Gene Variants Linked to Sweetness-Acid Balance in Watermelon Fruit

The flavor of a watermelon depends heavily on its sugar-acid ratio, the balance between soluble sugars and organic acids that determines whether a fruit tastes flat, sharp, or pleasantly sweet. Despite its importance to consumers and breeders, the genetic control of this trait in watermelon (Citrullus lanatus) has remained largely unmapped. A study published in BMC Plant Biology on 22 October 2026 now reports a set of candidate genes associated with this ratio, combining transcriptome-wide co-expression analysis with comparative genomics across two genetically contrasting watermelon accessions.

The research team, led by Fikru Tamiru Kenea and colleagues, compared an improved cultivar named ‘Xichunxuan’ (abbreviated Xi), which has a high sugar-acid ratio, with a landrace called ‘Sashenganiyougua’ (Sa), which has a low ratio. Fruit from both accessions was sampled at five developmental stages: 8, 14, 20, 26, and 32 days after pollination. Chemical profiling showed that ‘Xi’ accumulated higher levels of soluble solid contents and titratable acidity, along with greater amounts of fructose, sucrose, glucose, and the organic acids malic, citric, and oxalic. This combined profile produced the superior sugar-acid ratio observed in the improved line.

To identify the genes that might underlie this difference, the researchers applied weighted gene co-expression network analysis, a statistical method that groups thousands of genes into modules based on correlated expression patterns across tissues and time points. Four modules showed significant correlations with the sugar-acid ratio, and from within them the team prioritized seven hub genes, the most connected members of each network. Two of these stood out in the subsequent analyses.

The first, a pectin lyase-like superfamily protein gene (PLLSP), belongs to a family of enzymes involved in remodeling pectin, a major component of the plant cell wall. The authors propose that PLLSP may contribute to the sugar-acid ratio by facilitating cell wall disassembly and thereby redirecting carbon toward the synthesis of sugars and organic acids. The second, polyadenylate-binding protein-interacting protein 4-like (PbPIP4L), is thought to act through post-transcriptional regulation, potentially influencing the stability of messenger RNAs involved in fruit metabolism. Both genes showed the strongest positive correlations with the sugar-acid ratio among the candidates, with correlation coefficients of 0.85 for PLLSP and 0.73 for PbPIP4L, and both were expressed at higher levels in ‘Xi’, matching the pattern of ratio accumulation between the two accessions.

Comparative genomics then revealed structural differences between the accessions. In ‘Xi’, the PLLSP gene carries a 61-base-pair deletion in its first exon, while the promoter region of PbPIP4L contains a C/G polymorphism that generates a binding site for the GTGANTG10 transcription factor, a motif associated with fruit-ripening regulation. These sequence variants provide a plausible molecular link between genotype and the observed biochemical differences, although the study establishes association rather than demonstrated causation.

To test how widely these variants occur, the team validated them across 16 watermelon accessions. The 61-base-pair deletion in PLLSP was present in all of the high-ratio improved accessions examined but absent from the low-ratio landraces. The authors are careful to note that this association was observed in the limited germplasm included in the study, so broader screening across more diverse collections will be needed to confirm the marker’s utility.

Phylogenetic and multiple sequence alignment analyses added an evolutionary dimension to the findings. Both genes appear to be conserved across a range of fruit species, including melon, tomato, citrus, grape, apple, and peach. This conservation suggests that the pathways these genes participate in may be shared components of fruit flavor and quality control across distantly related crops, raising the possibility that comparable variants could be relevant beyond watermelon.

For breeders, the study offers concrete molecular targets. Marker-assisted selection based on the PLLSP deletion, or gene-editing approaches aimed at the identified variants, could in principle accelerate the development of watermelon lines with improved flavor balance without waiting for lengthy phenotypic screening. The authors frame the work as elucidating natural variation in promising candidate genes and providing targets for strategies aimed at enhancing fruit flavor.

Several caveats remain. The correlations were measured across two accessions and five developmental stages, and the validation panel covered only 16 accessions, so the findings should be read as well-supported associations within that scope rather than proven regulatory mechanisms. Functional validation of PLLSP and PbPIP4L, for example through mutant or transgenic analysis, was not part of this study. Even so, by linking specific sequence polymorphisms to a measurable flavor trait and situating the candidate genes within co-expression networks and an evolutionary framework, the research adds a genomic handle to a trait that has long been managed almost entirely through sensory selection.

Subject of Research: Candidate genes regulating the sugar-acid ratio in watermelon fruit identified through transcriptome co-expression network and genomic analysis

Article Title: Transcriptome based co-expression network analysis coupled with genomic analysis insights candidate genes regulate sugar-acid ratio in watermelon fruit

Article References: Kenea, F. T., Shao, Z., Lu, X., Sajjad, M. Z., He, N., Yang, D., Chen, G., Zhao, Y., Gonfa, M. T., Yousef, A. F., Luo, X., Zhang, Y., Chen, M., Su, Y., Kaseb, M. O., Zhu, H., & Liu, W. (2026). Transcriptome based co-expression network analysis coupled with genomic analysis insights candidate genes regulate sugar-acid ratio in watermelon fruit. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09973-x

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09973-x

Keywords: watermelon, sugar-acid ratio, transcriptomics, co-expression network analysis, WGCNA, candidate genes, pectin lyase-like protein, PbPIP4L, comparative genomics, fruit flavor, marker-assisted selection, BMC Plant Biology