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Article

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 and Phytohormone Treatments

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School of Life Sciences, Tsinghua University, Beijing 100084, China
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State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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Department of Biology, University of Western Ontario, 1151 Richmond St, London, ON N6A5B8, Canada
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Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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Forage & Range Research, United States Department of Agriculture, Agricultural Research Service, Logan, UT 84322, USA
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(1), 321; https://doi.org/10.3390/ijms21010321
Received: 4 December 2019 / Revised: 31 December 2019 / Accepted: 1 January 2020 / Published: 3 January 2020
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants 2020)
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. View Full-Text
Keywords: histone deacetylases; genome-wide analysis; fiber; abiotic stress; cotton histone deacetylases; genome-wide analysis; fiber; abiotic stress; cotton
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MDPI and ACS Style

Imran, M.; Shafiq, S.; Naeem, M.K.; Widemann, E.; Munir, M.Z.; Jensen, K.B.; Wang, R.R.-C. 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 and Phytohormone Treatments. Int. J. Mol. Sci. 2020, 21, 321. https://doi.org/10.3390/ijms21010321

AMA Style

Imran M, Shafiq S, Naeem MK, Widemann E, Munir MZ, Jensen KB, Wang RR-C. 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 and Phytohormone Treatments. International Journal of Molecular Sciences. 2020; 21(1):321. https://doi.org/10.3390/ijms21010321

Chicago/Turabian Style

Imran, Muhammad; Shafiq, Sarfraz; Naeem, Muhammad K.; Widemann, Emilie; Munir, Muhammad Z.; Jensen, Kevin B.; Wang, Richard R.-C. 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 and Phytohormone Treatments" Int. J. Mol. Sci. 21, no. 1: 321. https://doi.org/10.3390/ijms21010321

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