Genet Resour Crop Evol (2011) 58:1213–1224
DOI 10.1007/s10722-010-9654-5
RESEARCH ARTICLE
Role of informal seed system in promoting landrace
diversity and their on-farm conservation: a case study
of rice in Indian Himalayas
Avinash Pandey • I. S. Bisht • K. V. Bhat •
P. S. Mehta
Received: 12 October 2010 / Accepted: 13 December 2010 / Published online: 20 January 2011
Ó Springer Science+Business Media B.V. 2011
Abstract Role of informal seed system in landrace
diversification, in situ conservation on-farm and sus-
tainability in production were investigated as a case
study for rice diversity in Indian Himalayas. The
diachronic pattern of landrace occurrence revealed
substantial increase, both in landrace number and
frequency, in time. The local level seed supply in
Uttarakhand Himalaya revealed that about 96% seed
supply originated from informal system and a mere 4%
seed supply is met from formal seed supply networks.
In higher elevation ranges, beyond 1200 masl, largely
landrace cultivation is practiced and a greater landrace
diversification in traditional production was observed.
Substantial variations due to environmental adapta-
tions in niche habitats help provide important donor
germplasm for crop improvement to users. Further, the
population genetic structure also indicated enough
diversity being maintained on-farm. Developing path-
ways for strengthening local level seed system for
A. Pandey  I. S. Bisht (&)  K. V. Bhat
National Bureau of Plant Genetic Resources,
Pusa Campus, New Delhi 110012, India
e-mail: bishtis@nbpgr.ernet.in; bishtis@rediffmail.com
P. S. Mehta
NBPGR Regional Station Bhowali, Nainital,
UA 261132, India
Present Address:
A. Pandey
ICAR Research Complex for NEH Region Umiam,
Meghalaya 793103, India
landrace diversification linked to sustainability in food
production and conserving agro-biodiversity has been
emphasized.
Keywords In situ conservation on-farm 
Informal seed system  Landrace diversification 
Rice (Oryza sativa L.)  Sustainable crop production
Introduction
A seed system refers to the different ways that farmers
access seed at the farm level. Seed systems are complex
processes that are influenced by the agro-ecosystem
factors, nature of the crop as well as social, economic
and political environments (Jarvis et al. 2000). Two
types of seed supply systems are most commonly
recognized. Informal seed sources are common in the
marginal rainfed cropping areas where the resource-
constrained farmers plant security food crops of local
importance that are adapted to local ecological condi-
tions. Farmers obtain seed and varieties through
informal networks based on exchange or gift with
relatives and neighbors, or purchase them from other
farmers and local markets. Formal seed systems, on the
other hand, cover seed production and supply mech-
anisms, operated by public or private sector specialists.
They are guided by scientific methodologies for plant
breeding and controlled multiplication.
There is increasing recognition that the diverse
needs of resource-poor farmers cannot be addressed
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by the breeding of a restricted range of high-yielding,
high-input varieties. Yields of improved varieties in
favourable conditions have reached a plateau in many
countries or even subsequently declined (Win and
Win 1990). It has often been suggested that a range of
varieties are needed to fulfill specific socio-economic
as well as agroecological needs in the small farm
system and that breeding methods need to be
reassessed to increase the ability of formal sector
agricultural research to produce varieties useful to
small farmers (Cromwell 1990). An issue of great
relevance when discussing the conservation of
genetic diversity and seed sector development is that
small-scale farmers are predominantly practicing
subsistence farming and are only to a limited extent
involved in the cultivation of cash crops. Within this
context a critical question is whether or not farmers
have a real option to purchase ‘formal’ seed from
released ‘varieties’; even if seed is available to be
purchased, affordability remains a serious issue.
The formal system ignores the role that diversity
traditionally plays in what is considered to be the
common livelihood strategy of small-scale farmers
operating in complex, diverse, and risk-prone envi-
ronments. Small-scale farmers use a diversity of
crops and manage genetic diversity within a crop,
usually consisting of traditional varieties or land-
races, with the objective of keeping options open and
reducing the risk of crop failure (Pretty 1995).
Farmers approach these varieties in a dynamic
manner by exchanging and sharing varieties and
seeds, as they are always looking for new types of
seeds and enrich crop diversity. There could be other
motives of seed exchange as farmers sometime need
to replace the lost seed with new one or the seed that
has degenerated.
Local varieties and local crops are considered
critical as they are usually well adapted to the local
production system and are part of a strategy aiming
for food security. Such an emphasis happens to
coincide with principles that underpin in situ conser-
vation ‘on-farm’, thus supporting communities that
manage agrobiodiversity (Subedi et al. 2006; Hodg-
kin et al. 2007) and contributing to the conservation
of plant genetic resources.
Rice (Oryza sativa L.) is an important crop of
Indian subcontinent. Under improved management
the traditional landraces have been replaced by
modern cultivars during the post-green revolution
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Genet Resour Crop Evol (2011) 58:1213–1224
era but under marginal management landrace culti-
vation is still largely practiced. Sustainability in rice
production due to varietal diversification under
wheat-rice cropping system in Indo-Gangetic plains
have been reported. There is, however, no precise
documentation about loss of landrace diversity from
marginal subsistence agriculture.
This paper explores the context of local seed
exchange and agrobiodiversity conservation, dia-
chronic analysis of landrace occurrence at different
periods, the in situ on-farm conservation of landrace
diversity, and also outlines the importance of land-
race diversification in sustainability of agriculture in
marginal production of Uttarakhand Himalaya of
India.
Materials and methods
Inventorization of rice landrace diversity
and local level seed system
Data on rice landrace diversity from north-western
Himalayas in Uttarakhand state were collected from
primary sources with the help of planned structured
and unstructured questionnaire/interview schedules at
individual farm households level during 2007 crop-
ping season. Sample households were randomly
selected from 30 niche environment sites (Fig. 1) at
different elevations. Three to four villages were
randomly selected at each niche site. In each selected
village 10% households were randomly selected for
documenting information on rice landraces. During
the survey of the region, a non-participant observa-
tion method was also used while recording the crop
landrace diversity. Using participatory rural apprai-
sal, information was obtained on the total land area
under cultivation for individual rice landraces. Dia-
chronic information of two periods was also collected
on the loss and shift in landrace diversity, if any,
during 1970s and 2000s from each household. The
information for current (2000s) crop landrace diver-
sity status was validated by taking observations in the
field for rice landrace diversity under cultivation.
Respondent households were also asked to fill-in a
