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

This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea. Chickpea (Cicer arietinum L.) is a self pollinated, diploid (2n = 2x = 16) annual grain legume crop with a genome of size ~738 Mb 1. It is mostly cultivated in arid and semi-arid areas and ranks third in production among food legumes worldwide 1,2. Being a rich and economic source of proteins, vitamins and minerals, chickpea seeds are an important commodity, especially in the diet of the poor and vegetarian population of developing countries 3. The economic importance of chickpea seed therefore necessitates genetic and genomics studies especially related to traits such as seed yield as this is a major target of chickpea breeding. Attempts have been made to map QTLs responsible for seed traits in chickpea 3-5. However, since high density maps were not used for such purposes, it resulted in QTLs with low resolution. Moreover, due to the unavailability of the chickpea genome sequence earlier, identification of candidate genes for yield related traits had also not been possible. A linkage map, densely populated with molecular markers, is a prerequisite for successful QTL identification 6. Amongst all types of molecular markers, single nucleotide polymorphisms (SNPs) have proven to be the marker of choice because of their ubiquitous presence in high numbers, uniform distribution, biallelic nature and high heritability 7,8. Moreover, variations at a single nucleotide level within genes may