Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in Maize

Abstract

Maize is an important food crop, and 100-kernel weight (HKW) is one of the three key components of yield. In this study, 200 maize inbred lines were used as the material, and HKW was evaluated over three consecutive years in two environments. A genome-wide association study (GWAS) was conducted using the Blink and FarmCPU models with 44,935 SNP markers evenly distributed across the maize genome. A total of 25 SNPs significantly associated with HKW were identified, with three SNPs detected in both models. Six significant SNPs were located within previously mapped QTL bins associated with grain weight. In the linkage disequilibrium (LD) regions of the significant SNP loci, 198 candidate genes were identified, of which 74 had annotation information. Further analysis revealed 21 candidate genes related to HKW, such as GRMZM2G010555 (alternative oxidase), GRMZM2G102471 (ubiquitin-conjugating enzyme), GRMZM2G060669 (histone deacetylase), GRMZM2G090156 (methyltransferase), GRMZM2G002075 (BZIP transcription factor), and GRMZM2G138454 (bHLH transcription factor). The SNP loci and candidate genes identified in this study provide important references for marker-assisted selection, fine mapping, and gene cloning related to HKW in maize.

Keywords

• maize
• 100-kernel weight
• genome-wide association study
• candidate gene identification