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Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley

The WRKY transcription factors (WRKYs) are known for their crucial roles in biotic and abiotic stress responses, and developmental and physiological processes. In barley, early studies revealed their importance, whereas their diversity at the population scale remains hardly estimated. In this study,...

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Autores principales: Kan, Jinhong, Gao, Guangqi, He, Qiang, Gao, Qian, Jiang, Congcong, Ahmar, Sunny, Liu, Jun, Zhang, Jing, Yang, Ping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8160967/
https://www.ncbi.nlm.nih.gov/pubmed/34069581
http://dx.doi.org/10.3390/ijms22105354
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author Kan, Jinhong
Gao, Guangqi
He, Qiang
Gao, Qian
Jiang, Congcong
Ahmar, Sunny
Liu, Jun
Zhang, Jing
Yang, Ping
author_facet Kan, Jinhong
Gao, Guangqi
He, Qiang
Gao, Qian
Jiang, Congcong
Ahmar, Sunny
Liu, Jun
Zhang, Jing
Yang, Ping
author_sort Kan, Jinhong
collection PubMed
description The WRKY transcription factors (WRKYs) are known for their crucial roles in biotic and abiotic stress responses, and developmental and physiological processes. In barley, early studies revealed their importance, whereas their diversity at the population scale remains hardly estimated. In this study, 98 HsWRKYs and 103 HvWRKYs have been identified from the reference genome of wild and cultivated barley, respectively. The tandem duplication and segmental duplication events from the cultivated barley were observed. By taking advantage of early released exome-captured sequencing datasets in 90 wild barley accessions and 137 landraces, the diversity analysis uncovered synonymous and non-synonymous variants instead of loss-of-function mutations that had occurred at all WRKYs. For majority of WRKYs, the haplotype and nucleotide diversity both decreased in cultivated barley relative to the wild population. Five WRKYs were detected to have undergone selection, among which haplotypes of WRKY9 were enriched, correlating with the geographic collection sites. Collectively, profiting from the state-of-the-art barley genomic resources, this work represented the characterization and diversity of barley WRKY transcription factors, shedding light on future deciphering of their roles in barley domestication and adaptation.
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spelling pubmed-81609672021-05-29 Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley Kan, Jinhong Gao, Guangqi He, Qiang Gao, Qian Jiang, Congcong Ahmar, Sunny Liu, Jun Zhang, Jing Yang, Ping Int J Mol Sci Article The WRKY transcription factors (WRKYs) are known for their crucial roles in biotic and abiotic stress responses, and developmental and physiological processes. In barley, early studies revealed their importance, whereas their diversity at the population scale remains hardly estimated. In this study, 98 HsWRKYs and 103 HvWRKYs have been identified from the reference genome of wild and cultivated barley, respectively. The tandem duplication and segmental duplication events from the cultivated barley were observed. By taking advantage of early released exome-captured sequencing datasets in 90 wild barley accessions and 137 landraces, the diversity analysis uncovered synonymous and non-synonymous variants instead of loss-of-function mutations that had occurred at all WRKYs. For majority of WRKYs, the haplotype and nucleotide diversity both decreased in cultivated barley relative to the wild population. Five WRKYs were detected to have undergone selection, among which haplotypes of WRKY9 were enriched, correlating with the geographic collection sites. Collectively, profiting from the state-of-the-art barley genomic resources, this work represented the characterization and diversity of barley WRKY transcription factors, shedding light on future deciphering of their roles in barley domestication and adaptation. MDPI 2021-05-19 /pmc/articles/PMC8160967/ /pubmed/34069581 http://dx.doi.org/10.3390/ijms22105354 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kan, Jinhong
Gao, Guangqi
He, Qiang
Gao, Qian
Jiang, Congcong
Ahmar, Sunny
Liu, Jun
Zhang, Jing
Yang, Ping
Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley
title Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley
title_full Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley
title_fullStr Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley
title_full_unstemmed Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley
title_short Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley
title_sort genome-wide characterization of wrky transcription factors revealed gene duplication and diversification in populations of wild to domesticated barley
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8160967/
https://www.ncbi.nlm.nih.gov/pubmed/34069581
http://dx.doi.org/10.3390/ijms22105354
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