Genetic dissection of oil content in maize kernel using combined genome-wide association analysis and linkage mapping

Integration of multienvironment QTL mapping and GWAS revealed three candidate genes-ZmFum1, ZmDGAT1-1, and ZmLPAAT4-as potential key regulators of maize kernel oil content. With an exceptional energy density and high polyunsaturated fatty acid content, maize oil positions high-oil maize as multifunctional feedstocks. Exploring the genetic architecture of oil content (OC) in maize kernel is crucial for breeding high-oil maize varieties. Herein, a combination of genome-wide association study and linkage mapping was employed to explore the quantitative trait loci (QTL) and candidate genes underlying the OC in maize kernel under four environments. Linkage mapping identified 17 QTLs for the OC, among which three QTL were repeatedly detected under multiple environments. GWAS revealed 17 OC-associated SNPs, of which 12 SNPs had large phenotype contribution rates with one accounting for 17.2% of the phenotypic variance. By integrating three multienvironment QTL identified through linkage mapping with the 17 most significant SNPs detected by GWAS, a total of 1142 genes were identified as the candidate genes. Based on the functional annotations, expression profiling, and gene-based association analysis, three candidate genes were prioritized: Zm00001d029084, Zm00001d037760, and Zm00001d043267, which encode fumarate hydratase 1 (ZmFum1), diacylglycerol acyltransferase-type I2 (ZmDGAT1-1), and 1-acyl-sn-glycerol-3-phosphate acyltransferase 4 (ZmLPAAT4), respectively. The SNPs in the coding sequences of Zm00001d029084 and Zm00001d037760 were significantly associated with OC and result in amino acid substitutions, whereas the promoter and 3'UTR regions of Zm00001d043267 each harbor an SNP significantly associated with OC. These findings provide valuable insights into the genetic basis of OC and highlight potential targets for marker-assisted selection in high-oil maize breeding.