Development of chickpea EST-SSR markers and analysis of allelic variation across related species |
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Authors: | Shalu Choudhary Niroj Kumar Sethy Bhumika Shokeen Sabhyata Bhatia |
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Institution: | (1) National Institute of Plant Genome Research, Post Box Number 10531, Aruna Asaf Ali Marg, Jawaharlal Nehru University Campus, New Delhi, 110067, India;(2) Present address: Defence Institute of Physiology and Allied Sciences (DIPAS), Defence Research and Development Organization (DRDO), Timarpur, Delhi, 110 054, India |
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Abstract: | 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.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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