Unraveling the drought-responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixation
Common bean (Phaseolus vulgaris) can efficiently fix atmospheric nitrogen when associated with Rhizobia. However, drought stress impairs plant metabolic processes, especially the biological nitrogen fixation (BNF). Here, we assessed transcriptional responses in nodules of two common bean genotypes t...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2024-01-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1345379/full |
| _version_ | 1797346170127777792 |
|---|---|
| author | Helder Anderson Pinto da Silva Vanessa Santana Caetano Daniella Duarte Villarinho Pessôa Rafael Sanches Pacheco Carlos Henrique S. G. Meneses Jean Luiz Simões-Araújo Jean Luiz Simões-Araújo Jean Luiz Simões-Araújo |
| author_facet | Helder Anderson Pinto da Silva Vanessa Santana Caetano Daniella Duarte Villarinho Pessôa Rafael Sanches Pacheco Carlos Henrique S. G. Meneses Jean Luiz Simões-Araújo Jean Luiz Simões-Araújo Jean Luiz Simões-Araújo |
| author_sort | Helder Anderson Pinto da Silva |
| collection | DOAJ |
| description | Common bean (Phaseolus vulgaris) can efficiently fix atmospheric nitrogen when associated with Rhizobia. However, drought stress impairs plant metabolic processes, especially the biological nitrogen fixation (BNF). Here, we assessed transcriptional responses in nodules of two common bean genotypes to drought stress under BNF reliance. The RNA-Seq analysis yielded a total of 81,489,262 and 72,497,478 high quality reads for Negro Argel and BAT 477 genotypes, respectively. The reads were mapped to the Phaseolus vulgaris reference genome and expression analysis identified 145 and 1451 differentially expressed genes (DEGs) for Negro Argel and BAT 477 genotypes, respectively. Although BAT 477 had more DEGs, both genotypes shared certain drought-responsive genes, including an up-regulated heat shock protein (HSP) and a down-regulated peroxidase, indicating shared pathways activated during drought in nodule tissue. Functional analysis using MapMan software highlighted the up-regulation of genes involved in abiotic stress responses, such as HSPs and specific transcription factors (TFs), in both genotypes. There was a significant down-regulation in metabolic pathways related to antioxidant protection, hormone signaling, metabolism, and transcriptional regulation. To validate these findings, we conducted RT-qPCR experiments for ten DEGs in nodules from both genotypes, for which the expression profile was confirmed, thus reinforcing their functional relevance in the nodule responses to drought stress during BNF. BAT 477 genotype exhibited more pronounced response to drought, characterized by a high number of DEGs. The strong down-regulation of DEGs leads to transcriptional disturbances in several pathways related to stress acclimation such as hormone and antioxidant metabolism. Additionally, we identified several genes that are known to play key roles in enhancing drought tolerance, such as HSPs and crucial TFs. Our results provide new insights into the transcriptional responses in root-nodules, an underexplored tissue of plants mainly under drought conditions. This research paves the way for potential improvements in plant-bacteria interactions, contributing to common bean adaptations in the face of challenging environmental conditions. |
| first_indexed | 2024-03-08T11:27:56Z |
| format | Article |
| id | doaj.art-7dbdc44e057e41d1bdc4f46072737793 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-08T11:27:56Z |
| publishDate | 2024-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-7dbdc44e057e41d1bdc4f460727377932024-01-26T04:44:57ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-01-011510.3389/fpls.2024.13453791345379Unraveling the drought-responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixationHelder Anderson Pinto da Silva0Vanessa Santana Caetano1Daniella Duarte Villarinho Pessôa2Rafael Sanches Pacheco3Carlos Henrique S. G. Meneses4Jean Luiz Simões-Araújo5Jean Luiz Simões-Araújo6Jean Luiz Simões-Araújo7Programa de Pós-Graduação em Biotecnologia Vegetal, Centro de Ciências da Saúde (CCS), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, BrazilPrograma de Pós-Graduação em Biotecnologia Vegetal, Centro de Ciências da Saúde (CCS), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, BrazilPrograma de Pós-Graduação em Biotecnologia Vegetal, Centro de Ciências da Saúde (CCS), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, BrazilPrograma de Pós-graduação em Fitossanidade e Biotecnologia Aplicada, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, RJ, BrazilDepartamento de Biologia, Centro de Ciências Biológicas e da Saúde, Universidade Estadual da Paraíba, Campina Grande, BrazilPrograma de Pós-Graduação em Biotecnologia Vegetal, Centro de Ciências da Saúde (CCS), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, BrazilPrograma de Pós-graduação em Fitossanidade e Biotecnologia