Multistage temporal transcriptomic atlas unveils major contributor to reproductive phase in upland cotton

Abstract Flowering is a major developmental transition in plants, but asynchronous flowering hinders the utilization of wild cotton relatives in breeding programs. We performed comparative transcriptomic profiling of early‐ and late‐flowering Gossypium hirsutum genotypes to elucidate genetic factors influencing reproductive timing. Shoot apices were sampled from the photoperiod‐sensitive landrace G. hirsutum purpurascens ( GhP ) and early‐maturing variety ZhongMianSuo (ZMS) at five time points following the emergence of sympodial nodes. RNA‐sequencing revealed extensive transcriptional differences during floral transition. Numerous flowering‐associated genes exhibited genotype‐specific expression, including FLOWERING LOCUS T ( FT ) homologs upregulated in ZMS. FT‐interacting factors like SOC1 and CO ‐like also showed higher expression in ZMS, implicating florigen pathways in early flowering. Additionally, circadian clock and light signalling components were misregulated between varieties, suggesting altered photoperiod responses in GhP. Weighted co‐expression network analysis specifically linked a module enriched for circadian‐related genes to GhP's late flowering. Through an integrated transcriptome analysis, we defined a regulatory landscape of reproductive phase change in cotton. Differentially expressed genes related to photoperiod, circadian clock, and light signalling likely contribute to delayed flowering in wild cottons. Characterization of upstream flowering regulators will enable modifying photoperiod sensitivity and expand germplasm use for cotton improvement. This study provides candidate targets for elucidating interactive mechanisms that control cotton flowering time across diverse genotypes.