Genome-Wide Association Study Identifies Major Loci for Carcass Weight on BTA14 in Hanwoo (Korean Cattle)

Abstract

This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10−6) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was BTB-01280026 (P = 4.02×10−11), located in the 25 Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were Hapmap27934-BTC-065223 (P = 4.04×10−11) in 25.2 Mb, BTB-01143580 (P = 6.35×10−11) in 24.3 Mb, Hapmap30932-BTC-011225 (P = 5.92×10−10) in 24.8 Mb, Hapmap27112-BTC-063342 (P = 5.18×10−9) in 25.4 Mb, and Hapmap24414-BTC-073009 (P = 7.38×10−8) in 25.4 Mb, all on BTA 14. One SNP (BTB-01143580; P = 6.35×10−11) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73% to 10.55% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP (BTB-01280026; P = 4.02×10−11) had 16.96 kg of allele substitution effect, and the second most significant SNP (Hapmap27934-BTC-065223; P = 4.04×10−11) had 18.06 kg of effect on carcass weight, which correspond to 44% and 47%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.

Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population

“…A genome-wide SNP validation analysis was performed using 83 markers (Supplementary Tables S1 to S4), which were genotyped using the Illumina GoldenGate and Infinium genotyping assays to detect the association of SNPs with four phenotypes: CW, EMA, BF, and MS. The SNPs used in this study were selected from the previous GWAS results of Lee et al (2013b). Phenotypic data were provided by the abattoir (Table 1) and were recorded using standard measurement methods, i.e., CW (kg) was the weight after slaughter at 32 months of age, and EMA (cm 2 ), BF (mm), and MS were measured at the twelfth and thirteenth rib junctions after 24 hours of chilling.…”

“…Given the importance of validating markers, we genotyped 83 SNP markers, which were significantly identified in a previous GWAS performed by Lee et al (2013b), and validated the effects of those markers in a commercial Hanwoo population in this study.…”

“…Many genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) that are significantly associated with carcass traits in different cattle breeds (Nishimura et al, 2012; Lee et al, 2013b; Lu et al, 2013). In a previous GWAS study performed by Lee et al (2013b), statistically significant SNPs were identified on Bos taurus autosome (BTA) 14 for carcass traits in a progeny-tested Hanwoo population.…”

“…In a previous GWAS study performed by Lee et al (2013b), statistically significant SNPs were identified on Bos taurus autosome (BTA) 14 for carcass traits in a progeny-tested Hanwoo population. Before any SNP marker is delivered to the beef industry, a validation study that accurately estimates the additive genetic marker effect in a population different from the discovery population should be done.…”

Genome-wide Copy Number Variation in a Korean Native Chicken Breed

“…기존에 분자유전학적 품종 특성 평가를 위하 여 축산분야에서는 주로 각 품종에 대한 유전자 내 단일염 기 다형성(single nucleotide polymorphism, SNP)을 활용한 개 체식별 및 특성 평가 방법과 초위성체 DNA(microsatellite, MS)의 개체별 유전자형을 활용한 유전자 감식 기법 등이 개발되어 활용되었다 (Vignal et al, 2002). 최근 국내에서도 재래가축 가운데 제주 흑돼지와 한우에서 유전자 정보를 기 반으로 하는 분자유적학적 품종 특성 연구가 활발히 이뤄지 고 있다 (Han et al, 2008;Lee et al, 2013;Yoon et al, 2005). 특히 닭에서는 국내 복원 토종닭(적갈색 재래종, 황갈색 재 래종), 토종닭 실용계와 오골계 및 외래 품종(Hy-Line Brown: HB, White Leghorn: WL)을 대상으로 13종의 MS marker를 이용하여 누적 품종 식별력(cumulative power of discriminate, CPD)값을 보고하였으며 (Oh et al 2010) (Lee et al, 2011).…”