Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance

Detalhes bibliográficos
Autor(a) principal: Pimenta, Ricardo José Gonzaga
Data de Publicação: 2021
Outros Autores: Aono, Alexandre Hild, Burbano, Roberto Carlos Villavicencio, Coutinho, Alisson Esdras [UNESP], da Silva, Carla Cristina, dos Anjos, Ivan Antônio, Perecin, Dilermando [UNESP], Landell, Marcos Guimarães de Andrade, Gonçalves, Marcos Cesar, Pinto, Luciana Rossini, de Souza, Anete Pereira
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1038/s41598-021-95116-1
http://hdl.handle.net/11449/233361
Resumo: Sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.
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spelling Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistanceSugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Secretaría Nacional de Ciencia, Tecnología e InnovaciónFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Centre of Molecular Biology and Genetic Engineering (CBMEG) University of Campinas (UNICAMP)Gustavo Galindo Velasco Campus Littoral Polytechnic Superior School (ESPOL)São Paulo State University (UNESP)Advanced Centre for Technological Research in Sugarcane Agribusiness Agronomic Institute of Campinas (IAC/APTA)Plant Protection Research Centre Biological Institute (IB/APTA)Department of Plant Biology Institute of Biology University of Campinas (UNICAMP)São Paulo State University (UNESP)FAPESP: 2015/24346-9FAPESP: 2018/18588-8FAPESP: 2019/03232-6FAPESP: 2019/21682-9CNPq: 424050/2016-1Universidade Estadual de Campinas (UNICAMP)Littoral Polytechnic Superior School (ESPOL)Universidade Estadual Paulista (UNESP)Agronomic Institute of Campinas (IAC/APTA)Biological Institute (IB/APTA)Pimenta, Ricardo José GonzagaAono, Alexandre HildBurbano, Roberto Carlos VillavicencioCoutinho, Alisson Esdras [UNESP]da Silva, Carla Cristinados Anjos, Ivan AntônioPerecin, Dilermando [UNESP]Landell, Marcos Guimarães de AndradeGonçalves, Marcos CesarPinto, Luciana Rossinide Souza, Anete Pereira2022-05-01T07:58:54Z2022-05-01T07:58:54Z2021-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1038/s41598-021-95116-1Scientific Reports, v. 11, n. 1, 2021.2045-2322http://hdl.handle.net/11449/23336110.1038/s41598-021-95116-12-s2.0-85112014467Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengScientific Reportsinfo:eu-repo/semantics/openAccess2024-06-06T13:43:18Zoai:repositorio.unesp.br:11449/233361Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:50:52.961116Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
title Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
spellingShingle Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
Pimenta, Ricardo José Gonzaga
title_short Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
title_full Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
title_fullStr Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
title_full_unstemmed Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
title_sort Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
author Pimenta, Ricardo José Gonzaga
author_facet Pimenta, Ricardo José Gonzaga
Aono, Alexandre Hild
Burbano, Roberto Carlos Villavicencio
Coutinho, Alisson Esdras [UNESP]
da Silva, Carla Cristina
dos Anjos, Ivan Antônio
Perecin, Dilermando [UNESP]
Landell, Marcos Guimarães de Andrade
Gonçalves, Marcos Cesar
Pinto, Luciana Rossini
de Souza, Anete Pereira
author_role author
author2 Aono, Alexandre Hild
Burbano, Roberto Carlos Villavicencio
Coutinho, Alisson Esdras [UNESP]
da Silva, Carla Cristina
dos Anjos, Ivan Antônio
Perecin, Dilermando [UNESP]
Landell, Marcos Guimarães de Andrade
Gonçalves, Marcos Cesar
Pinto, Luciana Rossini
de Souza, Anete Pereira
author2_role author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual de Campinas (UNICAMP)
Littoral Polytechnic Superior School (ESPOL)
Universidade Estadual Paulista (UNESP)
Agronomic Institute of Campinas (IAC/APTA)
Biological Institute (IB/APTA)
dc.contributor.author.fl_str_mv Pimenta, Ricardo José Gonzaga
Aono, Alexandre Hild
Burbano, Roberto Carlos Villavicencio
Coutinho, Alisson Esdras [UNESP]
da Silva, Carla Cristina
dos Anjos, Ivan Antônio
Perecin, Dilermando [UNESP]
Landell, Marcos Guimarães de Andrade
Gonçalves, Marcos Cesar
Pinto, Luciana Rossini
de Souza, Anete Pereira
description Sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.
publishDate 2021
dc.date.none.fl_str_mv 2021-12-01
2022-05-01T07:58:54Z
2022-05-01T07:58:54Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1038/s41598-021-95116-1
Scientific Reports, v. 11, n. 1, 2021.
2045-2322
http://hdl.handle.net/11449/233361
10.1038/s41598-021-95116-1
2-s2.0-85112014467
url http://dx.doi.org/10.1038/s41598-021-95116-1
http://hdl.handle.net/11449/233361
identifier_str_mv Scientific Reports, v. 11, n. 1, 2021.
2045-2322
10.1038/s41598-021-95116-1
2-s2.0-85112014467
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Scientific Reports
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
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