You are on page 1of 59
T 2008
T
2008

B

No. 13
No. 13

Improving productivity and livelihood for fragile environments

T 2008 B No. 13 Improving productivity and livelihood for fragile environments

The International Rice Research Institute (IRRI) was established in 1960 by the Ford and Rockefeller Foundations with the help and approval of the Government of the Philippines. Today, IRRI is one of the 15 nonprofit international research centers supported by the Consultative Group on In- ternational Agricultural Research (CGIAR – www.cgiar.org). IRRI receives support from several CGIAR members, including the World Bank, European Union, Asian Development Bank, International Fund for Agricultural Development, Rockefeller Foundation, Food and Agriculture Organization of the United Nations, and agencies of the fol- lowing countries: Australia, Brazil, Canada, Denmark, France, Germany, India, Iran, Japan, Malaysia, Norway, People’s Republic of China, Repub- lic of Korea, Republic of the Philippines, Sweden, Switzerland, Thailand, United Kingdom, United States, and Vietnam. The responsibility for this publication rests with the International Rice Research Institute.

This publication is copyrighted by the International Rice Research Institute (2008) and is licensed for
This publication is copyrighted by the International Rice Research Institute
(2008) and is licensed for use under a Creative Commons Attribution-Non-
Commercial-ShareAlike 3.0 License (Unported). Unless otherwise noted, users are
free to copy, duplicate, or reproduce, and distribute, display, or transmit any of the
articles or portions of the articles, and to make translations, adaptations, or other
derivative works under the following conditions:
Attribution: The work must be attributed, but not in any way that suggests
endorsement by IRRI or the author(s).
NonCommercial: This work may not be used for commercial purposes.
ShareAlike: If this work is altered, transformed, or built upon, the resulting
work must be distributed only under the same or similar license to this one.
To view the full text of this license, visit
http://creativecommons.org/licenses/by-nc-sa/3.0/.

Mailing address: DAPO Box 7777, Metro Manila, Philippines Phone: +63 (2) 580-5600 Fax: +63 (2) 580-5699 Email: irri@cgiar.org Web: www.irri.org. Rice Knowledge Bank: www.knowledgebank.irri.org Courier address: Suite 1009, Security Bank Center 6776 Ayala Avenue, Makati City, Philippines Tel. +63 (2) 891-1236, 891-1174, 891-1258, 891-1303

Suggested Citation:

IRRI (International Rice Research Institute). 2008. Improving productivity and livelihood for fragile environments. IRRI Technical Bulletin No. 13. Los Baños (Philippines): IRRI. 54 p.

Editing: Bill Hardy

Layout and Design: Emmanuel Panisales

ISSN 0074-7807

Contents

 

Contents

III

Preface

IV

Physiological basis of tolerance of flash flooding during germination and early seedling establishment in rice

1

Abdelbagi M. smail, Evangelina S. Ella, Gina Vergara, Donna F. Holt-Stevens, Alvaro Pamplona, and Dave Mackill

Salinity tolerance in rice: physiological bases and implications for management strategies for better crop establishment

8

Abdelbagi M. smail, Babita Thapa, and James Egdane

Opportunities for direct seeding and improved weed control in the Barind of Bangladesh

15

M.A. Mazid, C.R. Riches, A.M. Mortimer, and D.E. Johnson

Breeding for submergence tolerance

20

D.J. Mackill, A.M. smail, S. Heuer, E. Septiningsih, A.M. Pamplona, R.M. Rodriguez, C.N. Neeraja, D. Sanchez, K. ftekhar, and G. Vergara

Participatory varietal selection of salinity-tolerant rice for the coastal wetlands of Bangladesh

27

M.A. Salam, G.B. Gregorio, D.L. Adorada, and R.D. Mendoza

Increasing profits from rice production in Bangladesh:

direct wet seeding of rice using a plastic drum seeder

32

M.

Zainul Abedin

Characterizing and understanding the socioeconomic conditions of farming households in rainfed rice environments: a case in eastern Uttar Pradesh

36

T. Paris, A.D. Cueno, and A. Singh

Preface

Improving Productivity and Livelihood for Fragile Environments is one of IRRI’s four programs and 11 projects stipulated in its Medium-Term Plan for 2006-2008. The Medium-Term Plan (MTP) for 2006-2008 reflects IRRI’s core agenda in addressing current and emerging problems in rice. It is guided by the broad framework of the strategic plan outlined in the document IRRI Toward 2020 published in 1996, and updated in November 2003. It also takes advantage of the scientific opportunities that assist the Institute in reaching its goals.

Improving Productivity and Livelihood for Fragile Environments is Program 3 of the MTP for 2006-2008. It examines risk reduction in rice cultivation. The program also focuses on helping increase yield and farm income via the development of stress-tolerant better-yielding varieties using efficient crop management practices.

In the past, the probability of success in research for building tolerance for abiotic stresses into better-yielding varieties was low, leading to inadequate allocation of research resources to solve these problems. But with the recent advances in molecular biology for tagging and characterizing genes and their transfer to other species, the probability of success in this area brightened. Since the environments are diverse and their domains vary across countries, the research is being done in partnership with the national agricultural research and extension systems, drawing on local scientific expertise and farmers’ indigenous knowledge.

Program 3: Improving Productivity and Livelihood for Fragile Environments attempts to solve the abovementioned problems in three projects―Project 7: Genetic enhancement for improving productivity and human health in fragile environments; Project 8: Natural resource management for rainfed lowland and upland rice ecosystems; and Project 9: Consortium for Unfavorable Rice Environments (CURE).

This Technical Bulletin showcases the studies and research results from each of the projects under Program 3.

V

Physiological basis of tolerance of flash flooding during germination and early seedling establishment in rice

Abdelbagi M. smail, Evangelina S. Ella, Gina Vergara, Donna F. Holt-Stevens, Alvaro Pamplona, and Dave Mackill

More than 16 million ha of lowland and deepwater rice areas are unfavorably affected by flooding because of complete submergence. Rice is the only crop plant adapted to aquatic environments because of its well-developed aerenchyma tissue that facilitates oxygen diffusion through continuous air spaces from shoot to root and avoids anoxia development in roots. However, complete submergence due to frequent flooding can adversely affect plant growth and yield. Two types of flooding cause damage to rice: flash flooding, which results in rapid ascending of water levels with complete submergence for about 1–2 weeks, and deep water, in which water depth exceeds 100 cm and persists for longer periods of up to several months. Plants may become completely submerged for short periods if flooding is severe. Elongation ability of leaves and internodes is essential in deepwater conditions to keep pace with the rising water levels and to escape complete submergence. Traditional varieties adapted to these environments are low yielding because of their low-tillering ability, susceptibility to lodging, and poor grain quality. Flash flooding can occur any time during the growing season and usually occurs more than once. It is usually more damaging if it occurs early in the season, particularly during early crop establishment. This is because younger seedlings are more sensitive to flooding. In direct-seeded areas, even waterlogging can be devastating because of the high sensitivity of all crop plants to low oxygen during germination.

Tolerance of flooding during germination and early seedling establishment

The likelihood of occurrence of flash flooding at different stages of growth requires different tolerance strategies. In rainfed lowlands, direct seeding is becoming more popular because of the escalating expense and scarcity of labor, and farmers are also enthusiastic to adopt it because of its additional benefits such as shortening crop duration and the enhanced tolerance of some stresses, particularly drought. Breeding cultivars with tolerance of flooding during germination and early seedling establishment will help avoid crop failures commonly encountered when early flooding occurs in both rainfed and irrigated ecosystems. Moreover, maintaining a shallow water head after seeding under irrigated conditions can help suppress weed growth and this could provide an effective, cheap, and sustainable method for weed management. However, this practice is stalled by the unavailability of suitable germplasm. Previous studies showed that rice is capable of germination underwater, but this capability is limited to coleoptile elongation, with failure to develop further. In an attempt to discern rice germplasm with higher tolerance of submergence during germination, we screened more than 8,000 genebank accessions and breeding lines and a few tolerant lines were identified. Screening was conducted by direct dry seeding in plastic trays containing a shallow layer of soil. Seeds of individual lines were sown in rows and immediately submerged by adding water to a depth of 10 cm. This depth is maintained for 2–3 weeks, when the percentage of seeds that germinate and successfully emerge from water

Table 1. Rice accessions most tolerant of flooding during germination.

Cultivar Origin Percent survival (first screening) Khaiyan – 90 Khao Hlan On Myanmar 75 Cody
Cultivar
Origin
Percent survival
(first screening)
Khaiyan
90
Khao Hlan On
Myanmar
75
Cody
United States
70
Dholamon 64-3
Bangladesh
80
Liu-Tiao-Nuo
China
70
Ma-Zhan (Red)
China
90
Sossoka
Guinea
85
Kaolack
Guinea
85
Kalonchi
90
Nanhi
ndia
80
R6855-00----
NPT-RR
75
R6855-00--3-
NPT-RR
55
Seedling survival (%)
00
A
80
Not submerged
60
Submerged
40
0
0
Khaiyan
Khao Hlan On
Tolerant
FR3A
R4
ntolerant

is determined. Through this method, about 12 lines were identified as being tolerant (Table 1) and the tolerance of some of them was further confirmed in replicated trials (Fig. 1A,B).

Traits associated with tolerance of flooding during germination and early growth

Tolerant lines and a few intolerant checks were evaluated for some agronomic traits to test their association with tolerance. A subset of these is shown in Table 2. Tolerant cultivars vary substantially with respect to mature plant height, days to flowering, and average grain weight. This variation provides opportunities for breeders to select appropriate parental lines for crossing to incorporate this trait. Tolerant lines seem to emerge faster from the soil and water (by about 2–3 d and 2–4 d, respectively) when compared with intolerant lines. The strong negative correlation of survival with

time of emergence from soil (R = –0.97) and water (R = –0.95) indicated that fast germination and growth under hypoxic conditions is crucial for survival. However, survival did not correlate with plant height at maturity, days to flowering, or average grain weight. Tolerant cultivars tend to grow faster underwater, produce taller seedlings with more leaves, and attain greater leaf area than intolerant lines (Fig. 2), traits that might also be useful for weed competitiveness early in the season.

Germination under anoxia (absence of O 2 )

Six tolerant and two sensitive cultivars were evaluated for their ability to germinate under anoxia. Seeds were sterilized using sodium hypochloride and tween 20, and then placed in a 1% stagnant agar solution deoxygenated by continuous bubbling of nitrogen gas.

Seedling survival (%) after dry seeding and submergence for 21 d

00 B 80 60 LSD 0.05 40 0 0 Cody Khaiyan Kalonch Nanh Khao FR3A
00
B
80
60
LSD 0.05
40
0
0
Cody
Khaiyan Kalonch
Nanh
Khao
FR3A
R
R8
R4
R64
Hlan On
Tolerant
ntolerant
Fig. 1. Average survival of selected lines over two separate replicated experiments. Vertical bars
indicate (A) S.E. and (B) LSD 0.05 .

Table 2. Comparison between selected tolerant and sensitive lines for selected agronomic traits and their associa- tion with survival.

Cultivar Origin Days to flowering Mature height 1,000-seed wt. Days to emergence Survival (%) (cm)
Cultivar
Origin
Days to flowering
Mature height
1,000-seed wt.
Days to emergence
Survival (%)
(cm)
Soil
Water
Tolerant lines
Dholamon
Bangladesh
7
03
.5
4
9
8
Liu-Tiao-Nuo
China
6
43
7.0
4
9
7
Khaiyan
?
66
60
8.
5
74
Khao Hlan On
Myanmar
85
45
8.3
4
9
73
Intolerant lines
R64
Philippines
65
30
0.0
7
3
7
FR3A
ndia
70
67
9.7
7
3
0
R4
Philippines
73
5
8.4
7
3
9
Correlation with
–0.47
0.50
–0.00
–0.97
–0.95
survival
Coleoptile length (cm)
Coleoptile length (cm)
3
8
6
4
0
0
Seedling height (cm)
Root length (cm)
Leaf area (cm )
Aerated tap water
Anoxic agar

Fig. 2. Average shoot height, root length, and leaf area of five tolerant (shaded columns) and three intolerant (black columns) cultivars germinated underwater. Results are means of 3 replicates taken 21 d after seeding.

