Genetic variants associated with leaf spot disease resistance in oil palm (Elaeis guineensis): A genome-wide association study

Leaf spot is considered as a common disease of oil palm, caused primarily by Curvularia spp. fungi. This disease mainly affects the early stages of oil palm and if not adequately controlled can cause plant death. Among the methods available to control the disease, breeding resistant varieties is the most economically effective and promising strategy. A genome-wide association study for leaf spot resistance was conducted on 210 individual tenera palms from seven different (origin) crosses. These palms were subsequently infected with Curvularia spp. pathogenic inoculum in a nursery trial located in an endemic area. The area under the disease progress curve was used as a phenotypic measure. In addition, a genotyping-by-sequencing (GBS) approach was used to obtain the genotyping data of each individual. We found two loci, at chromosome 2 and chromosome 13, that were significantly associated with leaf spot disease resistance. Six genetic variants at the two loci (five variants at chromosome 2 and one variant at chromosome 13) surpassed the threshold for genome-wide significance (p < 10(6)). These loci are linked with three widely known disease-related genes, namely, resistance gene analogue 3 (RGA3), resistance gene analogue 4 (RGA4) and receptor-like protein 9a (RLP9a). The loci identified here can be used for marker-assisted selection when developing leaf spot disease-resistant oil palm varieties.