生物学杂志

生物学杂志 ›› 2020, Vol. 37 ›› Issue (4): 96-.doi: 10.3969/j.issn.2095-1736.2020.04.096

• 技术方法 • 上一篇    下一篇

不同统计分析模型在大豆菌核病GWAS中的应用

  

  1. 1. 陕西理工大学 生物科学与工程学院, 汉中 723000；2. Département de Phytologie, Université Laval, Québec, QC G1V 0A6, Canada
  • 出版日期:2020-08-18 发布日期:2020-08-10
  • 作者简介:张羽，教授，研究方向为植物分子标记的开发与应用，E-mail:yuzhang20160315@outlook.com
  • 基金资助:
    陕西理工大学访问学者项目

Application of the different models of GWAS on Sclerotinia sclerotiorum resistance in soybean

  1. 1． School of Biological Sciences and Engineering, Shaanxi Sci-Tech University, Hanzhong 723000, China;2． Département de Phytologie, Université Laval, Québec, QC G1V 0A6, Canada
  • Online:2020-08-18 Published:2020-08-10

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摘要： 以126个大豆品系的Illumina Hiseq2000测序后的SNPs数据和对大豆主茎接种菌核病菌丝后病斑长度的表型值为例，利用2种方法(全部样本和极端类型)进行基于单个SNP-Trait和Haplotype-Trait的关联分析。结果表明：在α≤0.05时，MAF取值0.01、0.05和0.1的基因型-表型关联结果完全一致，MAF取值0.25的关联结果与前3个MAF取值关联结果有所区别，但在同一染色体上的关联位点相同，且每条染色体上的峰值SNP都出现在相应的Haplotype中；基于全部样品和极端表型的关联在PLINK v1.07和HAPLOVIEW4.2里分析结果差异较小；单个SNP-Trait和Haplotype-Trait的显著关联结果有差异，但较强关联差异较小。找到与大豆Sclerotinia sclerotiorum 抗性有关的一些潜在的显著SNP位点和相关基因。

关键词: 测序, SNP-Trait, Haplotype-Trait;全部样本;极端类型

Abstract: SNP results that had been previously obtained via Illumina Hiseq2000 sequencing of 126 soybean strains were analyzed using two methods (using all 126 samples and using only extreme phenotypes) for association with stem lesion length data that had been collected subsequent to inoculation with Sclerotinia sclerotiorum. The association analysis, based on both single SNPs and haplotypes, was performed. When α≤0.05, MAF values of 0.01, 0.05, and 0.1 yielded the same loci; however, a more restrictive MAF threshold of 0.25 resulted in relatively different association loci, with the exception of only a single chromosome. Furthermore, peak SNPs also appeared in their corresponding haplotypes. The analysis based on the association of all samples and extreme phenotypes in PLINK v1.07 and HAPLOVIEW4.2 showed little difference. The results of significant correlation by SNP-Trait association locus were significantly different from those of Haplotype-Trait association, However, there is less difference in stronger correlations. Some potential significant SNP loci and related genes related to soybean Sclerotinia sclerotiorum resistance were found.

Key words: sequencing, SNP-Trait, Haplotype-Trait, whole genotypes, extreme genotypes

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