
increase drought resistance through an improved rice root system.

References cited
Cruz R T, O’Toole J C, Dingkuhn M, Yambao E B, Thangaraj M, De Datta S K (1986)
Shoot and root responses to water deficits in rainfed lowland rice. Aust. J. Plant Physiol.
13:567-575.
Das D K, Jat R L (1977) Influence of three soil water regimes on root porosity and growth of four
rice varieties. Agron. J. 69:197-200.
Ghildyal B P, Tomar V S (1982) Soil physical properties that affect rice root systems under
drought. Pages 83-96 in Drought resistance in crops wih emphasis on rice. International Rice
Research Institute, P.O. Box 933, Manila, Philippines.
Greenland D J, Bhuiyan S I (1982) Rice research strategies in selected areas: environment
management and utilization. Pages 239-262 in Rice research strategies for the future.
International Rice Research Institute, P.O. Box 933, Manila, Philippines.
Hasegawa S, Thangaraj M, O’Toole J C (1985) Root behavior: field and laboratory studies.
Pages 383-395 in Soil physics and rice. International Rice Research Institute, P.O. Box 933,
Manila, Philippines.
Kar S, Varade S B, Ghildyal B P (1979) Pore size distribution and root growth relations of rice
in artificially synthesized soils. Soil Sci. 128:364-368.
Kar S, Varade S B, Subramanyam T K, Ghildyal B P (1974) Nature and growth pattern of rice
root system under submerged and unsaturated conditions. I1 Riso 23:173-179.
Kar S, Varade S B, Subramanyam T K, Ghildyal BP (1976) Soil physical conditions affecting
rice root growth: bulk density and submerged soil temperature regime effects. Agron. J.
68:23-26.
Mambani B, De Datta S K, Redulla C A (1989) Land preparation requirements for rainfed rice
as affected by climatic water balance and tillage properties of lowland soils. Soil Till. Res.
14:219-230.
Mambani B, De Datta S K, Redulla C A (1990) Soil physical behaviour and crop responses to
tillage in lowland rice soils of varying clay content. Plant Soil 126:227-235.
Maurya P R, Ghildyal B P (1975) Root distribution pattern of rice varieties evaluated under
upland and flooded soil conditions. I1 Riso 24:239-244.
Ogunrerni L T (1991) Influence of bulk density and moisture regime of a permeable soil on the
performance of a lowland rice, Oryza sativa L. Trop. Agric. 68:129-134.
O’Toole J C, Chang T T (1978) Drought and rice improvement in perspective. IRRI Res. Pap.
Ser. 14.
Pradhan S K, Varade S B, Kar S (1973) Influence of soil water conditions on growth and root
porosity of rice. Plant Soil 38:501-507.
Sharma P K, De Datta S K (1986) Physical properties and processes of puddled rice soils. Adv.
Soil Sci. 5:139-178.
Sharma P K, De Datta S K, Redulla C A (1987) Root growth and yield response of rainfed
lowland rice to planting method. Exp. Agric. 23:305-313.
Thangaraj M, O’Toole J C, De Datta S K (1990) Root response to water stress in rainfed lowland
rice. Exp. Agric. 26:287-296.

Rainfed lowland rice roots: soil and hydrological effects 65
Wiersum L K (1957) The relationship of the size and structural rigidity of pores to their
penetration by roots. Plant Soil 9:75-85.
Yoshida S (1981) Fundamentals of rice crop science. International Rice Research Institute, P.O.
Box 933, Manila, Philippines. 269 p.

Notes
Authors’ addresses: Pradeep K. Sharma, Department of Soil Science, HPKV, Palampur 176062
H.P., India; G. Pantuwan, Ubon Rice Research Center, P.O. Box 65, Ubon Ratchathani 34000,
Thailand; K.T. Ingram, Agronomy, Plant Physiology, and Agroecology Division, International
Rice Research Institute, P.O. Box 933, Manila, Philippines; S.K. De Datta, College of
Agriculture and Life Sciences, Virginia Polytechnic Institute and State University, Blacksburg,
VA 2401-0334, USA.
Citation information: Kirk G J D, ed. (1994) Rice roots: nutrient and water use. International
Rice Research Institute, P.O. Box 933, Manila, Philippines.

