Fine mapping and functional analysis of the candidate gene OFP17, regulating both seed and fruit sizes in cotton

Single cotton boll weight (BW) and seed index (SI, 100-seed weight) are key determinants of lint and seed yield, yet their genetic basis remains poorly understood. Here, a stable interploidy introgression line with small boll from Gossypium arboreum in Gossypium hirsutum, NB298, was employed to map quantitative trait loci (QTLs) of BW and SI. A moderate/minor-effect QTL on ChrA05 was preliminary mapped in the F₂ population of NB298 and TM-1, with the phenotypic variation explained of 6.21% and 1.65% for BW and SI, respectively, named q(BW+SI)-A05. Sixteen simple sequence repeat and insertion and deletion (InDel) markers were further developed for genotyping of individuals in F₂ and F₃ populations. A total of seven QTLs for three yield-related traits (BW, SI, and boll number per plant) were detected. Among them, stable QTLs for BW and SI were co-located in the interval between InDel-4353 and InDel-4370 in both F₂ and F₃ populations, with a length of 1354.55 kb. Then, the substitution mapping method demonstrated the QTL was located in an interval of 468.155 kb between the markers of InDel-4365 and InDel-4373. Comparisons of BW and SI between introgression lines with/without the introgression fragment showed they were significantly different. Combined with the RNA-seq of the ovules of 0, 3, and 5 days post anthesis, three differentially expressed genes were obtained and subjected to virus-induced gene silencing and overexpressing in cotton and ectopic expression in Arabidopsis thaliana. The identification of OFP17 (where OFP is ovate family protein) provides a molecular target for manipulating seed and fruit size to enhance cotton yield.