questionnaire for extracting information on their
knowledge regarding specific landraces, folk nomen-
clature of traditional landraces, their distinctive
properties etc. Information on farmer management
Genet Resour Crop Evol (2011) 58:1213–1224
Fig. 1 Map of Uttarakhand depicting areas of rice landrace collected at niche sites (denoted by ‘‘*’’) [the elevation range falling
between 30° 310 22.500 N and 28° 560 1.100 N latitude to 79° 040 32.300 E and 79° 550 25.900 E longitude]
of population structure, pattern of rice landrace
occurrence and gene flow was obtained following
Jarvis et al. (2000). All possible care was taken to
determine the consistency in farmers’ naming and
describing rice landraces by comparing information
from farmer households and different social groups.
The information on farmers’ decision on variety
choice was also documented. While recording the
names of crop cultivars/landraces, informant farmers
were visited for identification of the landrace in the
field. Information obtained was authenticated from
knowledgeable elderly farmers and other secondary
sources. Information was also recorded on ranking
the varieties in terms of area covered by each
landrace/variety. The source of seed, whether self,
from within the family, between farmers in commu-
nities, distant markets and traders was also deter-
mined. The questionnaire also contained questions
about farmers’ perceptions on various benefit enhanc-
ing options for farmers from local rice landrace
diversity for sustainable use at all study sites.
Morphological variations in rice landraces due
to environmental adaptations
The 69 distinct named rice landraces assembled from
above survey sites of Uttarakhand state including a few
landraces from parts of North-eastern Himalayas
(Arunachal Pradesh and Assam) were grown in an
1215
on-station trial for study of adaptive variations during
2008 cropping season at NBPGR Regional Station,
Bhowali (Nainital) Uttarakhand, situated at 1800 masl
elevation. The material was grown in randomized
block design, each accession grown in four 2 m row
plots, with a between-row spacing of 20 cm, and a
within-row spacing of 10 cm. Five rice varieties
developed through institutional breeding programmes
viz. VL 206, VL 207, VL 208, VL 209 and Majhera 7
were included as controls. Recommended agronomic
practices were followed through various stages of crop
growth. Observations on 22 characters, 15 quantitative
and 7 qualitative were recorded. As majority of the
Arunachal Pradesh populations were photoperiod
sensitive at Bhowali location, yield data of only four
populations from this region could be recorded in the
present study for adaptive environmental variations.
Data on quantitative traits were statistically analyzed
for range and pattern of variations using INDOSTAT
statistical software developed at the INDOSTAT
Services, Hyderabad. Classification (cluster analysis)
and ordination (principal components analysis) anal-
yses were performed. Skewed data on quantitative
traits were transformed before multivariate analysis.
Ward’s minimum variance clustering method was
used to classify accessions in discrete clusters (Sneath
and Sokal 1973). The phenotypic frequencies of both
quantitative and qualitative characters were also used
for computing Shannon–Weaver information index
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(Shannon and Weaver 1963) in order to estimate the
diversity in different clusters. The index (H) was
calculated as presented by Negassa (1985) and Engels
(1991):
X
n X
H¼ pi log pi
i¼1
where pi is the proportion of the accessions in the ith
class of an n-class character.
Population structure of rice landraces using STMS
markers
The experimental materials for population structure
comprised 20 rice landrace populations, 10 popula-
tions assembled from parts of Uttarakhand state in
North-western Himalayas and 10 collected from
North-eastern Himalayas (parts of Arunachal Pradesh
and Assam).
The DNA extracted from 24 individuals per
population was used for STMS analysis. Genomic
DNA was extracted using the CTAB method (Saghai-
Maroof et al. 1984). DNA samples were diluted to a
working concentration of approximately 10 ng ll-1.
Each 25 ll PCR contained 3.0 mM MgCl2, 1U Taq
DNA polymerase, 200 lM dNTP, 0.2 lM STMS
primers and 30 ng genomic DNA in 10 mM Tris–
HCl, 50 mM KCl pH 8.3. The amplification regime
as detailed in Cornell University website
www.gramene.com was followed. The gels were
stained with ethidium bromide and viewed under UV
light. Patterns were scored for presence of each allele
in an accession.
Thirty STMS primers were screened to identify
suitable primers for detailed molecular diversity
analysis of rice landrace populations. The primers
were selected from the sequence information
obtained from the Website of Cornell University.
Of the thirty primers screened, eleven informative
primer pairs were used in the present study for final
STMS analysis. Electrophoretic patterns were ana-
lysed by using the BioCalculator software supplied
with QIAxcel system. Allele calling is based on the
size of largest peak Capillary separations of most
STMS amplicons consist of a cluster of peaks in
electrogram. Only the peak which was most conspic-
uous was considered and the less conspicuous peaks
were considered as artefacts and rejected.
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Genet Resour Crop Evol (2011) 58:1213–1224
The polymorphism information content (PIC)
value described by Botstein et al. (1980) and
modified by Anderson et al. (1993) for self-pollinated
species was calculated as follows:
n
PICi ¼ 1  P2ij
j¼1
where, Pij is the frequency of the jth allele for the ith
marker, and summed over n alleles. PIC is also an
estimate of the discriminatory power of a SSR marker
locus.
Ten populations each from both groups of rice
landraces, group I from NW Himalayas and group II
from NE Himalayas were analysed using PopGene
Version 132 software (Yeh et al. 2000) to estimate
the various genetic diversity parameters. The Ewens-
Watterson test of neutrality was also performed,
using the above software, to detect deviations from a
neutral equilibrium model. The genetic distance
matrices were subjected to cluster analysis by
unweighted pair group method of arithmetic average
(UPGMA) analysis to generate dendrogram for all
populations using NTSYS-PC (ver 202j; Exeter
Software, NY, Rohlf 2000). Mantel’s correlation test
(Mantel 1967) was performed by calculating corre-
lations between Nei’s genetic distance and cophenet-
ic value for each pair of comparisons. The data
were subjected for analysis of molecular variation
(AMOVA) using Arlequin 31 software (Excoffier
et al. 2005). Population structure by AMOVA is
based on an analysis of variance of gene frequencies,
taking into account the number of mutational differ-
ences between molecular haplotypes. Fixation indices
(Weir and Cockerham 1984) and population pairwise
FST (pairwise estimates of the correlation of alleles
between populations) values were also computed.
The genetic structure of the populations was also
studied by using the Bayesian Model-based approach
proposed by Pritchard et al. (2000) to assign
the landraces into genetically structured groups.
The software package STRUCTURE version 20
(Pritchard et al. 2000) was used to perform this
analysis. With the knowledge of UPGMA clusters
analysis, STRUCTURE software was run for pre-
sumed populations (k) from 2 to 8, following the
admixture ancestry model. Run length of 1000 burn-
in period with10 replications was performed. The run
with maximum likelihood was used to assign
Genet Resour Crop Evol (2011) 58:1213–1224 1217

