Histone deacetylase (HDAC) gene family in allotetraploid cotton and its diploid progenitors: In silico identification, molecular characterization, and gene expression analysis under multiple abiotic stresses, DNA damage

Authors: IMRAN, MUHAMMAD - Chinese Academy Of Sciences; SHAFIQ, SARFRAZ - Comsats Institute Of Information Technology; NAEEM, MUHAMMAD - Chinese Academy Of Sciences; WIDEMANN, EMILIE - University Of Western Ontario; MUNIR, MUHAMMAD - Beijing Forestry University; Jensen, Kevin; Wang, Richard

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/4/2019
Publication Date: 1/3/2020
Publication URL: https://handle.nal.usda.gov/10113/6862108
Citation: Imran, M., Shafiq, S., Naeem, M., Widemann, E., Munir, M., Jensen, K.B., Wang, R. 2020. Histone deacetylase (HDAC) gene family in allotetraploid cotton and its diploid progenitors: In silico identification, molecular characterization, and gene expression analysis under multiple abiotic stresses, DNA damage. International Journal of Molecular Sciences. 21(1). https://doi.org/10.3390/ijms21010321.
DOI: https://doi.org/10.3390/ijms21010321

Interpretive Summary: Histone deacetylases (HDACs) maintain the homeotic balance of histone acetylation by removing the acetyl group and are linked to transcriptional repression and gene silencing. HDACs are well conserved in different organisms including, human, yeast and plants, and are generally classified into three distinct groups in plants. Numbers of HDAC genes are variable among different plants. Previous studies indicated the importance of HDACs in gene expression regulation during the plant development and in response to environmental stimuli. However, the identification and function of HDACs in cotton is yet to be investigated. In this study, we first identified HDAC genes from G. hirsutum, G. arboretum and G. raimondii, and then comprehensively analyzed through the phylogenetic classification, gene structure and chromosomal location, domain organization, and the cis-regulatory elements in their promoters. In addition to these bioinformatics analysis, gene expression patterns of G. hirsutum, HDACs were studied during the different stages of fiber development, phytohormone treatment, and diverse abiotic stresses including, Zn, Cd metal stress, cold, drought and salt. This study will lead to a long-term improvement of cotton as well as will be useful for functional genomic studies on the regulation of histone acetylation.

Technical Abstract: Histone deacetylases (HDACs) play a significant role in plant 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 3 groups (RPD3/HDA1, HD2-like ad SRT) based on their sequences and Gossypium HDACs within each subgroup share similar gene structure, conserved catalytic domains and motifs. Further analysis revealed that Gossypium HDACs are under strong purifying selection and are unevenly distributed on their chromosomes. Gene expression data revealed that Gossypium hirsutum HDACs are differentially expressed in various vegetative and reproductive tissues, as well as at different developmental stages of cotton fiber. Furthermore, some Gossypium hirsutum HDACs were co-localized with quantitative trait lock (QTLs) and single-nucleotide polymorphism (SNPs) of fiber related traits, indicating their function in fiber related traits. We also showed that Gossypium hirsutum HDACs are differentially regulated in response to plant hormones (ABA and auxin), DNA damage agent (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 of Gossypium hirsutum HDACs ad highlight their potential functions in cotton growth, fiber development and stress adaptations, which wil be helpful to devise innovative strategies for the improvement of cotton fiber and stress tolerance.