title: High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.).
abstract: 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 genotyping 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.
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi 110067,  India.
authors.forename: Rashmi
authors.initials: R
authors.lastname: Gaur
authors.forename: Sarwar
authors.initials: S
authors.lastname: Azam
authors.forename: Ganga
authors.initials: G
authors.lastname: Jeena
authors.forename: Aamir Waseem
authors.initials: AW
authors.lastname: Khan
authors.forename: Shalu
authors.initials: S
authors.lastname: Choudhary
authors.forename: Mukesh
authors.initials: M
authors.lastname: Jain
authors.forename: Gitanjali
authors.initials: G
authors.lastname: Yadav
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
authors.forename: Debasis
authors.initials: D
authors.lastname: Chattopadhyay
authors.forename: Sabhyata
authors.initials: S
authors.lastname: Bhatia
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D029863:Cicer / Q000235:genetics*; D008040:Genetic Linkage; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D005819:Genetic Markers