landraces to groups and to reveal the group member-
ship probability (inferred ancestry) of the landraces.
Results
Inventory of rice landraces and the local seed
systems
A detailed inventory of rice landraces at 30 collection
sites is presented in Table 1. About 80 distinct named
landraces have been documented in the present study,
two-thirds of which were categorized as rare and one-
third as common. The diachronic pattern of landrace
occurrence revealed substantial increase, both in
landrace number and frequency, in time at all sites
during 2000 s compared to 1970s.
The local level seed supply in Uttarakhand Hima-
laya revealed (Table 2) that about 43% seed supply
for planting is met from farm households’ own saved
seed of local landraces. About 30% seed supply is
met from landraces exchanged from other farm
households from within the village or from distant
neighbours’ and relatives in the region. About 27%
supply of seed of improved varieties is met mainly
from own saved seeds or from neighbours’/relatives.
A mere 4% seed supply is met from formal seed
supply network. Improved varieties are mainly grown
in valleys under assured irrigation at lower eleva-
tions. Under upland rainfed higher elevation ranges
largely landrace cultivation is practiced and almost
entire seed supply is met thro ugh informal system.
The farmers at a given site recalled many rice
landraces with their distinctive properties grown
during 1970s, which are not available locally now
but we found these landraces gown elsewhere at
several other sites in the region. There was no
consistency in landrace names and often it was
difficult to ascertain that all the farmer-named
varieties are genetically distinct. All care was,
however, taken to record only distinct landraces
based on farmer description of their varieties using
distinct naming criteria.
Morphological variations in rice landraces due
to environmental adaptations
The descriptive statistics for important quantitative
traits of 69 distinct rice landraces assembled from 30
niche sites has been presented in Table 3. Wide
variations for various agronomic traits like grain
yield per plant, panicle length, number of tillers/plant,

