Integrative transcriptome analysis and weighted co-expression network identify auxin signaling hub genes as key regulators of peach (Prunus davidiana) fruit weight

• WGCNA identified a key gene module strongly linked to peach fruit weight. • GO and KEGG implicate auxin signaling pathway in regulating fruit weight. • Hub gene expression in early development controls cell division and final fruit size. Fruit weight is an essential trait in peaches, yet its complex genetic regulation is poorly understood. We conducted our research on a genetically informative population of Peach ( Prunus davidiana ) that exhibits a natural bimodal variation of fruit sizes, categorized as Big and Small. The significant weight variation occurs in the early stages of cell division, and immediately visible after fruit set. Time-series transcriptome (RNA-Seq) analysis across four developmental stages identified 6031 differentially expressed genes (DEGs). Twenty different gene modules were identified through Weighted Gene Co-expression Network Analysis (WGCNA). Among these, the MEgreen module found the strongest positive correlation with fruit weight. Functional enrichment analyses “Gene ontology (GO) and Encyclopedia of Genes and Genomes (KEGG)” demonstrated that they are enriched with plant hormone signal transduction, particularly the auxin pathway, regulating this trait. There are five hub genes in the auxin signaling pathway. The Prupe.6G273000 ( AUX1 ), Prupe.1G368300 ( ARF ), Prupe.1G049200 ( AUX/IAA ), Prupe.8G137900 ( GH3 ), and Prupe.8G078700 ( SAUR ) showed high expression during the early stages of fruit development and were found to be differentially expressed in big and small fruits. The increased cell division and expansion in big and small fruits are strongly correlated with their expression patterns which were confirmed by qRT-PCR. Our study provides a dynamic network-level perspective on the genetic control of peach fruit weight, identifying key regulatory candidate genes and modules for breeding of high-yielding varieties.