Differential gene expression in roots of sugarcane hybrids provides insights into drought stress tolerance
Autor(a) principal: | |
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Data de Publicação: | 2024 |
Tipo de documento: | Tese |
Idioma: | eng |
Título da fonte: | Biblioteca Digital de Teses e Dissertações da USP |
Texto Completo: | https://www.teses.usp.br/teses/disponiveis/11/11137/tde-04042024-155905/ |
Resumo: | Sugarcane is one of the main crops that contributes to the Brazilian economy. A major challenge for sugarcane breeding programs has been developing cultivars that are more productive and tolerant to adverse environmental conditions, such as drought stresses. Gene expression analysis is an effective way to identify genes involved in drought response and understand how these genes regulate plant physiology under stress. The aim of this study was to identify genes in sugarcane roots that regulate the response to soil water deficit stress and to identify gene expression patterns associated with tolerance to drought. For this, we evaluated gene expression in six commercial sugarcane hybrids (RB867515, RB855113, RB855536, RB92579, SP79-1011, and SP80-3280). Roots were collected from a 2 x 2 factorial experiment in a greenhouse. One of the main factors tested was the effect of water availability in the soil (control treatment and treatment with water deprivation for five days) and the other factor was the effect of genotypes, grouped as susceptible or tolerant to drought. We performed RNA-seq for three biological replicates of roots of each treatment. These sequences were used to assemble a de novo transcriptome, which was functionally annotated and used as a reference to estimate gene expression levels in each sample from a quasi-mapping strategy. We then performed a differential gene expression analysis to identify genes responsive to the main effects of drought stress and cultivar group. Finally, we explored the interaction between these two main effects. We found 1,913 upregulated genes and 1,550 downregulated genes for the main effect of drought stress, showing common responses to stress between the two groups of cultivars. The majority of these genes were related to abiotic stress responses and include kinase precursors, transcription factors, and proteins that confer cellular homeostasis. In addition, we identified 12,939 differentially expressed genes (DEGs) for the main effect of cultivars, suggesting a significant divergence in gene expression between tolerant and susceptible cultivars. These genes are mostly related to biotic stress and the general response to stress. Finally, we identified 412 DEGs that have an interaction between the effects of the treatment and cultivar group, in which more than 86% were induced in tolerant genotypes under drought stress. Many of these genes enriched gene ontologies related to defined biological processes such as: ethylene-activated signaling pathway, negative cytokinin regulation, and cell signaling. Therefore, we conclude that drought tolerance is possibly associated with innate gene characteristics present in tolerant genotypes. Some of these genes are involved in hormonal signaling pathways and are induced in the roots of tolerant cultivars under drought stress. Thus, we suggest an in-depth investigation of the drought tolerance genes that we identified in this work, to better understand the role of each of these genes in regulating drought stress tolerance. These results are valuable in understanding the genetic mechanisms of drought tolerance, which will contribute to better efficiency in the development of new drought-tolerant sugarcane cultivars. |
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Differential gene expression in roots of sugarcane hybrids provides insights into drought stress toleranceExpressão gênica diferencial em raízes de híbridos de cana-de-açúcar fornece informações sobre a tolerância ao estresse por déficit hídricoSaccharumSaccharumAbiotic stressEstresse abióticoExpression profilePerfil de expressão gênicaRNA-SeqRNA-SeqSugarcane is one of the main crops that contributes to the Brazilian economy. A major challenge for sugarcane breeding programs has been developing cultivars that are more productive and tolerant to adverse environmental conditions, such as drought stresses. Gene expression analysis is an effective way to identify genes involved in drought response and understand how these genes regulate plant physiology under stress. The aim of this