Genome-wide association analyses of the 15th QTL-MAS workshop data using mixed model based single locus regression analysis.

Wei-Xuan Fu,Qin Zhang,Zhe Zhang,Jian-Feng Liu,Pei-Pei Ma,Chong-Long Wang,Zi-Qing Weng,Xiang-Dong Ding

doi:10.1186/1753-6561-6-s2-s5

Abstract

BackgroundThe mixed model based single locus regression analysis (MMRA) method was used to analyse the common simulated dataset of the 15th QTL-MAS workshop to detect potential significant association between single nucleotide polymorphisms (SNPs) and the simulated trait. A Wald chi-squared statistic with df =1 was employed as test statistic and the permutation test was performed. For adjusting multiple testing, phenotypic observations were permutated 10,000 times against the genotype and pedigree data to obtain the threshold for declaring genome-wide significant SNPs. Linkage disequilibrium (LD) in term of D' between significant SNPs was quantified and LD blocks were defined to indicate quantitative trait loci (QTL) regions.ResultsThe estimated heritability of the simulated trait is approximately 0.30. 82 genome-wide significant SNPs (P < 0.05) on chromosomes 1, 2 and 3 were detected. Through the LD blocks of the significant SNPs, we confirmed 5 and 1 QTL regions on chromosomes 1 and 3, respectively. No block was detected on chromosome 2, and no significant SNP was detected on chromosomes 4 and 5.ConclusionMMRA is a suitable method for detecting additive QTL and a fast method with feasibility of performing permutation test. Using LD blocks can effectively detect QTL regions.

Highlights

The mixed model based single locus regression analysis (MMRA) method was used to analyse the common simulated dataset of the 15th quantitative trait loci (QTL)-MAS workshop to detect potential significant association between single nucleotide polymorphisms (SNPs) and the simulated trait
Recently, the high-density single nucleotide polymorphism (SNP) arrays have been developed for almost all domestic animals, which offer the prerequisite of genome-wide association study (GWAS), a more powerful approach for high-resolution mapping of loci controlling phenotypic traits in domestic animals [1]
We found that 2,879 SNPs were homozygous (MAF = 0) for all the tested individuals and 715 SNPs had a minor allele frequency (MAF) less than 0.03

Summary

Results

The estimated heritability of the simulated trait is approximately 0.30. 82 genome-wide significant SNPs (P < 0.05) on chromosomes 1, 2 and 3 were detected. The estimated heritability of the simulated trait is approximately 0.30. 82 genome-wide significant SNPs (P < 0.05) on chromosomes 1, 2 and 3 were detected. Through the LD blocks of the significant SNPs, we confirmed 5 and 1 QTL regions on chromosomes 1 and 3, respectively. No block was detected on chromosome 2, and no significant SNP was detected on chromosomes 4 and 5

Background

Methods

Results and discussion

Conclusion

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