The extraction of high quality total ribonucleic acid (RNA) has become an essential step for downstream plant molecular biology research. In oil palm, several total RNA extraction protocols have been reported across specific tissues using either conventional method or commercial kits. To our knowledge, there is no specific total RNA extraction method described for oil palm whole fruit which contains lipids, polysaccharides, protein, polyphenols and other secondary metabolites. Here, a modified cetyltrimethylammonium bromidelithium chloride (CTAB-LiCl) method with addition of phenol was established to extract total RNA across various oil palm tissues, especially for whole fruit at eight weeks after anthesis (WAA) and 15 WAA. To assess the extracted total RNA, quality and quantity as well as integrity were evaluated using spectrophotometer and bioanalyser, respectively. It was found that modified CTAB-LiCl method with addition of phenol was able to produce good quality (both A 260 /A 280 and A 260 /A 230 ratios > 1.8) and intact (RIN > 7.4) total RNA. Furthermore, reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was successfully performed across all total RNA extracted using two reference genes (PD00569 and pOP-EA01332) and one gene of interest, ethylene-responsive transcription factor-3 like, designated as PD00088. The results indicated that the method is suitable for extraction of total RNA from whole fruit as well as other oil palm tissues and is amenable to RT-qPCR.

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).