66 Sharma et al
Rice root traits for drought
resistance and their genetic
variation
K.T. lngram, F.D. Bueno, O.S. Namuco, E.B. Yambao, and C.A. Beyrouty

The root traits that confer drought resistance are not well-defined. Glasshouse
research has shown that the root xylem vessel cross-sectional area does not explain
water relation differences across genotypes. In field experiments under upland
conditions, root length density (RLD) was negatively correlated with grain yield of
three rice genotypes grown under different levels of water deficit stress. On the other
hand, in minirhizotron experiments under rainfed lowland conditions, only RLD in the
10-20 and 20-30 cm soil layers were related to relative yields (30-d vegetative phase
stress yield/continuously flooded control yield) in 12 rainfed lowland genotypes and
only on 2 sampling days (86 and 89 d after sowing). Two root characteristics were
common to drought-resistant rainfed lowland genotypes: 1) rapid root responses to
changing soil moisture level in the 10-20 and 20-30 cm soil layers, and 2) greater
absolute RLD below 20 cm.

Capacity for water uptake may limit rice productivity even in flooded soils. Thus,
midday stomatal closure (a symptom of leaf water deficit) has been observed in rice
growing in flooded soils (Dingkuhn et al 1990). However, water uptake and transport
by rice roots are most important and have been primarily studied in nonflooded soils,
especially as they affect yields under water-limited conditions, i.e., drought resistance.
Drought is not a single stress. Rather, as suggested by O’Toole and De Datta (1986),
it is a syndrome. The three major dimensions of the drought syndrome are the timing,
duration, and intensity of water deficit within the crop life cycle. Stress effects in each
of these dimensions result from a complex interaction between crop, soil, and
atmospheric factors.
Just as drought is a syndrome rather than a single stress, plant adaptations that
maximize yields under water-limited conditions are numerous and diverse. O’Toole
and Chang (1979) identified four components of drought resistance: tolerance,
avoidance, escape, and recovery. The second component, avoidance, can be subdi-
vided by its mechanisms—those that allow the plant to maintain a high internal water
status when available water is less than evaporated demand—into a) water conserva-
tion and b) water collection. Plant mechanisms for water conservation include leaf
rolling and stomatal closure; which tend to reduce growth and yield. Mechanisms for
water collection result in increased capacity for water uptake (e.g., through deeper
rooting or more efficient water extraction from soils); which should reduce yield
losses.
This paper focuses on water collection mechanisms in roots. We will describe recent
research on genetic variation and heritability of rice root traits as well as the
interrelationships among root characters, drought resistance, and water use.

Variation and heritability of root traits
Research on the genetic variation and heritability of rice root traits was recently
reviewed by O’Toole and Bland (1987). The findings are summarized in Tables 1 and
2. It has been long thought that the best root system for drought resistance has deep and
thick roots (Armenta-Soto et al 1983, Chang and Loresto 1986), so most studies of root
traits to date have emphasized those traits directly or indirectly.

Table 1. Root traits showing genetic variation in rice.

Diameter/thickness
Water extraction
Maximum depth Japonica > indica
Deep root-shoot ratio
Xylem vessel diameter

Root dry weight 0-10 cm, indica >japonica
Thick root number below 30 cm, japonica > indica

Branching Indica > japonica
Number

Table 2. Narrow sense heritability (NSH) of root traits in rice.

NSH (%)

Maximum root length 35-61
Basal diameter 60-80
Acropetal diameter 49-62
Root dry weight 43-92
Root-shoot ratio 53
Root number 44
Number of thick roots 33-53
Root volume 18-55
Root length density 44-77
Uprooting force 39-47

Sources: Armenta-Soto et al 1983, Chang et al 1982, Ekanayake et al 1985 a,b.

