Genome-Wide Association Provides Insights into Exploitable Natural Variation for Developing Climate Smart Chickpeas

Chickpea (Cicer arietinum L.) is an important food legume crop for global food security in developing countries, but productivity is severely limited due to biotic and abiotic stress. In order to exploit the genome sequence for chickpea improvement, 429 chickpea genotypes of diverse origin were re-sequenced at 5X to 13X coverage. Using this data, we identified genome-wide variations including 4.9 million single nucleotide polymorphisms (SNPs), 596,100 Indels, 4,931 copy number variations, 60,742 presence absence variations and 70,159 structural variations. In addition, this analysis provides insights in to population structure, genetic diversity, gene loss, domestication and selection sweeps. For identifying marker-trait associations (MTAs) that can be applied in chickpea improvement, we used genome-side SNP data coupled with phenotyping data generated for drought and heat tolerance related traits from 1–6 seasons and 1–3 locations in India  and three locations in Africa. In total, 333 MTAs were identified for 13 traits, of which 249 were for drought tolerance related traits, 67 for heat tolerance related traits and 17 for heat tolerance index. Based on the physical position of associated SNP loci on the CDC Frontier reference genome, candidate genes like TIME FOR COFFE, RELATIVE OF EARLY FLOWERING 6, disease resistance etc., were identified. We report haplotype patterns shaping the genomic background of elite varieties used by farmers, and marker trait associations for drought and heat tolerance that can be deployed to accelerate chickpea improvement.