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Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.)

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Title Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.)
 
Creator Sethy, Niroj Kumar
Shokeen, Bhumika
Edwards, Keith J.
Bhatia, Sabhyata
 
Subject microsatellite markers
Chickpea
Cicer arietinum L.
intraspecific genetic variability
 
Description Paucity of polymorphic molecular markers in
chickpea (Cicer arietinum L.) has been a major limitation in the improvement of this important legume.
Hence, in an attempt to develop sequence-tagged
microsatellite sites (STMS) markers from chickpea, a
microsatellite enriched library from the C. arietinum cv.
Pusa362 nuclear genome was constructed for the identification of (CA/GT)n and (CT/GA)n microsatellite
motifs. A total of 92 new microsatellites were identified,
of which 74 functional STMS primer pairs were developed. These markers were validated using 9 chickpea
and one C. reticulatum accession. Of the STMS markers
developed, 25 polymorphic markers were used to analyze the intraspecific genetic diversity within 36 geographically diverse chickpea accessions. The 25 primer
pairs amplified single loci producing a minimum of 2
and maximum of 11 alleles. A total of 159 alleles were
detected with an average of 6.4 alleles per locus. The
observed and expected heterozygosity values averaged
0.32 (0.08–0.91) and 0.74 (0.23–0.89) respectively. The
UPGMA based dendrogram was able to distinguish all
the accessions except two accessions from Afghanistan
establishing that microsatellites could successfully detect
intraspecific genetic diversity in chickpea. Further,
cloning and sequencing of size variant alleles at two
microsatellite loci revealed that the variable numbers of
AG repeats in different alleles were the major source of
polymorphism. Point mutations were found to occur
both within and immediately upstream of the long tracts of perfect repeats, thereby bringing about a conversion
of perfect motifs into imperfect or compound motifs.
Such events possibly occurred in order to limit the
expansion of microsatellites and also lead to the birth of
new microsatellites. The microsatellite markers devel-
oped in this study will be useful for genetic diversity
analysis, linkage map construction as well as for
depicting intraspecific microsatellite evolution.
Financial assistance for this work was provided
by Department of Biotechnology, Government of India (BT/PR3518/AGR/02/179/2002) and National Centre for Plant Genome Research.
 
Date 2013-11-05T04:14:23Z
2013-11-05T04:14:23Z
2006
13 February 2006
 
Type Article
 
Identifier Theor. Appl. Genet., 112: 1416-1428
http://hdl.handle.net/123456789/58
 
Language en
 
Publisher Springer