Genome-Wide Association Study of Oil Palm Mesocarp Oil Yield Content and Its Application for Marker Selection

Oil palm is the most productive oil crop in the world and the most traded. While molecular markers have been deployed increasingly to understand underlying QTLs for traits of interest, most marker discovery programs in oil palm are still based on controlled cross-based QTL mapping. Although this approach is reasonably powerful, it identifies poorly localized QTLs for more complex phenotypes which may also be specific to the investigated population. To break through this bottleneck, we applied the first comprehensive application of genome-wide association study in oil palm where a total of 7,500 diverse palms were genotyped using a custom 200K-SNP array. After corrections to reduce false positives, we found 62 and 18 loci in 1,459 Deli dura x AVROS pisifera and 586 Nigerian dura x AVROS pisifera, respectively, to be significantly associated with an important breeding trait i.e. mesocarp oil content. The trait-associated SNPs were further validated in an independent breeding trial and indicated 4% improvement in oil content in the mesocarp was observed. These results demonstrate a promising way to integrate genomics into oil palm breeding programmes.