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2021
Santos, Ariana Silva; Andrade, Edson Mário; Sousa, Andressa Rodrigues Oliveira; Costa, Marcos Mota Carmo; Togawa, Roberto; Grynberg, Priscila; Pirovani, Carlos Priminho; Oliveira, Saulo Alves Silva; Filho, Walter Santos Soares; Filho, Mauricio Antônio Coelho; Gesteira, Abelmon Silva; Ferreira, Claudia Fortes
Transcriptome profile of drought responsive candidate genes in varieties of citrus rootstocks with different tolerance strategies Journal Article
In: Scientia Horticulturae, vol. 277, pp. 109838, 2021, ISSN: 0304-4238.
Abstract | Links | BibTeX | Tags: Citrus, drought, RNA-Seq, root, Sunki, Transcriptome
@article{nokey,
title = {Transcriptome profile of drought responsive candidate genes in varieties of citrus rootstocks with different tolerance strategies},
author = {Ariana Silva Santos and Edson Mário Andrade and Andressa Rodrigues Oliveira Sousa and Marcos Mota Carmo Costa and Roberto Togawa and Priscila Grynberg and Carlos Priminho Pirovani and Saulo Alves Silva Oliveira and Walter Santos Soares Filho and Mauricio Antônio Coelho Filho and Abelmon Silva Gesteira and Claudia Fortes Ferreira},
doi = {10.1016/J.SCIENTA.2020.109838},
issn = {0304-4238},
year = {2021},
date = {2021-01-01},
journal = {Scientia Horticulturae},
volume = {277},
pages = {109838},
publisher = {Elsevier},
abstract = {Sunki Maravilha' and 'Sunki Tropical' are citrus plants with different drought tolerance strategies. `Sunki Tropical' is considered as another rootstock alternative for use in drought prone areas, however, its genetic expression profiles regarding response to water deficit, are still unknown. In this study, the transcriptome of the ‘Sunki Maravilha’ and ‘Sunki Tropical’ rootstocks under control were analyzed by RNA-seq technique using the Illumina HiSeq-2500. A total of 109,114.164 reads were produced and mapped against the Citrus sinensis reference genome (version 1.1). 3.607 transcripts showed significant variation in expression between the water deficit and control treatments with 739 genes up-regulated and 2868 down-regulated during water deficit imposition. The differentially expressed genes (DEGs) identified are involved in more than 100 biological processes and molecular functions whereas most enriched for the function of oxidoreductase, protein phosporilation, transcriptional regulation, ligation processes and response to oxidative stress. DEGs related to the biosynthesis of ABA (Abscisic Acid), redox system, cell wall mechanism, root development, transcription factors (TFs) and kinase proteins (KPs), were also identified. This work lays the basic foundation for further investigation of the specific functions of genes in citrus rootstocks, Sunki Maravilha’ and Sunki Tropical’, with different strategies of survival under water deficit and also provides candidate genes for engineering or breeding of citrus plants aiming drought tolerance.},
keywords = {Citrus, drought, RNA-Seq, root, Sunki, Transcriptome},
pubstate = {published},
tppubtype = {article}
}
Sunki Maravilha' and 'Sunki Tropical' are citrus plants with different drought tolerance strategies. `Sunki Tropical' is considered as another rootstock alternative for use in drought prone areas, however, its genetic expression profiles regarding response to water deficit, are still unknown. In this study, the transcriptome of the ‘Sunki Maravilha’ and ‘Sunki Tropical’ rootstocks under control were analyzed by RNA-seq technique using the Illumina HiSeq-2500. A total of 109,114.164 reads were produced and mapped against the Citrus sinensis reference genome (version 1.1). 3.607 transcripts showed significant variation in expression between the water deficit and control treatments with 739 genes up-regulated and 2868 down-regulated during water deficit imposition. The differentially expressed genes (DEGs) identified are involved in more than 100 biological processes and molecular functions whereas most enriched for the function of oxidoreductase, protein phosporilation, transcriptional regulation, ligation processes and response to oxidative stress. DEGs related to the biosynthesis of ABA (Abscisic Acid), redox system, cell wall mechanism, root development, transcription factors (TFs) and kinase proteins (KPs), were also identified. This work lays the basic foundation for further investigation of the specific functions of genes in citrus rootstocks, Sunki Maravilha’ and Sunki Tropical’, with different strategies of survival under water deficit and also provides candidate genes for engineering or breeding of citrus plants aiming drought tolerance.
