Whole-Genome Resequencing Identifies SNPs in Sucrose Synthase and Sugar Transporter Genes Associated with Sweetness in Coconut

Coconut (Cocos nucifera L.) is an important agricultural commodity with substantial economic and nutritional value, widely used for various products, including coconut water. The sweetness is an important quality trait of coconut water, which is influenced by genetic and environmental factors. In this study, we utilized next-generation sequencing to identify genetic variations in the coconut genome associated with the sweetness of coconut water. Whole-genome resequencing of 49 coconut accessions, including diverse germplasm and an F2 population of 81 individuals, revealed ~27 M SNPs and ~1.5 M InDels. Sugar content measured by °Bx was highly variable across all accessions tested, with dwarf varieties generally sweeter. A comprehensive analysis of the sugar profiles revealed that sucrose was the major sugar contributing to sweetness. Allele mining of the 148 genes involved in sugar metabolism and transport and genotype–phenotype association tests revealed two significant SNPs in the hexose carrier protein (Cnu01G018720) and sucrose synthase (Cnu09G011120) genes associated with the higher sugar content in both the germplasm and F2 populations. This research provides valuable insights into the genetic basis of coconut sweetness and offers molecular markers for breeding programs aimed at improving coconut water quality. The identified variants can improve the selection process in breeding high-quality sweet coconut varieties and thus support the economic sustainability of coconut cultivation.