Integrated QTL Mapping and Transcriptome Analysis Reveal Multigenic Control of Fruit Shape Polymorphism in Melon

Fruit shape is a critical agronomic trait that determines market value, processing suitability, and consumer preference in melon. To elucidate the genetic basis of fruit shape polymorphism, we employed an integrated strategy combining high-density QTL mapping, structural variation (SV) analysis, and transcriptome profiling. Histological analysis revealed that the distinct fruit morphologies of the elongated YJM and round VED accessions are attributable to differential cell number and size. Additionally, F2 population derived from VED and YJM was used for high-resolution mapping. We identified nine QTLs across chromosome 3, 4, 6, 7, 9 and 10, including three QTLs for transverse diameter, two QTLs for vertical diameter, and four QTLs for fruit shape index, which contains total 1949 candidate genes. Subsequently, we integrated SVs, differential expression analysis, Venn analysis, GO enrichment, and WGCNA to prioritize candidate genes. This integrative approach narrowed down the pool to eight high-confidence candidates associated with melon fruit shape, selected based on their expression patterns and functional annotations, providing a crucial theoretical foundation for future molecular breeding.