68 lngram et al
Geneticists have estimated narrow sense heritability from observations in F1, F2, or
F3 populations growing in either soil or aeroponic media (Table 2). For most traits,
inheritance was shown to be additive and polygenic. Overall, the root traits studied
show strong potential for improvement through breeding, with the greatest breeding
limitation being the large quantity of labor required for screening most root traits.
For much of the above research, genetic variation and heritability were estimated
from indica-japonica comparisons. Such a comparison ignores the fact that drought
occurs over widely varying rice environments, since indica rices are grown primarily
in the rainfed lowland ecosystem and japonica rices in the uplands. Thus, differences
in root traits between rice ecotypes may not be of practical use in breeding for drought
resistance. Focusing on the genetic variation and heritability within a single rice
ecotype instead might more quickly yield progress toward drought resistance. Simi-
larly, as we consider whether root traits can be transferred from wild Oryza species or
from one rice ecotype to another, we need to recognize that a trait that confers drought
resistance in one soil and rainfall environment may not be useful in another.

Root growth and development
Field research with four cultivars under continuously flooded conditions showed that
wet seeded rice (WSR) had about 1.5 times as much total root length (TRL) as
transplanted rice (TPR) by 50 d after seeding (DAS) (Fig. 1). Binato, a traditional
cultivar, had greater TRL than the other three cultivars studied, which were all
improved indica types (Fig. 2). The greater TRL of WSR was accompanied by greater
maximum root depth (IRRI 1991). This difference was maintained through maturity
and through a ratoon crop. The peak and decline of TRL shortly after panicle initiation
was probably related to increased competition for assimilates by the developing

1. Total root length of wet seeded and transplanted rice through a plant and ratoon crop cycle.
Each point is the average of four cultivars. Vertical bars show significant differences by LSD at
P < 0.05. PI = panicle initiation, F = flowering, H = harvest.

Rice root traits for drought resistance and their genetic variation 69
2. Total root length of four rice cultivars through a plant and ratoon crop cycle. Each point is the
average of two establishment methods. Vertical bars show significant differences by LSD at
P < 0.05.

Table 3. Grain yields (av of 24 rainfed lowland rice genotypes) in response to vegetative water
deficit under transplanted and wet seeded crop establishment.

Transplanted Wet seeded

Well-watered Deficit Well-watered Deficit

3.1 a a 2.2 b 3.1 a 3.0 a

a Means followed by the same letter are not significantly different at P < 0.05 by LSD.

panicle. Similarly, the increase in TRL beginning about 15 d after panicle emergence
was probably associated with decreased competition for assimilates as grains reached
physiological maturity.
Although TRL changed greatly through the season, once roots had reached their
maximum depth, there were no significant changes in root distribution through the
profile (IRRI 199 1). Changes in TRL probably result mostly from death and initiation
of branch roots rather than from changes in primary root axes.
These results have important implications for both nutrient uptake and drought
resistance. Greater TRL and deeper roots may allow greater or more efficient nutrient
uptake in WSR than in TPR. These root system differences also explain differences in
drought resistance observed when TPR and WSR are subjected to water deficit. For 24
rainfed lowland rices, water deficit significantly reduced yields of TPR but not of WSR
(Table 3, IRRI 1988).

