High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS)

• DOI: 10.1038/srep17512
• Publication Date: 2015-12-03T10:16:35Z
• Authors: Subodh Verma; Shefali Gupta; Nitesh Bandhiwal; Tapan Kumar; Chellapilla Bhara...; Sabhyata Bhatia
• Keywords: Candidate gene; Family-based QTL mapping; SNP genotyping; Synteny; Genetic linkage

This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping recombinant inbred lines (RILs) an intra-specific mapping population chickpea contrasting seed traits. A total 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality 39.5% present in genic regions. Comparative analysis using physically mapped marker loci a higher degree synteny with Medicago comparison to soybean. The data was utilized construct one most saturated genetic linkage maps having 3,363 positions including 3,228 on 8 groups spanning 1006.98 cM at average inter distance 0.33 cM. map identify 20 quantitative trait (QTLs) associated traits accounting phenotypic variations ranging from 9.97% 29.71%. Analysis genomic sequence corresponding five robust QTLs led identification 684 putative candidate genes whose expression profiling that 101 exhibited specific expression. integrated approach utilizing identified along available genome transcriptome could serve as platform gene molecular breeding chickpea.