Mapping QTL for leaf area in oil palm using genotyping by sequencing

Leaf area is an important parameter in oil palm breeding as it is positively correlated with oil yield. However, measurement of leaf area is tedious and also destructive. In the present study, a breeding population with 145 palms derived from a cross between Deli Dura and Avros Pisifera was used to construct a high-density linkage map and identify quantitative trait loci (QTL) for leaf area in oil palm. Using genotyping by sequencing, a linkage map containing 2413 SNPs was constructed. The total length of the linkage map was 1161.89 cM, with an average marker spacing of 0.48 cM. Based on the continuous phenotyping of leaf area from 2010 to 2015, two suggestive QTL for leaf area were mapped on chromosomes (Chr) 3 and 9. The allelic effects of the QTL associated with leaf area in the mapping population were estimated by linear regression using ordinary least squares method. The QTL on Chr 9 explained 13.3% of phenotypic variation for leaf area. A candidate gene, ARC5, within the narrow interval of QTL on Chr 9 was identified. The gene was significantly higher expressed in leaf than root and fruit of oil palm. This high-quality and SNP-based map supplies a base to fine map QTL for agronomic traits in oil palm, and the markers closely linked to the stable QTL may be used in marker-assisted selection in oil palm breeding.