Genomics-Assisted Breeding for Climate Resilience in Tropical Maize

Around 80 per cent of the maize growing area in South Asia is rain-fed and vulnerable to extreme weather events such as drought and high temperatures. One-sixth of the hybrid maize grown in the region experience high temperature stress, especially during flowering. Under a USAID –sponsored initiative, CIMMYT in partnership with Purdue University, Pioneer Hi-Bred, several national agricultural research systems (NARS) and small & medium enterprises (SMEs) recently launched a project, “Heat Tolerant Maize for Asia (HTMA)”, which aims at developing and deploying high yielding maize cultivars with in-built climate resilience. In an effort to identify and validate favorable alleles/haplotypes controlling adaptation of maize to heat stress in the tropical environments of South Asia, we carried out a large-scale genome-wide association analysis involving ~400 lines from CIMMYT and other partner organizations. Three genomic regions on chromosomes 1, 3 and 5 were found to be significantly associated with heat tolerance based on test cross hybrid evaluations across multiple locations and two testers and their effect sizes ranged from 0.2 to 0.9 t/ha. Additionally, we carried out candidate gene-based association analyses, in which 17 genes were re-sequenced across a set of contrasting lines. Association analysis based on ~18,000 SNPs and TC phenotypes under heat stress revealed three candidate associations corresponding to Acc1,  Acco20, and CenH3. Acc1 and ACC oxidases have previously been strongly associated with lipid metabolism which regulates heat tolerance in a range of model species. Currently, the candidate associations are being validated in specific bi-parental populations.