Fine-mapping and candidate gene analysis of qFF3.1 conferring fruit firmness in a modern tomato variety

Tomato fruit firmness is a critical determinant of postharvest quality, dictating storage, ultimate shelf life, and market value. While previous research on tomato fruit firmness has largely confined to wild or heirloom accessions, the genetic basis underlying this trait in modern elite breeding lines remains largely unexplored. In this study, we dissect the genetic architecture of fruit firmness using a recombinant inbred line (RIL) population derived from a cross between the modern inbred line CF-1 and the conventional cultivar Moneymaker. Quantitative trait locus (QTL) mapping revealed three firmness-associated loci on chromosomes 3, 4, and 5. The major-effect QTL qFF3.1 on chromosome 3 accounted for 11.10% of the phenotypic variation and was further confirmed by bulked segregant analysis (BSA-seq). Fine-mapping in the F_2:3 population delimited qFF3.1 to a 111 kb interval containing 26 predicted gene models. After combined analysis of functional annotations and RNA-seq data from near-isogenic lines (NILs), we prioritized six candidate genes associated with cell wall development and ethylene response, and four of which exhibiting differential expression patterns across fruit ripening stages. To our knowledge, qFF3.1 is the first major-effect QTL for fruit firmness identified in a modern tomato breeding line. Our findings offer molecular insights into the regulation of fruit firmness, and provide a strategy for improving shelf life and other postharvest traits.