70 lngram et al
Root relationships with drought resistance and water use
When upland rice is grown in a range of soil moisture conditions, grain yields are
negatively related to RLD (Fig. 3). In contrast, Mambani and Lal (1983) reported that
for upland rice growing across a toposequence, grain yields are related to RLD. Several
researchers have reported that rice root growth under aeroponic or hydroponic culture
is well-correlated with root growth under upland field conditions (Ahmadi 1983,
Chang and Loresto 1986).
Unfortunately, root traits observed in aeroponic culture were not at all related to
drought resistance under rainfed lowland conditions (Ingram et al 1990). Also, neither
total RLD nor RLD by soil layer were significantly correlated with yields of 30 rainfed
lowland rices grown in a farmer’s field in Tarlac, Philippines (data not shown). The
lack of correlation between aeroponic and rainfed lowland field root growth under-
scores the need to consider the soil environment for which germplasm improvement
is targeted.
One hypothesis is that thick roots confer drought resistance because they have
greater xylem vessel radii, lower axial resistance to water flux, and hence, greater
capacity for water uptake from deeper soil layers (Yambao et al 1992). This hypothesis
is the opposite of that proposed for wheat grown on residual soil moisture—i.e., that
smaller root vessels confer drought resistance (Richards and Passioura 1989). In rice,
the axial resistance to water flux can be estimated by summing the individual
resistances for different root vessels, assuming that the vessels act as capillaries and
obey the Poiseuille-Hagan equation (Yambao et al 1992). Root box and hydroponic
research showed that differences in axial resistance to water flux explained shoot-water

3. Relationship between root length density and grain yield of upland rice.

Rice root traits for drought resistance and their genetic variation 71
4. For IR36, the response surfaces for relationships between equivalent root vessel radius,
transpiration, and leaf water potential as estimated by a) Poiseuille-Hagan equation or b) the
best-fitting curve. Variation in root vessel radius was achieved through root pruning in
hydroponic culture.

relations for a single cultivar (Fig. 4) but did not explain differences across cultivars
(Fig. 5). Clearly, factors other than axial resistance explain differences among cultivar
responses to water deficit.
Thick roots may also be hypothesized to confer drought resistance because
branching is directly related to root thickness (Fitter 1991). Thick roots persist longer,
produce more and larger branch roots, thereby increasing RLD and water uptake
capacity.

72 lngram et al
5. For 5 cultivars, the response surfaces for relationships between equivalent root vessel radius,
transpiration, and leaf water potential as estimated by a) Poiseuille-Hagan equation or b) the best-
fitting curve. Variation in root vessel radius was achieved through different cultivars and through
root pruning in hydroponic culture.

Root growth under water deficit stress
The minirhizotron has enabled us to make observations of the dynamic changes in root
distribution in response to water deficit. In field experiments, we grew 12 rice
genotypes under either continuously flooded conditions or drained 25-55 DAS. Total
root length for two of the genotypes throughout the season is shown in Figure 6. We
grouped the genotypes into three classes based on RLD under stress and nonstress

Rice root traits for drought resistance and their genetic variation 73
6. Total root length (0-70 cm soil layer) of IR46 and IR20 when continuously flooded or
nonflooded at 25-55 DAS throughout the full crop season.

conditions in the 10-30 cm soil layer, grading them high, medium, and low. We further
considered yield potential and effect of stress on maturity (Table 4).
The most important finding was that there was great genetic variation in root system
plasticity. In all genotypes, root length of stressed plants rapidly dropped below that
of continuously flooded plants when the plots were initially drained. There was also a
sharp dip in root length when stressed plants were reflooded (Fig. 6). After each dip,
genotypes with good root systems (e.g., IR46) produced greater root length in the
stressed than in the well-watered plots and had maximum RLDs greater than 0.5 cm
cm3 in the 20-30 cm soil layer. Genotypes with poor root systems (e.g., IR20) had
greater root length in the control than in the stressed plots and had RLDs less than 0.5
cm/cm 3.
The dynamic changes in root length are shown as the ratios of root length in stressed
and control treatments (Fig. 7). We hypothesize that these dynamic root responses to

74 lngram et al
Table 4. Root length and other characteristics related to drought resistance of 12 rice genotypes
under rainfed lowland conditions. a

Relative Maximum Yield Maturity Cultivar/line
nonstressed RLD stressed RLD potential delay by
stress

Good root characters
S >C High Good +/0 IR46
lR49612-45-6-2-2
S>C High Medium 0 IR46331-PMI-53-2-1-3
lR47310-117-1-3-3
lR13146-45-2-3
S>C High Low (blight) 0 lR43526-523-1-1-1

Poor root characters
C>S Low Good + IR20
IR19431-72-2
C>S Medium Good 0 IR43449-SKN-522-3-1-3
IR28626-33-3252-3

Intermediate root characters
C S High Excellent/Poor ++ IR72
Binato

a C = continuously flooded control: S = nonflooded 2555 DAS: +, ++ = less than 5 d and greater than 8 d delay
in maturity by stress, respectively.

