Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , , , |
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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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 |
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UNESP |
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Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1808128231638827008 |