Genome-Wide Association Study Reveals Major SNPs Associated with Pollen Viability and Spikelet Fertility in Wheat under Heat Stress

Heat stress during the reproductive stage significantly reduces wheat ( Triticum aestivum L.) productivity, primarily by impairing pollen viability and grain filling rate. This study employed genome-wide association study (GWAS) using 5,171 high-quality single nucleotide polymorphisms (SNPs) across 319 diverse wheat lines to identify genomic regions associated with pollen viability and spikelet fertility under reproductive-stage heat stress. Pollen viability was assessed from field-grown plants subjected to high temperature in a controlled setup using a thermal cycler. Spikelet fertility was evaluated in two years with heat treatment applied at the four different ear emergence stages. The wheat population showed significant genotypic and phenotypic variation. Chinese landraces formed a distinct cluster from other groups and generally exhibited lower pollen viability and spikelet fertility compared to Chinese commercial varieties. Pollen viability score showed moderate but significant correlation with spikelet fertility, especially at early ear-emergence stage. GWAS identified 15 significant SNPs associated with these two traits. Notably, AVRIG15341 on chromosome 1B and AVRIG21657 on chromosome 3A explained 20.31% and 11.9% of phenotypic variation in pollen viability, respectively. AVRIG26861 on chromosome 5A explained 17.09% of phenotypic variation in spikelet viability. This is the first report on SNPs linked to wheat pollen viability scores under heat stress. Combination of favorable alleles showed higher trait performance, suggesting strong potential for use in marker-assisted selection. Our pioneering study provides new insights into the genetic architecture of reproductive-stage heat tolerance in wheat and offers valuable genetic resources for breeding heat-resilient cultivars.