Abstract
Histone deacetylases (HDACs) play a significant role in a plant’s development and response to various environmental stimuli by regulating the gene transcription. However, HDACs remain unidentified in cotton. In this study, a total of 29 HDACs were identified in allotetraploid Gossypium hirsutum, while 15 and 13 HDACs were identified in Gossypium arboretum and Gossypium raimondii, respectively. Gossypium HDACs were classified into three groups (reduced potassium dependency 3 (RPD3)/HDA1, HD2-like, and Sir2-like (SRT) based on their sequences, and Gossypium HDACs within each subgroup shared a similar gene structure, conserved catalytic domains and motifs. Further analysis revealed that Gossypium HDACs were under a strong purifying selection and were unevenly distributed on their chromosomes. Gene expression data revealed that G. hirsutum HDACs were differentially expressed in various vegetative and reproductive tissues, as well as at different developmental stages of cotton fiber. Furthermore, some G. hirsutum HDACs were co-localized with quantitative trait loci (QTLs) and single-nucleotide polymorphism (SNPs) of fiber-related traits, indicating their function in fiber-related traits. We also showed that G. hirsutum HDACs were differentially regulated in response to plant hormones (abscisic acid (ABA) and auxin), DNA damage agent (methyl methanesulfonate (MMS)), and abiotic stresses (cold, salt, heavy metals and drought), indicating the functional diversity and specification of HDACs in response to developmental and environmental cues. In brief, our results provide fundamental information regarding G. hirsutum HDACs and highlight their potential functions in cotton growth, fiber development and stress adaptations, which will be helpful for devising innovative strategies for the improvement of cotton fiber and stress tolerance.
Highlights
Cotton is the most important crop worldwide that has contributed a lot for the textile industry through its natural and renewable fiber
We found that the open reading frame (ORF) length of Gossypium Histone deacetylases (HDACs) ranged from 606–2004 bp, which encoded the polypeptides from 201–667 amino acids
The expression of GhHDA1509 and GhSRT1501 decreased from 0–5 days post anthesis (DPA) and increased from 5–25 DPA of fiber development. These results indicate the functional divergence among different groups of G. hirsutum HDACs in fiber development
Summary
Cotton is the most important crop worldwide that has contributed a lot for the textile industry through its natural and renewable fiber. HDA6 interacts with DNA methyltransferase MET1 [40], histone demethylase Flowering Locus D (FLD) [41], and histone methyltransferases SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 4/5/6 (SUVH4/5/6) [27] These studies highlight the importance of HDACs in gene expression regulation during plant development and in response to environmental stimuli. We first identified HDACs from G. hirsutum, G. arboretum and G. raimondii, and comprehensively analyzed them through the phylogenetic classification, gene structure and chromosomal location, domain organization, and the cis-regulatory elements in their promoters In addition to these bioinformatics analyses, the gene expression patterns of G. hirsutum HDACs were studied during the different stages of fiber development, phytohormone treatment, and diverse abiotic stresses, including Zn and Cd metal stresses, cold, drought and salt. This study will lead to a long-term improvement of cotton and will be useful for functional genomic studies on the regulation of histone acetylation in cotton
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