Identification of major loci governing 13 agronomic traits and the fine-mapping of CaSUN29 regulating fruit length in pepper

Pepper (Capsicum spp.), one of the world's most important vegetable and spice crops, has attracted considerable attention due to its phenotypic diversity, abundant secondary metabolites (particularly capsaicinoids), and substantial economic value. However, current research on the genetic basis and key regulatory genes underlying most traits in pepper is limited. Therefore, in this study, we used two parental lines that presented multiple phenotypic differences-namely, BVRC1 and BVRC25-to generate a recombinant inbred line (RIL) population (F₁₀ generation, 216 lines), after which we performed whole-genome re-sequencing on all lines. Based on a high-resolution bin map, 19 significant loci were identified in association with 13 traits, explaining an average of 26% of the phenotypic variance in the RILs. On the basis of uncovering the major effect locus FL-3.2 (FS-3.1) for fruit shape/fruit length, we constructed new genetic populations to finely map and clone a novel minor-effect regulatory locus FL-10.1 for fruit length. Candidate gene CaSUN29 encoded an IQD protein that was specifically expressed in the early stage of fruit development, affected cell expansion in the pepper pericarp, and subsequently impacted fruit elongation. Virus-induced gene silencing of CaSUN29 in pepper resulted in shorter fruit, while heterologous CaSUN29 overexpression in tomato led to longer fruit. In contrast to the pleiotropic locus FL-3.2, which regulated fruit length, width, and shape simultaneously, FL-10.1 only regulated fruit length. Based on the identified loci, a trait-locus network was constructed to understand the correlations among traits based on the degree of locus linkage. These findings are helpful for our exploration of new genes regulating important traits, providing better understanding of the linkage relationships among complex traits.