Genome-wide association study dissects the genetic architecture of kernel rate and its component traits in maize

Kernel rate (KR), the ratio of kernel to ear weight, serves as a key metric of assimilate partitioning efficiency and determines single-ear yield stability under high planting densities. Despite its critical role in modern intensive agriculture, the genetic architecture of KR remains largely elusive. Here, we performed a genome-wide association study (GWAS) for KR and its component traits-ear weight (EW), kernel weight (KW), and cob weight (CW)-using a diverse panel of 502 maize inbred lines across seven environments. Phenotypic profiling revealed substantial variation and high heritability. Leveraging 10.77 million high-quality SNPs, we identified 202 significant associations, which were refined into 106 quantitative trait loci (QTL), each explaining 5%-12% of the phenotypic variance. Notably, four QTL hotspots exhibited co-located across multiple traits and environments, indicative of pleiotropic regulation. Integration of gene annotation with transcriptomic profiles narrowed these loci to 308 genes. Subsequent haplotype analysis prioritized two high-confidence candidates: ZmKR1 (encoding pentatricopeptide repeat protein, PPR, essential for kernel development) and ZmKR2 (encoding meiotic recombination 11b, a DNA repair component). Specifically, favorable haplotype (Hap1) of ZmKR1 and ZmKR2 (Hap1) were significantly associated with elevated KR. Furthermore, evolutionary analysis revealed that these two genes have been selected at domestication. Our findings provide comprehensive genetic dissection of KR and its components, offering fundamental insights into the regulation of assimilate partitioning and delivering valuable gene resources for breeding maize varieties with improved yield stability under high-density conditions.