Gaur, R. and Jeena, G. and Shah, N. and et al, .
(2015)
High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea.
Scientific Reports, 5 (13387).
pp. 1-11.
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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.
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