Santos, Ariana Silva; Andrade, Edson Mário; Sousa, Andressa Rodrigues Oliveira; Costa, Marcos Mota Carmo; Togawa, Roberto; Grynberg, Priscila; Pirovani, Carlos Priminho; Oliveira, Saulo Alves Silva; Filho, Walter Santos Soares; Filho, Mauricio Antônio Coelho; Gesteira, Abelmon Silva; Ferreira, Claudia Fortes
Transcriptome profile of drought responsive candidate genes in varieties of citrus rootstocks with different tolerance strategies Journal Article
In: Scientia Horticulturae, vol. 277, pp. 109838, 2021, ISSN: 0304-4238.
Abstract | Links | BibTeX | Tags: Citrus, drought, RNA-Seq, root, Sunki, Transcriptome
@article{nokey,
title = {Transcriptome profile of drought responsive candidate genes in varieties of citrus rootstocks with different tolerance strategies},
author = {Ariana Silva Santos and Edson Mário Andrade and Andressa Rodrigues Oliveira Sousa and Marcos Mota Carmo Costa and Roberto Togawa and Priscila Grynberg and Carlos Priminho Pirovani and Saulo Alves Silva Oliveira and Walter Santos Soares Filho and Mauricio Antônio Coelho Filho and Abelmon Silva Gesteira and Claudia Fortes Ferreira},
doi = {10.1016/J.SCIENTA.2020.109838},
issn = {0304-4238},
year = {2021},
date = {2021-01-01},
journal = {Scientia Horticulturae},
volume = {277},
pages = {109838},
publisher = {Elsevier},
abstract = {Sunki Maravilha' and 'Sunki Tropical' are citrus plants with different drought tolerance strategies. `Sunki Tropical' is considered as another rootstock alternative for use in drought prone areas, however, its genetic expression profiles regarding response to water deficit, are still unknown. In this study, the transcriptome of the ‘Sunki Maravilha’ and ‘Sunki Tropical’ rootstocks under control were analyzed by RNA-seq technique using the Illumina HiSeq-2500. A total of 109,114.164 reads were produced and mapped against the Citrus sinensis reference genome (version 1.1). 3.607 transcripts showed significant variation in expression between the water deficit and control treatments with 739 genes up-regulated and 2868 down-regulated during water deficit imposition. The differentially expressed genes (DEGs) identified are involved in more than 100 biological processes and molecular functions whereas most enriched for the function of oxidoreductase, protein phosporilation, transcriptional regulation, ligation processes and response to oxidative stress. DEGs related to the biosynthesis of ABA (Abscisic Acid), redox system, cell wall mechanism, root development, transcription factors (TFs) and kinase proteins (KPs), were also identified. This work lays the basic foundation for further investigation of the specific functions of genes in citrus rootstocks, Sunki Maravilha’ and Sunki Tropical’, with different strategies of survival under water deficit and also provides candidate genes for engineering or breeding of citrus plants aiming drought tolerance.},
keywords = {Citrus, drought, RNA-Seq, root, Sunki, Transcriptome},
pubstate = {published},
tppubtype = {article}
}
Sunki Maravilha' and 'Sunki Tropical' are citrus plants with different drought tolerance strategies. `Sunki Tropical' is considered as another rootstock alternative for use in drought prone areas, however, its genetic expression profiles regarding response to water deficit, are still unknown. In this study, the transcriptome of the ‘Sunki Maravilha’ and ‘Sunki Tropical’ rootstocks under control were analyzed by RNA-seq technique using the Illumina HiSeq-2500. A total of 109,114.164 reads were produced and mapped against the Citrus sinensis reference genome (version 1.1). 3.607 transcripts showed significant variation in expression between the water deficit and control treatments with 739 genes up-regulated and 2868 down-regulated during water deficit imposition. The differentially expressed genes (DEGs) identified are involved in more than 100 biological processes and molecular functions whereas most enriched for the function of oxidoreductase, protein phosporilation, transcriptional regulation, ligation processes and response to oxidative stress. DEGs related to the biosynthesis of ABA (Abscisic Acid), redox system, cell wall mechanism, root development, transcription factors (TFs) and kinase proteins (KPs), were also identified. This work lays the basic foundation for further investigation of the specific functions of genes in citrus rootstocks, Sunki Maravilha’ and Sunki Tropical’, with different strategies of survival under water deficit and also provides candidate genes for engineering or breeding of citrus plants aiming drought tolerance.
2019
Gonçalves, Luana P.; Camargo, Raquel L. Boscariol; Takita, Marco Aurélio; Machado, Marcos A.; Filho, Walter S. Dos Soares; Costa, Marcio G. C.
Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq Journal Article
In: BMC Genomics, vol. 20, iss. 1, pp. 1-14, 2019, ISSN: 14712164.
