Integrating GWAS, QTL Mapping, and RNA-seq to Identify Candidate Genes for Kernel Weight and Oil Traits in Maize (Zea...

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 SAD 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 FALDH 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 (qOC5) and one stable QTL related to arachidic acid (qAA9) were identified. Among them, the FAE2 gene was located in qAA9, which plays a crucial role in regulating the fatty acid content in plants. Additionally, the gene TT12, 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.