甘蔗对甘蔗花叶病毒抗性的多组学研究

IF 6 1区 农林科学 Q1 AGRONOMY
Ricardo José Gonzaga Pimenta , Alexandre Hild Aono , Roberto Carlos Villavicencio Burbano , Marcel Fernando da Silva , Ivan Antônio dos Anjos , Marcos Guimarães de Andrade Landell , Marcos Cesar Gonçalves , Luciana Rossini Pinto , Anete Pereira de Souza
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引用次数: 0

摘要

甘蔗马赛克病毒(SCMV)是甘蔗马赛克病的主要病原体,该病影响甘蔗和其他禾本科作物。尽管对控制玉米 SCMV 抗性的数量性状位点进行了广泛表征,但甘蔗这一性状的遗传基础在很大程度上仍未得到探索。在此,我们进行了一项全基因组关联研究,并利用机器学习和特征选择对不同甘蔗群体的 SCMV 抗性进行了基因组预测。九个单核苷酸多态性(SNPs)解释了高达 29.9% 的观察到的表型变异,73-SNP 集预测抗性的准确度、精确度、召回率和 F1 分数(精确度和召回率的调和平均值)都很高。这两组标记都在其他甘蔗基因型中进行了验证,其中 SNPs 解释了高达 23.6% 的表型变异,预测抗性的准确率最高达 69.1%。合成分析表明,玉米中对大多数 SCMV 具有抗性的基因在甘蔗中并不存在,这也解释了为什么这种主要抗性来源在甘蔗中尚未被发现。最后,利用甘蔗 RNA-Seq 数据,对与 SCMV 抗性相关的标记进行了注释,并构建了一个基因共表达网络,以确定抗性所涉及的预测生物过程。通过该网络可以确定候选抗性基因,并证实抗 SCMV 的过程涉及胁迫反应、光合作用以及转录和翻译调控。这些结果为甘蔗提供了一种实用的标记辅助育种方法,并为今后的 SCMV 抗性研究确定了目标基因。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Multiomic investigation of Sugarcane mosaic virus resistance in sugarcane

Sugarcane mosaic virus (SCMV) is the main etiological agent of sugarcane mosaic disease, which affects sugarcane and other grass crops. Despite the extensive characterization of quantitative trait loci controlling resistance to SCMV in maize, the genetic basis of this trait in sugarcane is largely unexplored. Here, a genome-wide association study was performed and machine learning coupled with feature selection was used for genomic prediction of resistance to SCMV in a diverse sugarcane panel. Nine single-nucleotide polymorphisms (SNPs) explained up to 29.9% of the observed phenotypic variance and a 73-SNP set predicted resistance with high accuracy, precision, recall, and F1 scores (the harmonic mean of precision and recall). Both marker sets were validated in additional sugarcane genotypes, in which the SNPs explained up to 23.6% of the phenotypic variation and predicted resistance with a maximum accuracy of 69.1%. Synteny analyses suggested that the gene responsible for the majority of SCMV resistance in maize is absent in sugarcane, explaining why this major resistance source has not been identified in this crop. Finally, using sugarcane RNA-Seq data, markers associated with resistance to SCMV were annotated, and a gene coexpression network was constructed to identify the predicted biological processes involved in resistance. This network allowed the identification of candidate resistance genes and confirmed the involvement of stress responses, photosynthesis, and the regulation of transcription and translation in resistance to SCMV. These results provide a practical marker-assisted breeding approach for sugarcane and identify target genes for future studies of SCMV resistance.

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来源期刊
Crop Journal
Crop Journal Agricultural and Biological Sciences-Agronomy and Crop Science
CiteScore
9.90
自引率
3.00%
发文量
638
审稿时长
41 days
期刊介绍: The major aims of The Crop Journal are to report recent progresses in crop sciences including crop genetics, breeding, agronomy, crop physiology, germplasm resources, grain chemistry, grain storage and processing, crop management practices, crop biotechnology, and biomathematics. The regular columns of the journal are Original Research Articles, Reviews, and Research Notes. The strict peer-review procedure will guarantee the academic level and raise the reputation of the journal. The readership of the journal is for crop science researchers, students of agricultural colleges and universities, and persons with similar academic levels.
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