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Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

BACKGROUND: The trihelix family of transcription factors plays essential roles in the growth, development, and abiotic stress response of plants. Although several studies have been performed on the trihelix gene family in several dicots and monocots, this gene family is yet to be studied in Chenopod...

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Autores principales: Li, Kuiyin, Fan, Yue, Zhou, Guangyi, Liu, Xiaojuan, Chen, Songshu, Chang, Xiangcai, Wu, Wenqiang, Duan, Lili, Yao, Maoxing, Wang, Rui, Wang, Zili, Yang, Mingfang, Ding, Yanqing, Ren, Mingjian, Fan, Yu, Zhang, Liyi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9271251/
https://www.ncbi.nlm.nih.gov/pubmed/35810309
http://dx.doi.org/10.1186/s12864-022-08726-y
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author Li, Kuiyin
Fan, Yue
Zhou, Guangyi
Liu, Xiaojuan
Chen, Songshu
Chang, Xiangcai
Wu, Wenqiang
Duan, Lili
Yao, Maoxing
Wang, Rui
Wang, Zili
Yang, Mingfang
Ding, Yanqing
Ren, Mingjian
Fan, Yu
Zhang, Liyi
author_facet Li, Kuiyin
Fan, Yue
Zhou, Guangyi
Liu, Xiaojuan
Chen, Songshu
Chang, Xiangcai
Wu, Wenqiang
Duan, Lili
Yao, Maoxing
Wang, Rui
Wang, Zili
Yang, Mingfang
Ding, Yanqing
Ren, Mingjian
Fan, Yu
Zhang, Liyi
author_sort Li, Kuiyin
collection PubMed
description BACKGROUND: The trihelix family of transcription factors plays essential roles in the growth, development, and abiotic stress response of plants. Although several studies have been performed on the trihelix gene family in several dicots and monocots, this gene family is yet to be studied in Chenopodium quinoa (quinoa). RESULTS: In this study, 47 C. quinoa trihelix (CqTH) genes were in the quinoa genome. Phylogenetic analysis of the CqTH and trihelix genes from Arabidopsis thaliana and Beta vulgaris revealed that the genes were clustered into five subfamilies: SIP1, GTγ, GT1, GT2, and SH4. Additionally, synteny analysis revealed that the CqTH genes were located on 17 chromosomes, with the exception of chromosomes 8 and 11, and 23 pairs of segmental duplication genes were detected. Furthermore, expression patterns of 10 CqTH genes in different plant tissues and at different developmental stages under abiotic stress and phytohormone treatment were examined. Among the 10 genes, CqTH02, CqTH25, CqTH18, CqTH19, CqTH25, CqTH31, and CqTH36, were highly expressed in unripe achenes 21 d after flowering and in mature achenes compared with other plant tissues. Notably, the 10 CqTH genes were upregulated in UV-treated leaves, whereas CqTH36 was consistently upregulated in the leaves under all abiotic stress conditions. CONCLUSIONS: The findings of this study suggest that gene duplication could be a major driver of trihelix gene evolution in quinoa. These findings could serve as a basis for future studies on the roles of CqTH transcription factors and present potential genetic markers for breeding stress-resistant and high-yielding quinoa varieties. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08726-y.
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spelling pubmed-92712512022-07-11 Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions Li, Kuiyin Fan, Yue Zhou, Guangyi Liu, Xiaojuan Chen, Songshu Chang, Xiangcai Wu, Wenqiang Duan, Lili Yao, Maoxing Wang, Rui Wang, Zili Yang, Mingfang Ding, Yanqing Ren, Mingjian Fan, Yu Zhang, Liyi BMC Genomics Research BACKGROUND: The trihelix family of transcription factors plays essential roles in the growth, development, and abiotic stress response of plants. Although several studies have been performed on the trihelix gene family in several dicots and monocots, this gene family is yet to be studied in Chenopodium quinoa (quinoa). RESULTS: In this study, 47 C. quinoa trihelix (CqTH) genes were in the quinoa genome. Phylogenetic analysis of the CqTH and trihelix genes from Arabidopsis thaliana and Beta vulgaris revealed that the genes were clustered into five subfamilies: SIP1, GTγ, GT1, GT2, and SH4. Additionally, synteny analysis revealed that the CqTH genes were located on 17 chromosomes, with the exception of chromosomes 8 and 11, and 23 pairs of segmental duplication genes were detected. Furthermore, expression patterns of 10 CqTH genes in different plant tissues and at different developmental stages under abiotic stress and phytohormone treatment were examined. Among the 10 genes, CqTH02, CqTH25, CqTH18, CqTH19, CqTH25, CqTH31, and CqTH36, were highly expressed in unripe achenes 21 d after flowering and in mature achenes compared with other plant tissues. Notably, the 10 CqTH genes were upregulated in UV-treated leaves, whereas CqTH36 was consistently upregulated in the leaves under all abiotic stress conditions. CONCLUSIONS: The findings of this study suggest that gene duplication could be a major driver of trihelix gene evolution in quinoa. These findings could serve as a basis for future studies on the roles of CqTH transcription factors and present potential genetic markers for breeding stress-resistant and high-yielding quinoa varieties. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08726-y. BioMed Central 2022-07-10 /pmc/articles/PMC9271251/ /pubmed/35810309 http://dx.doi.org/10.1186/s12864-022-08726-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Li, Kuiyin
Fan, Yue
Zhou, Guangyi
Liu, Xiaojuan
Chen, Songshu
Chang, Xiangcai
Wu, Wenqiang
Duan, Lili
Yao, Maoxing
Wang, Rui
Wang, Zili
Yang, Mingfang
Ding, Yanqing
Ren, Mingjian
Fan, Yu
Zhang, Liyi
Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions
title Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions
title_full Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions
title_fullStr Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions
title_full_unstemmed Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions
title_short Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions
title_sort genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (chenopodium quinoa willd.) under abiotic stress conditions
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9271251/
https://www.ncbi.nlm.nih.gov/pubmed/35810309
http://dx.doi.org/10.1186/s12864-022-08726-y
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