Developmental Transcriptome Profiling and WGCNA Identify Candidate Genes Associated with Sugar Accumulation and Fruit Enlargement in Lycium ruthenicum.

Background:Lycium ruthenicum, commonly known as Black goji berry, is a shrub species native to western China and is rich in bioactive compounds that contribute to its nutritional and health-promoting effects. However, the transcriptional dynamics associated with fruit development and quality formation in black goji berry remain incompletely understood. This study aimed to investigate transcriptional dynamics during fruit development and identify candidate genes associated with sugar accumulation and fruit enlargement. Methods: Fruits were sampled at five developmental stages (S1-S5), and RNA-seq was performed to investigate the alterations in gene expression. Differential expression analysis, temporal expression-pattern analysis, functional enrichment analysis, and weighted gene co-expression network analysis (WGCNA) were performed, followed by the integration of differential expression, temporal expression patterns, co-expression relationships, and functional annotation. Results: Fruit diameter, fresh weight, and total soluble sugar content increased markedly during the later developmental stages. Differential expression analysis revealed extensive transcriptional changes across successive developmental transitions, while temporal expression-pattern analysis identified distinct increasing and decreasing gene clusters. Functional enrichment analysis showed that the DEGs were mainly associated with carbohydrate metabolism, sugar transport, hormone-related processes, photosynthesis, and cell-wall modification. WGCNA identified 13 co-expression modules, among which MEyellow and MEbrown showed strong but opposite associations with developmental stage, total soluble sugar content, fruit diameter, and fruit fresh weight. The integrated analysis highlighted several candidate genes associated with sugar metabolism and transport during late fruit development. Conclusions: These findings provide a transcriptomic perspective on the coordinated changes in sugar accumulation and fruit enlargement during L. ruthenicum fruit development.