Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Upland Cotton (): Genome-Wide Identification and Expression Analysis in Fiber Development.

Zinc finger-homeodomain (ZHD) genes encode a family of plant-specific transcription factors that not only participate in the regulation of plant growth and development but also play an important role in the response to abiotic stress. The ZHD gene family has been studied in several model plants, including , and . However, a comprehensive study of the genes of the ZHD family and their roles in fiber development and pigmentation in upland cotton has not been completed. To address this gap, we selected a brown fiber cultivar for our study; brown color in cotton is one of the most desired colors in the textile industry. The natural colored fibers require less processing and little dying, thereby eliminating dye costs and chemical residues. Using bioinformatics approaches, we identified 37 genes from and then divided these genes into seven groups based on their phylogeny. The genes were mostly conserved in each subfamily with minor variations in motif distribution and gene structure. These genes were largely distributed on 19 of the 26 upland cotton chromosomes. Among the genomes, the paralogs and orthologs of the genes were identified and further characterized. Furthermore, among the paralogs, we observed that the ZHD family duplications in genomes (, and ) were probably derived from segmental duplication or genome-wide duplication (GWD) events. Through a combination of qRT-PCR and proanthocyanidins (PA) accumulation analyses in brown cotton fibers, we concluded that the candidate genes involved in early fiber development and fiber pigment synthesis include the following: , and This study delivers insights into the evolution of the genes in brown cotton, serves as a valuable resource for further studies, and identifies the conditions necessary for improving the quality of brown cotton fiber.