Cargando…
Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis
The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to dr...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505142/ https://www.ncbi.nlm.nih.gov/pubmed/23189148 http://dx.doi.org/10.1371/journal.pone.0049522 |
_version_ | 1782250718015520768 |
---|---|
author | Le, Dung Tien Nishiyama, Rie Watanabe, Yasuko Tanaka, Maho Seki, Motoaki Ham, Le Huy Yamaguchi-Shinozaki, Kazuko Shinozaki, Kazuo Tran, Lam-Son Phan |
author_facet | Le, Dung Tien Nishiyama, Rie Watanabe, Yasuko Tanaka, Maho Seki, Motoaki Ham, Le Huy Yamaguchi-Shinozaki, Kazuko Shinozaki, Kazuo Tran, Lam-Son Phan |
author_sort | Le, Dung Tien |
collection | PubMed |
description | The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to drought stress from late vegetative V6 and from full bloom reproductive R2 stages. Our data analyses showed that out of 46093 soybean genes, which were predicted with high confidence among approximately 66000 putative genes, 41059 genes could be assigned with a known function. Using the criteria of a ratio change > = 2 and a q-value<0.05, we identified 1458 and 1818 upregulated and 1582 and 1688 downregulated genes in drought-stressed V6 and R2 leaves, respectively. These datasets were classified into 19 most abundant biological categories with similar proportions. There were only 612 and 463 genes that were overlapped among the upregulated and downregulated genes, respectively, in both stages, suggesting that both conserved and unconserved pathways might be involved in regulation of drought response in different stages of plant development. A comparative expression analysis using our datasets and that of drought stressed Arabidopsis leaves revealed the existence of both conserved and species-specific mechanisms that regulate drought responses. Many upregulated genes encode either regulatory proteins, such as transcription factors, including those with high homology to Arabidopsis DREB, NAC, AREB and ZAT/STZ transcription factors, kinases and two-component system members, or functional proteins, e.g. late embryogenesis-abundant proteins, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins. A detailed analysis of the GmNAC family and the hormone-related gene category showed that expression of many GmNAC and hormone-related genes was altered by drought in V6 and/or R2 leaves. Additionally, the downregulation of many photosynthesis-related genes, which contribute to growth retardation under drought stress, may serve as an adaptive mechanism for plant survival. This study has identified excellent drought-responsive candidate genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans. |
format | Online Article Text |
id | pubmed-3505142 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35051422012-11-27 Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis Le, Dung Tien Nishiyama, Rie Watanabe, Yasuko Tanaka, Maho Seki, Motoaki Ham, Le Huy Yamaguchi-Shinozaki, Kazuko Shinozaki, Kazuo Tran, Lam-Son Phan PLoS One Research Article The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to drought stress from late vegetative V6 and from full bloom reproductive R2 stages. Our data analyses showed that out of 46093 soybean genes, which were predicted with high confidence among approximately 66000 putative genes, 41059 genes could be assigned with a known function. Using the criteria of a ratio change > = 2 and a q-value<0.05, we identified 1458 and 1818 upregulated and 1582 and 1688 downregulated genes in drought-stressed V6 and R2 leaves, respectively. These datasets were classified into 19 most abundant biological categories with similar proportions. There were only 612 and 463 genes that were overlapped among the upregulated and downregulated genes, respectively, in both stages, suggesting that both conserved and unconserved pathways might be involved in regulation of drought response in different stages of plant development. A comparative expression analysis using our datasets and that of drought stressed Arabidopsis leaves revealed the existence of both conserved and species-specific mechanisms that regulate drought responses. Many upregulated genes encode either regulatory proteins, such as transcription factors, including those with high homology to Arabidopsis DREB, NAC, AREB and ZAT/STZ transcription factors, kinases and two-component system members, or functional proteins, e.g. late embryogenesis-abundant proteins, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins. A detailed analysis of the GmNAC family and the hormone-related gene category showed that expression of many GmNAC and hormone-related genes was altered by drought in V6 and/or R2 leaves. Additionally, the downregulation of many photosynthesis-related genes, which contribute to growth retardation under drought stress, may serve as an adaptive mechanism for plant survival. This study has identified excellent drought-responsive candidate genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans. Public Library of Science 2012-11-19 /pmc/articles/PMC3505142/ /pubmed/23189148 http://dx.doi.org/10.1371/journal.pone.0049522 Text en © 2012 Le et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Le, Dung Tien Nishiyama, Rie Watanabe, Yasuko Tanaka, Maho Seki, Motoaki Ham, Le Huy Yamaguchi-Shinozaki, Kazuko Shinozaki, Kazuo Tran, Lam-Son Phan Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis |
title | Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis |
title_full | Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis |
title_fullStr | Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis |
title_full_unstemmed | Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis |
title_short | Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis |
title_sort | differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505142/ https://www.ncbi.nlm.nih.gov/pubmed/23189148 http://dx.doi.org/10.1371/journal.pone.0049522 |
work_keys_str_mv | AT ledungtien differentialgeneexpressioninsoybeanleaftissuesatlatedevelopmentalstagesunderdroughtstressrevealedbygenomewidetranscriptomeanalysis AT nishiyamarie differentialgeneexpressioninsoybeanleaftissuesatlatedevelopmentalstagesunderdroughtstressrevealedbygenomewidetranscriptomeanalysis AT watanabeyasuko differentialgeneexpressioninsoybeanleaftissuesatlatedevelopmentalstagesunderdroughtstressrevealedbygenomewidetranscriptomeanalysis AT tanakamaho differentialgeneexpressioninsoybeanleaftissuesatlatedevelopmentalstagesunderdroughtstressrevealedbygenomewidetranscriptomeanalysis AT sekimotoaki differentialgeneexpressioninsoybeanleaftissuesatlatedevelopmentalstagesunderdroughtstressrevealedbygenomewidetranscriptomeanalysis AT hamlehuy differentialgeneexpressioninsoybeanleaftissuesatlatedevelopmentalstagesunderdroughtstressrevealedbygenomewidetranscriptomeanalysis AT yamaguchishinozakikazuko differentialgeneexpressioninsoybeanleaftissuesatlatedevelopmentalstagesunderdroughtstressrevealedbygenomewidetranscriptomeanalysis AT shinozakikazuo differentialgeneexpressioninsoybeanleaftissuesatlatedevelopmentalstagesunderdroughtstressrevealedbygenomewidetranscriptomeanalysis AT tranlamsonphan differentialgeneexpressioninsoybeanleaftissuesatlatedevelopmentalstagesunderdroughtstressrevealedbygenomewidetranscriptomeanalysis |