Evaluation of percent germination, length of coleoptiles, as well as appearance of roots was carried out after 7 d of continuous anoxia. Tolerant lines had greater coleoptile length under both anoxic and normal conditions (Fig. 3).

Physiological mechanisms associated with tolerance of flooding during germination

Total amylase activity The ability to break down starches into simple sugars is a major factor limiting germination under flooded conditions. This is because of the high sensitivity of key enzymes involved

Fig. 3. Average coleoptile length of six tolerant (open columns) and two intolerant (black columns) cultivars under anoxia and aerated conditions. Data are from 7-d-old seedlings and vertical bars indicate ± S.E.

in this process to low oxygen. Total amylase activity was measured using two tolerant and two sensitive lines germinated in flooded soils for 3 days. The activity of these enzymes increased substantially in germinating seeds of tolerant lines under flooding but did not change significantly in sensitive lines (Fig. 4). Higher activity of these enzymes in germinating seeds of tolerant lines under flooding indicated that these lines are able to break down stored starch into simple sugars better than sensitive lines, and this step is essential for germination and growth. Metabolic breakdown of simple sugars is much less sensitive to low oxygen than the

Amylase activity (units mg – protein) 50 A 40 Not submerged Submerged 30 0 0
Amylase activity (units mg – protein)
50
A
40
Not submerged
Submerged
30
0
0
0 Khaiyan
Khao Hlan On
Tolerant
FR3A
R4
ntolerant
Plant survival (%) 6 B 4 R = 0.9  0 0 0 30 40
Plant survival (%)
6
B
4
R = 0.9
0
0
0
30
40
50

Amylase activity

Fig. 4. (A) Total amylase activity in germinating seeds of two tolerant and two intolerant rice cultivars sown in submerged soils for 3 days. Vertical bars are S.E. (B) Correlation between amylase activity and seedling survival.

processes involved in starch degradation. Total activities of these enzymes correlated positively with shoot and root length (R = 0.85, 0.83, respectively), and with plant survival (Fig. 4B), suggesting a strong relationship between the activity of these enzymes and the ability of seeds to germinate and seedlings to grow under submerged conditions.

Plant hormones Germinating seeds of tolerant lines produced more ethylene than susceptible ones under submergence (Fig. 5). Ethylene is known to counteract ABA synthesis and increase synthesis of and sensitivity to GA. High levels of ABA in seeds are associated with the inhibition of seed germination and dormancy; however, high GA is associated with activation of amylase enzymes and breakdown of stored starches to be used for further growth of germinating seeds.

Peroxidase activity Peroxidases are responsible for the assembly of lignins and proteins in the cell wall and for the binding of ferulic acid to cell walls by the formation of diferuloyl cross-links to

Ethylene content (mg seedling )

30

Khao Hlan On (N) Khao Hlan On (S) IR42 (N) IR42 (S)
Khao Hlan On (N)
Khao Hlan On (S)
IR42 (N)
IR42 (S)

5

0

5

0

5

0

4

5

7

8

0

Days of incubation in soil

Fig. 5. Ethylene content of germinating seeds of one tolerant and one sensitive line under submerged conditions. N = normal, S = stress.

matrix polysaccharides, both of which are associated with reduced cell wall extensibility. Higher peroxidase activity is closely associated with reduced growth in other plants such as in mung bean and peanut. We measured peroxidase activity in germinating seeds of two tolerant (Khaiyan and Khao Hlan On) and two sensitive (R64 and IR22) cultivars to evaluate its involvement in growth under low-oxygen conditions. Tolerant genotypes showed much

less peroxidase activity than intolerant ones (Fig. 6A). A strong negative correlation was observed between peroxidase activity and shoot growth (R = –0.69) and seedling survival (Fig. 6B). The ability of seedlings to elongate underwater and emerge quickly is critical for survival. This may also suggest that lower peroxidase activity in seedlings germinating under anoxia could be used as an indicator for ability to germinate and grow under flooded conditions.

Nonstructural carbohydrate content and ex- pression of key enzymes involved in carbo- hydrate catabolism Nonstructural carbohydrate content. Seed starch and soluble sugars are the main sources of energy for embryo growth in germinating seeds and, under anaerobic conditions, breakdown of starch into sugars decreases greatly because of reduced activity or expression of the enzymes involved in starch catabolism under low-oxygen conditions. Comparisons of total starch levels were made between tolerant Khaiyan and intolerant IR42 from 0 to 5 d of hypoxia (0.03 mol O 2 m 3 ). We found that total starch was

always higher for the tolerant cultivar for up to

5 d of hypoxia and did not change significantly

between time points. The availability of total soluble sugars (TSS) was compared between tolerant Khaiyan and intolerant IR42 at 0 d, 1 d, 3 d, and 5 d of hypoxia. TSS levels at 0 d (25 to 32 µg per seed dry wt.) were not significantly different between tolerant and

intolerant rice cultivars. However, after 1 d of hypoxic treatment, availability of TSS declined rapidly, by 60%, and then increased at 3 d in germinating embryos. We found significant differences in TSS between tolerant Khaiyan and intolerant IR42 starting at 3 d and up to

5 d of hypoxia (Fig. 7). The increased levels

of available TSS may stem from the higher carbohydrate breakdown brought about by the higher amylase activity found in Khaiyan, which in turn contributes to the greater ability of Khaiyan to survive flooding and low-oxygen stress during germination.

Peroxidase activity (µg α-naphthylamine consumed g DW h )

5 A  LSD 0.05 9 6 3 0 Khaiyan Khao Hlan On R64 R
5
A
LSD 0.05
9
6
3
0
Khaiyan
Khao Hlan On
R64
R
Tolerant
ntolerant

% survival

60 B 40 R = –0.7 0 0 0 3 6 9
60
B
40
R = –0.7
0
0 0
3
6
9

Peroxidase activity

Fig. 6. (A) Peroxidase activity in seedlings incubated in anoxic agar solution for 5 d and (B) correlation between peroxidase activity and seedling survival. Vertical bar in A indicates LSD at P = 0.05.

Alpha-amylases. Starches are a major energy source for developing rice embryos and the total amylases needed to break them down were generally found to be higher for tolerant cultivars under low-oxygen or submerged conditions than for intolerant lines. Analyses of transcriptional activity of rice α-amylases (RAmy1A, RAmy2A, RAmy3C, RAmy3D, and RAmy3E) were performed using RT-PCR of RNA extracted from germinating embryos of tolerant (Khaiyan) and intolerant (IR42) genotypes subjected to hypoxia: air (0.25 mol O 2 m 3 ) or anoxia (<0.003 mol O 2 m 3 ) treatments for

Total soluble sugars (µg per seed dry wt.) 35 Khaiyan 30 R4 5 0 5
Total soluble sugars (µg per seed dry wt.)
35
Khaiyan
30
R4
5
0
5
0
5
0
0
3
5
Treatment days

Fig. 7. Total soluble sugars of Khaiyan and IR42 at different time points after hypoxia treatment.

0 h, 12 h, 24 h, 48 h, and 72 h. Rice α-amylases (RAmy1A, RAmy3C, RAmy3D, and RAmy3E) generally showed up-regulation starting at 12

h following treatment (Fig. 8). RAmy2A was not

expressed. During hypoxia, RAmy3D, which

is important for oligosacharride degradation,

showed relatively higher expression in the tolerant Khaiyan than in the intolerant IR42. RAmy1A, which breaks down soluble starch, was less induced during anoxia but not during hypoxia in tolerant cultivars. No differences in expression levels were found for RAmy3C and RAmy3E in the three O 2 regimes. Using RT-PCR analyses, we found that rice α- amylases were rapidly induced in germinating embryos. RAmy3D, a key and major enzyme for carbohydrate use for germinating embryos, was expressed at higher levels in tolerant cultivars during hypoxia and this probably helps provide and sustain energy during germination. Sucrose synthases. Sucrose is another major energy source for germinating embryos. It can be hydrolyzed via the sucrose synthase (Sus) pathway or the invertase pathway. Under low-O 2 stress, Sus transcript levels increase while those of invertase decrease, suggesting that sucrose synthase is the principal enzyme that converts sucrose to phosphorylated hexose under low oxygen. Comparison of

transcriptional activity of sucrose synthase patterns in tolerant and intolerant rice embryos showed no differences between treatments under aerated conditions or during hypoxia or anoxia. We showed the induction of Sus1 during the first 72 h of treatment, whereas Sus3 activity was completely shut down after 24 h of treatment (Fig. 8). Overall, the result suggests that Sus1, but not Sus3, appeared to contribute to sucrose degradation during germination. Pyruvate decarboxylases and alcohol dehydrogenases. Rice seedlings under low-oxygen stress are capable of survival for a limited time by shifting to the fermentative pathway to generate ATP for cellular metabolism. Using RT-PCR analyses, we showed that Pdc1, Adh1, and Adh2 transcripts were induced during the first 72 h of rice seedling growth whether in air or under hypoxic or anoxic conditions (Fig. 8). Although oxidative phosphorylation provides major ATP needs for rapid growth under aerobic conditions, our results showed that germinating rice embryos do experience anaerobic conditions and partly use the fermentative pathway to generate energy. PDC and ADH activity. For total PDC and ADH enzyme activity levels, marked differences were observed between tolerant and intolerant cultivars under hypoxic compared with aerobic conditions (Fig. 9). PDC activity was 1.6x higher immediately after 12 h of

H ours

RAmy1A

RAmy3C

RAmy3D

RAmy3E

Sus1

Sus3

Pdc1

Adh1

Adh2

Gapdh

0

Hypoxia

Khaiyan

12

24

48

72

0

IR42

12

24

48

72

Air

Khaiyan

IR42

24

48

72

24

48

72

Anoxia

Khaiyan

IR42

24

48

72

24

48

72

IR42 24 48 72 24 48 72 Anoxia Khaiyan IR42 24 48 72 24 48 72

Fig 8. RT-PCR of key enzymes involved in carbohydrate metabolism.

PDC levels (µ min – mg – protein) . A Air Khaiyan .0 Air R4
PDC levels (µ min – mg – protein)
.
A Air Khaiyan
.0
Air R4
Hypoxia Khai
Hypoxia R4
0.8
0.6
0.4
0.
0.0
0 h
h
4 h
48 h
7 h
ADH levels (µ min – mg – protein) .4 B . .0 0.8 0.6 0.4
ADH levels (µ min – mg – protein)
.4
B
.
.0
0.8
0.6
0.4
0.
0.0
0 h
h
4 h
48 h
7 h

Fig 9. (A) PDC and (B) ADH activities. Means with the same letter are statistically not different at each time point. The asterisks indicate significant differences between genotypes and treatment at particular time point (P<0.01). Vertical bars indicate ± S.E.

hypoxia in tolerant Khaiyan and 1.48x higher for intolerant IR42. At the end of 72 h, PDC levels increased 4x for Khaiyan and only 2x for IR42 under hypoxic vs. aerobic conditions.

