• Journal of agriculture & life science
• /
• v.50 no.3
• /
• pp.99-117
• /
• 2016

Data on primal cuts were collected from 1,829 steers of Hanwoo progeny testing programs, between 2010 and 2015 for the ssGWAS. SNP data were analyzed by using Illumina Bovine 50K Beadchip. The SNP data that matches with phenotype data was 674 animals. As a first step, the genomic estimated breeding value(GEBV) of the loin and rib cuts were estimated, which was used in the estimation of SNP marker effects and their variances related to the traits. Then, the estimated variance explained by each marker was expressed as a proportion to the total genetic variance. Finally, the SNP loci and their significance to any possible QTL were examined. Among the 20 best SNP loci explaining a larger proportion of SNP variance to the total genetic variance for tender loin yield, the region between 12,812,193 ~ 12,922,313bp on BTA 10 harbored a cluster of SNPs that explained about 7.32 to 7.34% of the total genetic variance. For strip loin yield, a peak for higher effects for multiple SNPs was found in BTA24, between 38,158,543 and 38,347,278bp distances, which explained about 8.36 to 8.56% of the observed variance for this trait. For loin yield had relatively smaller effects in terms of the total genetic variance. Therefore, loin yield might be affected by a few loci with moderate effects and many other loci with smaller effects across the genome.

• Journal of Life Science
• /
• v.22 no.3
• /
• pp.366-372
• /
• 2012

This study was conducted to estimate the extent of linkage disequilibrium (LD) and effective population size using whole genomic single nucleotide polymorphisms (SNP) genotyped by DNA chip in Hanwoo. Using the blood samples of 35 young bulls born from 2005 to 2008 and their progenies (N=253) in a Hanwoo nucleus population collected from Hanwoo Improvement Center, 51,582 SNPs were genotyped using Bovine SNP50 chips. A total of 40,851 SNPs were used in this study after elimination of SNPs with a missing genotyping rate of over 10 percent and monomorphic SNPs (10,730 SNPs). The total autosomal genome length, measured as the sum of the longest syntenic pairs of SNPs by chromosome, was 2,541.6 Mb (Mega base pairs). The average distances of all adjacent pairs by each BTA ranged from 0.55 to 0.74 cM. Decay of LD showed an exponential trend with physical distance. The means of LD ($r^2$) among syntenic SNP pairs were 0.136 at a range of 0-0.1 Mb in physical distance and 0.06 at a range of 0.1-0.2 Mb. When these results were used for Luo's formula, about 2,000 phenotypic records were found to be required to achieve power > 0.9 to detect 5% QTL in the population of Hanwoo. As a result of estimating effective population size by generation in Hanwoo, the estimated effective population size for the current status was 84 heads and the estimate of effective population size for 50 generations of ancestors was 1,150 heads. The average decreasing rates of effective population size by generation were 9.0% at about five generations and 17.3% at the current generation. The main cause of the rapid decrease in effective population size was considered to be the intensive use of a few prominent sires since the application of artificial insemination technology in Korea. To increase and/or sustain the effective population size, the selection of various proven bulls and mating systems that consider genetic diversity are needed.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
• /
• 2005.10a
• /
• pp.123-126
• /
• 2005

본 연구는 고등동물의 불포화지방산 생합성의 핵심 효소로 알려져 있는 Stearoyl-CoA desaturase(SCD) 유전자의 특정한 단일염기다형(single nucleotide polymorphism; SNP)이 한우의 도체 및 육질형질에 미치는 영향을 분석하기 위해 SCD 유전자의 Intron 7번 영역의 특정부위를 포함하는 primer를 제작하고, 염기서열 분석을 통하여 유전자 구조를 해석한 결과 총 211bp 크기를 갖는 염기서열의 122번째에서 아데닌(A)${\leftrightarrow}$구아닌(G) 염기치환으로 발생한 단일염기다형(SNP) 부위를 발견하였다. 이들 단일염기다형 염기서열 부위를 PCR-SSCP(single-strand conformation polymorphism) 기법을 이용하여 분석한 결과 3종류의 SNP 유전자형(A/A, A/G 및 G/G)을 검출하였다. 이 가운데 A/G 유전자형이 한우의 근내지방도와 등지방두께와 고도의 유의적 연관성이 있다는 새로운 사실을 발견하였다. 따라서, 본 연구를 통해 개발된 한우 SCD 유전자의 특정한 단일 염기다형 표지인자는 한우의 연령 및 성별에 관계없이 육질이 우수한 고급육을 생산하는 우량 한우의 조기식별에 매우 유용한 DNA 표지인자로 활용할 수 있을 것으로 기대된다.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
• /
• 2006.05a
• /
• pp.112-116
• /
• 2006

