Translational Genomics for Developing Climate-Change Ready Chickpeas

Chickpea (Cicer arietinum) is the second most important food legume crop that is generally grown in marginal environments of Asia and sub-Saharan Africa. Due to exposure of crop to several abiotic and biotic stresses, the crop productivity is very low. With an objective to develop superior varieties with enhanced tolerance/resistance to abiotic and biotic stresses, genomics-assisted breeding efforts have been initiated. Large scale genomic resources including draft genome sequence as well as specialized genetic stocks such as reference set, MAGIC and TILLING populations have been developed. After analyzing large-scale phenotyping and genotyping data on two RIL populations, one genomic region (“QTL-hotspot”) harboring QTLs for several drought tolerance traits has been identified. Similarly, QTLs for biotic stress prevalent in warmer (Fusarium wilt) and cool, cloudy and humid climatic conditions (Ascochyta blight) were mapped. In parallel, genome wide association study (GWAS) using genotyping data for 1882 markers and sequence data for 10 genes together with phenotyping data for 24 drought tolerance traits on the reference set comprising 300 genotypes provided 335 significant marker-trait associations (MTAs). This study has been extended now after re-sequencing the reference set at 5-10X coverage. Introgression of the “QTL-hotspot” into elite chickpea lines have shown significant yield improvement under irrigated as well as rainfed conditions. Similarly introgression lines for QTLs for FW and AB showed higher level of resistance to these diseases. Genomic selection approach is also being used to enhance genetic gain. Above mentioned translational genomics approaches should help breeding community to develop climate-change ready chickpea varieties.