Table 1 Rice landrace scenario in traditional productions during 1970s and 2000s in Uttarakhand Himalayas
Elevation (masl) Landrace scenario Common Rare
1970s 2000s 1970s 2000s

\1200 Average no. of landraces per household per site 2.0 3.0 4.0 6.0
Frequency 70.0 80.0 10.0 22.0
Total named landraces grown at all study sites 13.0 18.0 22.0 34.0
Total no. of improved varieties grown 5.0 7.0 – –
1200–1800 Average no. of landraces per household per site 3.0 4.0 7.0 8.0
Frequency 60.0 73.0 17.0 33.0
Total named landraces grown at all study sites 18.0 26.0 31.0 46.0
Total no. of improved varieties grown 3.0 5.0 – –
[1800 Average no. of landraces per household per site 3.0 3.0 7.0 9.0
Frequency 53.0 67.0 21.0 32.0
Total named landraces grown at all study sites 11.0 23.0 27.0 49.0
Total no. of improved varieties grown – – – –
Average (at all elevations) Average no. of landraces per household per site 2.7 3.3 6.0 7.7
Frequency 61.0 73.3 16.0 29.0
Total named landraces grown at all study sites 14.0 22.3 26.7 43.0
Total no. of improved varieties grown 2.7 4.0 – –

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Table 2 Comparative estimates of rice seed supply (%) at household level

Seed source \1200 masl 1200–1800 masl [1800 masl Average
seed supply

Own landraces 33.0 44.0 53.0 43.3

Neighbours’ landraces from the village 11.0 12.0 18.0 13.7
Distant neighbours’/relatives’ landraces in the region 12.0 16.0 20.0 16.0
Own improved variety 10.0 10.0 2.0 7.3
Neighbours’ improved variety within the village 11.0 8.0 2.0 7.0
Distant neighbours’/relatives’ improved variety within the region 14.0 7.0 5.0 9.0
Other improved variety from formal seed supply network 9.0 3.0 – 4.0

Table 3 Range of variation for various quantitative traits of rice landraces from high altitude ranges of Uttarakhand state
Character Range K S Mean CV (%)

Days to 75% panicle emergence 103.00–175.00 10.52a -1.87a 154.51 6.15

Plant height 58.67–164 0.48 -0.07 111.67 18.52
Flag leaf length (cm) 3.56–11.62 5.97a 1.68a 5.81 21.34
Flag leaf width (cm) 0.22–0.45 0.52 -0.13 0.32 12.92
Penultimate leaf length (cm) 5.55–12.88 -0.54a -0.36 9.25 18.37
Penultimate leaf width (cm) 0.16–0.42 0.40 -0.44 0.30 16.67
Panicle length (cm) 0.00–5.95 16.42a -2.67a 4.42 16.58
No. of grains/panicle 12.68–54.56 -0.12 0.36 28.95 29.48
Days to 80% maturity 137.00–203 5.44a -1.31a 181.58 6.13
Grain length (cm) 0.81–1.47 -0.14 0.30 1.14 12.48
Grain width (cm) 0.32–0.68 -0.22 0.50a 0.47 17.71
100 grains weight (g) 0.61–2.94 -0.60a -0.26 1.85 29.04
Grain yield/plant (g) 0.10–22.73 0.13 0.62a 7.81 65.94
No. of tillers/plant 0.88–4.84 0.65a 0.78a 2.38 34.74
K Kurtosis, S Skewness
a
Significant at 0.05 probability

