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Development of chickpea EST-SSR markers and analysis of allelic variation across related species

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Title Development of chickpea EST-SSR markers and analysis of allelic variation across related species
 
Creator Choudhary, Shalu
Sethy, Niroj Kumar
Shokeen, Bhumika
Bhatia, Sabhyata
 
Subject chickpea
EST-SSR markers
 
Description Despite chickpea being the third important grain legume, there is a limited availability of genomic resources, especially of the expressed sequence tag (EST)-based markers. In this study, we generated 822 chickpea ESTs from immature seeds as well as exploited 1,309 ESTs from the chickpea database, thus utilizing a total of 2,131 EST sequences for development of functional EST-SSR markers. Two hundred and forty-six simple sequence repeat (SSR) motifs were identified from which 183 primer pairs were designed and 60 validated as functional markers. Genetic diversity analysis across 30 chickpea accessions revealed ten markers to be polymorphic producing a total of 29 alleles and an observed heterozygosity average of 0.16 thereby exhibiting low levels of intra-specific polymorphism. However, the markers exhibited high cross-species transferability ranging from 68.3 to 96.6% across the six annual Cicer species and from 29.4 to 61.7% across the seven legume genera. Sequence analysis of size variant amplicons from various species revealed that size polymorphism was due to multiple events such as copy number variation, point mutations and insertions/deletions in the microsatellite repeat as well as in the flanking regions. Interestingly, a wide prevalence of crossability-group-specific sequence variations were observed among Cicer species that were phylogenetically informative. The neighbor joining dendrogram clearly separated the chickpea cultivars from the wild Cicer and validated the proximity of C. judaicum with C. pinnatifidum. Hence, this study for the first time provides an insight into the distribution of SSRs in the chickpea transcribed regions and also demonstrates the development and utilization of genic-SSRs. In addition to proving their suitability for genetic diversity analysis, their high rates of transferability also proved their potential for comparative genomic studies and for following gene introgressions and evolution in wild species, which constitute the valuable secondary genepool in chickpea.
Financial assistance for this
work was provided by National Institute for Plant Genome Research
(NIPGR), New Delhi, India and also the Department of Biotechnology (DBT), Government of India by means of a project grant.
 
Date 2013-11-18T10:50:18Z
2013-11-18T10:50:18Z
2009
24 October 2008
 
Type Article
 
Identifier Theor. Appl. Genet., 118(3): 591-608
http://hdl.handle.net/123456789/108
 
Language en
 
Publisher Springer