Integrated phylogenomic and transcriptomic analyses reveal GhTZP3 as a key gene regulating flowering time and undergoing artificial selection in upland cotton (Gossypium hirsutum).

Although the TANDEM ZINC-FINGER/PLUS3 (TZP) gene family is known to regulate growth and development in Arabidopsis thaliana, its biological functions in upland cotton remain largely unknown. In this study, members of the upland cotton TZP gene family were systematically identified and analyzed at the genome-wide level. By integrating published RNA-seq data and real-time quantitative polymerase chain reaction (qRT‒PCR) assays, we identified candidate genes. Subsequently, the function of the target gene was validated using virus-induced gene silencing (VIGS) technology, and breeding and evolutionary analyses were conducted to develop molecular markers. The results revealed that 16 GhTZPs were distributed unevenly across 14 chromosomes in the upland cotton genome. An expression analysis revealed significant differences in GhTZP3 expression between early- and late-maturing cultivars. VIGS analysis demonstrated that the suppression of GhTZP3 expression significantly delayed the budding and flowering time of upland cotton. Furthermore, a single-nucleotide polymorphism (SNP) was detected within the GhTZP3 exon region, which was significantly associated with flowering time. The 'A' allele, linked to early-flowering traits, exhibited higher distribution frequencies in varieties from the northwestern inland region (NIR) and showed a gradual increase from the early-season to the modern varieties. On the basis of this variant site, a kompetitive allele-specific PCR (KASP) marker was successfully developed. In summary, these results suggest that GhTZP3 participates in regulating the flowering period of upland cotton and has undergone natural or artificial selection during variety improvement. KEY MESSAGES: Silencing of GhTZP3 delays cotton flowering, and a KASP marker was developed for a flowering-associated site within this gene.