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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
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Gonzaga Pimenta, Ricardo Jose [1] ; Aono, Alexandre Hild [1] ; Villavicencio Burbano, Roberto Carlos [2] ; Coutinho, Alisson Esdras [3] ; da Silva, Carla Cristina [1] ; Antonio dos Anjos, Ivan [4] ; Perecin, Dilermando [3] ; de Andrade Landell, Marcos Guimaraes [4] ; Goncalves, Marcos Cesar [5] ; Pinto, Luciana Rossini [4] ; de Souza, Anete Pereira [6, 1]
Total Authors: 11
Affiliation:
[1] Univ Campinas UNICAMP, Ctr Mol Biol & Genet Engn CBMEG, Campinas, SP - Brazil
[2] Littoral Polytech Super Sch ESPOL, Gustavo Galindo Velasco Campus, Guayaquil - Ecuador
[3] Sao Paulo State Univ Unesp, Jaboticabal, SP - Brazil
[4] Agron Inst Campinas IAC APTA, Adv Ctr Technol Res Sugarcane Agribusiness, Ribeirao Preto, SP - Brazil
[5] Biol Inst IB APTA, Plant Protect Res Ctr, Sao Paulo, SP - Brazil
[6] Univ Campinas UNICAMP, Inst Biol, Dept Plant Biol, Campinas, SP - Brazil
Total Affiliations: 6
Document type: Journal article
Source: SCIENTIFIC REPORTS; v. 11, n. 1 AUG 3 2021.
Web of Science Citations: 1
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. (AU)

FAPESP's process: 19/21682-9 - Associative mapping and transcriptomic in the investigation of sugarcane yellow leaf virus resistance
Grantee:Ricardo José Gonzaga Pimenta
Support type: Scholarships in Brazil - Doctorate (Direct)
FAPESP's process: 18/18588-8 - Association mapping in sugarcane targeting tolerance to yellow leaf virus
Grantee:Ricardo José Gonzaga Pimenta
Support type: Scholarships in Brazil - Master
FAPESP's process: 15/24346-9 - Allelic variation analysis in genes of economic importance among hom(oe)ologous regions of sugarcane (Saccharum spp.) genome
Grantee:Carla Cristina da Silva
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 19/03232-6 - Genome wide selection in sugarcane using machine learning and complex networks for economically important traits
Grantee:Alexandre Hild Aono
Support type: Scholarships in Brazil - Doctorate (Direct)