Putative regulatory candidate genes for QTL linked to fruit traits in oil palm (Elaeis guineensis Jacq.)

Palm oil is among the most important vegetable oils, contributing to a quarter of the world’s oils and fats market. The oil palm (Elaeis guineensis Jacq.) fruitlets, which are the source of palm oil, vary from 8 to 20 g in weight. Palm oil content in the fruitlets is approximately 45–50% by weight and an increase in the percentage of mesocarp-to-fruit is likely to have a positive effect on oil yield. In this study, we report a quantitative trait loci (QTL) associated with two yield related components, namely fruit and mesocarp content in a commercial breeding population (Deli dura × Yangambi pisifera). The QTL confidence interval of about 12 cM (~ 6.7 Mbp) was fine-mapped with 31 markers (17 SNPs and 14 SSRs) consisting of 20 nuclear markers derived from the maternal parent, six paternal and five co-segregating markers. Interestingly, inheritance of the paternal alleles leads to a larger difference in both fruit and mesocarp weight, when comparing genotypes in the progeny palms. Candidate genes and transcription factors were mined from the QTL region by positioning markers on the oil palm EG5 genome build. Putative genes and transcription factors involved in various biological processes including flower organ development, flowering, photosynthesis, microtubule formation, nitrogen and lipid metabolism were identified within this QTL interval on pseudo-chromosome 3. This genome-based approach allowed us to identify a number of potential candidate gene markers associated with oil palm fruit and mesocarp weight which can be further evaluated for potential use in marker-assisted breeding.