number of grains per panicle, etc. were recorded
among different populations. Least variations were
observed for days to flowering and maturity. For
qualitative traits, striking variations were recorded for
seed coat colour, husk colour, panicle exertion,
presence of aroma, presence of awn and threshability.
Representations of frequency distribution for all
quantitative traits revealed skewness, both positive
and negative.
The clustering pattern as revealed by Ward’s
minimum variance dendrogram classified the acces-
sions into five distinct groups. Cluster I with 16
accessions was mainly characterized as early flower-
ing and dwarf types. Cluster II was characterized by
populations with medium flowering and high yield
potential. Cluster III comprised accessions late in
flowering and low grain weight. Cluster IV was
characterized with bold seeded accessions and mod-
erate yield. Cluster V comprised accessions with
relatively poor yield. Association of geographical
origin and genetic diversity was somewhat evident.
The Shannon–Weaver diversity indices (SDI), for
both quantitative and qualitative characters, showed
wide variations between characters cluster-wise. The
pooled diversity indices by characters (quantitative
traits) indicate relatively high diversity for grain
width, 100-grain weight and number of tillers/plant
whereas for other quantitative traits, diversity was
moderate. Based on cluster-wise pooled diversity
over all the characters, cluster III was the most

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diverse followed by accessions in cluster V, I, II and Table 4 Estimates of Shannon–Weaver diversity indices
IV. Among qualitative traits, seed coat colour and (SDI) for landraces occurring at different elevation ranges for
different morphological traits
panicle exertion recorded relatively greater diversity.
Accessions in cluster I were relatively more diverse Characters Elevation range (masl)
for these qualitative traits followed by accessions \1200 1200–1800 [1800
from cluster V, II, IV and III. Cluster III and V, with
greater diversity indices, can be a valuable aid for Quantitative traits
selection of parental lines with desired adaptive Days to 75% panicle emergence 0.25 0.60 0.86
variations. Plant height 0.54 0.75 0.78
Principal components analysis performed on quan- Flag leaf length (cm) 0.52 0.58 0.79
titative traits revealed that the first three most Flag leaf width (cm) 0.55 0.64 0.77
informative components accounted for 65.72% var- Penultimate leaf length (cm) 0.63 0.66 0.74
iance. It also presented the characters with greater Penultimate leaf width (cm) 0.67 0.79 0.83
weightings in each of the three principal component Panicle length (cm) 0.54 0.54 0.52
axes. Important characters with greater weightings in No. of grains/panicle 0.63 0.64 0.78
principal component axis I include 100-grain weight, Days to 80% maturity 0.57 0.69 0.71
yield/plant and plant height. Important characters Grain length (cm) 0.43 0.43 0.78
with greater weightings in principal component axis Grain width (cm) 0.71 0.90 0.86
II include days to flowering, days to maturity and 100 grains weight (g) 0.54 0.78 0.73
grain length. No. of grains/panicle had greater Grain yield/plant (g) 0.76 0.70 0.82
weightings in principal component axis III. The No. of tillers/plant 0.64 0.86 0.83
principal components analysis in general confirmed Qualitative traits
the groupings obtained through cluster analysis. Early plant vigour 0.12 0.20 0.40
The pooled SDI values were relatively greater for Panicle exertion 0.30 0.28 0.37
landraces assembled from higher elevation areas Husk colour 0.31 0.10 0.10
(Table 4). A positive relationship was therefore Threshability 0.25 0.16 0.40
evident between informal seed exchange and greater Seed coat colour 0.39 0.35 0.42
diversity with increasing elevation. Pooled SDI 9.35 10.65 12.49

Population structure of rice landraces using STMS

markers
A total of 71 alleles were detected in twenty rice
landrace populations by using eleven STMS markers
(RM11, RM19, RM25, RM164, RM216, RM217,
RM218, RM224, RM241, RM242 and RM263). The
number of alleles per locus and their allele size
ranged from 4 to 10, with an average of 6.45 alleles
per locus. The polymorphism information content
(PIC) value of STMS loci ranged from 0.461 to 0.826
with mean value of 0.705 for each locus. The overall
size of amplified products ranged from 108 to 298 bp.
The genotypes of 24 individuals of each landrace
populations were not identical at eleven studied
STMS loci. Of the total 71 alleles recorded, 46 (65%)
alleles were present in both group I (populations from
NW Himalaya) and group II (populations from NE
Himalaya). Nine (3 rare, frequency less than 0.05)
alleles were present in group I but not in group II
whereas, 16 (7 rare) alleles were present in group II
but not in group I. Three alleles were rare in both
groups, 5 alleles were rare in group I but not in group
II and nine alleles were rare in group II but not in
group I. Nine (2 rare) alleles were found unique and
present in any one of the rice landrace populations.
The total number of alleles per population ranged
from 16 to 37 (Table 5). Allelic richness was greater
for population from mid to low elevation ranges
compared to higher elevations. At higher elevations,
the populations largely comprise locally common
unique alleles.
Population differentiation as revealed by FST
values ranged from 0.30 to 0.79 with the mean value
of 0.47 in group I, whereas in group II the FST values
ranged from 0.27 to 0.83 with the mean of 0.61.
Overall, the FST values ranged from 0.40 to 0.80 with
the mean value of 0.58 per locus. This indicates high
genetic differentiation among populations. The gene

