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

Abstract

BackgroundThe 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.ResultsIn total, 836 animals were genotyped using the Illumina PorcineSNP60 BeadChip and 14 customized SNPs from regions of known candidate genes related to the traits of interest. The power of SNP-based GWAS was greater than that of haplotype-based GWAS in a simulation analysis. In real data analysis, a larger number of significant regions was obtained by SNP-based GWAS than by haplotype-based GWAS. For SNP-based GWAS, 23 genome-wide significant SNP regions were detected for 17 traits, and 120 genome-wide suggestive SNP regions were detected for 27 traits. For haplotype-based GWAS, 6 genome-wide significant SNP regions were detected for four traits, and 11 genome-wide suggestive SNP regions were detected for eight traits. All genome-wide significant SNP regions detected by haplotype-based GWAS were located in regions also detected by SNP-based GWAS. Four regions detected by SNP-based GWAS were significantly associated with multiple traits: on Sus scrofa chromosome (SSC) 1 at 304 Mb; and on SSC7 at 35–39 Mb, 41–42 Mb, and 103 Mb. The vertnin gene (VRTN) in particular, was located on SSC7 at 103 Mb and was significantly associated with vertebrae number and carcass lengths. Mapped QTL regions contain some candidate genes involved in skeletal formation (FUBP3; far upstream element binding protein 3) and fat deposition (METTL3; methyltransferase like 3).ConclusionOur results show that a multigenerational pig population is useful for detecting QTL, which are typically segregated in a purebred population. In addition, a novel significant region could be detected by SNP-based GWAS as opposed to haplotype-based GWAS.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0368-3) contains supplementary material, which is available to authorized users.

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

“…In DG and BF, suggestive QTL were detected by haplotype-based GWAS, but no QTL were detected in LEA (Sato et al 2016). In addition, significant QTL were detected by SNPbased GWAS in DG and BF, but not detected in LEA (Sato et al 2016). As for IMF, no QTL was detected by haplotype-based GWAS, but some suggestive QTL on chromosome 7 located in a similar region were detected by SNP-based GWAS (Sato et al 2016).…”

“…In LEA, the estimated heritability of the NRM was the highest in all three matrices. In DG and BF, suggestive QTL were detected by haplotype-based GWAS, but no QTL were detected in LEA (Sato et al 2016). In addition, significant QTL were detected by SNPbased GWAS in DG and BF, but not detected in LEA (Sato et al 2016).…”

“…In addition, the QTL effect was generated from a gamma distribution, which means total genetic variance is composed of a few QTL with large and polygenic effects . For G H , G H could overestimate the QTL variance around QTL and thus overestimate the total genetic variance, because haplotype-based GWAS cannot perform finer mapping than SNP-based GWAS does in this population (Sato et al 2016). For G S and the NRM, the trends of the estimated heritability (NRM ≤ G S ) were shown in the SNP-QTL scenario, because G S could capture all of the total genetic variance under perfect LD between QTL and SNPs on the array.…”

“…Genotypes, phenotypes and pedigree information for this study were obtained from previously published data by a genome-wide association study (GWAS) (Sato et al 2016). All procedures involving animals followed the Guidelines for the Care and Use of Laboratory Animals established by the National Livestock Breeding Center.…”

“…All procedures involving animals followed the Guidelines for the Care and Use of Laboratory Animals established by the National Livestock Breeding Center. Complete descriptions of the experimental population, phenotypes and SNP information were reported previously by Sato et al (2016). In short, a total of 836 Duroc purebred pigs were used in this study.…”