Aplicada, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, RJ, BrazilCentro Nacional de Pesquisa de Agrobiologia, CNPAB – Embrapa, Laboratório de Genética e Bioquímica, Seropédica, RJ, BrazilCommon bean (Phaseolus vulgaris) can efficiently fix atmospheric nitrogen when associated with Rhizobia. However, drought stress impairs plant metabolic processes, especially the biological nitrogen fixation (BNF). Here, we assessed transcriptional responses in nodules of two common bean genotypes to drought stress under BNF reliance. The RNA-Seq analysis yielded a total of 81,489,262 and 72,497,478 high quality reads for Negro Argel and BAT 477 genotypes, respectively. The reads were mapped to the Phaseolus vulgaris reference genome and expression analysis identified 145 and 1451 differentially expressed genes (DEGs) for Negro Argel and BAT 477 genotypes, respectively. Although BAT 477 had more DEGs, both genotypes shared certain drought-responsive genes, including an up-regulated heat shock protein (HSP) and a down-regulated peroxidase, indicating shared pathways activated during drought in nodule tissue. Functional analysis using MapMan software highlighted the up-regulation of genes involved in abiotic stress responses, such as HSPs and specific transcription factors (TFs), in both genotypes. There was a significant down-regulation in metabolic pathways related to antioxidant protection, hormone signaling, metabolism, and transcriptional regulation. To validate these findings, we conducted RT-qPCR experiments for ten DEGs in nodules from both genotypes, for which the expression profile was confirmed, thus reinforcing their functional relevance in the nodule responses to drought stress during BNF. BAT 477 genotype exhibited more pronounced response to drought, characterized by a high number of DEGs. The strong down-regulation of DEGs leads to transcriptional disturbances in several pathways related to stress acclimation such as hormone and antioxidant metabolism. Additionally, we identified several genes that are known to play key roles in enhancing drought tolerance, such as HSPs and crucial TFs. Our results provide new insights into the transcriptional responses in root-nodules, an underexplored tissue of plants mainly under drought conditions. This research paves the way for potential improvements in plant-bacteria interactions, contributing to common bean adaptations in the face of challenging environmental conditions.https://www.frontiersin.org/articles/10.3389/fpls.2024.1345379/fullsymbiotic nitrogen assimilationwater deficitgenetic transcript profileRT-qPCRcandidate genes |
| spellingShingle | Helder Anderson Pinto da Silva Vanessa Santana Caetano Daniella Duarte Villarinho Pessôa Rafael Sanches Pacheco Carlos Henrique S. G. Meneses Jean Luiz Simões-Araújo Jean Luiz Simões-Araújo Jean Luiz Simões-Araújo Unraveling the drought-responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixation Frontiers in Plant Science symbiotic nitrogen assimilation water deficit genetic transcript profile RT-qPCR candidate genes |
| title | Unraveling the drought-responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixation |
| title_full | Unraveling the drought-responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixation |
| title_fullStr | Unraveling the drought-responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixation |
| title_full_unstemmed | Unraveling the drought-responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixation |
| title_short | Unraveling the drought-responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixation |
| title_sort | unraveling the drought responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixation |
| topic | symbiotic nitrogen assimilation water deficit genetic transcript profile RT-qPCR candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1345379/full |
| work_keys_str_mv | AT helderandersonpintodasilva unravelingthedroughtresponsivetranscriptomesinnodulesoftwocommonbeangenotypesduringbiologicalnitrogenfixation AT vanessasantanacaetano unravelingthedroughtresponsivetranscriptomesinnodulesoftwocommonbeangenotypesduringbiologicalnitrogenfixation AT danielladuartevillarinhopessoa unravelingthedroughtresponsivetranscriptomesinnodulesoftwocommonbeangenotypesduringbiologicalnitrogenfixation AT rafaelsanchespacheco unravelingthedroughtresponsivetranscriptomesinnodulesoftwocommonbeangenotypesduringbiologicalnitrogenfixation AT carloshenriquesgmeneses unravelingthedroughtresponsivetranscriptomesinnodulesoftwocommonbeangenotypesduringbiologicalnitrogenfixation AT jeanluizsimoesaraujo unravelingthedroughtresponsivetranscriptomesinnodulesoftwocommonbeangenotypesduringbiologicalnitrogenfixation AT jeanluizsimoesaraujo unravelingthedroughtresponsivetranscriptomesinnodulesoftwocommonbeangenotypesduringbiologicalnitrogenfixation AT jeanluizsimoesaraujo unravelingthedroughtresponsivetranscriptomesinnodulesoftwocommonbeangenotypesduringbiologicalnitrogenfixation |