PDC levels were significantly higher in Khaiyan than in IR42 germinating seeds from 12 h to

72 h. ADH activity was also higher in Khaiyan

than in IR42 after 24 h of hypoxia treatment. The tolerant cultivar Khaiyan showed as much as 3x greater ADH activity compared with

only a 1.5x increase in the intolerant IR42 after

72 h of hypoxia compared with that under

aerated conditions. The higher PDC and ADH activities suggest the involvement of the alcohol fermentation pathway in the tolerant cultivars during hypoxia. Higher PDC and ADH enzyme activity probably supports the faster growth and development of tolerant lines than intolerant ones during hypoxia.

Conclusions

These studies demonstrated substantial genetic variation in rice in ability to germinate and establish underwater; however, the trait is relatively rare. Tolerance is associated with faster root and shoot growth and leaf area development, faster coleoptile growth under hypoxia and anoxia, enhanced activity of total amylases, increased ethylene levels in germinating seeds, and lower peroxidase activity. Tolerant lines also seem to maintain

greater soluble sugars, particularly a few days after imbibition under hypoxia, and maintain higher activity of the key enzymes involved in anaerobic respiration (ADH and PDC). Further studies are ongoing to establish the full array of physiological and biochemical mechanisms associated with tolerance as well as to unravel their genetic bases. Backcross populations were developed and are being used to map this trait. Crosses were also made and are being selected and advanced to incorporate tolerance into modern varieties, for both irrigated and rainfed ecosystems.

Salinity tolerance in rice: physiological bases and implications for management strategies for better crop establishment

Abdelbagi M. smail, Babita Thapa, and James Egdane

In most coastal areas, salinity is high in both soil and water during the dry season, mostly between December and July, and with the peak during May-June. Salinity then decreases progressively with time after the onset of the monsoon season. This poses great challenges for farming during the dry season, when most of these areas are often left barren or are grown to limited short-maturing crops when freshwater resources are available. For wet- season rice, the main problems are encountered during crop establishment in June-July, when salinity is still high at the beginning of the rainy season. This is particularly important because rice is highly sensitive to salt stress during early seedling growth, which is a major obstacle because of high seedling mortality and difficulty in establishing a sufficient crop stand. Varieties with reasonable genetic tolerance as well as proper management strategies during crop establishment are needed to ensure a good stand to significantly enhance and stabilize productivity in these coastal areas. For transplanted rice, damage to young seedlings is further provoked by the fact that more salt is absorbed passively through the injured roots, coupled with the fact that seedling growth and uptake of nutrients are greatly hindered during the first week after transplanting and until the seedlings are well established. Osmotic stress of the soil solution together with a massive uptake of salts and low nutrient uptake will make nutritional deficiencies even higher for some minerals and toxicities of others, causing higher seedling mortality and poor stand establishment. Based on our understanding of the mechanisms associated with tolerance of salt stress, we attempt to develop management strategies

that can reduce seedling mortality after transplanting and enhance crop establishment. Another objective is to compare rice cultivars contrasting in tolerance of salt stress for their responsiveness to such stress-mitigating options.

Nursery management for enhanced seed- ling survival

The effects of seedling N status, seedling age, and handling at transplanting on seedling survival after transplanting in saline soils were investigated. Two rice lines were used, a moderately tolerant variety, IR64, and a tolerant breeding line, IR651-4B-10-3 (referred to as IR651 henceforth). The two cultivars were grown in grid plastic trays, with one seedling per partition and half of the seedlings supplied with extra N at planting. Twenty-d-old and 40- d-old seedlings with and without N treatments were transplanted either after washing their roots or with soil left attached to their root system (unwashed). The trial was repeated once with 4 replications each time. Average standard evaluation system (SES) scores of 6.4 and 1 were observed for plants grown under salt stress and normal conditions, respectively (Table 1). Average scores were significantly lower for the tolerant cultivar (5.1) than for the moderately tolerant cultivar (7.8), suggesting that IR651 experienced less salt injury and had better growth under salt stress than IR64. Likewise, transplanting older seedlings and seedlings with soil attached to their roots resulted in substantially better overall growth as evidenced from visual observations. The artificially salinized plot seems ideal for evaluating plants for salt stress

Table 1. Standard evaluation system (SES) scores and per- centage survival of rice seedlings as affected by cultivar, age of seedlings in the nursery, and seedling handling under salt stress and normal conditions. Measurements were taken 20 d after transplanting.

Variables

SES scores

% survival

Cultivar

R65

5.06

55.9

R64

7.75

37.7

Seedling age

0 days old

7.56

35.4

40 days old

5.0

58.

Seedling handling

Roots washed

6.93

38.6

Roots not washed

5.87

55.6

Salinity

EC 8 dS m

6.40

46.9

Normal

.00

00.0

Significance

Cultivar

*** a

**

Age

***

***

Seedling handling

**

***

Salinity

***

***

LSD 0.05 (others)

0.47

3.3

LSD 0.05 for salinity

0.3

7.0

a *,**, *** = significant at P< 0.05, 0.0, and 0.00, respectively.

tolerance where a drastic reduction (53%) in plant establishment was observed compared with the normal plot (100%). Using older seedlings and seedlings transplanted with soil intact on roots showed survival of 58% and 56% compared with 35% and 39% for younger seedlings and seedlings with their roots washed before transplanting, respectively. The salt-tolerant line IR651 maintained significantly higher seedling survival than IR64. These results showed that survival of seedlings transplanted in saline soils could be enhanced substantially if older seedlings of tolerant varieties were used, particularly if their roots were protected during transplanting. Older seedlings have higher shoot and root dry weights and green leaf area; they also maintain higher starch content in the shoot, all of which are positively associated with survival

Table 2. Correlations of seedling survival with dry weight and carbohydrate content at transplanting.

Trait

R-value a

Seedling dry weight

0.65**

Green leaf area

0.60*

Root dry weight

0.68**

Shoot dry weight

0.6*

Total carbohydrates

0.6**

Stem starch

0.60*

Leaf starch

0.68**

Shoot starch

0.5*

Root starch

0.40 ns

a ns = not significant; *, ** = significant at P< 0.05 and 0.0, respectively.

after transplanting (Table 2). High nonstructural carbohydrates in shoot and root could probably act as a reserve source of energy at the time of transplanting to overcome the period of slow growth until the transplanted seedlings retain their full capacity for photosynthetic carbon fixation. The older seedlings were taller and experienced less reduction in plant height under salt stress than the younger ones. IR651 had more tillers per plant under both saline and normal conditions and showed significantly lower reduction in tiller number under salinity. Younger seedlings produced more tillers per plant under normal conditions whereas the older seedlings produced more tillers under saline conditions and transplanted younger seedlings showed a higher percent reduction in tiller number (61%) than the older seedlings (41%) under salt stress. Salt stress delayed maturity by about 11 d, with greater delays in younger seedlings when roots are washed and in sensitive cultivars (Table 3). This study demonstrated that salinity stress at transplanting can reduce seedling survival by >50% and further decrease grain yield of surviving plants by about 37%, mainly because of a reduction in number of panicles per plant as determined by the number of surviving tillers and number of spikelets per panicle. Grain yield under salt stress also correlated positively with the number of panicles per plant

Table 3. Plant height, tiller number at 20 d after transplanting, and days to maturity as affected by cultivar, seedling age, and handling under salt stress and normal conditions. Values are means of 4 replications.

tem

Plant height (cm)

 

Tiller number

 

Days to maturity

 
 

Normal

EC 8

% change

Normal

EC 8

% change

Normal

EC 8

% change

Cultivar

R659

50.5

39.5

7.8

0.37

5.5

46.77

4.6

0.9

6.3

R64

48.

44.

8.

9.8

3.9

60.04

98.0

4.6

6.6

Age of seedlings

0 days old

4.4

33.4

9.3

0.7

4.4

6.44

05.4

8.8

3.4

40 days old

5.5

43.

6.

9.48

5.58

4.3

07.4

6.9

9.5

Seedling handling

Roots washed

5.7

4.9

6.9

9.30

5.0

46.0

06.9

.8

5.9

Roots not washed

48.

40.

6.7

0.80

5.03

53.4

05.9

3.8

7.9

Salinity

49.

4.0

6.6

0.08

5.03

50.0

06.4

7.9

.7

Significance a

LSD 0.05

Significance

LSD 0.05

Significance

LSD 0.05

Cultivar

ns

**

0.49

***

.

Age

**

3.7

*

0.50

ns

Seedling handling

ns

ns

***

.04

Salinity

***

3.

***

0.5

**

.06

Cultivar*salinity

ns

***

0.69

**

1.98

a ns = not significant; *, **, *** = significant at P < 0.05, 0.0, 0.00, respectively.

and spikelets per panicle and to a lesser extent with individual grain weight but not with fertility. This is probably because salinity stress declined gradually 30 d after transplanting to simulate the actual conditions of coastal saline areas, and number of panicles as well as spikelets was determined earlier. Fertility, on the other hand, is mainly affected by pollen grain development and pollination, both of which occur at a time when salinity stress is low. The negative effects on individual grain weight are probably because of the effect of early stress on photosynthetic leaf area and stored assimilates. Older seedlings had higher dry matter and starch content that correlated positively with seedling survival under salt stress. In summary, seedlings transplanted with protected roots had higher shoot dry matter, less salt uptake, and earlier maturity. The positive consequences of using older seedlings and root protection are more evident in the salt-tolerant IR651 than in the moderately tolerant IR64. This enhanced responsiveness of the salt-tolerant cultivar to stress-mitigating

0

amendments suggests that combining salt tolerance with proper nursery and seedling handling options can substantially improve crop establishment and early growth in salt- affected areas, which can later be reflected in higher grain yield.

Nutrient management to enhance seedling establishment under direct seeding

Despite the well-documented beneficial effects of Ca + in mitigating salt stress in different plant species, contrasting observations were noted in rice. This is probably because in most of the studies conducted so far, only one or a few sensitive lines were used. Salt stress often coexists with P deficiency because affected soils are often either acidic (saline) or alkaline (sodic), and both conditions promote P fixation in forms that are poorly available for plants. Thus, the induced P deficiency in these soils could further worsen the detrimental effects of salt stress with consequent high seedling mortality. Salt tolerance is also associated with restricted toxic ion absorption and adequate uptake of essential inorganic nutrients, such as K + , to overcome the

nutritional imbalances caused by salinity stress. Here, we attempt to investigate the effects of calcium and phosphorus in enhancing tolerance of salt stress and in reducing seedling mortality. Furthermore, we used rice cultivars contrasting in salinity tolerance to test whether differential responses to additional Ca 2+ and P could be observed in these genotypes. Two experiments were conducted using culture solutions; in each experiment, two levels of P (2 and 10 µL L 1 ) and three levels of Ca 2+ (20, 40, and 60 µL L 1 ) were used under normal or salt stress (12 dS m 1 ) conditions. Three rice cultivars were used, one tolerant (IR651), one moderately tolerant (IR64), and one sensitive (IR29). The tolerant line had higher leaf area, higher root and shoot dry weight, and lower SES scores when evaluated 3 weeks after the start of the stress treatment (Table 4). The addition of higher levels of P and Ca 2+ enhanced leaf area; however, P enhanced shoot growth while

Ca 2+ enhanced root growth under salt stress. Higher levels of both nutrients resulted in better tolerance of salt stress across cultivars as shown by the significantly lower SES scores. Increasing P from 2 µL L 1 to 10 µL L 1 in the nutrient solution resulted in about a 145% increase in P concentration in shoots. It also enhanced the uptake of Mg 2+ and Ca 2+ and significantly reduced Na + concentration in plant tissue under salt stress. However, the effect of higher P was greater in IR64, followed by IR651, and with IR29 showing an opposite effect, in which Na + concentration in plant tissue increased at higher P. This result suggests that tolerant and moderately tolerant cultivars are more responsive to higher P in a nutrient medium. Increasing calcium concentration in the culture solution significantly reduced sodium concentration in shoots of all three cultivars and with a relatively greater reduction

Table 4. Leaf area (cm 2 seedling 1 ), shoot and root dry weights (g), and SES scores of rice cultivars under normal conditions and salt stress (12 dS m 1 ) measured 21 d after the start of a salt-stress treatment.

tem

Leaf area

Shoot dry wt.

