Genome-Wide Association Study Dissects the Genetic Architecture of Oil Biosynthesis in Maize Kernels

Association mapping through linkage disequilibrium (LD) analysis is a powerful tool for the dissection of complex agronomic traits and for the identification of alleles that can contribute to the enhancement of a target trait. With the developments of high throughput genotyping techniques and advanced statistical approaches as well as the assembling and characterization of multiple association mapping panels, maize has become the model crop for association analysis. The rapid development in genome-wide genotyping techniques promises to improve the power of association mapping and significantly refine our understanding of the genetic architecture of complex quantitative traits. We have build up a maize association mapping panel containing 500 diverse maize inbred lines which has been genotyped by using Maize 50K SNP chip and deep RNA sequencing technology. Totally, 1.06 million high quality maize SNPs were obtained and the genetic architecture of oil biosynthesis was further extensively examined. We identified 74 loci significantly associated with kernel oil concentration and fatty acid composition which were further examined using eQTL mapping, linkage mapping, and co-expression analysis. More than half of the identified loci co-localized within mapped QTL intervals and one-third of the candidate genes were annotated as enzymes in oil metabolic pathway. The 26 loci associated with oil concentration could explain up to 83% of the phenotypic variation using a simple additive model. Results illuminate the process of oil synthesis in maize kernels, and may facilitate marker based breeding for oil quantity and quality.