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Table 5 Summary diversity of twenty rice landrace populations based on STMS markers
Population Na Ne I He Total no. of No. of
alleles present polymorphic loci*

North-western Himalayas
IC-556525 3.27 ± 0.79 1.93 ± 0.79 0.74 ± 0.39 0.41 ± 0.22 36 11 (100)
IC-556528 2.18 ± 1.47 1.65 ± 0.76 0.44 ± 0.52 0.26 ± 0.30 24 5 (45.45)
IC-556531 2.90 ± 0.83 1.75 ± 0.25 0.72 ± 0.16 0.43 ± 0.07 32 11 (100)
IC-556532 2.09 ± 1.13 1.45 ± 0.65 0.38 ± 0.42 0.22 ± 0.25 23 6 (54.55)
IC-556533 2.90 ± 1.81 1.69 ± 0.61 0.60 ± 0.49 0.33 ± 0.27 32 7 (63.64)
IC-556544 3.09 ± 1.38 2.11 ± 1.03 0.78 ± 0.45 0.44 ± 0.23 34 10 (90.91)
IC-556555 2.90 ± 1.04 2.03 ± 0.72 0.77 ± 0.34 0.46 ± 0.18 32 11 (100)
IC-556557 2.45 ± 1.03 1.81 ± 0.57 0.63 ± 0.37 0.39 ± 0.22 27 9 (81.82)
IC-556559 2.36 ± 0.67 1.35 ± 0.23 0.43 ± 0.21 0.25 ± 0.13 26 10 (90.91)
IC-556560 2.45 ± 0.69 1.60 ± 0.49 0.54 ± 0.20 0.33 ± 0.19 27 11 (100)
North-eastern Himalayas
IC-558249 3.36 ± 1.02 1.89 ± 0.65 0.76 ± 0.33 0.43 ± 0.18 37 11 (100)
IC-558259 1.73 ± 0.79 1.23 ± 0.28 0.26 ± 0.28 0.16 ± 0.17 19 6 (54.55)
IC-558275 1.45 ± 0.52 1.20 ± 0.33 0.19 ± 0.25 0.12 ± 0.18 16 5 (45.45)
IC-558293 1.54 ± 0.69 1.67 ± 0.26 0.18 ± 0.25 0.11 ± 0.16 17 5 (45.45)
IC-558298 3.36 ± 1.13 2.26 ± 0.75 0.90 ± 0.32 0.51 ± 0.16 37 11 (100)
IC-558304 2.09 ± 0.30 1.48 ± 0.47 0.45 ± 0.24 0.29 ± 0.17 23 11 (100)
IC-558306 2.55 ± 1.12 1.60 ± 0.41 0.56 ± 0.35 0.34 ± 0.20 28 9 (81.82)
IC-558308 1.72 ± 0.78 1.17 ± 0.23 0.22 ± 0.26 0.13 ± 0.15 19 6 (54.55)
IC-558313 1.73 ± 0.64 1.23 ± 0.33 0.25 ± 0.27 0.15 ± 0.17 19 7 (63.64)
IC-558330 2.36 ± 1.50 1.70 ± 0.84 0.50 ± 0.53 0.30 ± 0.30 26 6 (54.55)
Na Observed number of alleles, Ne Effective number of alleles, I Shannon’s Information index, He Expected heterozygosity
* Percent polymorphism in parentheses

flow ranged from 0.14 to 0.60 with the mean of 0.28
for group I, whereas it ranged from 0.05 to 0.67 with
the mean of 0.16 for group II.
The UPGMA dendrogram based on Nei’s genetic
distances classified all twenty populations into three
major clusters. Cluster I comprised seven landrace
populations from NW Himalayas while seven land-
races from NE Himalaya were present in cluster II.
The remaining six landraces, three each from both
regions, formed the cluster III. The validity of the
grouping observed in the dendrogram was tested by
calculating Mantel’s correlation between cophenetic
values and Nei’s genetic distance. The Mantel’s
correlation coefficient (r) between Nei’s genetic
distance and cophenetic value was 0.80.
STRUCTURE software was used to perform
model-based cluster analysis. In 10 replicated runs
for different K values from 2 to 8 (presumed number
of populations) based on the distribution of 71
different alleles at 11 SSR loci among 480 individ-
uals (24 individuals for each 20 landraces). Accord-
ing to STRUCTURE documentation, the smallest
value of K that captures the major structure in the
data is frequently the most appropriate choice. In
present study the most appropriate number of groups
(K) was identified at K = 3 with a constant alpha
*0.037 and the natural log probability of the data
which is proportional to the posterior probability
were maximized (LnP(D) = -10059.4). At K = 3,
the sample is divided into 3 model clusters consisting
of individuals from 6 landrace populations from NW
Himalayas in cluster I, individuals from 7 landraces
from NE Himalaya in cluster II and individuals from
7 landraces from both NW Himalaya and NE
Himalaya in cluster III (Fig. 2). Fifteen rice landraces
may be categorised as pure landrace as the average

