Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
Abstract 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 t...
Guardado en:
| Autores principales: | , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Nature Portfolio
2021
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/b5c606fce2b24919aee73627285c9fee |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:b5c606fce2b24919aee73627285c9fee |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:b5c606fce2b24919aee73627285c9fee2021-12-02T18:49:32ZGenome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance10.1038/s41598-021-95116-12045-2322https://doaj.org/article/b5c606fce2b24919aee73627285c9fee2021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95116-1https://doaj.org/toc/2045-2322Abstract 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.Ricardo José Gonzaga PimentaAlexandre Hild AonoRoberto Carlos Villavicencio BurbanoAlisson Esdras CoutinhoCarla Cristina da SilvaIvan Antônio dos AnjosDilermando PerecinMarcos Guimarães de Andrade LandellMarcos Cesar GonçalvesLuciana Rossini PintoAnete Pereira de SouzaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-18 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Ricardo José Gonzaga Pimenta Alexandre Hild Aono Roberto Carlos Villavicencio Burbano Alisson Esdras Coutinho Carla Cristina da Silva Ivan Antônio dos Anjos Dilermando Perecin Marcos Guimarães de Andrade Landell Marcos Cesar Gonçalves Luciana Rossini Pinto Anete Pereira de Souza Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance |
| description |
Abstract 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. |
| format |
article |
| author |
Ricardo José Gonzaga Pimenta Alexandre Hild Aono Roberto Carlos Villavicencio Burbano Alisson Esdras Coutinho Carla Cristina da Silva Ivan Antônio dos Anjos Dilermando Perecin Marcos Guimarães de Andrade Landell Marcos Cesar Gonçalves Luciana Rossini Pinto Anete Pereira de Souza |
| author_facet |
Ricardo José Gonzaga Pimenta Alexandre Hild Aono Roberto Carlos Villavicencio Burbano Alisson Esdras Coutinho Carla Cristina da Silva Ivan Antônio dos Anjos Dilermando Perecin Marcos Guimarães de Andrade Landell Marcos Cesar Gonçalves Luciana Rossini Pinto Anete Pereira de Souza |
| author_sort |
Ricardo José Gonzaga Pimenta |
| title |
Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance |
| 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 |
| publisher |
Nature Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/b5c606fce2b24919aee73627285c9fee |
| work_keys_str_mv |
AT ricardojosegonzagapimenta genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT alexandrehildaono genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT robertocarlosvillavicencioburbano genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT alissonesdrascoutinho genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT carlacristinadasilva genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT ivanantoniodosanjos genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT dilermandoperecin genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT marcosguimaraesdeandradelandell genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT marcoscesargoncalves genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT lucianarossinipinto genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance AT anetepereiradesouza genomewideapproachesfortheidentificationofmarkersandgenesassociatedwithsugarcaneyellowleafvirusresistance |
| _version_ |
1718377585112514560 |