Computational protocol: The genetic architecture of water-soluble protein content and its genetic relationship to total protein content in soybean

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Protocol publication

[…] SNPs with MAF ≥ 0.05 and the number of accessions with the minor allele ≥10 in the diverse panel were used to carry out GWAS. As a result, the final set of 201,994 SNPs (MAF ≥ 0.05) and the phenotypic values for all genotypes from the association panel across six environments and the BLUP over all environments, were used to perform marker-trait association analysis. GWAS was performed with a compressed mixed linear model using the GAPIT package. The population structure was accounted for by principle component analysis (PCA) and the relatedness was calculated by VanRaden method using GAPIT. Markers were identified as significantly associated with traits by comparison with the significant threshold of P-value < 1/n (P < 4.95 × 10−6).The genome-wide epistatic interaction test was implemented in PLINK version 1.07. To remedy the shortcoming of a less stringent significance threshold (1/n), we also carried out multi-locus GWAS by using ISIS EM-BLASSO and mrMLM (with the software rmMLM: https://cran.r-project.org/web/packages/mrMLM/index.html) simultaneously in natural population. […]

Pipeline specifications

Software tools GAPIT, PLINK, mrMLM
Application GWAS
Organisms Glycine max
Diseases Water Intoxication