Root dry wt.

SES scores

Normal

Stress

Normal

Stress

Normal

Stress

Normal

Stress

Cultivar

 

R9

43.6

9.8

0.407

0.5

0.46

0.054

.00

8.83

R64

54.7

33.

0.460

0.3

0.36

0.079

.9

7.83

R65

6.7

36.4

0.444

0.348

0.30

0.03

.9

6.36

Phosphorus

 

µL L

50.6

6.3

0.408

0.70

0.65

0.08

.90

7.83

0 µL L

56.8

33.3

0.466

0.33

0.60

0.077

.00

7.5

Calcium

 

0 µL L

5.

4.9

0.45

0.83

0.4

0.066

.00

8.4

40

µL L

53.4

7.7

0.454

0.94

0.6

0.08

.9

7.78

60

µL L

55.5

36.7

0.444

0.97

0.80

0.089

.9

7.

Mean

53.7

9.8

0.437

0.9

0.37

0.079

.94

7.67

Significance a

 

Salinity (S)

Cultivar (C)

 

***

***

***

***

Phosphorus (P)

***

***

***

***

Calcium (Ca)

***

***

ns

***

 

**

ns

***

***

LSD 0.05

Salinity

 

4.

0.056

0.00

0.5

Cultivar

3.6

0.048

0.08

0.46

P

.9

0.039

0.

Ca

3.6

0.08

0.46

Na + total uptake in roots (µg SDW )

Na + uptake in shoots (µg SDW )

8 A 4 3 0 Ca 0 ppm Ca 40 ppm Ca 60 ppm 8
8
A
4
3
0
Ca 0 ppm
Ca 40 ppm
Ca 60 ppm
8
6
4
0
K + total uptake in roots (µg SDW – )
8 B 6 4 3 0 N + /K + ratio in roots .5 C
8
B
6
4
3
0
N + /K + ratio in roots
.5
C
.0
.5
.0
0.5
0.0
R9
R64
R65

Cultivar

70 D 60 50 40 30 0 0 0
70
D
60
50
40
30
0
0
0

K + uptake in shoots (µg SDW )

70 E 60 50 40 30 0 0 0 N + /K + ratio in
70
E
60
50
40
30
0
0
0
N + /K + ratio in shoots
3.5
F
3.0
.5
.0
.5
.0
0.5
0.0
R9
R64
R65

Cultivar

Fig. 1. Uptake of Na + and K + and Na + /K + ratio in roots (A, B, C) and shoots (D, E, F) of three contrasting rice cultivars as affected by different levels of Ca 2+ in nutrient solution. SDW = shoot dry weight, RDW = root dry weight. Vertical bars indicate standard error.

with increasing genetic tolerance. Sodium concentration decreased by 14%, 24%, and 35% in IR29, IR64, and IR651, respectively, with increasing Ca 2+ concentration from 20 to 60 µL L 1 . This also suggests that the response to higher calcium under salt stress is strongly dependent on the level of tolerance, with salt- tolerant cultivars being substantially more responsive. This is also clearly reflected in the total uptake of sodium in the shoot of salt- tolerant cultivars, in which total uptake was substantially lower in IR651 under higher calcium in the nutrient solution (Fig. 1D). Potassium concentration in plant tissue as well as total uptake into shoots (Fig. 1E) increased with increasing calcium concentration. Consequently, Na + /K + ratio in shoots decreased significantly with increasing concentrations of calcium in the growth medium (Fig. 1F). Under salt stress, increasing Ca 2+ levels also increased Ca 2+ concentrations in all cultivars, but with a greater increase in IR651 and IR64, in which it increased by about 19% and 17%, respectively, compared with only 8% in IR29. Higher Ca 2+ concentrations also reduced Na + /Ca 2+ ratios in all cultivars. Root total Na + uptake increased with increasing Ca 2+ concentration in the culture solution in all cultivars (Fig. 1A), which contrasts with the trend observed for total sodium uptake into shoots, particularly in IR651 (Fig. 1D). Salt-tolerant cultivar IR651 showed the highest total sodium uptake into roots, whereas salt-sensitive cultivar IR29 showed the lowest Na + uptake into roots. This greater compartmentation of sodium into roots of IR651 may partially explain its greater tolerance of salt stress, which seems to be further enhanced by supplementary Ca 2+ . Higher Na + in roots could also act as an osmoticum to allow water uptake into roots of tolerant lines without much detriment to shoot growth. Total uptake of K + into roots also increased with increasing calcium concentration in the nutrient solution and with the uptake being relatively higher in IR651, followed by IR64. Thus, Na + /K + ratio in roots was highest at lower Ca 2+ in IR64 and

IR651.

The accumulation of Na + in rice tissues under salt stress seems to influence the overall nutrient balance by changing the internal ion concentrations in shoots. Na + concentration in plant tissue was negatively associated with K +

(R = –0.61**), Ca 2+ (R = –0.30**), and Mg 2+ (R = –0.28**), but positively correlated with Na + /K + ratio (R = 0.89**) under salt stress, suggesting that the optimum balance of these essential nutrients could be deleteriously affected with increasing sodium uptake. Phosphorus showed

a positive correlation with Mg 2+ under both

normal and salt-stress conditions. However, Ca 2+ concentration in shoots under salt stress showed a strong positive correlation with Mg 2+ (R = 0.72**), P (R = 0.38**), and K + (R = 0.29**), and a negative correlation with Na + . Based on these findings, it seems that an addition of more calcium under saline conditions is beneficial because it helps reduce Na + uptake while enhancing the uptake of other essential nutrients such as magnesium, phosphorus, and potassium, whose uptake was negatively affected under higher salt stress. The synergistic effects of the use of genetic tolerance combined with the mitigating effects of P and Ca + are further summarized in Figure

2, in which a lower ratio of Na + /K + in the shoot is taken as an indicator of lower salt injury. The ratio is very high in IR29 but decreased with the addition of Ca 2+ as well as when both Ca 2+ and

P were combined. IR64 with its intermediate

level of tolerance showed a better response to both P and Ca 2+ when applied separately, and a

Na + /K + ratio in shoots .0 Cultivar (C) .6 + P C +
Na + /K + ratio in shoots
.0
Cultivar (C)
.6
+ P
C
+ Ca
C
+ P + Ca
C
.
0.8
0.4
0.0

R9

R64

Cultivar

R65

Fig. 2. Na + /K + ratio in shoots as affected by genotype and P and Ca 2+ in three rice cultivars contrasting in their response to salt stress.

3

greater response when the two nutrients were combined. IR651, on the other hand, showed a response similar to that of IR29 but with a strong genetic effect, particularly when the two nutrients were added together. A genotype effect is also obvious. Na + /K + ratio in plant tissue drops to <0.4 when genetic tolerance is combined with higher Ca 2+ and P. So, these amendments seem to be effective only when combined with intermediate or high levels of genetic tolerance. In summary, our studies demonstrated a few nursery and nutrient management strategies that can effectively enhance crop establishment

4

in salt-affected areas. However, these strategies may be effective only if they are applied using salt-tolerant cultivars. This is because the incremental effects of genetic tolerance seem to act additively to the effects of these mitigating strategies. Combining salt tolerance with proper nursery and nutrient management options can therefore substantially improve crop establishment and early growth in salt- affected coastal areas, which can subsequently enhance and stabilize rice productivity in these ecosystems. Further studies are needed to validate these strategies under farmers’ field conditions.

Opportunities for direct seeding and improved weed control in the Barind of Bangladesh

M.A. Mazid, C.R. Riches, A.M. Mortimer, and D.E. Johnson

In the High Barind Tract, in northwest Bangladesh, a single crop of transplanted rainfed rice (TPR), grown in the monsoon aman season from June to October, provides a major component of rural livelihoods. Aman rice is vulnerable to late-season drought during grain filling in October and in the rabi (winter) season much of the land lies fallow. Cultivation intensity in much of the Barind is considerably less than in districts where irrigation allows two or three rice crops to be grown each year. Farmers’ lands are typically distributed over a shallow sloping landscape or toposequence. Two challenges of agricultural improvement in such areas are to simultaneously improve the reliability and yield of aman rice while increasing total system productivity. Research in recent years has demonstrated that these objectives can be achieved through the introduction of dry-seeded rice (DSR) and the planting of short-duration rabi crops (e.g., mustard or chickpea) on residual moisture immediately after the rice harvest. Late onset of the monsoon or low rainfall can delay rice transplanting as a minimum of 600 mm of cumulative rainfall is needed to complete land preparation and transplanting. Dry seeding, on the other hand, can be completed after land preparation by a power tiller after much less rainfall and the earlier planted DSR crop matures 1–2 weeks before TPR, thus reducing the risk of terminal drought, and allows earlier planting of a following nonrice crop. TPR requires less labor and draft power for rice establishment than DSR, but the high costs associated with weed control in DSR are a major constraint to its adoption. Monitoring of farmer-managed transplanted aman rice crops in the Barind revealed that labor availability constrains the timeliness of first weeding for

many households and, with current practices, 34% of farmers lose more than 0.5 t ha 1 of the attainable yield because of weed competition (Mazid et al 2001). Farmers in the Barind have a strong preference for the late-maturing rice cultivar Swarna. Use of this cultivar, however, reduces the opportunity for establishing chickpea or other rabi crops on residual moisture, whereas growing earlier maturing modern cultivars may contribute to an earlier harvest. This report summarizes selected findings (after Mazid et al 2003) from a long- term field experiment in the Barind designed to explore the contribution of rice establishment method, rice cultivar duration, and weed control practices to aman rice performance and the likely long-term impact on the composition of the rice weed flora.

Methods

Rice establishment, nutrient management, and weeding practices have been investigated on farmland at Rajabari, Rajshahi, in northwest Bangladesh from 2001 in an ongoing long-term trial as described in greater detail in Mazid et al (2001). The results for rice crops in 2000, 2001, and 2002 are reported, comparing rice crop establishment methods and weed management practices. Treatments were (1) transplanted rice (TPR)—soil is puddled prior to transplanting; the crop is hand-weeded twice at 30 and 45 days after transplanting (DAT); (2) direct-seeded rice (DSR)—soil is plowed prior to seeding in rows by hand, with hand weeding at 21, 33, and 45 days after sowing (DAS); (3) direct-seeded rice with chemical weed control (DSRH)—as for DSR but with oxadiazon (375 g a.i. ha 1 ) applied 2–4 days after seeding, followed by one hand weeding at 33 DAS. Plots of these treatments were sown to the cultivars Swarna (maturity

5

140–145 days) and BRRI dhan39 (maturity 120–125 days). Rice was harvested in 5-m 2 plots. Biomass of individual weed species was recorded in two unweeded quadrats per plot at 28 days DAS/DAT and total weed biomass at 45 DAS/DAT and again at harvest.

Results

Crop establishment method With the exception of BRRI dhan39 in 2000, yields from direct seeding of this and cv. Swarna were as good as or better than from transplanting, the usual method of rice culture in the district (Fig. 1). Early-season weed control by preemergence application of herbicide resulted in the highest yields, except for BRRI dhan39 in 2000.

