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