study was to identify genes in sugarcane roots that regulate the response to soil water deficit stress and to identify gene expression patterns associated with tolerance to drought. For this, we evaluated gene expression in six commercial sugarcane hybrids (RB867515, RB855113, RB855536, RB92579, SP79-1011, and SP80-3280). Roots were collected from a 2 x 2 factorial experiment in a greenhouse. One of the main factors tested was the effect of water availability in the soil (control treatment and treatment with water deprivation for five days) and the other factor was the effect of genotypes, grouped as susceptible or tolerant to drought. We performed RNA-seq for three biological replicates of roots of each treatment. These sequences were used to assemble a de novo transcriptome, which was functionally annotated and used as a reference to estimate gene expression levels in each sample from a quasi-mapping strategy. We then performed a differential gene expression analysis to identify genes responsive to the main effects of drought stress and cultivar group. Finally, we explored the interaction between these two main effects. We found 1,913 upregulated genes and 1,550 downregulated genes for the main effect of drought stress, showing common responses to stress between the two groups of cultivars. The majority of these genes were related to abiotic stress responses and include kinase precursors, transcription factors, and proteins that confer cellular homeostasis. In addition, we identified 12,939 differentially expressed genes (DEGs) for the main effect of cultivars, suggesting a significant divergence in gene expression between tolerant and susceptible cultivars. These genes are mostly related to biotic stress and the general response to stress. Finally, we identified 412 DEGs that have an interaction between the effects of the treatment and cultivar group, in which more than 86% were induced in tolerant genotypes under drought stress. Many of these genes enriched gene ontologies related to defined biological processes such as: ethylene-activated signaling pathway, negative cytokinin regulation, and cell signaling. Therefore, we conclude that drought tolerance is possibly associated with innate gene characteristics present in tolerant genotypes. Some of these genes are involved in hormonal signaling pathways and are induced in the roots of tolerant cultivars under drought stress. Thus, we suggest an in-depth investigation of the drought tolerance genes that we identified in this work, to better understand the role of each of these genes in regulating drought stress tolerance. These results are valuable in understanding the genetic mechanisms of drought tolerance, which will contribute to better efficiency in the development of new drought-tolerant sugarcane cultivars.A cana-de-açúcar é uma das principais culturas que contribuem para a economia brasileira. Os programas de melhoramento genético de cana-de-açúcar têm sido desafiados a desenvolver cultivares cada vez mais produtivas e que possam tolerar condições ambientais adversas, como o estresse hídrico. A análise da expressão gênica é uma forma eficaz de identificar genes envolvidos na resposta à seca e entender como esses genes regulam as respostas fisiológicas da planta. O objetivo deste trabalho foi identificar genes em raízes de cana-de-açúcar que regulam a resposta ao estresse por déficit hídrico no solo e identificar padrões de expressão gênica associados à tolerância à seca. Para isso, avaliamos a expressão gênica em seis híbridos comerciais de cana-de-açúcar (RB867515, RB855113, RB855536, RB92579, SP79-1011 e SP80-3280). Foram coletadas raízes de um experimento em esquema fatorial 2 x 2 instalado em casa de vegetação, em que os fatores corresponderam aos efeitos de disponibilidade de água no solo (tratamento controle e tratamento com privação de água por cinco dias) e ao efeito de genótipos, agrupados em suscetíveis ou tolerantes à seca. Nós coletamos raízes e realizamos RNA-seq para três réplicas biológicas de cada tratamento. Essas sequências foram utilizadas para montar um transcriptoma de novo, que foi anotado funcionalmente e utilizado como referência para estimar os níveis de expressão gênica a partir de uma estratégia de quase-mapping. Em seguida, fizemos uma análise de expressão gênica diferencial para identificar os principais genes responsivos aos efeitos principais de estresse por seca e de grupo de cultivar. Foram encontrados 1.913 genes com expressão aumentada e 1.550 genes