Grain yield (t ha – ) 5 A 4 000 00 00 3  5
Grain yield (t ha – )
5
A
4
000
00
00
3
5
B
4
3
DSR
DSRH TPR
DSR
DSRH TPR
DSR
DSRH TPR

Establishment method

Fig. 1. Effect of establishment and weed control practices on the yield (mean ±S.E.M) of rice cultivars BRRI dhan39 (A) and Swarna (B). DSR = direct-seeded, hand-weeded; DSRH = direct-seeded + herbicide; TPR = transplanted rice + hand-weeded.

Weed species shifts The weed flora of rainfed rice in the Barind is diverse and exhibits high interseasonal variability depending on water regimes at rice establishment and soil moisture status of toposequence position. Weed species present in the experiment included Alternanthera sessilis, Ammania baccifera, Cyanotis axillaris, Cynodon dactylon, Cyperus difformis, Cyperus iria, Cyperus rotundus, Cyperus tenuispica, Echinochloa

6

colona, Eclipta prostrata, Eriocaulon cinereum, Fimbristylis dichotoma, Fimbristylis miliacea, Hedyotis corymbosa, Lindernia ciliata, Ludwigia sp., Monochoria vaginalis, Paspalum distichum, and Sphaeranthus indicus. At harvest, there were significantly higher densities of weeds in DSR (228 m 2 ) than in TPR (75 m 2 ; P 0.023). As expected, however, at 45 DAS/DAT, the least weed density and biomass were recorded in DSRH. The range of responses by individual weed species over three consecutive seasons to crop establishment and weed management practices is shown in Figure 2. An increase in abundance (biomass at 28 DAS/DAT) of the broadleaf species Alternanthera sessilis, Eclipta prostrata, Lindernia ciliata, and Ludwigia sp. and the sedges Cyperus difformis and Fimbristylis miliacea was noticeable in DSR. Conversely, the biomass of Monochoria vaginalis was decreased by direct seeding. The most noticeable increase in abundance was seen in the perennial grass Paspalum distichum. A long-term trial has demonstrated that, although rice yield can be maintained with the switch from transplanting to direct seeding, farmers will face a greater weed problem early in the crop season. Not only is there an increased burden of weeds in direct-seeded rice but the change in establishment practice also leads to a shift in the relative abundance of important species. Previous findings indicate that direct seeding was associated with higher labor inputs for first weeding than is the case for transplanting. With the labor constraint, late first weeding, and a significant yield gap due to weeds on many farms in transplanted rice with current weed control practices (Mazid et al 2001), it is clear that the adoption of direct seeding will need to be associated with the use of chemical weed control. Studies suggest that herbicides may find a ready market in Rajshahi District because (1) weeding is done almost exclusively by hired labor and (2) the supply of hired labor is local, with very little weeding done by seasonal migrant labor. Together, these factors will create intense competition for labor, especially on larger farms, which would be intensified by the adoption of direct seeding.

DSR DSRH TPR

Mean dry biomass g m- at 8 DAS/DAT 7 9 Alternanthera sessilis 7 5 5
Mean dry biomass g m- at 8 DAS/DAT
7
9
Alternanthera sessilis
7
5
5
3
3
5
50
Eclipta prostrata
3
30
0
9
5
Lindernia ciliata
7
0
5
3
5
0 Cyperus difformis Cyperus iria 5 0 5 8 Fimbristylis miliacea Ludwigia sp. 6 4
0
Cyperus difformis
Cyperus iria
5
0
5
8
Fimbristylis miliacea
Ludwigia sp.
6
4
00
Monochoria vaginalis
Paspalum distichum
50
00
50
DSR DSRH TPR
DSR DSRH TPR

Establishment method

Fig. 2. Effect of establishment and weed control practices on the biomass of nine rice weeds at 28 days after planting in unweeded plots. See text for details.

Direct seeding advanced the rice harvest by 7 to 10 days. Earlier harvest reduces the problem of terminal drought in rice when rains end abruptly in October and will ensure that postrice crops are sown while seedbeds are moist. Farmers with the least land under cultivation (0.6 ha for the lowest quartile of households) on average plant 43% to postrice crops, often on the least favorable land where moisture is limiting (Mazid et al 2003). Our trials suggest that this group can maximize rice yield and achieve timely planting of a high- value chickpea crop by direct seeding rice. On larger farms (> 2.5 ha for the upper quartile), a lower proportion of land is planted after rice, using more favorable soils. Adoption of DSR by this group could increase the area planted to chickpea.

A single rice crop, combined with land pressure and a high level of sharecropping in the Barind Tract, leads farmers to place a premium on optimizing rice yield and household food security. This study demonstrates that, although the widely grown rice cultivar Swarna performs well under direct seeding, the shorter duration BR39 is not well adapted for this planting practice. This is because of the high levels of sterility in this cultivar associated with flowering during wet periods. An earlier maturing variety with yields to match those of Swarna could contribute further to avoiding late-season drought during grain filling and also allow earlier planting of postrice crops. This challenge requires a broad- based approach combining rice breeding with agronomy and weed science.

7

Information availability With a shift to direct seeding, farmers will be increasingly dependent on information from outside sources. Indeed, successful adoption and correct decision making would be likely only if farmers had a greater availability of current knowledge. Direct seeding and associated weed management comprise not single recommendations but a wide range of options that will be dependent on toposequence, seasonal effects/rainfall pattern, the weeds present, and farmers’ resources. Decision trees can provide farm-level information in the form of structured questions that enable answers “in the form of options” to be chosen (Johnson and Mortimer 2004). These trees specifically focus on technical issues related to the adoption of a particular system and they may be useful tools to help refine technology options for researchers and extension staff. For a farmer in the favorable

rainfed environment, such as the Barind, the question “What are my options for rice establishment?” might initiate a tree involving several steps and covering the range of direct- seeding options (see Fig. 3 for an example). In this example, the decision process recognizes that a primary consideration will be the ability of a farmer to drain his field as only if this is possible should direct seeding be recommended because of the risk of early flooding. A second decision level will involve the choice between wet and dry cultivation and this will depend on the ability to dry-cultivate and/or the presence of perennial weeds. Further levels indicate choices for row or broadcast seeding and weed control options. Such a diagram allows a structured approach to the range of options available, and a more complex decision tree may comprise weed control options for individual or groups of weeds.

CAN FIELD BE DRAINED?

Yes

for individual or groups of weeds. CAN FIELD BE DRAINED? Yes CAN FIELD BE DRY-CULTIVATED? Is

CAN FIELD BE DRY-CULTIVATED? Is Cynodon dactylon or Cyperus rotundus ABSENT?

No TRANSPLANT
No
TRANSPLANT

CROP ESTABLISHMENT

Yes DRY SEEDING into a seedbed
Yes
DRY SEEDING
into a seedbed

ARE SOIL CONDITIONS SUITABLE FOR LINE SEEDING BY MACHINERY?

No WET SEEDING sowing onto puddled saturated soil
No
WET SEEDING
sowing onto puddled saturated
soil

IS THERE A NEED FOR INTERROW CULTIVA- TION OR SUBSTANTIAL HAND WEEDING?

No Yes No Yes BROADCAST DRILL-SEED BROADCAST DRUM-SEED WEED MANAGEMENT ARE ANNUAL GRASSES ABSENT? IS
No
Yes
No
Yes
BROADCAST
DRILL-SEED
BROADCAST
DRUM-SEED
WEED MANAGEMENT
ARE ANNUAL GRASSES ABSENT?
IS GOOD WATER MANAGEMENT POSSIBLE?
Yes
No
APPLY HERBICIDE
+ LIMITED MANUAL WEEDING
APPLY HERBICIDE
+ MANUAL WEEDING OR
INTERROW CULTIVATION

Fig. 3. Illustrative decision tree for the adoption of direct seeding with respect to favorable rainfed lowland rice.

8

The transition to direct seeding and the management of challenging weed problems will require substantial information to enable farmers to judge objectively what the best technology options are. Gaining access to such information may be a major obstacle for potential adopters. The challenge for researchers is to adequately address the variability of the rice-farming systems for which they are making recommendations and to synthesize the results in ways that will make the conclusions available to those who will use them. Studies on direct seeding, weed management, and decision tools are ongoing.

Acknowledgments

The research in Rajshahi was conducted by the Bangladesh Rice Research Institute, Natural Resources Institute (UK), and University of Liverpool in association with the Consortium for Unfavorable Rice Environments (CURE), and was partially funded under the Crop Protection Programme by the Department for International Development, UK.

References

Johnson DE, Mortimer AM. 2004. Issues for integrated weed management and decision support in direct-seeded

rice. In: Rice is life: scientific perspectives for the 21st

century. Proceedings of the World Rice Research Conference held in Tokyo and Tsuukuba, Japan, 4-7 November 2004. Los Baños (Philippines): International Rice Research Institute, and Tsukuba (Japan): Japan

International Research Center for Agricultural Science.

CD. p 211-214.

Mazid MA, Jabber MA, Riches CR, Robinson EJZ, Mortimer M, Wade LJ. 2001. Weed management implications of introducing dry-seeded rice in the Barind Tract of Bangladesh. Proceedings of the BCPC Conference – Weeds 2001. 1:211-216. Mazid M, Jabber MA, Mortimer M, Wade L, Riches CR, Orr AW. 2003. Improving rice-based cropping systems in north-west Bangladesh: diversification and weed management. Proceedings of the BCPC International Congress on Crop Science and Technology — 2003, SECC, Glasgow, UK. p 1029-1034.

9

Breeding for submergence tolerance

D.J. Mackill, A.M. smail, S. Heuer, E. Septiningsih, A.M. Pamplona, R.M. Rodriguez, C.N. Neeraja, D. Sanchez, K. ftekhar, and G. Vergara

Purpose

This project aims to develop submergence- tolerant cultivars that will improve the livelihood and food security of farmers and rice consumers in submergence-prone areas. The major objective is to convert widely grown varieties in rainfed lowland areas into submergence-tolerant varieties through incorporation of the Sub1 QTL on chromosome 9.

Background

Some 11 million hectares of shallow rainfed lowland rice in South and Southeast Asia are submergence-prone, and another 5 million ha of medium-deep area experience stagnant flooding of up to 50 cm. Submergence also affects some of the areas classified as deepwater (sustained water depths above 50 cm) on around 4 million ha in Asia. Some estimates indicate that submergence stress causes annual losses of around US$1 billion in Asia (Dey and Upadhyaya 1996, Herdt 1991). The “normalized” yield loss (an index taking into account several parameters) in submergence-prone areas was estimated at about 80 kg ha 1 , causing a production loss of about 3.2 million tons per year, with a value of about $384 million. About 140 million people are at risk from flooding damage in Bangladesh and five states of eastern India. With an average poverty ratio of 45%, approximately 74 million poor people stand to benefit significantly from improved submergence-tolerant rice cultivars. Modern high-yielding rice cultivars are seriously damaged if they are completely submerged for a few days; however, a few tolerant landraces were identified that can withstand inundation for up to 2 weeks. In these tolerant landraces, the Sub1 major

0

QTL accounts for most of the variation in the trait. DNA markers linked to the Sub1 locus have facilitated its transfer into widely grown cultivars that are locally adapted and possess the quality aspects preferred by local consumers. Those tolerant Sub1 cultivars have considerably higher survival and yield under submergence than susceptible cultivars. Rice production can therefore be improved and stabilized in submergence-prone areas of South and Southeast Asia predominantly inhabited by resource-poor farmers. The value of submergence tolerance could be further enhanced by combining it with tolerance for medium-deep stagnant flooded conditions and tolerance for submergence during germination. Yield of these tolerant cultivars can be further increased and stabilized through proper management strategies.