123
Genet Resour Crop Evol (2011) 58:1213–1224 1221

Fig. 2 Dendrogram of
twenty rice landrace
populations based on Nei’s
(1972) genetic distance

shared ancestry of 24 individuals of respective Discussion

landrace for a model cluster is more than [90%
while other shows admixture. The level of admixture The present study demonstrated that more than 95%
was more in north-western landrace populations than seed planted by farmers in higher Himalayan ranges
north-western populations. The model based cluster- originates from informal system. Under marginal
ing pattern found similar to the UPGMA clustering subsistence agriculture, beyond 1600 masl, mainly
pattern with minor deviations. traditional landraces are cultivated and the entire seed
Analysis of molecular variance (AMOVA) requirement of farmers is met from informal systems.
revealed maximum percentage of variation among Merely 4–5% seed supply is met through formal seed
populations within group (57.18%) followed by system, mainly in valleys at lower elevations where
31.60% within populations and rest 11.22% among improved varieties are also cultivated under assured
groups (Table 6). Pairwise genetic differentiation irrigation.
(FST) among the 20 rice landraces ranged from 0.02 Increase in number of rice landrace populations
to 0.92. IC-558259 from NE Himalaya showed high over time could be attributed to enhanced informal
genetic differentiation with all other populations with seed exchange under marginal productions. It has
an average FST of 0.69 and a range of 0.89 to 0.45. been earlier reported from Uttarakhand Himalaya that
IC-556557 from NW Himalaya had the lowest farmers with larger land holdings grow more com-
average differentiation (FST = 0.37). mon landraces occupying greater area owing to their
high yield potential (Bisht et al. 2006, 2007). Big
farmers also grow rare localized landraces which
Table 6 Analysis of molecular variance (AMOVA) fetch premium prices or are important for aesthetic
Source of variation df Sum of Variance Percentage reasons. Small farmers, on the other hand, largely
squares component of variation cultivate rare landraces. At higher elevational ranges
the landraces grown were unique and rare localized.
Among groups 2 132.49 0.25Va 11.22
There was no consistency in landrace names and
Among population 17 521.33 1.25Vb 57.18
often it was difficult to ascertain that all the farmer-
within group
named varieties are genetically distinct. The small
Within population 460 317.50 0.69Vc 31.6
farmers use either their own-saved seed or are
Total 479 971.32 2.18
dependent on neighbours’ landraces, whereas the