본 연구는 인간과 동물의 식욕조절, 에너지 대사, 체지방 축적 및 지방 대사에 핵심적인 역할을 담당하는 비만 유전자 leptin의 SNP를 검색하고, 이들 SNP 마커와 한우의 도체 및 육질형질들과의 연관성을 구명하여 고급육 생산 한우 조기 선발 및 육질 진단을 위한 분자 표지 마커로 활용하기 위하여 수행하였다. 한우 leptin 유전자의 exon 2 및 3번 영역을 포함한 염기서열 분석결과 총 3개의 SNP를 검출하였고, PCR-RFLP및 SSCP기법을 이용하여 SNP유전자형을 분석한 결과 exon 2 영역 내 C1180T SNP부위가 한우의 근내 지방도 및 등지방 두께와 유의적인 연관성(p<0.05)이 있는 것으로 나타났다. 따라서, 본 연구를 통해 개발된 한우 leptin 유전자의 특정한 SNP marker는 근내 지방도가 우수한 고급육을 생산하는 한우의 조기식별 및 마블링 등 육질진단에 매우 유용한 DNA 표지인자로 활용할 수 있을 기대된다.

• Journal of the Korean Data and Information Science Society
• /
• v.22 no.4
• /
• pp.661-669
• /
• 2011

By direct sequencing of 12 STS marker, we identified 10 polymorphic SNPs. As a result of genotype frequency analysis between 10 polymorphic SNPs and extreme population (n=20) for marbling score in Hanwoo (n=233), there was over 40 percent of frequency difference of HWSNP_1-1 and HWSNP_9-4 SNP. HWSNP_1-1 SNP was significantly associated with marbling score in large-scale population (n=233). Therefore we suggested that HWSNP_1-1 SNP can be useful as a positional candidate for beef quality for marker-assisted selection in Hanwoo.

• Journal of Life Science
• /
• v.30 no.3
• /
• pp.230-238
• /
• 2020

Carcass traits are the most economically important traits in Hanwoo (Korean cattle). Recently, the development of the field of genomics has made it possible to identify DNA markers for the genetic evaluation of carcass and meat quality traits in beef cattle. The objective of this study was to assess the genetic effects of single nucleotide polymorphism (SNP) markers related to carcass traits by field evaluations in a commercial Hanwoo population. We evaluated 15 SNP markers (TG g.371T>C, APM1 g.1454G>A, FABP4 g.2834C>G, FABP4 g.3533T>A, FABP4 g.3691G>A, SCD g.10153A>G, SCD g.10329T >C, CPE g.601T>C, EDG1 g.166A>G, NPY g.4271T>C, GPD1 g.2766C>T, PDE1B g.17122A>G, PDE1B g.17507A>C, TNNT1 g.6650C>T, and RORC g.20152A>G) related to carcass traits in Hanwoo. Genotyping of these SNP markers was performed using PCR-RFLP analysis in Hanwoo steers (n = 1,536) to evaluate their association with carcass traits. Seven SNPs, APM1 g.1454G>, FABP4 g.3691G>A, SCD g.10153A>G, CPE g.601T>C, PDE1B g.17122A>G, TNNT1 g.6650C>T, and RORC g.20152A>G, were significantly associated with carcass traits such as marbling score (MS), backfat thickness (BF), musculus longissimus dorsi area (LDA), carcass weight (CW), meat grade (MG), meat color (MC), and maturity score (MA). The results suggest that these SNPs may be used as DNA markers for the selection of Hanwoo with higher meat quality.

• Journal of Animal Science and Technology
• /
• v.53 no.1
• /
• pp.1-6
• /
• 2011

This simulation study was performed to investigate the accuracy of the estimated breeding value by using genomic information (GEBV) by way of Bayesian framework. Genomic information by way of single nucleotide polymorphism (SNP) from a chromosome with length of 100cM were simulated with different marker distance (0.1cM, 0.5cM), heritabilities (0.1, 0.5) and half sibs families (20 heads, 4 heads). For generating the simulated population in which animals were inferred to genomic polymorphism, we assumed that the number of quantitative trait loci (QTL) were equal with the number of no effect markers. The positions of markers and QTLs were located with even and scatter distances, respectively. The accuracies of estimated breeding values by way of indicating correlations between true and estimated breeding values were compared on several cases of marker distances, heritabilities and family sizes. The accuracies of breeding values on animals only having genomic information were 0.87 and 0.81 in marker distances of 0.1cM and 0.5cM, respectively. These accuracies were shown to be influenced by heritabilities (0.87 at $h^2$ =0.10, 0.94 at $h^2$ =0.50). According to half sibs' family size, these accuracies were 0.87 and 0.84 in family size of 20 and 4, respectively. As half sibs family size is high, accuracy of breeding appeared high. Based on the results of this study it is concluded that the amount of marker information, heritability and family size would influence the accuracy of the estimated breeding values in genomic selection methodology for animal breeding.