7. Idealized relative root length density (root length stress divided by root length control) for
drought-resistant and drought-susceptible rice cultivars through a full crop season.

Rice root traits for drought resistance and their genetic variation 75
soil moisture are mostly a result of the shedding of old branch roots and the production
of new ones. According to our hypothesis, branch roots produced during stress are
adapted to aerobic conditions and have little or no aerenchyma; those produced after
reflooding are adapted to anaerobic conditions, with aerenchyma.

Summary and conclusions
Among the root traits studied, TRL is the most strongly related to drought resistance
under upland conditions. Root traits found to confer drought resistance under rainfed
lowland conditions were RLD in the 10-30 cm soil layer and dynamic shedding of roots
and production of root length in response to changing moisture conditions.
There are still large gaps in our knowledge of the overall function and specific
genetic traits of roots in relation to water uptake. The potential for transferring desirable
root traits from upland japonicas to lowland indicas is uncertain, although it may be
possible to accomplish these transfers with molecular biological tools. The sensing
mechanisms that determine root responses to changes in soil moisture or to soil strength
are little understood. Many of the root traits that have been proposed as contributing
to drought resistance have not yet been fully evaluated. These include maximum depth
of longest roots, number of vertically oriented root axes, root osmotic adjustment, and
hardpan penetration.

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drought resistance of rice. J. Exp. Bot. 43(252):925-932.

Notes
Authors’ addresses: K.T. Ingram, F.D. Bueno, O.S. Namuco, and E.B. Yambao, Agronomy,
Plant Physiology, and Agroecology Division, International Rice Research Institute, P.O. Box
933, Manila, Philippines; C.A. Beyrouty, Depatment of Agronomy, University of Arkansas,
Fayetteville, Arkansas 72701, USA.
Citation information: Kirk G J D, ed. (1994) Rice roots: nutrient and water use. International
Rice Research Institute, P.O. Box 933, Manila, Philippines.

Rice root traits for drought resistance and their genetic variation 77
Use of molecular markers
to exploit rice root traits
for drought tolerance
H.T. Nguyen, J.D. Ray, and Long-Xi Yu

Current progress in the application of molecular markers and root-specific gene
expression to exploit root traits for drought tolerance in rice is reviewed. The root
system is central to the mechanisms by which plants resist or escape drought.
Research indicates significant genetic variability in the associated root traits,
especially root morphology and the ability to penetrate compacted soil layers.
However, genetic improvement for root traits is difficult using conventional
phenotypic selection criteria. Recent advances in molecular biology and genome
mapping may provide new strategies for incorporating root traits into breeding
programs.

Plants have various means by which they escape or resist periods of limited water
availability (drought) (Ludlow and Muchow 1990). In this paper, we consider the role
of the root system in the response of rice to drought and the use of molecular markers
as selection tools for incorporating root traits in improved rice cultivars.

