Integrating GWAS, QTL Mapping, and RNA-seq to Identify Candidate Genes for Kernel Weight and Oil Traits in Maize ( <i>Zea mays</i> ssp. <i>mays</i> )

The evaluation of the kernel oil content and fatty acid composition in maize is crucial for understanding maize nutrition. This study utilized an association population of 278 inbred lines and a F₂ population of 229 individuals to identify candidate genes for 8 kernel weight and oil traits. By employing two genome-wide association study (GWAS) models, the K model and Q+K model, key SNP loci and candidate genes were identified. A total of 10 pleiotropic quantitative trait loci (QTLs) were discovered that collectively encompassed 82 candidate genes. Notably, the <i>SAD</i> gene catalyzed the conversion of stearoyl-acyl carrier protein (ACP) to oleoyl-ACP, playing a crucial role in regulating the content of unsaturated fatty acids in plants. Three candidate genes were identified through three methods (GWAS, QTL mapping, and RNA-seq), with the <i>FALDH</i> gene playing a role in regulating the grain oil content. Through the integration of GWAS analysis and QTL mapping, one stable QTL related to the oil content (<i>qOC5</i>) and one stable QTL related to arachidic acid (<i>qAA9</i>) were identified. Among them, the <i>FAE2</i> gene was located in <i>qAA9</i>, which plays a crucial role in regulating the fatty acid content in plants. Additionally, the gene <i>TT12</i>, identified through a combination of GWAS and RNA-seq analyses, has been found to play a pivotal role in seed development. Overall, these findings provide a foundation for deeper insights into the genetic mechanisms underlying maize oil traits and offer valuable insights for molecular marker-assisted breeding.