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

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.

Characterization and Functional Divergence of a Novel DUF668 Gene Family in Rice Based on Comprehensive Expression Patterns

“…Cis-acting regulatory elements might provide clues for determining gene expression patterns in various organs or under environmental stresses [36]. Previous studies reported a significant positive relationship between response genes and their cis-elements in upstream promoter regions [37,38]. Here, we manifested potential cis-regulatory elements in the 2 Kb upstream regions of the OsDUF668s examined via the PlantCARE database.…”

Genome-Wide Identification and Functional Characterization of the Trans-Isopentenyl Diphosphate Synthases Gene Family in Cinnamomum camphora

“…We analyzed cis-elements in the promoter of the CcTIDS genes to better understand their potential regulation and function. In total, 343 cis-acting elements were identified, and they were grouped into three categories, which were responsible for plant growth and development, phytohormone responsiveness, and stress responsiveness, according to previous research ( Abdullah et al, 2018 ). Of these, nine belong to the plant growth and development category, of which AAGAA motifs (involved in the endosperm) and AS-1 elements (involved in shoot expression) accounted for the highest proportion (19.05%).…”

Zinc Finger-Homeodomain Transcriptional Factors (ZF-HDs) in Wheat (Triticum aestivum L.): Identification, Evolution, Expression Analysis and Response to Abiotic Stresses

“…In this study, we identified 37 TaZF-HD genes in wheat including 28 TaZF-HD genes and nine TaMIF genes ( Figure 1 and Table S1 ). The number of TaZF-HD genes was relatively higher than that identified in Arabidopsis (17) [ 11 ], tomato (22) [ 16 ], Chinese cabbage (31) [ 12 ] and Tartary buckwheat (20) [ 18 ] and the same as that in cotton (37) [ 17 ], suggesting that genome duplication events might have contributed to the expansion of TaZF-HD genes in wheat. Thirty-six paralogous gene pairs were identified in wheat, which all had undergone WGD or segmental duplication events and a strong purifying selection pressure ( Figure 4 and Table S3 ).…”

“…ZF-HD proteins were first identified in the C4 plant Flaveria as a potential regulator of the gene encoding C4 phosphoenolpyruvate carboxylase (PEPCase) [ 13 ]. Subsequently, ZF-HD genes were identified in several plant species such as Arabidopsis thaliana [ 11 ], tomato ( Solanum lycopersicum ) [ 16 ], cotton ( Gossypium hirsutum ) [ 17 ], Chinese cabbage [ 12 ] and Tartary buckwheat ( Fagopyrum tataricum ) [ 18 ]. In Arabidopsis , ZFHD10 recruits TANDEM ZINC-FINGER PLUS3 (TZP) to bind to light-regulated elements and regulate hypocotyl elongation [ 19 ].…”