• Journal of Animal Science and Technology
• /
• v.53 no.1
• /
• pp.7-13
• /
• 2011

The aim of this study was to identify the polymorphism on exostosin-1 (EXT1) gene and to associate with economic traits in Hanwoo (Korean cattle). We sequenced for detection of single nucleotide polymorphism (SNP) with 24 unrelated individuals and identified four SNPs (T272196A, C272359T, G290964A and A302092G). Relationship between the genotypes of 583 Hanwoo individuals by PCR-RFLP and economic traits were analyzed by general linear model. In EXT1 gene, there were four SNPs associated with economic traits such as eye muscle area breeding value, marbling score breeding value, backfat and thickness breeding value (p<0.05 to p<0.01). In conclusion, this study indicates an important role of EXT1 gene in determining the meat quality or economic characteristics in Hanwoo.

• Journal of Animal Science and Technology
• /
• v.52 no.5
• /
• pp.357-366
• /
• 2010

The emergence of next-generation sequencing technologies has lead to application of new computational and statistical methodologies that allow incorporating genetic information from entire genomes of many individuals composing the population. For example, using single-nucleotide polymorphisms (SNP) obtained from whole genome amplification platforms such as the Ilummina BovineSNP50 chip, many researchers are actively engaged in the genetic evaluation of cattle livestock using whole genome relationship analyses. In this study, we estimated the genomic relationship matrix (GRM) and compared it with one computed using a pedigree relationship matrix (PRM) using a population of Hanwoo. This project is a preliminary study that will eventually include future work on genomic selection and prediction. Data used in this study were obtained from 187 blood samples consisting of the progeny of 20 young bulls collected after parentage testing from the Hanwoo improvement center, National Agriculture Cooperative Federation as well as 103 blood samples from the progeny of 12 proven bulls collected from farms around the Kyong-buk area in South Korea. The data set was divided into two cases for analysis. In the first case missing genotypes were included. In the second case missing genotypes were excluded. The effect of missing genotypes on the accuracy of genomic relationship estimation was investigated. Estimation of relationships using genomic information was also carried out chromosome by chromosome for whole genomic SNP markers based on the regression method using allele frequencies across loci. The average correlation coefficient and standard deviation between relationships using pedigree information and chromosomal genomic information using data which was verified using a parentage test andeliminated missing genotypes was $0.81{\pm}0.04$ and their correlation coefficient when using whole genomic information was 0.98, which was higher. Variation in relationships between non-inbred half sibs was $0.22{\pm}0.17$ on chromosomal and $0.22{\pm}0.04$ on whole genomic SNP markers. The variations were larger and unusual values were observed when non-parentage test data were included. So, relationship matrix by genomic information can be useful for genetic evaluation of animal breeding.

• Journal of Animal Science and Technology
• /
• v.49 no.5
• /
• pp.577-584
• /
• 2007

Adipocyte-specific secretory factor(ADSF)/resistin, an hormone, is a small cysteine-rich protein secreted from adipose tissue and ADSF/resistin has been implicated in modulating adipogenesis in human and rodents. Although the exact role of ADSF/resistin in bovine has not been identified, it may have directly or indirectly involved in adipocyte differentiation. The objective of this study was to investigate its DNA polymorphism associated with carcass traits in Korean Native Cattle(Hanwoo). To investigate DNA polymorphism in Hanwoo ADSF/resistin gene, blood samples were taken from 295 Hanwoo steers belonging to progeny testing at Hanwoo Improvement Center in Korea. Seven single nucleotide polymorphisms(SNPs) were found in intron regions but not in any other regions including promoter (1.7kb) and 4 exons. The highest frequency among SNPs was C186A(0.16/0.84) following G964A (0.156/0.884). The significant correlation(P<0.05) between the SNPs and economic traits was found on 764Ains associated with marbling but not from any other SNPs determined.  A computer simulation was also conducted to assess the efficiency of marker assisted selection(MAS) versus the conventional breeding scheme.  Results revealed that MAS was more efficient as a breeding tool compared to the conventional. In conclusion, ADSF/Resistin gene is one of candidate genes to evaluate the quality, especially marbling score, in Hanwoo.