Drought and root systems
Roots can moderate the effects of drought by growing deeper or thicker to reach more
water (and thus increase water supply) or by changing the rate at which water becomes
available (Gregory 1989). Individual root characteristics such as thickness, depth of
rooting, and penetration ability have been associated with drought avoidance (O’Toole
and Chang 1979, Yoshida and Hasegawa 1982, Ekanayake et al 1985). O’Toole and
De Datta (1986) suggest that increased root depth and root density in rice increase the
capacity to extract available soil water and may be responsible for increased drought
avoidance in some rice genotypes. Thangaraj et al (1990) suggest that during water
stress, water use is primarily determined by root system density and depth. While
exploitation of a deeper soil volume may be beneficial in avoiding drought, water in
these deeper regions is often unavailable due to the presence of compacted soil layers.
Compacted soil layers are often found in lowland ricefields, formed as a result of
the cultural practices used in preparing land for rice (O’Toole and De Datta 1986).
Mechanical disruption of such layers is expensive and short-lived, as the compacted
layer often reforms in a few years (Threadgill 1982, Busscher et al 1986). Under these
conditions, the ability of roots to penetrate compacted soil layers is an important
characteristic associated with drought avoidance.

Effect of compacted soil layers on root systems
Compacted soil layers—variously known as hardpans, plowpans, tillage pans, plow
soles, and tillage soles (Taylor 1974)—impede root growth. They are one of the most
important factors determining root elongation and proliferation (Bengough and
Mullins 1990, Tu and Tan 1991). They cause changes in both root morphology and
physiology, including a decrease in cell length and a corresponding increase in cell
thickness and a decrease in the rate of cell division. Other physiological changes such
as osmotic adjustment and changes in plant growth regulator activity are also involved
(Bengough and Mullins 1990, Glinski and Lipiec 1990).
The effects of this mechanical impedance to roots on plant growth and development
include decreased transpiration rates, decreased leaf area expansion, and decreased dry
matter accumulation (Masle and Passioura 1987, Ludlow et al 1989, Assaeed et al
1990, Masle 1992). These effects may be direct consequences of reduced root access
to water and nutrients. Masle and Passioura (1987), however, found that the effects of
soil compaction on shoot growth were manifest before the supply of water and nutrients
to the shoot was affected and concluded that plant growth regulators produced in the
roots triggered the shoot response (Ludlow et al 1989).

Genetic variability in root systems
O’Toole and Bland (1987) have reviewed the genetic variability of root systems in crop
plants. Most examples of genetic variation in root system traits indicate quantitative
control (Schiefelbein and Benfey 1991). In rice, significant genetic variation in several
root characteristics associated with drought avoidance has been reported (O’Toole and
Chang 1979; Kandasamy 1981; O’Toole 1982; Chang et al 1982; Ekanayake et al 1985,
1986). The inheritance of root system characteristics in rice, including root length
density, root thickness, and root mass, was reported by Chang et al (1982) and
Ekanayake et al (1985). These studies indicate that genetic improvement for several
root morphological traits in rice is possible through early generation selection.
Genotypic variation in root penetration ability has been reported for cotton
(Kasperbauer and Busscher 199l), wheat and barley (Masle 1992), and rice (Kandasamy
1981, O’Toole 1982). We have evaluated root penetration by upland and lowland rice
cultivars using a wax layer system (Taylor and Gardner 1960) to simulate a compacted
soil layer. We found that root penetration ability varied with genotype and that upland

80 Nguyen et al
rice genotypes had a greater penetration ability than lowland rice genotypes. Moreover,
root penetration ability was positively correlated with root thickness (unpubl. data).

Use of molecular genetic markers in tagging root characteristics
Incorporation of root traits in breeding programs is hampered by the difficulty of
measuring root traits in the field and the consequent lack of reliable and efficient
screening techniques (Gregory 1989, O’Toole 1989). The quantitative nature of many
root characteristics is a further complication. Attempts made to correlate root charac-
teristics with more readily measurable shoot characteristics have met with limited
success. For example, deep root systems have been positively correlated with plant
height in rice (Armenta-Soto et al 1983, Ekanayake et al 1985, Chang et al 1986).
However, while selection for plant height could result in selection for deeper root
systems, the ideotype upland rice plant is of short or intermediate height with a deep
root system (Ekanayake et al 1985). Ekanayake et al (1985) did obtain recombinant
plants with short height and deep root systems, but obviously selection based on plant
height alone would not have identified these plants. This illustrates the need for more
effective selection criteria for root characteristics. One solution may be the identifica-
tion of molecular genetic markers associated with specific root traits, such as penetra-
tion ability.

