Abstract
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 Solanum lycopersicum, Zea mays, Oryza sativa, and Arabidopsis thaliana. 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 GhZHD genes from Gossypium hirsutum and then divided these genes into seven groups based on their phylogeny. The GhZHD 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 Gossypium genomes, the paralogs and orthologs of the GhZHD genes were identified and further characterized. Furthermore, among the paralogs, we observed that the ZHD family duplications in Gossypium genomes (G. hirsutum, G. arboreum, and G. raimondii) 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: GhZHD29, GhZHD35, GhZHD30, GhZHD31, GhZHD11, GhZHD27, GhZHD18, GhZHD15, GhZHD16, GhZHD22, GhZHD6, GhZHD33, GhZHD13, GhZHD5, and GhZHD23. This study delivers insights into the evolution of the GhZHD 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.
Highlights
Zinc finger-homeodomain (ZHD) transcription factors (TFs) are major regulators of the body plan specification of higher plants and are especially involved in plant development and stress responses (Wang et al, 2015; Khatun et al, 2017)
Our results provide a valuable foundation for future studies on ZHD proteins in brown cotton to facilitate functional analysis
After removing repetitive sequences and any sequence lacking the ZHD domain, we obtained a total of 37 non-redundant GhZHD genes
Summary
Zinc finger-homeodomain (ZHD) transcription factors (TFs) are major regulators of the body plan specification of higher plants and are especially involved in plant development (fiber development) and stress responses (Wang et al, 2015; Khatun et al, 2017). In plant and animal genomes, homeobox genes are part of a large gene family. Zinc finger genes were categorized into the following groups: KNOX, ZM-HOX, BELL, AT-HB8, HAT, and GAL2 (Bharathan et al, 1997; Bhattacharjee et al, 2015). Homeobox genes in rice were classified into ten subclasses: HDZip I, HD-Zip II, HD-Zip III, HD-Zip IV, KNOX I, KNOX II, BLH, WOX, PHD, and ZF-HD. Another systematic study on homeobox genes was carried out in which the genes were categorized into 14 subclasses, including the addition of some new classes, such as DDT, NDX, PHD, SAWADEE, LD, and PINTOX (Mukherjee et al, 2009). While some zinc fingers (C2H2, C2C2, and C3H) interact with one zinc ion, new approaches demonstrated that the animal Lin-11/Is1-1/Mec-3 (LIM) domain and plant RING finger domains interact with two zinc ions (Halbach et al, 2000; Englbrecht et al, 2004; Yanagisawa, 2004; Wang et al, 2014)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
