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High-Throughput SNP discovery and genotyping for constructing a saturated linkage map of Chickpea (Cicer arietinum L.)

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Title High-Throughput SNP discovery and genotyping for constructing a saturated linkage map of Chickpea (Cicer arietinum L.)
 
Creator Gaur, Rashmi
Azam, Sarwar
Jeena, Ganga
Khan, Aamir Waseem
Choudhary, Shalu
Jain, Mukesh
Yadav, Gitanjali
Tyagi, Akhilesh K.
Chattopadhyay, Debasis
Bhatia, Sabhyata
 
Subject Chickpea
SNP
linkage map
genotyping
NGS
 
Description The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms
(SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e.
Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific
reference mapping population of chickpea. Development and validation of a high-throughput SNP geno-
typing assay based on Illumina’s GoldenGate Genotyping Technology and its application in building a
high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs
were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool
All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating
a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368
co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was
constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning
1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one
of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which
revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The
first set of validated SNPs and map resources developed in this study will not only facilitate QTL
mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor
scaffolds arising out of the whole-genome sequencing of chickpea.
 
Date 2014-05-09T05:08:00Z
2014-05-09T05:08:00Z
2012
5 July 2012
 
Type Article
 
Identifier DNA Res., 19(5): 357-373
http://hdl.handle.net/123456789/230
 
Language en
 
Publisher Oxford University Press