123
1222
big and wealthy farmers largely use their own-saved
seed. The improved varieties are mainly grown by big
farmers thereby permitting geneflow through intro-
duction of new diversity into the traditional produc-
tion systems.
As has been observed, in recent past, some farmers
to a limited extent are involved in cultivation of cash
crops, by substituting the minor local crops, in the
area (Bisht et al. 2006, 2007). The area under wheat
and rice has, however, almost been static since the
last three-four decades. It was observed that
improved varieties or rice developed through institu-
tional breeding for which ‘formal’ seed is available
fail to provide the yield security that farmers need
and/or do not possess the traits they require. It was
also observed that local varieties performed better for
yield, drought and disease tolerance, and other
properties than improved varieties recommended for
the region. Similar reports are available that local rice
varieties in Nepal were preferred by farmers over
modern varieties when grown under local conditions
as they were better adapted to specific agro-ecolog-
ical niches and possessed specific quality traits (Rana
et al. 2007).
Further, in context of deploying traditional land-
races through informal seed system, little information
is available about landrace diversity loss over time
and space. In an interesting recent study, rice genetic
diversity from high altitude region of Nepal, how-
ever, has been predicted to increase even when
number of varieties decreases. Genetic diversity has
been reported to be maintained even when landraces
are displaced by modern varieties. Model case studies
demonstrated that the partial replacement of land-
races increased genetic diversity if the modern
varieties were adopted on up to 65% of the area.
Only above these levels did overall diversity decline
(Steele et al. 2009).
A wide variation due to environmental adaptations
was recorded in rice landraces occurring in Uttarak-
hand Himalayas. The pooled SDI values based on
morphological characters indicate that level of diver-
sity increases with increasing elevation (Table 4).
Close perusal of Tables 1, 2 and 4 indicate that there
is a positive relationship between local level seed
exchange and overall genetic diversity in the region.
Local level seed exchange is expected to positively
impact level of diversity with increasing landraces
over time at individual household level. Number of
123
Genet Resour Crop Evol (2011) 58:1213–1224
landraces has increased over time with increasing
elevation but the area under rice cultivation has been
almost static. At higher elevation ranges mainly rare
landraces are grown owing to high environmental
heterogeneity and limited area suitable for rice
cultivation. Jarvis et al. (2000) suggested two mea-
sures to classify each landrace according to whether
or not it is widespread (occurs in more than a few
fields) versus localized (restricted to a few fields), and
secondly whether it is common (defined as grown at
least on some farms, in large numbers, in above-
average field sizes) versus rare (in small fields only).
At higher elevation ranges mainly rare localized
landraces are prevalent.
Population genetic parameters on selected land-
races based on STMS markers, however, revealed
greater diversity at mid and low elevation ranges. This
was attributed to greater area under rice cultivation at
mid and lower elevations. As a few populations from
different elevation ranges were analyzed for molec-
ular diversity parameters, no definite relationship
between diversity level and elevation could be
established. Similarly, it was also not possible to
relate the local level seed exchange and diversity at
individual household level. Moreover, populations
from higher elevation ranges, both from NW and NW
regions, represented locally common unique alleles. A
more structured sampling is therefore required for
population studies to understand if increasing number
of farmer varieties and increasing genetic diversity
(allelic richness) are positively correlated. Further, It
could be that the genetic diversity contained in a few
varieties in some villages is similar to the amount of
genetic diversity contained in villages with many
varieties. To make rational conservation plans, it is
important to test whether villages with a few varieties
are conserving as much diversity as villages with
many varieties. The locally rare varieties at higher
elevations normally has high proportion of locally
common alleles of adaptive significance and are
therefore important for conservation and interesting
for users (Kumar et al. 2010).
The population genetic parameters indicate that the
NW Himalayan populations were more diverse than
the NE Himalayan landraces with relatively greater
values for mean effective number of alleles, observed
and expected heterozygosity, and Shannon’s infor-
mation index. The population differentiation was,
however, greater for NE Himalayan landraces
Genet Resour Crop Evol (2011) 58:1213–1224
(FST = 0.61) as compared to NW Himalayan land-
races (FST = 0.47). The comparison on population
structure of farmer landraces from both these geo-
graphically isolated areas was, however, not conclu-
sive as the landrace populations were not true
representative of the respective regions. More popu-
lations through structured sampling representing the
respective regions need to be analyzed for making
precise diversity assessment at household, village and
regional level.
The UPGMA dendrogram of the 20 landrace
populations (Fig. 2) revealed three clusters. Cluster I
and II comprised accessions representing populations
from NE and NW Himalayas, respectively, and
largely represented locally common alleles. The
clusters III comprise populations from both regions
and largely represent common widespread alleles
based on Marshall and Brown (1975) criteria. This
also revealed the presence of large scale seed
exchange even at geographically distant locations in
the region.
The proportion of genetic diversity in autogamous
species, such as rice, is expected to be greater amongst
than within each landrace. The analysis of molecular
variance showed that there is enough variation present
between and within landrace populations in a region.
The variations present among the landraces is more
than variation present within the landraces. Thus, for
conservation point of view it is important to conserve
as many landrace populations as possible with opti-
mum population size from these regions.
The variations due to environmental adaptations
provide important donor germplasm for crop
improvement to users. Further, understanding the
population genetic structure will be helpful in mon-
itoring diversity loss over time and space, and also for
devising a rational conservation plan for management
of farmer landraces on-farm. Developing pathways
for enhancing seed security while strengthening seed
system robustness has been emphasized. By present-
ing a coherent and non-conflicting framework, the
seemingly contradictory forces of increasing food
production and conserving agro-biodiversity has been
reconciled by de De Boef et al. (2010).
On-farm conservation of rice and other minor
crops those receiving less attention in research, such
as minor millets, pseudocereals (amaranths, buck-
wheat), minor legumes etc. are well-adapted to
marginal rainfed cultivation of Indian Himalayas
1223
and play a very important role as security food crops.
As most of these crops are heavily dominated by the
informal seed system with on-farm seed production
playing a very important part. Uncomplicated infor-
mal seed systems, diverse uses and easy agronomic
practices have aided in the on-farm maintenance of
landraces. As has been widely recognized that
although the main impetus for on-farm conservation
of farmer landraces is food and income generation,
other factors, such as the role of these crops in social
and cultural functions, determine what is grown and
the level of diversity (Masinde 2001).
Acknowledgments The authors are thankful to the Director,
NBPGR for providing the facilities for the study. The
scholarship provided to the senior author (AP) by the CSIR
for doctoral degree is gratefully acknowledged.
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