Abstract | Links | BibTeX | Tags: Abiotic stress, Citrus, Transcriptome, water deficit
@article{nokey,
title = {Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq},
author = {Luana P. Gonçalves and Raquel L. Boscariol Camargo and Marco Aurélio Takita and Marcos A. Machado and Walter S. Dos Soares Filho and Marcio G. C. Costa},
url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5481-z},
doi = {10.1186/S12864-019-5481-Z/FIGURES/3},
issn = {14712164},
year = {2019},
date = {2019-01-01},
journal = {BMC Genomics},
volume = {20},
issue = {1},
pages = {1-14},
publisher = {BioMed Central Ltd.},
abstract = {Background: Citrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available for citrus propagation, 'Rangpur' lime is known to confer enhanced tolerance to drought as compared to other citrus rootstocks. The objective of this study was to investigate the poorly understood molecular responses underlying the rootstock-induced drought tolerance in sweet orange. Results: RNA-Seq transcriptome analysis was carried out in leaves of sweet orange grafted on 'Rangpur' lime subjected to control and drought-stress treatments, under greenhouse conditions, using the Illumina HiSeq platform. A total of 41,827 unique transcripts were identified, among which 1764 transcripts showed significant variation (P ≤ 0.001) between the treatments, with 1081 genes induced and 683 repressed by drought-stress treatment. The transcripts were distributed in 44 different categories of cellular component, molecular function and biological process. Several genes related to cell metabolism, including those involved in the metabolisms of cell wall, carbohydrates and antioxidants, light reactions, biotic and abiotic stress responses, as well as genes coding for transcription factors (TFs), protein kinases (PKs) and proteins involved in the abscisic acid (ABA) and ethylene signaling pathways, were differentially regulated by drought stress. RNA-Seq data were validated by quantitative real-time PCR (qPCR) analysis and comparative analysis of expression of the selected genes between sweet orange grafted on drought-tolerant and -sensitive rootstocks revealed new candidate genes for drought tolerance in citrus. Conclusions: In conclusion, our results showed that only a relatively small but functionally diverse fraction of the sweet orange transcriptome, with functions in metabolism, cellular responses and regulation, was differentially regulated by drought stress. The data suggest that the rootstock-induced drought tolerance in sweet orange includes the transcriptional activation of genes related to the cell wall, soluble carbohydrate and antioxidant metabolisms, biotic and abiotic stress responses, TFs, PKs and ABA signaling pathway, and the downregulation of genes involved in the starch metabolism, light reactions and ethylene signaling. Future efforts to elucidate their functional roles and explore their potential in the citrus genetic improvement should benefit from this data.},
keywords = {Abiotic stress, Citrus, Transcriptome, water deficit},
pubstate = {published},
tppubtype = {article}
}
Background: Citrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available for citrus propagation, 'Rangpur' lime is known to confer enhanced tolerance to drought as compared to other citrus rootstocks. The objective of this study was to investigate the poorly understood molecular responses underlying the rootstock-induced drought tolerance in sweet orange. Results: RNA-Seq transcriptome analysis was carried out in leaves of sweet orange grafted on 'Rangpur' lime subjected to control and drought-stress treatments, under greenhouse conditions, using the Illumina HiSeq platform. A total of 41,827 unique transcripts were identified, among which 1764 transcripts showed significant variation (P ≤ 0.001) between the treatments, with 1081 genes induced and 683 repressed by drought-stress treatment. The transcripts were distributed in 44 different categories of cellular component, molecular function and biological process. Several genes related to cell metabolism, including those involved in the metabolisms of cell wall, carbohydrates and antioxidants, light reactions, biotic and abiotic stress responses, as well as genes coding for transcription factors (TFs), protein kinases (PKs) and proteins involved in the abscisic acid (ABA) and ethylene signaling pathways, were differentially regulated by drought stress. RNA-Seq data were validated by quantitative real-time PCR (qPCR) analysis and comparative analysis of expression of the selected genes between sweet orange grafted on drought-tolerant and -sensitive rootstocks revealed new candidate genes for drought tolerance in citrus. Conclusions: In conclusion, our results showed that only a relatively small but functionally diverse fraction of the sweet orange transcriptome, with functions in metabolism, cellular responses and regulation, was differentially regulated by drought stress. The data suggest that the rootstock-induced drought tolerance in sweet orange includes the transcriptional activation of genes related to the cell wall, soluble carbohydrate and antioxidant metabolisms, biotic and abiotic stress responses, TFs, PKs and ABA signaling pathway, and the downregulation of genes involved in the starch metabolism, light reactions and ethylene signaling. Future efforts to elucidate their functional roles and explore their potential in the citrus genetic improvement should benefit from this data.
Gonçalves, Luana P.; Camargo, Raquel L. Boscariol; Takita, Marco Aurélio; Machado, Marcos A.; Filho, Walter S. Dos Soares; Costa, Marcio G. C.
Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq Journal Article
In: BMC Genomics, vol. 20, iss. 1, pp. 1-14, 2019, ISSN: 14712164.
