Deus Mugabe, Mohsen Yoosefzadeh-Najafabadi, Istvan Rajcan
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This study sought to understand the genetic basis underlying SSR resistance particularly in soybean grown in Canada. Consequently, a panel of 193 genotypes was assembled based on maturity group and genetic diversity as representative of Canadian soybean cultivars. Plants were inoculated and screened for SSR resistance in controlled environments, where variation for SSR phenotypic response was observed. The panel was also genotyped via genotyping-by-sequencing and the resulting genotypic data were imputed using BEAGLE v5 leading to a catalogue of 417 K SNPs. Through genome-wide association analyses (GWAS) using FarmCPU method with threshold of FDR-adjusted p-values < 0.1, we identified significant SNPs on chromosomes 2 and 9 with allele effects of 16.1 and 14.3, respectively. Further analysis identified three potential candidate genes linked to SSR disease resistance within a 100 Kb window surrounding each of the peak SNPs. 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引用次数: 0
摘要
关键信息:开发具有抗性基因的大豆栽培品种是控制具有破坏性的大豆茎腐病(SSR)的关键。在此,一项针对加拿大大豆的 GWAS 研究确定了潜在的标记-性状关联和候选基因,为更有效的 SSR 育种方法铺平了道路。由真菌病原体 Sclerotinia sclerotiorum 引起的茎腐病(SSR)是导致加拿大和全世界大豆产量大幅下降的最重要病害之一。培育具有抗病基因的大豆栽培品种是控制这种病害的最廉价、最可靠的方法。然而,由于大豆对 SSR 的遗传抗性非常复杂,抗性育种受到阻碍。本研究试图了解 SSR 抗性的遗传基础,尤其是加拿大大豆的 SSR 抗性。因此,根据加拿大大豆栽培品种的成熟度组和遗传多样性,组建了一个由 193 个基因型组成的小组。在受控环境中对植物进行接种并筛选 SSR 抗性,观察 SSR 表型反应的变化。此外,还通过基因分型测序对面板进行了基因分型,并使用 BEAGLE v5 对由此产生的基因型数据进行了估算,从而得到了 417 K SNPs 的目录。通过使用 FarmCPU 方法进行全基因组关联分析(GWAS),以 FDR 调整后的 p 值为阈值
Genetic diversity and genome-wide association study of partial resistance to Sclerotinia stem rot in a Canadian soybean germplasm panel.
Key message: Developing genetically resistant soybean cultivars is key in controlling the destructive Sclerotinia Stem Rot (SSR) disease. Here, a GWAS study in Canadian soybeans identified potential marker-trait associations and candidate genes, paving the way for more efficient breeding methods for SSR. Sclerotinia stem rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is one of the most important diseases leading to significant soybean yield losses in Canada and worldwide. Developing soybean cultivars that are genetically resistant to the disease is the most inexpensive and reliable method to control the disease. However, breeding for resistance is hampered by the highly complex nature of genetic resistance to SSR in soybean. This study sought to understand the genetic basis underlying SSR resistance particularly in soybean grown in Canada. Consequently, a panel of 193 genotypes was assembled based on maturity group and genetic diversity as representative of Canadian soybean cultivars. Plants were inoculated and screened for SSR resistance in controlled environments, where variation for SSR phenotypic response was observed. The panel was also genotyped via genotyping-by-sequencing and the resulting genotypic data were imputed using BEAGLE v5 leading to a catalogue of 417 K SNPs. Through genome-wide association analyses (GWAS) using FarmCPU method with threshold of FDR-adjusted p-values < 0.1, we identified significant SNPs on chromosomes 2 and 9 with allele effects of 16.1 and 14.3, respectively. Further analysis identified three potential candidate genes linked to SSR disease resistance within a 100 Kb window surrounding each of the peak SNPs. Our results will be important in developing molecular markers that can speed up the breeding for SSR resistance in Canadian grown soybean.
期刊介绍:
Theoretical and Applied Genetics publishes original research and review articles in all key areas of modern plant genetics, plant genomics and plant biotechnology. All work needs to have a clear genetic component and significant impact on plant breeding. Theoretical considerations are only accepted in combination with new experimental data and/or if they indicate a relevant application in plant genetics or breeding. Emphasizing the practical, the journal focuses on research into leading crop plants and articles presenting innovative approaches.