Unravelling rubber tree growth by integrating GWAS and biological network-based approaches
Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs.
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Language: | eng |
Subjects: | Hevea brasiliensis, locus des caractères quantitatifs, Transcription génique, génome, phytogénétique, expression des gènes, marqueur génétique, génotype, phénotype, caoutchouc, croissance, http://aims.fao.org/aos/agrovoc/c_3589, http://aims.fao.org/aos/agrovoc/c_37974, http://aims.fao.org/aos/agrovoc/c_35128, http://aims.fao.org/aos/agrovoc/c_3224, http://aims.fao.org/aos/agrovoc/c_49985, http://aims.fao.org/aos/agrovoc/c_27527, http://aims.fao.org/aos/agrovoc/c_24030, http://aims.fao.org/aos/agrovoc/c_3225, http://aims.fao.org/aos/agrovoc/c_5776, http://aims.fao.org/aos/agrovoc/c_6678, http://aims.fao.org/aos/agrovoc/c_3394, |
Online Access: | http://agritrop.cirad.fr/599926/ http://agritrop.cirad.fr/599926/1/EN2660.pdf |
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Hevea brasiliensis locus des caractères quantitatifs Transcription génique génome phytogénétique expression des gènes marqueur génétique génotype phénotype caoutchouc croissance http://aims.fao.org/aos/agrovoc/c_3589 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_6678 http://aims.fao.org/aos/agrovoc/c_3394 Hevea brasiliensis locus des caractères quantitatifs Transcription génique génome phytogénétique expression des gènes marqueur génétique génotype phénotype caoutchouc croissance http://aims.fao.org/aos/agrovoc/c_3589 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_6678 http://aims.fao.org/aos/agrovoc/c_3394 |
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Hevea brasiliensis locus des caractères quantitatifs Transcription génique génome phytogénétique expression des gènes marqueur génétique génotype phénotype caoutchouc croissance http://aims.fao.org/aos/agrovoc/c_3589 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_6678 http://aims.fao.org/aos/agrovoc/c_3394 Hevea brasiliensis locus des caractères quantitatifs Transcription génique génome phytogénétique expression des gènes marqueur génétique génotype phénotype caoutchouc croissance http://aims.fao.org/aos/agrovoc/c_3589 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_6678 http://aims.fao.org/aos/agrovoc/c_3394 Francisco, Felipe Roberto Hild Aono, Alexandre Da Silva, Carla Cristina Gonçalves, Paulo S. Scaloppi Junior, Erivaldo José Le Guen, Vincent Fritsche-Neto, Roberto Moura Souza, Livia Pereira de Souza, Anete Unravelling rubber tree growth by integrating GWAS and biological network-based approaches |
description |
Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs. |
format |
article |
topic_facet |
Hevea brasiliensis locus des caractères quantitatifs Transcription génique génome phytogénétique expression des gènes marqueur génétique génotype phénotype caoutchouc croissance http://aims.fao.org/aos/agrovoc/c_3589 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_6678 http://aims.fao.org/aos/agrovoc/c_3394 |
author |
Francisco, Felipe Roberto Hild Aono, Alexandre Da Silva, Carla Cristina Gonçalves, Paulo S. Scaloppi Junior, Erivaldo José Le Guen, Vincent Fritsche-Neto, Roberto Moura Souza, Livia Pereira de Souza, Anete |
author_facet |
Francisco, Felipe Roberto Hild Aono, Alexandre Da Silva, Carla Cristina Gonçalves, Paulo S. Scaloppi Junior, Erivaldo José Le Guen, Vincent Fritsche-Neto, Roberto Moura Souza, Livia Pereira de Souza, Anete |
author_sort |
Francisco, Felipe Roberto |
title |
Unravelling rubber tree growth by integrating GWAS and biological network-based approaches |
title_short |
Unravelling rubber tree growth by integrating GWAS and biological network-based approaches |
title_full |
Unravelling rubber tree growth by integrating GWAS and biological network-based approaches |
title_fullStr |
Unravelling rubber tree growth by integrating GWAS and biological network-based approaches |
title_full_unstemmed |
Unravelling rubber tree growth by integrating GWAS and biological network-based approaches |
title_sort |
unravelling rubber tree growth by integrating gwas and biological network-based approaches |
url |
http://agritrop.cirad.fr/599926/ http://agritrop.cirad.fr/599926/1/EN2660.pdf |
work_keys_str_mv |
AT franciscofeliperoberto unravellingrubbertreegrowthbyintegratinggwasandbiologicalnetworkbasedapproaches AT hildaonoalexandre unravellingrubbertreegrowthbyintegratinggwasandbiologicalnetworkbasedapproaches AT dasilvacarlacristina unravellingrubbertreegrowthbyintegratinggwasandbiologicalnetworkbasedapproaches AT goncalvespaulos unravellingrubbertreegrowthbyintegratinggwasandbiologicalnetworkbasedapproaches AT scaloppijuniorerivaldojose unravellingrubbertreegrowthbyintegratinggwasandbiologicalnetworkbasedapproaches AT leguenvincent unravellingrubbertreegrowthbyintegratinggwasandbiologicalnetworkbasedapproaches AT fritschenetoroberto unravellingrubbertreegrowthbyintegratinggwasandbiologicalnetworkbasedapproaches AT mourasouzalivia unravellingrubbertreegrowthbyintegratinggwasandbiologicalnetworkbasedapproaches AT pereiradesouzaanete unravellingrubbertreegrowthbyintegratinggwasandbiologicalnetworkbasedapproaches |
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1792500279301636096 |
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dig-cirad-fr-5999262024-01-29T05:44:29Z http://agritrop.cirad.fr/599926/ http://agritrop.cirad.fr/599926/ Unravelling rubber tree growth by integrating GWAS and biological network-based approaches. Francisco Felipe Roberto, Hild Aono Alexandre, Da Silva Carla Cristina, Gonçalves Paulo S., Scaloppi Junior Erivaldo José, Le Guen Vincent, Fritsche-Neto Roberto, Moura Souza Livia, Pereira de Souza Anete. 2021. Frontiers in Plant Science, 12:768589, 20 p.https://doi.org/10.3389/fpls.2021.768589 <https://doi.org/10.3389/fpls.2021.768589> Unravelling rubber tree growth by integrating GWAS and biological network-based approaches Francisco, Felipe Roberto Hild Aono, Alexandre Da Silva, Carla Cristina Gonçalves, Paulo S. Scaloppi Junior, Erivaldo José Le Guen, Vincent Fritsche-Neto, Roberto Moura Souza, Livia Pereira de Souza, Anete eng 2021 Frontiers in Plant Science Hevea brasiliensis locus des caractères quantitatifs Transcription génique génome phytogénétique expression des gènes marqueur génétique génotype phénotype caoutchouc croissance http://aims.fao.org/aos/agrovoc/c_3589 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_6678 http://aims.fao.org/aos/agrovoc/c_3394 Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/599926/1/EN2660.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.3389/fpls.2021.768589 10.3389/fpls.2021.768589 info:eu-repo/semantics/altIdentifier/doi/10.3389/fpls.2021.768589 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.3389/fpls.2021.768589 info:eu-repo/semantics/reference/purl/https://CRAN.R-project.org/package=snpReady |