Association of SNP markers with height increment in mpob-angolan natural oil palm populations

Abstract

Low height increment is one of the desired traits in oil palm breeding and improvement programmes, as dwarf palms facilitate fruit harvesting and extend the economic life of the crop. In this study, 346 natural oil palms collected from Angola and maintained by the Malaysian Palm Oil Board (MPOB) were used. Analysis of variance (ANOVA) for height increment showed a significant difference (P ≤ 0.001) among families in populations, indicating substantial genetic variation for marker-trait association study. We applied nine carefully selected single nucleotide polymorphism (SNP) markers to genotype the oil palms via cleaved amplified polymorphic sequence (CAPS) method. Population structure analysis involving 18 SNP alleles divided the palms into two sub-populations, with no obvious relative kinship (values < 0.3). For association analysis between the SNP markers and height increment, three models were tested. The incorporation of population structure (Q) and relative kinship (K) as correction factors in the model had helped reduce false positive associations. Generally, the mixed linear model (MLM) with Q + K exhibited a more stringent model with less spurious associations detected. Based on this model, one significant marker SNPG00006_FatI corresponding to indole-3-acetic acid (IAA)-amido synthetase gene was identified to be associated with height increment (P ≤ 0.05). The marker, although potentially specific to MPOB-Angolan germplasm, can assist in introgressing the dwarf phenotype into advanced breeding materials through marker-assisted selection (MAS).