Previous studies on submergence tolerance

The effects of flooding on rice as well as the physiological bases of tolerance were recently reviewed (Ram et al 2002, Jackson and Ram 2003). Plant survival in flooded areas depends on various aspects of floodwater environments, particularly the limitation of gas diffusion, irradiance level, and water temperature. Among the important plant traits associated with tolerance are high nonstructural carbohydrate content before submergence, slower underwater shoot extension, optimum alcoholic fermentation when O 2 is low, an efficient protective system upon air entry after exposure to low O 2 , and limited leaf chlorosis (Setter et al 1997, Ram et al 2002, Jackson and Ram 2003, Ella et al 2003). Carbohydrates remaining after submergence are necessary for recovery growth and are correlated better with survival than

carbohydrate level before submergence (Das et al 2005). A rapid regeneration growth following submergence is essential under frequent or prolonged flooding as this can ensure early recovery and the production of sufficient biomass for high yield. Rice plants that exhibit only limited elongation during submergence are more tolerant of complete flooding and a strong association between limited underwater shoot growth and survival is commonly observed (Jackson and Ram 2003, Das et al 2005). Evidence is also accumulating for the role of postsubmergence events in tolerance for submergence. Tolerant cultivars acquired a more efficient protective system to suppress the level of active oxygen species and to lower the extent of lipid peroxidation upon exposure to air (Kawano et al 2002). Ethylene, a plant hormone, accumulates in plant tissue during submergence because of both enhanced synthesis and entrapment, and this promotes underwater leaf senescence. This effect is suppressed in tolerant cultivar FR13A. Ella et al (2003) found that blocking ethylene enhanced chlorophyll retention and carbohydrate content in the plant tissue and improved survival of intolerant cultivar IR42. Early flooding can cause poor crop establishment in direct-seeded rice areas. Landraces tolerant of these conditions emerge faster from the soil during flooding, produce taller seedlings with more leaves, and attain greater leaf area than intolerant lines. These cultivars also maintain higher activity of enzymes involved in the breakdown of starches, for example, total amylases, under flooding and this correlated positively with survival. Other studies showed increased activity of some of the enzymes involved in the fermentative pathways during anaerobic conditions (Xie and Wu 1989, Hossin et al 1996). Phosphofructokinase (Fukao et al 2003) and pyruvate orthophosphate dikinase (Huang et al 2005) were found to be induced under low-oxygen stress, both of which could enable substrate cycle operation of adenosine tri-phosphates (ATPs) necessary for energy production during germination. Breeding improved submergence-tolerant cultivars has been ongoing for more than

three decades (Mackill 1986, Mohanty and Chaudhary 1986, Singh and Dwivedi 1996). The initial work focused on transferring the trait from traditional landraces into semidwarf breeding lines. However, these lines were low-yielding and had many undesirable traits. Additional crosses resulted in the development of tolerant breeding lines with improved agronomic characteristics (Mackill et al 1993, Mackill and Xu 1996, Mohanty et al 2000). Although the lines with the highest levels of tolerance had some yield penalty, some breeding lines, such as IR49830-7, had a yield equivalent to that of the irrigated checks. These improved lines have been used for further crosses. New breeding lines with submergence tolerance were developed through the Eastern Indian Rainfed Lowland Shuttle Breeding Network (Singh et al 1998, Mallik et al 2002). Some of these lines have been released or recommended for release in India, such as Kishori, Satyam, OR1234-12-1, CN 1035-61 (Bhudev), CRLC 899 (Varshadhan), TTB 238-3- 38-3 (Prafulla), NDR 8002, CR 2003-2, CR 2003- 3, CR 978-8-2, and IR54112-B2-1-6-2-2-2-CR2-1. These lines together with Sub1 introgression lines would serve as a basis for studies on crop management and farmer participatory research. Genetically, submergence tolerance is largely governed by a single major QTL, designated Sub1, located on rice chromosome 9 (Xu and Mackill 1996). Almost all strongly tolerant cultivars possess the Sub1 QTL (Setter et al 1997); however, additional QTLs of smaller effect appear to give increasing amounts of tolerance (Nandi et al 1997). Through positional cloning, a cluster of three putative ethylene response factor (ERF) genes has been identified in the Sub1 locus. ERFs are transcription factors unique to plants, in which they constitute a large multigene family related to Apetala2 (AP2) and dehydration-responsive element binding (DREB) factors (McGrath et al 2005). ERF genes are induced in response to several biotic and abiotic stresses, and by ethylene and other plant hormones, and might be involved in cross-talk between the different pathways (for review, see Gutterson and Reuber 2004). In addition, it was shown in rice and tomato

that phosphorylation of the proteins enhances DNA binding affinity (Cheong et al 2003, Gu et al 2000) and that ERFs act as transcriptional activators and repressors, respectively (Fujimoto et al 2000, Ohta et al 2001). An allelic survey of the Sub1 ERF genes in a range of tolerant and intolerant germplasm revealed tolerant-specific alleles for Sub1A (Sub1A-1) and Sub1C (Sub1C-1). The tolerant and intolerant alleles (Sub1A-2; Sub1C-2 to 8) show differences in several putative phosphorylation sites and are differentially expressed during submergence. Whereas Sub1A-1 is highly expressed in tolerant lines and expressed at a very low level in intolerant accessions, Sub1C shows the opposite expression pattern. Overexpression of Sub1A-1 in an intolerant variety conferred submergence tolerance, suggesting that Sub1A-1 is the major determinant of tolerance (Xu et al 2006). The sequence information of these three genes facilitated the development of ideal markers suitable for backcrossing this locus into widely grown varieties. The use of marker- assisted backcrossing has been shown to be effective in transferring Sub1 into a widely grown Thai cultivar (Siangliw et al 2003). In a previous project, the Sub1 genes were introduced into widely grown varieties in the rainfed areas of Asia. The sequences are also being used to screen new landraces for the presence of this gene. Preliminary data indicate that some tolerant varieties such as FARO 27 do not have the typical Sub1 gene and might possess a different mechanism of tolerance. Preliminary evaluation of Sub1 introgression lines showed that Sub1 can be effective in conferring tolerance for 10–14 days, depending on floodwater conditions. However, submergence sometimes occurs for a longer duration or more than once. Identification of new sources of tolerance and genes additive to Sub1 will therefore be highly desirable.

Recent studies at IRRI

The physiological basis of tolerance for flash flooding is now reasonably well understood. Two main factors were identified as being

important in contributing to injury when rice is completely inundated: limited gas exchange and reduced illumination. The consequences of these are reduced underwater photosynthesis, accelerated stem and leaf extension, and enhanced chlorosis and leaf senescence, resulting in a shortage in energy supply for maintenance of metabolism. The mechanisms by which tolerant cultivars depress the damaging effects of submergence are becoming more evident. Identification of the traits associated with submergence tolerance will help in designing efficient evaluation methods to pyramid component traits and in gene discovery. In addition, suitable management strategies could be efficiently designed and tuned toward exploiting the potential of the traits that are important for survival and recovery. Initial work at IRRI indicated that submergence tolerance in the most tolerant cultivars is mainly controlled by Sub1 and that the most tolerant cultivars such as FR13A, Goda Heenati, and Kurkaruppan all possess this locus (Xu and Mackill 1996, Setter et al 1997, Xu et al 2006). However, data suggest that other genes are needed to gain higher submergence tolerance. We have identified a tolerant-specific allele of the Sub1C gene and have shown differential expression of this gene in tolerant and intolerant accessions upon submergence. It is currently unclear whether the relative abundance of Sub1A and Sub1C gene products is important for tolerance or whether Sub1 modulating factors are absent from intolerant varieties. Such factors might be present in additional minor QTLs controlling submergence tolerance (Nandi et al 1997, Kamolsukyunyong et al 2001) and could explain why some tolerant breeding lines do not have as high a tolerance as FR13A. Crosses were made with these lines for further genetic and mechanistic analysis. Breeders have been using the sources of submergence tolerance such as FR13A and Kurkaruppan to develop highly tolerant cultivars with a high-yielding plant type. The initial semidwarf breeding lines with submergence tolerance similar to that of FR13A

were developed in the late 1970s (described in Mackill and Xu 1996). Breeding lines with submergence tolerance from FR13A and high yield potential were developed in the late 1980s (Mackill et al 1993). More recently, breeding lines developed from these sources have shown promise in eastern India and a few of them were released as new varieties.

Summary of recent achievements

Development of Swarna with submergence tolerance: A submergence-tolerant version of Swarna was produced in 2 years by marker-assisted backcrossing (MAB):

only the small fragment carrying the QTL Sub1 was introduced. A large number of BC 1 F 1 seeds were produced. Based on five informative markers from the Sub1 region, 54% of the plants were detected to be Sub1+, out of which 3% (21 plants) had desired recombination for the Sub1 region. Background selection was performed for the 12 chromosomes with 58 markers (approx. 5 markers per chromosome). From the progeny of 320 plants from the second backcross, four plants were selected based on foreground and background selection. Out of 937 BC 2 F 2 progeny from the selected plants, one plant was selected for its maximum recipient genome and its target locus.

Providing NARES partners with multiplied seeds of Swarna-Sub1: The seeds of Swarna-Sub1 have been multiplied and used by CRRI, BRRI, and NDUAT for phenotypic evaluation. In preliminary yield trials at Rangpur, Bangladesh, and Cuttack, India, Swarna-Sub1 was evaluated against other elite breeding lines and checks. Swarna-Sub1 showed higher survival (25% for Swarna vs. 100% for Swarna- Sub1), a lower level of elongation under submergence, and earlier maturity and it did not lodge after 10 days of submergence. Data on yield and other attributes are being analyzed. Swarna-Sub1 was evaluated for adaptation to local conditions by growing it

in normal farmers’ fields at Cuttack, Orrissa, India, and Rangpur, Bangladesh. In India, both Swarna and Swarna-Sub1 produced similar yields in farmers’ fields (approx. 5.5 t ha 1 ), whereas, at Rangpur, Swarna- Sub1 slightly outyielded Swarna (3.9 t ha 1 ) and the local check Red Swarna (3.5 t ha 1 ). Swarna-Sub1 also had good plant height and panicle number. Seeds of Swarna-Sub1 were multiplied at two sites in both India and Bangladesh to produce sufficient seeds for large-scale testing in multiple farmers’ fields in 2007 through participatory varietal selection trials.

Identification of diagnostic markers for precise MAB of Sub1: Previously, two cleaved amplified polymorphic markers (CAPs) were designed targeting a silent single nucleotide polymorphism (SNP) located in the Sub1A gene and a unique phosphorylation site in the Sub1C gene. To more precisely measure the introgression region of the Sub1 locus and to obtain markers specific for functional genes underlying the QTL, additional allele- specific markers were developed. A second SNP where the IR40931 allele causes an amino acid change in the Sub1A protein (CCG in Teqing encoding for proline and TCG in IR40931-33 encoding for serine) was targeted for marker design. Since no restriction enzyme sites were located at the SNP locus that could be used to develop a CAP marker, a dominant STS marker was developed by designing a PCR primer with the SNP at the 3′ end. In addition, several CAPs and indel (insertion/deletion) markers were also designed in the promoter region of Sub1A and Sub1C. Several of these gene-based markers have been used in our MAB program, and have been found very useful as alternative foreground markers. The Sub1A marker has already been used in CRRI, India, to confirm the presence of the gene in some of their landraces and improved varieties.

3

Identification of additional microsatellite markers for foreground/recombinant selection of the Sub1 locus: Additional highly polymorphic SSR primers from the International Rice Genome Sequencing Project (IRGSP) were identified in the region of Sub1. Two of them were tightly linked and located upstream of the Sub1 locus, that is, RM23865 (6.2 Mb) and RM23869 (6.3 Mb). These two SSR markers have been very useful in minimizing the size of introgression of the Sub1 locus since previously there were no tightly linked polymorphic SSR markers located upstream of the Sub1 locus.

