Analysis of differential mechanisms in flavonoid synthesis in the exocarp of virescens and nigrescens fruits and development of KASP molecular markers

BACKGROUND: Oil palm is an important tropical woody oilseed crop. Its fruit is rich in flavonoids, which possess high nutritional value and exhibit antioxidant, anti-inflammatory, and antibacterial activities. The molecular mechanism underlying flavonoid biosynthesis in oil palm remains unclear. In this study, we performed LC-MS/MS and RNA-Seq analyses to investigate the molecular regulatory mechanism of flavonoid accumulation in oil palm exocarp. Exocarps from virescens (FS) and nigrescens (FT) at 95, 125, and 185 days after pollination were used as experimental materials to characterize the metabolome and transcriptome at different developmental stages. Our objectives were to identify flavonoid metabolite types, key biosynthetic genes, and related biological metabolic pathways in oil palm exocarp. RESULTS: A total of 274 flavonoids were identified in FS and 275 in FT. Across the three developmental stages, the flavonoid content in FT was higher than that in FS. The differentially accumulated metabolites were mainly enriched in three pathways: flavonoid biosynthesis, flavone and flavonol biosynthesis, and anthocyanin biosynthesis. Combined metabolomic and transcriptomic analyses allowed the reconstruction of the flavonoid biosynthetic pathway and the identification of enzyme genes and metabolites involved in flavonoid synthesis. For FS, six enzyme genes and seven differentially accumulated metabolites were involved. For FT, eight enzyme genes and nine metabolites were involved. This study preliminarily developed 9 pairs of KASP molecular markers (K2-K10). In field tests using 30 FS individuals and 30 FT individuals, these markers were used to evaluate the consistency between genotypes and corresponding phenotypes.The identification accuracy reached 100% within the tested population.These 9 marker pairs are closely linked to the EgDFR gene and can effectively distinguish FS from FT. CONCLUSIONS: This study clarifies the flavonoid biosynthesis mechanism in the exocarp of oil palm fruits and develops markers associated with flavonoid biosynthesis. It helps improve the ornamental value of oil palm, and allows the identification of variety purity and type at the seedling stage. This shortens the breeding cycle of oil palm. It provides a resource basis for the breeding and utilization of oil palm varieties, the screening of high‑flavonoid germplasm, and the development of related products.