Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq
Drought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2016-07-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01044/full |
| _version_ | 1811233752663195648 |
|---|---|
| author | Wei Chen Qiuming Yao Gunvant Baliram Patil Gaurav Agarwal Rupesh Kailasrao Deshmukh Li Lin Biao Wang Yongqin Wang Silvas J Prince Li Song Dong Xu Yong-Qiang An Babu Valliyodan Rajeev K Varshney Henry T Nguyen |
| author_facet | Wei Chen Qiuming Yao Gunvant Baliram Patil Gaurav Agarwal Rupesh Kailasrao Deshmukh Li Lin Biao Wang Yongqin Wang Silvas J Prince Li Song Dong Xu Yong-Qiang An Babu Valliyodan Rajeev K Varshney Henry T Nguyen |
| author_sort | Wei Chen |
| collection | DOAJ |
| description | Drought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. In this study, differentially expressed genes under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. A total of 2,724 and 3,498 differentially expressed genes (DEGs) were identified under drought and flooding treatments, respectively. These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement. |
| first_indexed | 2024-04-12T11:24:27Z |
| format | Article |
| id | doaj.art-a0f2fedd019d4ef9b5dc4d85ab21a9b9 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T11:24:27Z |
| publishDate | 2016-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-a0f2fedd019d4ef9b5dc4d85ab21a9b92022-12-22T03:35:15ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-07-01710.3389/fpls.2016.01044209431Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-SeqWei Chen0Qiuming Yao1Gunvant Baliram Patil2Gaurav Agarwal3Rupesh Kailasrao Deshmukh4Li Lin5Biao Wang6Yongqin Wang7Silvas J Prince8Li Song9Dong Xu10Yong-Qiang An11Babu Valliyodan12Rajeev K Varshney13Henry T Nguyen14University of MissouriUniversity of MissouriUniversity of MissouriInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT)University of MissouriUniversity of MissouriShanghai Jiao Tong UniversityUniversity of MissouriUniversity of MissouriUniversity of MissouriUniversity of MissouriUSDA-ARS, Donald Danforth Plant Science CenterUniversity of MissouriInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT)University of MissouriDrought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. In this study, differentially expressed genes under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. A total of 2,724 and 3,498 differentially expressed genes (DEGs) were identified under drought and flooding treatments, respectively. These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01044/fullGene ExpressionstressdroughtSoybeanRNA-Seqflooding |
| spellingShingle | Wei Chen Qiuming Yao Gunvant Baliram Patil Gaurav Agarwal Rupesh Kailasrao Deshmukh Li Lin Biao Wang Yongqin Wang Silvas J Prince Li Song Dong Xu Yong-Qiang An Babu Valliyodan Rajeev K Varshney Henry T Nguyen Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq Frontiers in Plant Science Gene Expression stress drought Soybean RNA-Seq flooding |
| title | Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq |
| title_full | Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq |
| title_fullStr | Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq |
| title_full_unstemmed | Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq |
| title_short | Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq |
| title_sort | identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by rna seq |
| topic | Gene Expression stress drought Soybean RNA-Seq flooding |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01044/full |
| work_keys_str_mv | AT weichen identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT qiumingyao identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT gunvantbalirampatil identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT gauravagarwal identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT rupeshkailasraodeshmukh identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT lilin identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT biaowang identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT yongqinwang identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT silvasjprince identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT lisong identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT dongxu identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT yongqiangan identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT babuvalliyodan identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT rajeevkvarshney identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq AT henrytnguyen identificationandcomparativeanalysisofdifferentialgeneexpressioninsoybeanleaftissueunderdroughtandfloodingstressrevealedbyrnaseq |