Development of Samba Mahsuri and IR64 with submergence tolerance: Previously, it was reported that Samba Mahsuri-Sub1 and IR64-Sub1 were produced within two

rounds of backcrossing and one generation

of self-pollination by MAB. Only the small

fragment around the tip of chromosome 9, where the QTL Sub1 is located, was introduced into Samba Mahsuri, a popular variety from India, and IR64. In addition, another version of Samba Mahsuri-Sub1 with a smaller introgression of the Sub1 region was selected among 48 BC 3 F 2 progenies derived from a double-side crossover type of BC 3 F 1 plant. A similar process was conducted for IR64. Seven hundred BC 3 F 2 plants derived from three selected BC 3 F 1 plants have been genotyped; however, no double-side crossover has been found. Nevertheless, several promising recombinants having a smaller region of Sub1 have been identified. We will genotype the BC 3 F 3 progenies of these recombinants to identify the best plants having the smallest introgression region of the Sub1 locus. This plant can then be multiplied and used as an alternative seed source of IR64-Sub1. Both versions of Samba Mahsuri-Sub1 (BC 2 F 2

and BC 3 F 2 ) and IR64-Sub1 (BC 2 F 2 and BC 2 F 3 ) have been used for seed multiplication.

A preliminary submergence field test has

shown that Samba Mahsuri-Sub1 and IR64- Sub1 were comparable with the tolerant check.

4

Development of TDK1 with submergence tolerance: Because of the small size of this population from the earlier backcross and several markers that were biased toward the tolerant parent, there were no optimal plants to be selected out of the BC 2 F 2 population. However, several BC 3 F 1 with very small Sub1 introgression regions having no or one background introgression have been identified. In addition, plenty of BC 3 F 2 -derived BC 3 F 1 seeds are available to maximize the probability of finding the best version of TDK1-Sub1. These BC 3 F 2 plants have been planted and will soon be ready for genotyping.

Development of BR11 with submergence tolerance: A special case study was done

for BR11. Four selection strategies associated with a marker-assisted backcross breeding program were compared for validating suitable selection strategies for an efficient and effective MAB breeding program. The four treatments related to the development of BR11-Sub1 were as follows:

a. Foreground, recombinant, and background selection

b. Foreground and phenotypic selection

c. Foreground, phenotypic, and background selection

d. Foreground, recombinant, and phenotypic selection

As many as 1,430 BC 1 F 1 plants were grown from 44 F 1 plants, and the best BC 2 F 1 progenies had been selected. Selection activities are ongoing in the BC 2 F 2 generation for treatment “b” and in the BC 3 F 1 generation for treatment “c.” However, we could not advance the selection processes a further generation for treatment “d” because of the unavailability of double-recombinant-type plants segregating in the BC 2 F 1 generation. Preliminary results showed that phenotypic selection cannot be used as an alternative for a marker-based background in the MAB scheme.

Development of CR1009 with submergence tolerance: DNA of CR1009 BC 2 F 2 and BC 3 F 1 plants has been isolated and is ready for genotyping.

References

Cheong YH, Moon BC, Kim JK, Kim CY, Kim MC, Kim IH, Park CY, Kim JC, Park BO, Koo SC, Yoon HW, Chung WS, Lim CO, Lee SY, Cho MJ. 2003. BWMK1, a rice nitrogen-activated protein kinase, locates in the nucleus and mediates pathogenesis-related gene expression by activation of a transcription factor. Plant Physiol.

132(4):1961-1972.

Das KK, Sarkar RK, Ismail AM. 2005. ElongationElongation abilityability and non-structural carbohydrate levels in relation to submergence tolerance in rice. Plant Sci. 168:131-136. Dey MM, Upadhyaya HK. 1996. Yield loss due to drought, cold and submergence tolerance. In: Evenson RE, Herdt RW, Hossain M, editors. Rice research in Asia: progress and priorities. CAB International, Wallingford, UK.

p 291-303.

Ella ES, Kawano N, Yamauchi Y, Tanaka K, Ismailil AM.AM.

2003. BlockingBlocking ethyleneethylene perceptionperception enhancesenhances ����oodingooding tolerance in rice seedlings. Func. Plant Biol. 30:813-819. Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M. 2000. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell 12:393-

404.

Fukao TR, Kennedy A, Yamasue Y, Rumpho ME. 2003. Genetic and biochemical analysis of anaerobically- induced enzymes during seed germination of

Echinochloa crus-galli varieties tolerant and intolerant of anoxia. J. Exp. Bot. 54:1421-1429. Gu YQ, Yang C, Thara VK, Zhou J, Martin GB. 2000. Pti4 is induced by ethylene and salicylic acid, and its product

is phosphorylated by the Pto kinase. Plant Cell 12:771-

786.

Gutterson N, Reuber TL. 2004. Regulation of disease resistance pathways by AP2/ERF transcription factors.

Herdt RW. 1991. Research priorities for rice biotechnology. In: Khush GS, Toenniessen GH, editors. Rice biotechnology. Oxon (UK): CAB International. p 19-54. Hossin MA, Huq E, Growver A, Dennis ES, Peacock WJ, Hodeg TK. 1996. Characterization of pyruvate decarboxylase genes from rice. Plant Mol. Biol. 31:761-

770.

Huang S, Greenway H, Colmer TD, Millar AH. 2005. Protein synthesis by rice coleoptiles during prolonged anoxia: implications for glycolysis, growth and energy utilization. Ann. Bot. 96:703-715. Jackson MB, Ram PC. 2003. Physiological and molecular basis of susceptibility and tolerance of rice plants to complete submergence. Ann.Ann. Bot.Bot. 91:227-241.91:227-241. Kawano N, Ella E, Ito O, Yamauchi Y, Tanaka K. 2002. Comparison of adaptability to ��ash ��ood between rice cultivars differing in ��ash ��ood tolerance. Soil Sci. Plant Nutr. 48:659-665.

Kamolsukyunyong W, Ruanjaichon V, Siangliw M,

Kawasaki S, Sasaki T, Vanavichit A, Tragoonrung S.

2001. Mapping of quantitative trait locus related to

submergence tolerance in rice with aid of chromosome walking. DNA Res. 8:163-171. Mackill DJ. 1986. Rainfed lowland rice improvement in South and Southeast Asia: results of a survey. In: Progress in rainfed lowland rice. Los Baños (Philippines): International Rice Research Institute. p 115-144. Mackill DJ, Amante MM, Vergara BS, Sarkarung S. 1993. Improved semidwarf rice lines with tolerance to submergence of seedlings. Crop Sci. 33:749-753. Mackill DJ, Xu K. 1996. Genetics of seedling-stage submergence tolerance in rice. In: Khush GS, editor. Rice genetics III. Manila (Philippines): International Rice Research Institute. p 607-612. Mallik S, Mandal BK, Sen SN, Sarkarung S. 2002. Shuttle-

breeding: an effective tool for rice varietal improvement in rainfed lowland ecosystem in eastern India. Curr. Sci. 83:1097-1102. McGrath KC, Dombrecht B, Manners JM, Schenk PM, Edgar CI, Maclean DJ, Scheible WR, Udvardi MK, Kazan K.

2005. Repressor- and activator-type ethylene response

factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of

Arabidopsis transcription factor gene expression. Plant Physiol. 139:949-959. Mohanty HK, Chaudhary RC. 1986. Breeding for submergence tolerance in rice in India. In: Progress in rainfed lowland rice. Los Baños (Philippines):

International Rice Research Institute. p 191-200. Mohanty HK, Mallik S, Grover A. 2000. Prospects of improving ��ooding tolerance in lowland rice varieties by conventional breeding and genetic engineering. Curr. Sci. 78:132-137. Nandi S, Subudhi PK, Senadhira D, Manigbas NL, Sen-Mandi S, Huang N. 1997. Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol. Gen. Genet. 255:1-8. Ohta M, Matsui K, Hiratsu K, Shinshi H, Ohme-Takagi M.

2001. Repression domains of class II ERF transcriptional

repressors share an essential motif for active repression. Plant Cell 13:1959-1968. Ram PC, Singh BB, Singh AK, Ram P, Singh PN, Singh HP, Boamfa EI, Harren FJM, Santosa E, Jackson MB. 2002. Physiological basis of submergence tolerance in rainfed lowland rice: prospects of germplasm improvement through marker aided breeding. Field Crops Res.

76:131-152.

Setter TL, Ellis M, Laureles EV, Ella ES, Senadhira D, Mishra SB, Sarkarung S, Datta S. 1997. Physiology and genetics of submergence tolerance in rice. Ann. Bot. 79:67-77. Siangliw M, Toojinda T, Tragoonrung S, Vanavichit A.

2003. Thai jasmine rice carrying QTL ch9 (SubQTL) is

submergence tolerant. Ann. Bot. 91:255-261. Singh RK, Dwivedi JL. 1996. Rice improvement for rainfed lowland ecosystem: breeding methods and practices in Eastern India. In: Fukai S et al, editors. Breeding strategies for rainfed lowland rice in drought-prone environments. Proc. Intl. Workshop, Ubon, Thailand,

5-8 Nov. 1996. ACIAR Proceedings 77:50-57.

5

Singh S, Singh ON, Singh RK. 1998. A shuttle breeding approach to rice improvement for rainfed lowland ecosystem in eastern India. In: Sustainable agriculture for food, energy and industry. James & James (Science Publishers) Ltd., UK. p 105-115. Xie Y, Wu R. 1989. Rice alcohol dehydrogenase genes:

anaerobic induction, organ specific expression and

characterization of cDNA clones. Plant Mol. Biol. 13:53-

68.

6

Xu K, Mackill DJ. 1996. A major locus for submergence tolerance mapped on rice chromosome 9. Mol. Breed.

2:219-224.

Xu K, Xia X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AI, Bailey-Serres J, Ronald PC, Mackill DJ. 2006. Sub1A is an ethylene response factor-like gene that confers submergence tolerance to rice. Nature

442:705-708.

Participatory varietal selection of salinity-tolerant rice for the coastal wetlands of Bangladesh

M.A. Salam, G.B. Gregorio, D.L. Adorada, and R.D. Mendoza

Soil salinity is one of the major constraints to rice production on about 1 million ha of the coastal areas of Bangladesh. To reduce salinity, major engineering infrastructure and expensive soil amendments are needed. However, these amendments require large investments to tailor rice plants to adapt to salt stress. In the past, it was difficult to release high-yielding varieties in the coastal areas because no single rice variety could be adapted to the varied soil and climatic conditions of those areas. The urgent need for the development of saline-tolerant varieties in the coastal areas of Bangladesh was therefore prioritized as a researchable issue in a stakeholder analysis. The Bangladesh Rice Research Institute (BRRI) and International Rice Research Institute (IRRI) developed advanced lines that can tolerate salt stress of 8–10 dS m 1 and with a large range of plant characters. All these genotypes were grown on the saline-prone farms of BRRI research stations at Sonagazi and Satkhira. Three sets composed of 72 lines for the wet season (T. aman), 76 for the irrigated (boro) season, and 86 for uplands were selected for evaluation in “mother and baby” trials of participatory varietal selection (PVS). PVS trials were conducted at five sites in the saline-prone coastal districts. Table 1 shows the soil salinity status of the mother trial plots across the three crop seasons. All the trial plots had initial soil salinity above the critical level (>4.0 dS m 1 ) except for Noakhali in the T. aman season. The mean salinity level was highest in boro, followed by upland and T. aman plots. The mother trial for T. aman was conducted at four sites, Char-Sonapur (Sonagazi), Char- Lawrence (Laxmipur), Char-Jabbar (Noakhali), and Benerpota (Satkhira), in 2001, followed by

baby trials in 2002 and evaluation in farm-walk farmers’ fields at three villages in 2003. A mother trial of the upland ecosystem was carried out at the Sonagazi BRRI farm in 2002 and at Upakul Villa (Char-Lawrence, Laxmipur) in 2003. Similarly, a mother trial of the boro season was carried out at Benerpota (Satkhira) and Gobindopur (Kaliganj) sites in 2000-01 and also at Benerpota in 2001-02, followed by baby trials in 2001-02 and 2002-03 crop seasons. Farm- walks of farmers were organized for baby trials at seven villages in this season. Nonreplicated mother trials and researcher- managed on-farm experiments were done in cooperation with the participating farmers. PVS was launched at crop maturity. The Department of Agriculture and Extension (DAE) and five NGOs (Gurpukur, Uttaran, Sushilan, Proshika, and BRAC) organized 25–40 RPFs, including 0– 15 women for the mother trials, across the sites and crop seasons. A briefing was given on the importance of involving farmers in the progress of variety development through PVS. The participating farmers were divided into three to four groups (8–10 farmers per group), and a researcher led each group. All farmers were given a simple PVS evaluation sheet asking them to choose one or two genotypes to grow

Table 1. Soil salinity of mother trial plots at five sites across rice crop seasons.

