Identification of candidate genes for early-maturity traits by combining BSA-seq and QTL mapping in upland cotton (Gossypium hirsutum L.)

Cotton breeding for the development of early maturing varieties is an effective way to improve the multiple cropping indexes and alleviate the conflict in cultivated fields between grains and cotton in China. In the present study, we aimed to find upland cotton quantitative trait loci (QTLs) and candidate genes related to early maturity traits, including whole growth period (WGP), flowering timing (FT), node of the first fruiting branch (NFFB), height of the node of the first fruiting branch (HNFFB) and plant height (PH). An early-maturing variety, CCRI50, and a late-maturing variety, Guoxinmian 11 were crossed to obtain biparental populations. These populations were used to map QTLs for the early-maturity traits for two years (2020 and 2021). With BSA-seq analysis based on the data of population 2020, the candidate regions related to early maturity were found to be located on chromosome D03. Then, we developed 22 polymorphic Indel makers to further narrow down the candidate regions, resulting in detection of five and four QTLs in the 2020 and 2021 populations, respectively. According to the results of QTL mapping, two candidate regions (InDelG286-InDelG144 and InDelG24-InDelG43) were detected. In these regions, three genes (GHD03G0451, GHD03G0649, and GHD03G1180) have non-synonymous mutations in the exon and one gene (GHD03G0450) has SNP variations in the upstream sequence between CCRI50 and Guoxinmian11. These four genes also showed a dominant expression in the floral organs. The expression of GHD03G0451, GHD03G0649 and GHD03G1180 in CCRI50 was significantly higher than in Guoxinmian11 during the bud differentiation stages, while GHD03G0450 showed an opposite trend. Further functional verification of GHD03G0451 showed that the GHD03G0451-silenced plants showed a delay in the flowering time. These results may suggest that these are the candidate genes for cotton early maturity and may further be used for cotton breeding aiming for early-maturity.