不同统计分析模型在大豆菌核病GWAS中的应用

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

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。

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.Whenα≤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.