RFLP molecular genetic markers
Plant breeders and geneticists have long made use of genetic markers in selection
programs, inheritance evaluations, phylogenic studies, genotype identification, and
construction of linkage maps. Classical linkage maps are constructed on the basis of
linked morphological characters and have existed since the early 1900s. Other genetic
markers have made use of biochemical differences, the most common of which are
allozyme (isozyme) markers developed in the 1950s. Since the 1970s, the development
of techniques to analyze DNA directly has led to a new class of genetic markers called
molecular markers, the most common being restriction fragment length polymorphism
(RFLP).
RFLP molecular markers have several advantages over more conventional morpho-
logical genetic markers. They are usually inherited codominately, exhibit phenotypic
neutrality, rarely have epistatic or pleiotropic interactions, and are typically tissue- and
phenologically independent (Beckmann and Soller 1986, Tanksley et al 1989). These
characteristics and the potentially unlimited number of RFLP loci in a population speed
the construction and increase the resolution of linkage maps. Other potential uses of
RFLP markers are described elsewhere (Helentjaris et al 1985, Beckmann and Seller
1986, Landry and Michelmore 1987, Tanksley et al 1989).
Restriction fragment length polymorphisms are the result of differences
(polymorphisms) in DNA fragments obtained by cleaving the DNA with restriction
endonucleases. Such polymorphisms are detected as changes in length (molecular
weight) of otherwise homologous DNA fragments relative to the restriction site of a
specific endonuclease. The changes in the length of the fragments are due to base pair

Use of molecular markers to exploit rice root traits for drought tolerance 81
changes in the highly specific recognition site of the endonuclease; DNA remangements
resulting in the relocation of the site; or to insertion/deletion events within one of the
fragments (Botstein et al 1980; Beckmann and Soller 1983, 1986).
Botstein et al (1980) first proposed the use of RFLPs as genetic markers in humans.
By 1983, the potential applications of RFLPs in plants were being suggested (Burr et
al 1983, Soller and Beckmann 1983, Tanksley 1983), and by the mid-l980s, RFLP
linkage maps were published for maize and tomato (Bernatzky and Tanksley 1986,
Helentjaris et al 1986). In varying degrees of resolution, RFLP linkage maps are now
available for a large number of species including rice (McCouch et al 1988, McCouch
and Tanksley 1991).
High-resolution linkage maps increase the possibility of identifying markers linked
to traits of interest, including quantitative trait loci (QTL) (McCouch et al 1988, Knapp
et al 1990, McCouch and Tanksley 1991). The rice RFLP linkage map is presently of
sufficient resolution (about 1 cM, McCouch and Tanksley 1991) to permit mapping of
QTLs. Identification of RFLP markers linked to desirable quantitative root character-
istics would greatly facilitate their selection in breeding programs (Hanson et al 1990).
Identification of RFLP markers would also minimize the requirement for exhaustive
experiments to characterize root systems since REPS analyze the DNA directly and
are tissue-independent.

