Finding a Home for an Orphan, an Example of Chickpea

Chickpea, though an important grain legume crop in semi-arid regions of the world, was used to be called “orphan’’ crop because of not being subject of extensive genomics and molecular studies. With an objective to find genes and evaluate their functions in chickpea genome for their utilization in crop improvement through genomics-assisted breeding (GAB), draft genome sequence has been assembled for CDC Frontier variety. In this context, a total of 544.73 Mb sequence data were assembled indicating that 73.8% of the genome is captured in scaffolds. Genome analysis predicted 28,269 genes in chickpea. Examination of synteny with other legume and selected non-legume dicot genomes revealed extensive conservation between chickpea and six other plant species. Analysis of 239.29 Gb re-sequence data were generated on 90 lines has provided 4.46 million variants and also the genomic region that might have undergone selection pressure during domestication and breeding. In parallel, by using linkage mapping approach, one genomic region harbouring QTLs for several drought component traits was identified. This QTL region has been introgressed in 3 leading varieties (e.g. JG 11, Chefe, KAK2) by using marker-assisted backcrossing (MABC) approach. Multi-location evaluation of these MABC lines provided several lines that have up to 24% higher yield than the recurrent varieties. Such advances in genomics and GAB have started to elevated so called “orphan” crop to genomic resource rich crop now.