suprimidos para efeito principal de estresse por seca. A grande maioria desses genes são relacionados a respostas para estresses abióticos, e incluem precursores de quinases, fatores de transcrição e proteínas que conferem homeostase celular. Complementarmente, identificamos 12.939 genes diferencialmente expressos (DEGs) para o efeito principal de cultivares, sugerindo divergência significativa de expressão gênica entre cultivares tolerantes e suscetíveis. Esses genes estão, em sua maioria, relacionados ao estresse biótico e à resposta geral à estresses. Por fim, identificamos 412 DEGs que possuem interação entre os efeitos de tratamento e de grupo de cultivar, dos quais mais de 86% foram induzidos em genótipos tolerantes sob estresse por seca. Muitos desses genes enriqueceram ontologias gênicas relacionadas a processos biológicos definidos como: via de sinalização ativada por etileno, regulação negativa de citocinina e sinalização celular. Concluímos que a tolerância à seca está possivelmente associada a características gênicas inatas presentes nos genótipos tolerantes. Alguns desses genes estão envolvidos em vias de sinalização hormonal e são induzidos em raízes de cultivares tolerantes sob estresse por seca. Sugerimos, portanto, um estudo aprofundado para os genes de tolerância à seca que identificamos neste trabalho, para buscar compreender os mecanismos envolvidos na regulação desses genes. Esses resultados são valiosos na compreensão de mecanismos genéticos de tolerância a seca, que contribuirá com a melhor eficiência no desenvolvimento de novas cultivares cana-de-açúcar tolerantes ao estresse por seca.Biblioteca Digitais de Teses e Dissertações da USPMargarido, Gabriel Rodrigues AlvesGarcia, Ana Letycia Basso2024-01-24info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisapplication/pdfhttps://www.teses.usp.br/teses/disponiveis/11/11137/tde-04042024-155905/reponame:Biblioteca Digital de Teses e Dissertações da USPinstname:Universidade de São Paulo (USP)instacron:USPReter o conteúdo por motivos de patente, publicação e/ou direitos autoriais.info:eu-repo/semantics/openAccesseng2024-04-04T20:08:02Zoai:teses.usp.br:tde-04042024-155905Biblioteca Digital de Teses e Dissertaçõeshttp://www.teses.usp.br/PUBhttp://www.teses.usp.br/cgi-bin/mtd2br.plvirginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.bropendoar:27212024-04-04T20:08:02Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)false |
dc.title.none.fl_str_mv |
Differential gene expression in roots of sugarcane hybrids provides insights into drought stress tolerance Expressão gênica diferencial em raízes de híbridos de cana-de-açúcar fornece informações sobre a tolerância ao estresse por déficit hídrico |
title |
Differential gene expression in roots of sugarcane hybrids provides insights into drought stress tolerance |
spellingShingle |
Differential gene expression in roots of sugarcane hybrids provides insights into drought stress tolerance Garcia, Ana Letycia Basso Saccharum Saccharum Abiotic stress Estresse abiótico Expression profile Perfil de expressão gênica RNA-Seq RNA-Seq |
title_short |
Differential gene expression in roots of sugarcane hybrids provides insights into drought stress tolerance |
title_full |
Differential gene expression in roots of sugarcane hybrids provides insights into drought stress tolerance |
title_fullStr |
Differential gene expression in roots of sugarcane hybrids provides insights into drought stress tolerance |
title_full_unstemmed |
Differential gene expression in roots of sugarcane hybrids provides insights into drought stress tolerance |
title_sort |
Differential gene expression in roots of sugarcane hybrids provides insights into drought stress tolerance |
author |
Garcia, Ana Letycia Basso |
author_facet |
Garcia, Ana Letycia Basso |
author_role |
author |
dc.contributor.none.fl_str_mv |
Margarido, Gabriel Rodrigues Alves |
dc.contributor.author.fl_str_mv |
Garcia, Ana Letycia Basso |
dc.subject.por.fl_str_mv |
Saccharum Saccharum Abiotic stress Estresse abiótico Expression profile Perfil de expressão gênica RNA-Seq RNA-Seq |
topic |
Saccharum Saccharum Abiotic stress Estresse abiótico Expression profile Perfil de expressão gênica RNA-Seq RNA-Seq |
description |
