Candidate genes for kernel ratio in maize identified via combined GWAS and QTL mapping across multiple environments

This study is the first to establish an association between Zm00001eb257890 and maize kernel ratio (KR), offering novel insights into the genetic mechanisms regulating KR. These findings enhance our understanding of the genetic architecture of KR and provide promising targets for molecular breeding strategies aimed at improving maize yield. Kernel Ratio (KR) is a crucial trait determining kernel yield and the efficiency of assimilate partitioning to maize kernels. To explore its genetic basis, a multi-parent population (MPP) was developed by crossing the temperate inbred line Ye107 with five tropical/temperate inbred lines, generating 678 F₉ recombinant inbred lines (RILs). Phenotypic evaluation of KR was conducted across three environments (21JH, 22YS, 23YS), and best linear unbiased prediction (BLUP) values were estimated for subsequent analysis. Genome-wide SNPs were identified through whole-genome resequencing (WGRS), followed by combined genome-wide association study (GWAS) and QTL mapping to identify key loci and candidate genes regulating KR. GWAS identified 99 SNPs significantly associated with KR, 34 of which were consistently detected across multiple environments, explaining 1.56% to 9.00% of the phenotypic variation (PVE). QTL mapping identified 35 QTLs, including two stable QTLs, qKR5-3 and qKR5-7, that were consistently detected across multiple environments. Co-localization analysis identified five SNPs overlapping six QTL intervals. Notably, a non-synonymous mutation (SNP5_222146671) was located in the exon of Zm00001eb257890, which encodes a serine/threonine protein kinase VPS15, showing high expression in maize ear primordia. qRT-PCR and gene structure analyses demonstrated that Zm00001eb257890 was upregulated in low-KR parents (Chang7-2, Shen137) due to a G/A mutation (V₁₃₂₂I). Critically, in transgressive segregants from three RIL populations, the expression of Zm00001eb257890 was consistently and significantly higher in low-KR lines than in high-KR lines, showing a significant negative correlation with KR values (r = -0.83 to -0.96), providing notable functional evidence for its regulatory role. Epistatic analysis further revealed a significant interaction between SNP5_222146671 and SNP4_15864100 (STAT = 8.13), highlighting the polygenic regulatory network underlying KR. Taken together, these data significantly suggest Zm00001eb257890 as a key candidate gene regulating maize KR and provide valuable genetic targets for improving maize yield.