Identification of EXPA4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplasts
Abstract Background Salinity stress impairs cotton growth and fiber quality. Protoplasts enable elucidation of early salt-responsive signaling. Elucidating crop tolerance mechanisms that ameliorate these diverse salinity-induced stresses is key for improving agricultural productivity under saline co...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-024-05958-w |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832594840625348608 |
|---|---|
| author | Qiankun Liu Pengtao Li Muhammad Jawad Umer Mubashir Abbas Yongqing Zhao Yu Chen Yanfang Li Aiming Zhang Yuling Liu Yangyang Wei Quanwei Lu Mengying Yang Yiman Liu Xiaoyan Cai Zhongli Zhou Shuxun Yu Fang Liu Renhai Peng |
| author_facet | Qiankun Liu Pengtao Li Muhammad Jawad Umer Mubashir Abbas Yongqing Zhao Yu Chen Yanfang Li Aiming Zhang Yuling Liu Yangyang Wei Quanwei Lu Mengying Yang Yiman Liu Xiaoyan Cai Zhongli Zhou Shuxun Yu Fang Liu Renhai Peng |
| author_sort | Qiankun Liu |
| collection | DOAJ |
| description | Abstract Background Salinity stress impairs cotton growth and fiber quality. Protoplasts enable elucidation of early salt-responsive signaling. Elucidating crop tolerance mechanisms that ameliorate these diverse salinity-induced stresses is key for improving agricultural productivity under saline conditions. Results Herein, we performed transcriptome profiling of Gossypium arboreum root tips and root tips-derived protoplasts to uncover salt tolerance genes and mechanisms. Differentially expressed genes (DEGs) were significantly enriched in the plant hormone signal transduction and MAPK signaling pathways. Transcriptome based weighted gene coexpression network analysis (WGCNA) clustered 885 commonly differentially expressed genes into four distinct modules. Black and yellow modules were highly upregulated under salt treatment, containing hub genes integral to signaling and transport, highlighting their importance. Differential expression analysis revealed more dynamic changes in protoplasts, identifying key genes including the Ga-α-expansin 4 (GaEXPA4). Silencing of the GaEXPA4 gene through virus-induced gene silencing heightened cotton’s sensitivity to salt stress, leading to increased wilting, elevated lipid peroxidation, and impaired antioxidant activity under salt conditions compared to controls. Conclusion These findings underscore the functional significance of GaEXPA4 in the salt stress response. Future research should focus on elucidating the precise mechanisms of putative salt tolerance genes like GaEXPA4 and evaluating the potential of signaling pathways, such as MAPK, for engineering enhanced salt resilience in cotton. Integrating multi-omics approaches could further expand the genetic resources available for improving cotton cultivation in saline environments. |
| format | Article |
| id | doaj-art-84496246229a497e9d837658bc67eca9 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-84496246229a497e9d837658bc67eca92025-01-19T12:16:42ZengBMCBMC Plant Biology1471-22292025-01-0125111910.1186/s12870-024-05958-wIdentification of EXPA4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplastsQiankun Liu0Pengtao Li1Muhammad Jawad Umer2Mubashir Abbas3Yongqing Zhao4Yu Chen5Yanfang Li6Aiming Zhang7Yuling Liu8Yangyang Wei9Quanwei Lu10Mengying Yang11Yiman Liu12Xiaoyan Cai13Zhongli Zhou14Shuxun Yu15Fang Liu16Renhai Peng17National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural SciencesCollege of Biology and Food Engineering, Anyang Institute of TechnologyNational Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural SciencesNational Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural SciencesCollege of Biology and Food Engineering, Anyang Institute of TechnologyState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityCollege of Biology and Food Engineering, Anyang Institute of TechnologyCollege of Biology and Food Engineering, Anyang Institute of TechnologyCollege of Biology and Food Engineering, Anyang Institute of TechnologyCollege of Biology and Food Engineering, Anyang Institute of TechnologyCollege of Biology and Food Engineering, Anyang Institute of TechnologyZhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou UniversityZhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou UniversityNational Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural SciencesNational Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural SciencesNational Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural SciencesNational Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural SciencesNational Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural SciencesAbstract Background Salinity stress impairs cotton growth and fiber quality. Protoplasts enable elucidation of early salt-responsive signaling. Elucidating crop tolerance mechanisms that ameliorate these diverse salinity-induced stresses is key for improving agricultural productivity under saline conditions. Results Herein, we performed transcriptome profiling of Gossypium arboreum root tips and root tips-derived protoplasts to uncover salt tolerance genes and mechanisms. Differentially expressed genes (DEGs) were significantly enriched in the plant hormone signal transduction and MAPK signaling pathways. Transcriptome based weighted gene coexpression network analysis (WGCNA) clustered 885 commonly differentially expressed genes into four distinct modules. Black and yellow modules were highly upregulated under salt treatment, containing hub genes integral to signaling and transport, highlighting their importance. Differential expression analysis revealed more dynamic changes in protoplasts, identifying key genes including the Ga-α-expansin 4 (GaEXPA4). Silencing of the GaEXPA4 gene through virus-induced gene silencing heightened cotton’s sensitivity to salt stress, leading to increased wilting, elevated lipid peroxidation, and impaired antioxidant activity under salt conditions compared to controls. Conclusion These findings underscore the functional significance of GaEXPA4 in the salt stress response. Future research should focus on elucidating the precise mechanisms of putative salt tolerance genes like GaEXPA4 and evaluating the potential of signaling pathways, such as MAPK, for engineering enhanced salt resilience in cotton. Integrating multi-omics approaches could further expand the genetic resources available for improving cotton cultivation in saline environments.https://doi.org/10.1186/s12870-024-05958-wCottonSalt stressTranscriptomeProtoplast dissociationEXPA4 gene |
| spellingShingle | Qiankun Liu Pengtao Li Muhammad Jawad Umer Mubashir Abbas Yongqing Zhao Yu Chen Yanfang Li Aiming Zhang Yuling Liu Yangyang Wei Quanwei Lu Mengying Yang Yiman Liu Xiaoyan Cai Zhongli Zhou Shuxun Yu Fang Liu Renhai Peng Identification of EXPA4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplasts BMC Plant Biology Cotton Salt stress Transcriptome Protoplast dissociation EXPA4 gene |
| title | Identification of EXPA4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplasts |
| title_full | Identification of EXPA4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplasts |
| title_fullStr | Identification of EXPA4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplasts |
| title_full_unstemmed | Identification of EXPA4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplasts |
| title_short | Identification of EXPA4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplasts |
| title_sort | identification of expa4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplasts |
| topic | Cotton Salt stress Transcriptome Protoplast dissociation EXPA4 gene |
| url | https://doi.org/10.1186/s12870-024-05958-w |
| work_keys_str_mv | AT qiankunliu identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT pengtaoli identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT muhammadjawadumer identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT mubashirabbas identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT yongqingzhao identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT yuchen identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT yanfangli identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT aimingzhang identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT yulingliu identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT yangyangwei identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT quanweilu identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT mengyingyang identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT yimanliu identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT xiaoyancai identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT zhonglizhou identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT shuxunyu identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT fangliu identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts AT renhaipeng identificationofexpa4asakeygeneincottonsaltstressadaptationthroughtranscriptomicandcoexpressionnetworkanalysisofroottipprotoplasts |