Sugarcane is one of the main crops that contributes to the Brazilian economy. A major challenge for sugarcane breeding programs has been developing cultivars that are more productive and tolerant to adverse environmental conditions, such as drought stresses. Gene expression analysis is an effective way to identify genes involved in drought response and understand how these genes regulate plant physiology under stress. The aim of this study was to identify genes in sugarcane roots that regulate the response to soil water deficit stress and to identify gene expression patterns associated with tolerance to drought. For this, we evaluated gene expression in six commercial sugarcane hybrids (RB867515, RB855113, RB855536, RB92579, SP79-1011, and SP80-3280). Roots were collected from a 2 x 2 factorial experiment in a greenhouse. One of the main factors tested was the effect of water availability in the soil (control treatment and treatment with water deprivation for five days) and the other factor was the effect of genotypes, grouped as susceptible or tolerant to drought. We performed RNA-seq for three biological replicates of roots of each treatment. These sequences were used to assemble a de novo transcriptome, which was functionally annotated and used as a reference to estimate gene expression levels in each sample from a quasi-mapping strategy. We then performed a differential gene expression analysis to identify genes responsive to the main effects of drought stress and cultivar group. Finally, we explored the interaction between these two main effects. We found 1,913 upregulated genes and 1,550 downregulated genes for the main effect of drought stress, showing common responses to stress between the two groups of cultivars. The majority of these genes were related to abiotic stress responses and include kinase precursors, transcription factors, and proteins that confer cellular homeostasis. In addition, we identified 12,939 differentially expressed genes (DEGs) for the main effect of cultivars, suggesting a significant divergence in gene expression between tolerant and susceptible cultivars. These genes are mostly related to biotic stress and the general response to stress. Finally, we identified 412 DEGs that have an interaction between the effects of the treatment and cultivar group, in which more than 86% were induced in tolerant genotypes under drought stress. Many of these genes enriched gene ontologies related to defined biological processes such as: ethylene-activated signaling pathway, negative cytokinin regulation, and cell signaling. Therefore, we conclude that drought tolerance is possibly associated with innate gene characteristics present in tolerant genotypes. Some of these genes are involved in hormonal signaling pathways and are induced in the roots of tolerant cultivars under drought stress. Thus, we suggest an in-depth investigation of the drought tolerance genes that we identified in this work, to better understand the role of each of these genes in regulating drought stress tolerance. These results are valuable in understanding the genetic mechanisms of drought tolerance, which will contribute to better efficiency in the development of new drought-tolerant sugarcane cultivars. |
publishDate |
2024 |
dc.date.none.fl_str_mv |
2024-01-24 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/doctoralThesis |
format |
doctoralThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://www.teses.usp.br/teses/disponiveis/11/11137/tde-04042024-155905/ |
url |
https://www.teses.usp.br/teses/disponiveis/11/11137/tde-04042024-155905/ |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
|
dc.rights.driver.fl_str_mv |
Reter o conteúdo por motivos de patente, publicação e/ou direitos autoriais. info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Reter o conteúdo por motivos de patente, publicação e/ou direitos autoriais. |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.coverage.none.fl_str_mv |
|
dc.publisher.none.fl_str_mv |
Biblioteca Digitais de Teses e Dissertações da USP |
publisher.none.fl_str_mv |
Biblioteca Digitais de Teses e Dissertações da USP |
dc.source.none.fl_str_mv |
reponame:Biblioteca Digital de Teses e Dissertações da USP instname:Universidade de São Paulo (USP) instacron:USP |
instname_str |
Universidade de São Paulo (USP) |
instacron_str |
USP |
institution |
USP |
reponame_str |
Biblioteca Digital de Teses e Dissertações da USP |
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Biblioteca Digital de Teses e Dissertações da USP |
repository.name.fl_str_mv |
Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP) |
repository.mail.fl_str_mv |
virginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.br |
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1815256655330279424 |