Abstract | Links | BibTeX | Tags: Abiotic stress, Citrus, Transcriptome, water deficit
@article{nokey,
title = {Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq},
author = {Luana P. Gonçalves and Raquel L. Boscariol Camargo and Marco Aurélio Takita and Marcos A. Machado and Walter S. Dos Soares Filho and Marcio G. C. Costa},
url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5481-z},
doi = {10.1186/S12864-019-5481-Z/FIGURES/3},
issn = {14712164},
year = {2019},
date = {2019-01-01},
journal = {BMC Genomics},
volume = {20},
issue = {1},
pages = {1-14},
publisher = {BioMed Central Ltd.},
abstract = {Background: Citrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available for citrus propagation, 'Rangpur' lime is known to confer enhanced tolerance to drought as compared to other citrus rootstocks. The objective of this study was to investigate the poorly understood molecular responses underlying the rootstock-induced drought tolerance in sweet orange. Results: RNA-Seq transcriptome analysis was carried out in leaves of sweet orange grafted on 'Rangpur' lime subjected to control and drought-stress treatments, under greenhouse conditions, using the Illumina HiSeq platform. A total of 41,827 unique transcripts were identified, among which 1764 transcripts showed significant variation (P ≤ 0.001) between the treatments, with 1081 genes induced and 683 repressed by drought-stress treatment. The transcripts were distributed in 44 different categories of cellular component, molecular function and biological process. Several genes related to cell metabolism, including those involved in the metabolisms of cell wall, carbohydrates and antioxidants, light reactions, biotic and abiotic stress responses, as well as genes coding for transcription factors (TFs), protein kinases (PKs) and proteins involved in the abscisic acid (ABA) and ethylene signaling pathways, were differentially regulated by drought stress. RNA-Seq data were validated by quantitative real-time PCR (qPCR) analysis and comparative analysis of expression of the selected genes between sweet orange grafted on drought-tolerant and -sensitive rootstocks revealed new candidate genes for drought tolerance in citrus. Conclusions: In conclusion, our results showed that only a relatively small but functionally diverse fraction of the sweet orange transcriptome, with functions in metabolism, cellular responses and regulation, was differentially regulated by drought stress. The data suggest that the rootstock-induced drought tolerance in sweet orange includes the transcriptional activation of genes related to the cell wall, soluble carbohydrate and antioxidant metabolisms, biotic and abiotic stress responses, TFs, PKs and ABA signaling pathway, and the downregulation of genes involved in the starch metabolism, light reactions and ethylene signaling. Future efforts to elucidate their functional roles and explore their potential in the citrus genetic improvement should benefit from this data.},
keywords = {Abiotic stress, Citrus, Transcriptome, water deficit},
pubstate = {published},
tppubtype = {article}
}
Background: Citrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available for citrus propagation, 'Rangpur' lime is known to confer enhanced tolerance to drought as compared to other citrus rootstocks. The objective of this study was to investigate the poorly understood molecular responses underlying the rootstock-induced drought tolerance in sweet orange. Results: RNA-Seq transcriptome analysis was carried out in leaves of sweet orange grafted on 'Rangpur' lime subjected to control and drought-stress treatments, under greenhouse conditions, using the Illumina HiSeq platform. A total of 41,827 unique transcripts were identified, among which 1764 transcripts showed significant variation (P ≤ 0.001) between the treatments, with 1081 genes induced and 683 repressed by drought-stress treatment. The transcripts were distributed in 44 different categories of cellular component, molecular function and biological process. Several genes related to cell metabolism, including those involved in the metabolisms of cell wall, carbohydrates and antioxidants, light reactions, biotic and abiotic stress responses, as well as genes coding for transcription factors (TFs), protein kinases (PKs) and proteins involved in the abscisic acid (ABA) and ethylene signaling pathways, were differentially regulated by drought stress. RNA-Seq data were validated by quantitative real-time PCR (qPCR) analysis and comparative analysis of expression of the selected genes between sweet orange grafted on drought-tolerant and -sensitive rootstocks revealed new candidate genes for drought tolerance in citrus. Conclusions: In conclusion, our results showed that only a relatively small but functionally diverse fraction of the sweet orange transcriptome, with functions in metabolism, cellular responses and regulation, was differentially regulated by drought stress. The data suggest that the rootstock-induced drought tolerance in sweet orange includes the transcriptional activation of genes related to the cell wall, soluble carbohydrate and antioxidant metabolisms, biotic and abiotic stress responses, TFs, PKs and ABA signaling pathway, and the downregulation of genes involved in the starch metabolism, light reactions and ethylene signaling. Future efforts to elucidate their functional roles and explore their potential in the citrus genetic improvement should benefit from this data.