Site

Plot location

Soil EC in crop seasons

 

T. aman

Boro

Upland

Sonagazi

Sonapur

5.9

6.

Laxmipur

Char-Lawrence

8.3

0.0

Noakhali

Char-Jabbar

3.6

Satkhira

Benerpota

6.9

6.9

Kaligonj

Gobindopur

0.5

Mean

6.

8.7

8.

7

as baby trials on their land under their own management. After a field visit, PVS sheets were collected and two or three farmers from each group were called immediately on a random basis to express their views and opinions on the selection made. All the PVS farmers were supplied with 500 g of seed of the chosen genotypes to be grown in their fields as baby trials. On the other hand, the farm-walk farmers selected seeds from baby-trial farmers’ fields. Baby trials and the farm-walk farmers’ plots were monitored using a household-level questionnaire (HLQ).

Varieties selected through PVS

PVS is the selection of fixed lines done by farmers in a target environment using their own selection criteria. In PVS, access to and selection of breeding lines are decentralized, with farmers’ participation. Plant materials, which have all the combinations of characteristics, are selected by the farmers for the appropriate plant type and yielding ability on their respective salt-stressed farms instead of researchers themselves selecting for the farmers in the coastal areas of Bangladesh. In three years, 245 salt-tolerant genotypes from IRRI and BRRI were placed in PVS mother trials at five coastal sites of Bangladesh.

PVS in T. aman season In 2001, 87 farmers took part in PVS at four mother- trial sites. The farmers selected 10 of the 72 lines and these genotypes were designated as PVS-T1 to

PVS-T10 representing T. aman (Table 2). Variation was great in the choice of PVS-T genotypes by the farmers across locations. The advanced lines had site-specific preference. BRRI dhan40 (PVS-T9) and BRRI dhan41 (PVS-T10) were chosen by a

majority of the farmers, followed by PVS-T7 at all

the sites. The farmers’ preferences for choosing the

genotypes were the following: lodging tolerance, high yield, freeness from disease, uniformity in maturity, and short growth duration. The choice of varieties by farmers also depended on the location.

This confirms the location specificity of varieties for complex environments such as coastal areas. There is considerable variation in yield and other agronomic characteristics of the 10 PVS-T genotypes (Table 3). Most of the farmers’ preferred varieties had growth duration of 140 ± 5 days except for PVS-T4, with early growth duration, and they were chosen at Sonagazi and Satkhira for highlands and crop diversification. The PVS-T farmers grew their selected genotypes as baby trials in 2002, under their own management practices. Data from HLQs showed that 50% of the farmers were discouraged by the results because of water stagnation in the field, which ranged from 30 to 50

cm from transplanting to maximum tillering stage.

The farm walks for baby trials in which 96 farmers partipated were conducted at three villages where there was no high water stagnation. Five PVS-T genotypes showed promising results and were

selected by farmers (Table 4). Two sister lines (PVS-

T5 and PVS-T7) were selected at Sonapur, whereas

two sister lines (PVS-T1 and PVS-T2) and PVS-T 4 were chosen at Satkhira and Kaliganj.

Table 2. Selected genotypes from mother trials and the number of PVS farmers across locations, T. aman, 2001-02.

Entry

Designation

Number of farmers

 
 

Sonagazi

Noakhali

Laxmipur

Satkhira

Total

PVS-T

BR5778-56--3-HR

5

6

3

PVS-T

BR5778-56--3-HR4

5

8

8

5

PVS-T3

BR5778-56--3-HR5

6

4

6

36

PVS-T4

R6640-B-4--

3

9

3

PVS-T5

BR5999-8-3--HR

8

3

4

3

38

PVS-T6

BR5999-8-3--HR0

0

3

3

5

3

PVS-T7

BR5999-8-3--HR6

6

3

8

8

55

PVS-T8

BR5333-34-4-6

4

4

PVS-T9

BRR dhan40

6

9

9

9

63

PVS-T0

BRR dhan4

8

8

8

86

8

Table 3. Agronomic performance of PVS genotypes in mother trials across locations, T. aman, 2001-02.

Entry

Plant height

Yield (t ha )

Duration

(cm)

Sonagazi

Noakhali

Laxmipur

Satkhira

Mean

(days)

PVS-T

6

.4

5.9

.

3.8

3.3

35

PVS-T

0

.

4.7

.

3.7

3.0

35

PVS-T3

4

.

5.4

.3

4.3

3.3

36

PVS-T4

06

.0

.9

.5

3.0

.3

6

PVS-T5

30

3.6

6.4

5.

4.7

5.0

35

PVS-T6

30

3.5

5.4

4.5

4.7

4.5

36

PVS-T7

30

.

4.4

3.8

3.8

3.5

35

PVS-T8

.9

5.4

4.

4.

46

PVS-T9

36

.7

4.9

4.5

3.8

3.7

38

PVS-T0

38

.8

4.4

4.

3.7

3.7

44

Table 4. Performance of PVS-T genotypes in baby trials and number of farm-walk farmers that selected each genotype, T. aman, 2002-03.

Genotype

Plant

Growth

Number of

Yield (t ha )

 

height

duration

preferring

L a

L

L3

X

(cm)

(days)

farmers

PVS-T

3

6

7

4.5

5.0

4.8

PVS-T

33

6

8

5.0

5.

5.

PVS-T4

9

34

4.5

3.4

4.0

PVS-T5

40

4

9

5.0

5.0

PVS-T7

39

40

7

5.0

5.0

a L1 = Parkumira, Tala; L2 = Gobindapur, Kaliganj; L3 = Sonapur, Feni.

All the farm-walk farmers grew their individual selection under their own management practices in T. aman 2003. PVS-T4 showed high- temperature sensitivity at the reproductive phase and consequently heterogeneity of heading and sterile panicles were observed. PVS-T4 is a short- duration genotype; thus, its flowering coincided with the high-temperature spell (>35 °C) during early to mid-October. On the other hand, PVS-T1, PVS-T2, PVS-T5, and PVS-T7 were relatively tall in stature and prone to lodging at wind speed of 30–50 km h 1 , a usual phenomenon in the coastal areas in early November. Thus, PVS in T. aman was terminated in the subsequent season.

PVS in saline-prone upland culture In 2002, a mother trial for 85 short-duration (120–130 d) IR genotypes was conducted at a BRRI farm in Sonagazi. The prevailing crop growing conditions in upland culture in coastal wetlands are the following:

1.

Dry direct seeding using the dibbling method,

2.

A drought spell plus salinity (6–8 dS m 1 ) stress from seedling to tillering stage,

3.

Water stagnation of 20–50 cm at tillering through maturity stage depending on elevation, and

4.

Harvesting of the upland rice crop at or

before mid-August for the transplanting of the main rice crop (T. aman). Considering the above-mentioned diversified and difficult conditions, a mother trial was conducted at the Sonagazi station. Crop establishment was done using dry direct seeding with the dibbling method. The crop received drought after seeding and also stagnation of water at 20–30 cm at maximum tillering up to maturity. PVS activity was conducted in collaboration with DAE and two NGOs (Proshika and BRAC) of Sonagazi at crop maturity in August 2002. Twenty-nine farmers, including two women, joined the PVS activity and 12 salt-tolerant genotypes with good yielding ability were selected. The performance of the farmers’ selected varieties demonstrated higher yield than BRRI dhan27 and varieties with shorter plant height. Farmers finally selected four PVS-A genotypes out of the 85 short-duration genotypes introduced. Seeds of the selected PVS-A genotypes were distributed to farmers

for adaptability tests in their own fields in aus

2004.

9

A mother trial composed of 22 genotypes, including 12 PVS-A, was conducted at Upakul Villa under Char Alexgender of Laxmipur in 2003. Proshika, BRAC, and DAE organized 31 farmers, including five women, to join the PVS activity. The male farmers visited the trial and selected four PVS-A genotypes (Table 5). Seeds (500 g) of the PVS genotypes were supplied to the PVS farmers’ baby trials to be conducted on their own farms for the 2004 crop season.

PVS in boro season Researcher-managed on-farm mother trials composed of 76 salt-tolerant (8–10 dS m 1 ) genotypes were conducted at Satkhira and Kaligonj sites in 2000-01. Thirty-seven farmers took part in the PVS activity at crop maturity in cooperation with the Department of Agricultural Extension (DAE) and three NGOs, Gurpukur, Uttaran, and Sushilan. Government officials, block supervisors of DAE, field-level workers of the NGOs, and local leaders (union council members and the chairman) participated. The 24 genotypes selected by participating farmers were designated as PVS-B1 to PVS-B24, representing the boro season. Since handling such a large number of genotypes was difficult, we distributed seeds of PVS-B1 to PVS-B8 and decided to conduct another PVS with the remaining PVS-B genotypes in the 2001-02 crop seasons. In 2001-02, at Benerpota, 42 farmers, including 15 women from Kaliganj, Tala, and Satkhira, participated in the PVS activity. The PVS farmers selected 12 genotypes as shown in Table 6. The performance of the PVS-B genotypes was highly accepted by farmers, especially for yielding ability and shorter growth duration. The farmers’ criteria for the selection of PVS genotypes were short growth duration and yield-contributing characters (high number of panicles per plant, high number of grains per panicle, and low sterility percentage). The fields with initial soil salinity of 8–10 dS m 1 had 2–3 dS m 1 at transplanting. Salnity gradually increased and exceeded the critical level (4.0 dS m 1 ) from late April. Thus, farmers preferred short-duration genotypes for saline conditions because they noted that, with longer

Table 5. Performance of selected genotypes in mother trials and number of farmers who chose PVS genotypes at Char Alexgen- der, Laxmipur, upland rice, 2002-03.

Entry

Designation

Plant

Growth

Yield (t ha )

No. of

 

height

duration

farmers

(cm)

(days)

PVS-A

R7046-B-R-6-3-

85

7

3.0

7

PVS-A6

R63307-4B-4-3

03

0

3.

PVS-A9

R6449-3B-4-3

9

04

.7

6

PVS-A0

BRR dhan7

3

00

.

0

Table 6. Performance of genotypes selected from mother trials and number of participating farmers at Benerpota, Satkhira, boro season, 2001-02.

PVS no.

Designation

Number

Plant

Yield (t ha )

 

of farmers

height

 

(cm)

PVS-B

BR5778-56--3-HR

4

99

6.7

PVS-B3

R63307-4B-4-3

7

6.

PVS-B4

R6449-3B-4-3

94

5.6

PVS-B5

R659-4B-4-

3

78