Integrated analysis of auxin-related gene families and WGCNA reveals regulatory mechanisms underlying reproductive organ development in pear.

Auxin-related gene families potentially interact with PpyFUL and play a crucial role in regulating reproductive organ development in pear. The Rosaceae family is a major angiosperm lineage, yet the molecular basis of reproductive organ development and fruit-type diversification remains poorly characterized. Here, we conducted a comparative genomic analysis of gene family expansion and contraction throughout 12 representative Rosaceae species. Gene families associated with auxin-related biological processes were enriched among convergently expanded families in pear, strawberry, and raspberry, but among convergently contracted families in peach. These patterns suggest an important role for auxin-associated pathways in the evolution of reproductive organs. Pear exhibited the most pronounced expansion and was chosen for further analysis, accounting for 149 auxin-related genes involved in auxin biosynthesis, transport, and signal transduction across eight gene families and 19 subgroups. Gene duplication analysis revealed that 85.23% of these genes arose from whole-genome or segmental duplications associated with polyploidization, with purifying selection predominating. Transcriptome and RT-qPCR analyses showed that auxin-related genes exhibited peak expression at 12 DAF in ovules and the ovary wall, but not in the hypanthium. Co-expression network analysis and protein-protein interaction predictions identified PpyFUL as a candidate regulator associated with auxin-related pathways. Dual-luciferase assays showed that PpyFUL activated the promoter activities of PpyARF30 and PpyARF16. Functional assays demonstrated that PpyFUL overexpression promoted early flowering, increased silique size, and altered floral organ development in Arabidopsis thaliana. This study presents an evolutionary and regulatory framework for auxin-related genes in Rosaceae, revealing an auxin-MADS-box co-regulatory network underlying reproductive organ development.