Single-nucleus transcriptome sequencing reveals the developmental trajectory of shoot apex in upland cotton (Gossypium hirsutum L.) (PRJCA037504)
With the decreased cultivated land area and the intensification of harsh environments, early maturity has become an important breeding target trait in upland cotton. The mechanism of flower bud differentiation, which is the decisive factor affecting the flowering time and the early maturity in upland cotton, has not been clarified. Here, the main cell types of upland cotton shoot apex were identified by single nucleus transcriptomic sequencing (snRNA-seq) of the first, third, and fifth true leaf stages (S1, S3, S5) in early-maturing cotton CCRI50 and late-maturing cotton Guoxinmian11 (GX11). The reconstruction of shoot apex cells development trajectory revealed that CCRI50 started flower bud differentiation in S1 or earlier, while GX11 began to transition from vegetative growth to reproductive growth in S3. To further elucidate the regulatory role of hormones on bud differentiation in upland cotton, plant hormone content in the same samples was detected and 8 candidate genes were identified, all of which could regulate flowering time to different degrees. CRISPR/Cas9 editing and overexpression experiments proved that VASCULAR PLANT ONE-ZINC FINGER1 (GhVOZ1), one of these 8 candidate genes, could positively regulate flowering in upland cotton. Using DNA affinity purification sequencing (DAP-seq) and RNA sequencing (RNA-seq), the motif specifically bound by GhVOZ1 and its downstream target genes were identified, and the molecular mechanism of GhVOZ1 regulation of flowering was further analyzed in upland cotton. In this study, the development model and differentiation process of upland cotton shoot apex were proposed, which provided the theoretical basis and breeding materials for the study of early maturity.