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Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton

As one of the pioneer crops widely planted in saline-alkaline areas, Gossypium provides daily necessities, including natural fiber, vegetable proteins, and edible oils. However, cotton fiber yield and quality are highly influenced by salt stress. Therefore, elucidating the molecular mechanisms of co...

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Autores principales: Liu, Qiankun, Li, Pengtao, Cheng, Shuang, Zhao, Zilin, Liu, Yuling, Wei, Yangyang, Lu, Quanwei, Han, Jiangping, Cai, Xiaoyan, Zhou, Zhongli, Umer, Muhammad Jawad, Peng, Renhai, Zhang, Baohong, Liu, Fang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8911145/
https://www.ncbi.nlm.nih.gov/pubmed/35269989
http://dx.doi.org/10.3390/ijms23052845
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author Liu, Qiankun
Li, Pengtao
Cheng, Shuang
Zhao, Zilin
Liu, Yuling
Wei, Yangyang
Lu, Quanwei
Han, Jiangping
Cai, Xiaoyan
Zhou, Zhongli
Umer, Muhammad Jawad
Peng, Renhai
Zhang, Baohong
Liu, Fang
author_facet Liu, Qiankun
Li, Pengtao
Cheng, Shuang
Zhao, Zilin
Liu, Yuling
Wei, Yangyang
Lu, Quanwei
Han, Jiangping
Cai, Xiaoyan
Zhou, Zhongli
Umer, Muhammad Jawad
Peng, Renhai
Zhang, Baohong
Liu, Fang
author_sort Liu, Qiankun
collection PubMed
description As one of the pioneer crops widely planted in saline-alkaline areas, Gossypium provides daily necessities, including natural fiber, vegetable proteins, and edible oils. However, cotton fiber yield and quality are highly influenced by salt stress. Therefore, elucidating the molecular mechanisms of cotton in response to salinity stress is importance to breed new cultivars with high tolerance. In this study, we first developed a method for single-cell RNA-seq based on isolating protoplast from cotton root tips; then, we studied the impact of salinity stress on gene expression profiling and their dynamic changes using the developed high-efficiency method for protoplast dissociation suitable for single-cell RNA-seq. A total of 3391 and 2826 differentially expressed genes (DEGs) were identified in salt-treated samples before and after protoplast dissociation, respectively, which were enriched into several molecular components, including response to stimulus, response to stress, and cellular macromolecule metabolic process by gene ontology (GO) analysis. Plant hormone signal transduction, phenylpropanoid biosynthesis, and MAPK signaling pathway were found to be enriched via Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Twenty-two and nine salinity-responsive DEGs participated in plant hormone signaling and MAPK signaling in roots, before and after protoplast dissociation, respectively; six upregulated DEGs were involved in ABA signaling transduction, namely, Ga04G2111, Ga07G0142, Ga09G2061, Ga10G0262, Ga01G0063, and Ga08G1915 which indicates their potential functions on plants adapting to salt stress. Additionally, 384 and 257 transcription factors (TFs) were differentially expressed in salt-stress roots before and after protoplast dissociation, respectively, of which significantly up-regulated TFs mainly belonged to the AP2/ERF-ERF family, which implied their potential roles responding to salt stress. These results not only provide novel insights to reveal the regulatory networks in plant’s root response to salt stress, but also lay the solid foundation for further exploration on cellular heterogeneity by single-cell transcriptome sequencing.
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spelling pubmed-89111452022-03-11 Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton Liu, Qiankun Li, Pengtao Cheng, Shuang Zhao, Zilin Liu, Yuling Wei, Yangyang Lu, Quanwei Han, Jiangping Cai, Xiaoyan Zhou, Zhongli Umer, Muhammad Jawad Peng, Renhai Zhang, Baohong Liu, Fang Int J Mol Sci Article As one of the pioneer crops widely planted in saline-alkaline areas, Gossypium provides daily necessities, including natural fiber, vegetable proteins, and edible oils. However, cotton fiber yield and quality are highly influenced by salt stress. Therefore, elucidating the molecular mechanisms of cotton in response to salinity stress is importance to breed new cultivars with high tolerance. In this study, we first developed a method for single-cell RNA-seq based on isolating protoplast from cotton root tips; then, we studied the impact of salinity stress on gene expression profiling and their dynamic changes using the developed high-efficiency method for protoplast dissociation suitable for single-cell RNA-seq. A total of 3391 and 2826 differentially expressed genes (DEGs) were identified in salt-treated samples before and after protoplast dissociation, respectively, which were enriched into several molecular components, including response to stimulus, response to stress, and cellular macromolecule metabolic process by gene ontology (GO) analysis. Plant hormone signal transduction, phenylpropanoid biosynthesis, and MAPK signaling pathway were found to be enriched via Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Twenty-two and nine salinity-responsive DEGs participated in plant hormone signaling and MAPK signaling in roots, before and after protoplast dissociation, respectively; six upregulated DEGs were involved in ABA signaling transduction, namely, Ga04G2111, Ga07G0142, Ga09G2061, Ga10G0262, Ga01G0063, and Ga08G1915 which indicates their potential functions on plants adapting to salt stress. Additionally, 384 and 257 transcription factors (TFs) were differentially expressed in salt-stress roots before and after protoplast dissociation, respectively, of which significantly up-regulated TFs mainly belonged to the AP2/ERF-ERF family, which implied their potential roles responding to salt stress. These results not only provide novel insights to reveal the regulatory networks in plant’s root response to salt stress, but also lay the solid foundation for further exploration on cellular heterogeneity by single-cell transcriptome sequencing. MDPI 2022-03-05 /pmc/articles/PMC8911145/ /pubmed/35269989 http://dx.doi.org/10.3390/ijms23052845 Text en © 2022 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
Liu, Qiankun
Li, Pengtao
Cheng, Shuang
Zhao, Zilin
Liu, Yuling
Wei, Yangyang
Lu, Quanwei
Han, Jiangping
Cai, Xiaoyan
Zhou, Zhongli
Umer, Muhammad Jawad
Peng, Renhai
Zhang, Baohong
Liu, Fang
Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton
title Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton
title_full Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton
title_fullStr Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton
title_full_unstemmed Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton
title_short Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton
title_sort protoplast dissociation and transcriptome analysis provides insights to salt stress response in cotton
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8911145/
https://www.ncbi.nlm.nih.gov/pubmed/35269989
http://dx.doi.org/10.3390/ijms23052845
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