Genomic evaluation using SNP- and haplotype-based genomic relationship matrices in a closed line of Duroc pigs.

A simulation analysis and real phenotype analysis were performed to evaluate the impact of three different relationship matrices on heritability estimation and prediction accuracy in a closed-line breeding of Duroc pigs. The numerator relationship matrix (NRM), single nucleotide polymorphism (SNP)-based genomic relationship matrix (GRM) (G ), and haplotype-based GRM (G ) were applied in this study. We used PorcineSNP60 genotype array data (38 114 SNPs) of 831 Duroc pigs with four selection traits.

Genome-wide association studies reveal additional related loci for fatty acid composition in a Duroc pig multigenerational population.

The aim of the present study was to detect quantitative trait loci affecting fatty acid composition in back fat and intramuscular fat in a Duroc pig population comprising seventh-generation pedigrees using genome-wide association studies (GWAS). In total, 305 animals were genotyped using single nucleotide polymorphisms (SNPs) array and five selected SNPs from regions containing known candidate genes related to fatty acid synthesis or metabolism. In total, 24 genome-wide significant SNP regions were detected in 12 traits, and 76 genome-wide suggestive SNP regions were detected in 33 traits.

SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population.

Background: The aim of the present study was to compare the power of single nucleotide polymorphism (SNP)-based genome-wide association study (GWAS) and haplotype-based GWAS for quantitative trait loci (QTL) detection, and to detect novel candidate genes affecting economically important traits in a purebred Duroc population comprising seven-generation pedigree. First, we performed a simulation analysis using real genotype data of this population to compare the power (based on the null hypothesis) of the two methods. We then performed GWAS using both methods and real phenotype data comprising 52 traits, which included growth, carcass, and meat quality traits.