Seed dormancy and size are two crucial traits influencing crop yield,and they have undergone strong selection during cereal domestication and improvement. However,the genetic basis underlying the antagonistic effects between seed dormancy and seed size remains poorly understood.

Based on genome-wide association study, we perform a comprehensive comparative analysis of 545 global wheat accessions to dissect the genetic architecture of these two traits during wheat improvement. We detect a strong negative correlation between the accumulation of favorable alleles for seed dormancy and the accumulation of favorable alleles for seed size. At the wheat genome level, a set of SNPs harboring antagonistic alleles explain up to 26.56% and 47.21% of the phenotypic variation for seed dormancy and seed size, respectively. In contrast, a set of SNPs with synergistic alleles account for only0.54%and 1.12% of the variation in both traits. During wheat breeding improvement, favorable alleles associated with increased seed size are preferentially selected, resulting in a compromise in seed dormancy. Under different climate conditions, the frequencies of haplotypes of the pleiotropic genes with antagonistic effects and synergistic loci collectively shape wheat diversity through balancing seed dormancy and seed size.

Our findings reveal the genetic architecture underlying the observed weakening of seed dormancy as seed size increases during wheat improvement,enabling further genome-informed cultivar breeding to balance and improve seed dormancy and seed size traits.