Linkage Mapping and Genome-Wide Association Reveal Candidate Genes Conferring Thermotolerance of Seed-Set in Maize

J Exp Bot. 2019 Sep 24;70(18):4849-4864. doi: 10.1093/jxb/erz171.


It is predicted that high-temperature stress will increasingly affect crop yields worldwide as a result of climate change. In order to determine the genetic basis of thermotolerance of seed-set in maize under field conditions, we performed mapping of quantitative trait loci (QTLs) in a recombinant inbred line (RIL) population using a collection of 8329 specifically developed high-density single-nucleotide polymorphism (SNP) markers, combined with a genome-wide association study (GWAS) of 261 diverse maize lines using 259 973 SNPs. In total, four QTLs and 17 genes associated with 42 SNPs related to thermotolerance of seed-set were identified. Among them, four candidate genes were found in both linkage mapping and GWAS. Thermotolerance of seed-set was increased significantly in near-isogenic lines (NILs) that incorporated the four candidate genes in a susceptible parent background. The expression profiles of two of the four genes showed that they were induced by high temperatures in the maize tassel in a tolerant parent background. Our results indicate that thermotolerance of maize seed-set is regulated by multiple genes each of which has minor effects, with calcium signaling playing a central role. The genes identified may be exploited in breeding programs to improve seed-set and yield of maize under heat stress.

Keywords: Calcium signaling; GWAS; candidate genes; high-density SNP markers; high-temperature stress; linkage mapping; maize; seed-set; thermotolerance.

Publication types

  • Research Support, Non-U.S. Gov't