Cargando…

Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum

Auxin response factors (ARFs) are critical components of the auxin signaling pathway, and are involved in diverse plant biological processes. However, ARF genes have not been investigated in flax (Linum usitatissimum L.), an important oilseed and fiber crop. In this study, we comprehensively analyze...

Descripción completa

Detalles Bibliográficos
Autores principales: Qi, Yanni, Wang, Limin, Li, Wenjuan, Dang, Zhao, Xie, Yaping, Zhao, Wei, Zhao, Lirong, Li, Wen, Yang, Chenxi, Xu, Chenmeng, Zhang, Jianping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10341394/
https://www.ncbi.nlm.nih.gov/pubmed/37446183
http://dx.doi.org/10.3390/ijms241311006
_version_ 1785072251437056000
author Qi, Yanni
Wang, Limin
Li, Wenjuan
Dang, Zhao
Xie, Yaping
Zhao, Wei
Zhao, Lirong
Li, Wen
Yang, Chenxi
Xu, Chenmeng
Zhang, Jianping
author_facet Qi, Yanni
Wang, Limin
Li, Wenjuan
Dang, Zhao
Xie, Yaping
Zhao, Wei
Zhao, Lirong
Li, Wen
Yang, Chenxi
Xu, Chenmeng
Zhang, Jianping
author_sort Qi, Yanni
collection PubMed
description Auxin response factors (ARFs) are critical components of the auxin signaling pathway, and are involved in diverse plant biological processes. However, ARF genes have not been investigated in flax (Linum usitatissimum L.), an important oilseed and fiber crop. In this study, we comprehensively analyzed the ARF gene family and identified 33 LuARF genes unevenly distributed on the 13 chromosomes of Longya-10, an oil-use flax variety. Detailed analysis revealed wide variation among the ARF family members and predicted nuclear localization for all proteins. Nineteen LuARFs contained a complete ARF structure, including DBD, MR, and CTD, whereas the other fourteen lacked the CTD. Phylogenetic analysis grouped the LuARFs into four (I–V) clades. Combined with sequence analysis, the LuARFs from the same clade showed structural conservation, implying functional redundancy. Duplication analysis identified twenty-seven whole-genome-duplicated LuARF genes and four tandem-duplicated LuARF genes. These duplicated gene pairs’ K(a)/K(s) ratios suggested a strong purifying selection pressure on the LuARF genes. Collinearity analysis revealed that about half of the LuARF genes had homologs in other species, indicating a relatively conserved nature of the ARFs. The promoter analysis identified numerous hormone- and stress-related elements, and the qRT-PCR experiment revealed that all LuARF genes were responsive to phytohormone (IAA, GA3, and NAA) and stress (PEG, NaCl, cold, and heat) treatments. Finally, expression profiling of LuARF genes in different tissues by qRT-PCR indicated their specific functions in stem or capsule growth. Thus, our findings suggest the potential functions of LuARFs in flax growth and response to an exogenous stimulus, providing a basis for further functional studies on these genes.
format Online
Article
Text
id pubmed-10341394
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-103413942023-07-14 Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum Qi, Yanni Wang, Limin Li, Wenjuan Dang, Zhao Xie, Yaping Zhao, Wei Zhao, Lirong Li, Wen Yang, Chenxi Xu, Chenmeng Zhang, Jianping Int J Mol Sci Article Auxin response factors (ARFs) are critical components of the auxin signaling pathway, and are involved in diverse plant biological processes. However, ARF genes have not been investigated in flax (Linum usitatissimum L.), an important oilseed and fiber crop. In this study, we comprehensively analyzed the ARF gene family and identified 33 LuARF genes unevenly distributed on the 13 chromosomes of Longya-10, an oil-use flax variety. Detailed analysis revealed wide variation among the ARF family members and predicted nuclear localization for all proteins. Nineteen LuARFs contained a complete ARF structure, including DBD, MR, and CTD, whereas the other fourteen lacked the CTD. Phylogenetic analysis grouped the LuARFs into four (I–V) clades. Combined with sequence analysis, the LuARFs from the same clade showed structural conservation, implying functional redundancy. Duplication analysis identified twenty-seven whole-genome-duplicated LuARF genes and four tandem-duplicated LuARF genes. These duplicated gene pairs’ K(a)/K(s) ratios suggested a strong purifying selection pressure on the LuARF genes. Collinearity analysis revealed that about half of the LuARF genes had homologs in other species, indicating a relatively conserved nature of the ARFs. The promoter analysis identified numerous hormone- and stress-related elements, and the qRT-PCR experiment revealed that all LuARF genes were responsive to phytohormone (IAA, GA3, and NAA) and stress (PEG, NaCl, cold, and heat) treatments. Finally, expression profiling of LuARF genes in different tissues by qRT-PCR indicated their specific functions in stem or capsule growth. Thus, our findings suggest the potential functions of LuARFs in flax growth and response to an exogenous stimulus, providing a basis for further functional studies on these genes. MDPI 2023-07-02 /pmc/articles/PMC10341394/ /pubmed/37446183 http://dx.doi.org/10.3390/ijms241311006 Text en © 2023 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
Qi, Yanni
Wang, Limin
Li, Wenjuan
Dang, Zhao
Xie, Yaping
Zhao, Wei
Zhao, Lirong
Li, Wen
Yang, Chenxi
Xu, Chenmeng
Zhang, Jianping
Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum
title Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum
title_full Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum
title_fullStr Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum
title_full_unstemmed Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum
title_short Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum
title_sort genome-wide identification and expression analysis of auxin response factor gene family in linum usitatissimum
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10341394/
https://www.ncbi.nlm.nih.gov/pubmed/37446183
http://dx.doi.org/10.3390/ijms241311006
work_keys_str_mv AT qiyanni genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT wanglimin genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT liwenjuan genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT dangzhao genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT xieyaping genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT zhaowei genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT zhaolirong genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT liwen genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT yangchenxi genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT xuchenmeng genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum
AT zhangjianping genomewideidentificationandexpressionanalysisofauxinresponsefactorgenefamilyinlinumusitatissimum