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High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

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Title High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea
 
Creator Gaur, Rashmi
Jeena, Ganga
Shah, Niraj
Gupta, Shefali
Pradhan, Seema
Tyagi, Akhilesh K.
Jain, Mukesh
Chattopadhyay, Debasis
Bhatia, Sabhyata
 
Subject Agricultural genetics
Plant genetics
 
Description Accepted date: 29 July 2015
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.
This work was funded by the Department of Biotechnology, Government of India, under the Next
Generation Challenge Programme on Chickpea Genomics (grant number BT/PR12919/AGR/02/676/2009).
SG and SP acknowledge the award of research fellowship from the Council for Scientific and Industrial
Research (CSIR) and Department of Biotechnology (DBT), respectively.
 
Date 2016-01-04T06:29:51Z
2016-01-04T06:29:51Z
2015
 
Type Article
 
Identifier Scientific Reports, 5: 13387
2045-2322
http://172.16.0.77:8080/jspui/handle/123456789/503
http://www.nature.com/articles/srep13387
10.1038/srep13387
 
Language en_US
 
Publisher Nature Publishing Group