Application of Genotyping-by-Sequencing (GBS) for SNP-Based Linkage Mapconstruction and Identification of QTL Associated with Trunk Height in Oil Palm

Oil palm (Elaeis guineensis) has become one of the most important oil crops in the world. Marker-assisted selections have played a pivotal role in oil palm breeding programs as they reduce the amount of time and resources required to develop new cultivars. Single nucleotide polymorphisms (SNPs) have recently become markers of choice owing to their abundance in the genome. We applied a genotyping-by-sequencing (GBS) approach for a large-scale SNP discovery and genotyping of a mapping population. We subsequently used the SNP-based linkage map for the identification of quantitative trait loci (QTL) associated with trunk height. Reduced representation libraries of 108 F₂ progeny were sequenced and a total of 524 million reads covering 56 Gb of high-quality data were obtained. We detected 21,471 single nucleotide substitutions, most of which represented transition events. Of 3,417 fully informative SNP markers, we were able to place 1,085 on a linkage map, with an average of 64 SNPs per linkage group. The map spanned 1,429 cM and had an average of one marker every 1.26 cM. Three QTL affecting trunk height were detected on LG 10, 14 and 15. Interestingly, the QTL governing stem stature identified on LG 14 was linked to two open reading frames encoding a putative gibberellin 2-oxidase and a putative DELLA protein GAI1. Both proteins have been implicated in plant height regulation via gibberellin homeostasis and signaling pathway. Finally, two SNP markers associated with the major QTL were validated using the TaqMan assays in the population with similar genetic background.