RAPD molecular genetic markers
A new class of molecular genetic markers has recently been developed based on
randomly amplified polymorphic DNA (RAPD, pronounced “rapid”) (Williams et al
1990, Welsh and McClelland 1990). The RAPD technique is based on the use of single
arbitrary sequence oligodeoxynucleotides as primers for polymerase chain reactions
(PCR). When primers bind to opposite strands of DNA within an amplifiable distance,
the intervening DNA segment can be amplified using PCR. The length of the amplified
DNA segments depends on the sequence and length of the primer in conjunction with
the reaction conditions (reaction buffer, annealing temperature, etc.). Comparison of
the amplified DNA segments by electrophoresis in agarose gels allows the detection
of differences (polymorphisms) between DNA from different sources. Polymorphisms
may be the result of changes in the primer binding sites, DNA insertions resulting in
the binding sites being too far apart for amplification, or DNA insertions or deletions
that change the length of the amplified segment (Williams et al 1990).
The RAPD polymorphisms are molecular genetic markers and have been used as
diagnostic tools in the same manner as RFLP molecular genetic markers (Hu and
Quiros 1991, Crowhurst et al 1991, Klein-Lankhorst et al 1991, Martin et al 1991,
Paran et al 1991). They have advantages over RFLP markers because they are easier
to use, less costly, and faster (Anderson and Fairbanks 1990). An additional advantage
is that they do not use radioisotopes, although nonradioactive hybridization techniques
have recently been developed for RFLP markers.
It has been suggested that RAPD markers could be used to develop linkage maps
with greater efficiency and higher resolution than do RFLP linkage maps (Williams et
al 1990). However, there are some disadvantages and difficulties in using arbitrary

82 Nguyen et al
primers in constructing linkage maps, such as the dominant nature of RAPD markers
which prevents direct determination of heterozygosity (Devos and Gale 1992, Halward
et al 1992).

Root-specific gene expression
Numerous genes that are expressed in specific tissues have been isolated in plants.
However, only a limited number of genes that are specifically expressed in roots have
been isolated. These include genes from tobacco (Conkling et al 1990, Keller and Lamb
1989), barley (Lerner and Raikhel 1989), and rice (Pater and Schilperoort 1992). The
function of the protein coded by the gene isolated from rice is unknown. Gene
expression in roots remains little explored, probably due to the difficulty inherent in
studying roots and the limited understanding of root biochemical processes.
However, isolation of root genes and characterization of the regulatory elements
governing their expression during drought or in response to other environmental
stimuli (such as a compacted soil layer) could lead to an understanding of the
mechanisms involved in drought avoidance. Recently, a review by Schiefelbien and
Benfey (1991) emphasized the lack of genetic and molecular studies on roots compared
with shoots. Research using molecular approaches is needed to characterize the
patterns of gene expression and isolate genes associated with root penetration ability
in rice. Such genes are expected to play a role in allowing the root tip region to grow
and penetrate through the compacted soil layers. Understanding the genetic organiza-
tion and expression of these genes is essential to establish the molecular basis of root
penetration traits in plants. In addition, the isolated cDNAs can be used as molecular
markers for breeding applications.

Conclusions
Incorporation of selection for root characteristics such as root penetration ability into
breeding programs offers the possibility of developing genotypes better able to exploit
soil water. Better exploitation of soil water reserves would allow plants to avoid the
adverse effects of periods of low rainfall. Phenotypic selection of root characteristics
in large breeding programs is difficult and requires too much time and labor, thus
limiting progress in developing improved genotypes. One solution is to use indirect
selection criteria based on the correlation between root characteristics and more readily
identifiable shoot phenotypes. However, this may not always be feasible or reliable. A
more direct approach is through the use of molecular genetic markers tightly linked to
the root characteristic of interest. The first step in using molecular markers in breeding
programs is to identify markers associated with desirable root characteristics. We have
begun this process in our laboratory with the tentative identification of four RFLP
molecular genetic markers associated with root penetration ability in rice (Texas
Technical University, unpubl. data). The identification of such markers will provide
breeders with better selection criteria for incorporation of desirable root characteristics
into improved cultivars.

Use of molecular markers to exploit rice root traits for drought tolerance 83
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Notes
Authors’ addresses: H.T. Nguyen, J.D. Ray, and Long-Xi Yu, Plant Molecular Genetics
Laboratory, Institute for Biotechnology and Department of Agronomy, Horticulture, and
Entomology, Texas Technological University, Box 42122, Lubbock, Texas 79409, USA.
Citation information: Kirk G J D, ed. (1994) Rice roots: nutrient and water use. International
Rice Research Institute, P.O. Box 933, Manila, Philippines.

86 Nguyen et al