<![CDATA[Reliable normalization and accurate quantification are essential for gene expression studies in oil palm mesocarp. This study assessed three candidate reference genes (Actin, GAPDH, and EF1α) for stability using four algorithms (ΔCt, BestKeeper, NormFinder, and GeNorm). Actin was consistently identified as the most stable single housekeeping gene (HKG) (stability value 0.021), while the combination of GAPDH and EF1α provided the most stable normalization pair (stability value 0.017), supporting their use as internal controls for normalization. Normalized expression analysis of two key biosynthetic genes, acetyl-CoA carboxylase (ACCase) and phytoene synthase (Psy), was conducted in contrasting phenotypes differing in oil yield and carotene content. The high-yielding, high-carotene genotype displayed lower ΔCt values for both ACCase (4.67 vs. 6.19) and Psy (4.75 vs. 5.26), corresponding to 2.86-fold and 1.42-fold higher expression, respectively. These expression differences aligned closely with phenotypic outcomes, as the superior traits achieved a 40.8% increase in oil yield and a 155.3% increase in carotene content. Expression patterns showed stage-specific specialization: ACCase was upregulated during the unripe stage, enhancing fatty acid biosynthesis, while Psy was most differentially expressed during ripening, coinciding with carotenoid accumulation. Together, these findings suggest that transcript abundance of oil and carotenoid pathways may be coordinated in elite oil palm and provide a framework for linking gene expression with metabolic output, which may inform future efforts to improve oil yield and quality.]]>
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