title: High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea.
abstract: This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties.
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India.
authors: Rashmi
authors: R
authors: Gaur
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India.
authors: Ganga
authors: G
authors: Jeena
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India.
authors: Niraj
authors: N
authors: Shah
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India.
authors: Shefali
authors: S
authors: Gupta
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India.
authors: Seema
authors: S
authors: Pradhan
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India.
authors: Akhilesh K
authors: AK
authors: Tyagi
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India.
authors: Mukesh
authors: M
authors: Jain
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India.
authors: Debasis
authors: D
authors: Chattopadhyay
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India.
authors: Sabhyata
authors: S
authors: Bhatia
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D029863:Cicer / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D015810:Linkage Disequilibrium / Q000235:genetics; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D026801:Synteny / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*