Cotton seeds, as the main by-product of cotton, are not only an important raw material for edible oil and feed but also a source of biofuel. The quality of cotton seeds directly affects cotton planting and is closely related to the yield and fiber quality. However, the molecular mechanism governing cotton seed size remains largely unexplored. This study investigates the regulatory mechanisms of cotton seed size by focusing on two cotton genotypes, N10 and N12, which exhibit notable phenotypic variations across multiple environments. Developing seeds were sampled at various stages (5, 20, 30, and 35 DPA) and subjected to RNA-seq. Temporal pattern clustering and WGCNA on differentially expressed genes identified 413 candidate genes, including these related to sugar metabolism that were significantly enriched in transcriptional regulation. A genetic transformation experiment indicated that the overexpression of the GhUXS5 gene encoding UDP-glucuronate decarboxylase 5 significantly increased seed size, suggesting an important role of GhUXS5 in regulating cotton seed size. This discovery provides crucial insights into the molecular mechanisms controlling cotton seed size, helping to unravel the complex regulatory network and offering new strategies and targets for cotton breeding to enhance the economic value of cotton seeds and overall cotton yield.

Cotton (Gossypium spp.) is a major global oilseed crop, ranking sixth in production worldwide and fifth in China. Protein arginine methyltransferases (PRMTs) catalyze arginine methylation, playing pivotal roles in DNA repair in Gossypium. However, their functions in cotton lipid metabolism remain unexplored. In this study, we identified 7, 9, 24, and 32 PRMT genes in Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively. Phylogenetic analysis classified these genes into 7 distinct clades, with structural conservation suggesting functional preservation during cotton evolution. Collinearity analysis indicated segmental duplication as a major driver of PRMT family expansion. Expression profiling revealed significantly divergent expression patterns of GhPRMT5 between high-oil and low-oil cotton accessions, particularly during the critical oil accumulation phase. Heterologous expression in yeast showed that GhPRMT5 overexpression significantly increased total lipid content by 14.13 % (p < 0.05), providing direct evidence for its role in promoting lipid biosynthesis. At the same time, GhPRMT5-silenced lines also exhibited a 15.3 % reduction in cottonseed oil content, with significant alterations in fatty acid composition: saturated fatty acids (e.g., myristic acid [C14:0] and stearic acid [C18:0]) increased by 22.67 % and 26.84 %, respectively, whereas unsaturated fatty acids showed elevated oleic acid (C18:1, +20.90 %) and reduced linoleic acid (C18:2, -8.88 %) (p < 0.01).These results not only confirm the critical role of GhPRMT5 in regulating cottonseed oil accumulation but also reveal its role in modulating fatty acid composition. We are the first to report the connection between the PRMT family and lipid biosynthesis in cotton, and our findings provide novel genetic targets for improving cottonseed oil yield and nutritional quality, offering potential applications in industrial oilseed crop breeding.

Cotton seeds as the main by-product of cotton are not only an important raw material for edible oil and feed but also a source of biofuel. The quality of cotton seeds directly affects cotton planting and is closely related to the yield and fiber quality. However, the molecular mechanism governing cotton seed size remains largely unexplored. This study investigates the regulatory mechanisms of cotton seed size by focusing on two cotton genotypes, N10 and N12, which exhibit notable phenotypic variations across multiple environments. Developing seeds were sampled at various stages (5, 20, 30, and 35 DAP) and subjected to RNA-seq. The temporal pattern clustering and WGCNA on differentially expressed genes identified 413 candidate genes, including these related to sugar metabolism that were significantly enriched in transcriptional regulation. A genetic transformation experiment indicated that the overexpression of the GhUXS5 gene encoding UDP-glucuronate decarboxylase 5 significantly increased seed size, suggesting an important role of GhUXS5 in regulating cotton seed size. This discovery provides crucial insights into the molecular mechanisms controlling cotton seed size, helping to unravel the complex regulatory network and offering new strategies and targets for cotton breeding to enhance the economic value of cotton seeds and overall cotton yield.