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.


RESULTS
In 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).


CONCLUSIONS
Our 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.
National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan. s0sato@nlbc.go.jp.
Shuji
S
Sato
National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
Yoshinobu
Y
Uemoto
National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
Takashi
T
Kikuchi
Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, 886-0004, Japan.
Sachiko
S
Egawa
National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
Kimiko
K
Kohira
National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
Tomomi
T
Saito
National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
Hironori
H
Sakuma
Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, 886-0004, Japan.
Satoshi
S
Miyashita
Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, 886-0004, Japan.
Shinji
S
Arata
National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
Takatoshi
T
Kojima
Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 981-8555, Japan.
Keiichi
K
Suzuki
D000818:Animals; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000235:genetics; D030541:Databases, Genetic; D005260:Female; D056726:Genetic Association Studies / Q000379:methods*; D060005:Genotyping Techniques; D006239:Haplotypes; D008297:Male; D008780:Methyltransferases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D000069466:Red Meat; D013552:Swine / Q000235:genetics* / Q000254:growth & development; D014157:Transcription Factors / Q000235:genetics
D004268:DNA-Binding Proteins; D014157:Transcription Factors; D008780:Methyltransferases
Duroc pigs; Haplotype-based GWAS; Known candidate genes; Production traits; SNP-based GWAS