• Asian-Australasian Journal of Animal Sciences
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• v.24 no.11
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• pp.1504-1513
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• 2011

It is important to identify genetic interactions related to human diseases or animal traits. Many linear statistical models have been reported but they did not consider genetic interactions. Genotype matrix mapping (GMM) has been developed to identify genetic interactions. This study uses the GMM method to detect superior SNP combinations of the CCDC158 gene that influences average daily gain, marbling score, cold carcass weight and longissimus muscle dorsi area traits in Hanwoo. We evaluated the statistical significance of the major SNP combinations selected by implementing the permutation test of the F-measure. The effect of g.34425+102 A>T (AA), g.8778G>A (GG) and g.4102+36T>G (GT) SNP combinations produced higher performance of average daily gain, marbling score, cold carcass weight and the longissimus muscle dorsi area traits than the effect of a single SNP. GMM is a fast and reliable method for multiple SNP analysis with potential application in marker-assisted selection. GMM may prospectively be used for genetic assessment of quantitative traits after further development.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.6
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• pp.817-820
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• 2007

The effects of diacylglycerol O-acyltransferase (DGAT1) candidate gene polymorphism on the economic traits of Hanwoo were studied. Through sequencing analysis, two polymorphism sites at K232A and T11993C were established and were analyzed by PCR-RFLP. The PCR-RFLP analysis for K232A showed that the frequencies of alleles K and A were 0.75 and 0.25, respectively, and the frequencies of genotypes for K/K, K/A and A/A were estimated as 0.509, 0.491 and 0, respectively. In the PCR-RFLP analysis for T11993C, we found allele frequencies of 0.773 and 0.227 for T and A, respectively, and 0.546, 0.454 and 0 for the T/T, T/C and C/C genotype frequencies, respectively. No significant effects on economic traits in Hanwoo were found in the separate analysis of K232A and T11993C polymorphisms, but the interaction between K232A and T11993C showed a significant effect (p<0.005) on marbling score. The DGAT1 candidate gene was found to have a significant effect not only on milk yield and component traits but also on the metabolism of intramuscular fat.

• Korean Journal of Agricultural Science
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• v.39 no.2
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• pp.219-226
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• 2012

The acyl-CoA dehydrogenase, C-2 to C-3 short chain (ACADS) gene is known to be related with fat metabolism, especially coverts the fat to the energy sources in cattle. In human, the mutations in this gene cause SCAD deficiency, which is one of the fatty acid metabolism disorders. The ACADS gene is located on bovine chromosome 17. The objective of this study was to identify SNPs in Hanwoo ACADS gene and identify the relationships with economic traits. In this study, two SNPs, T1570G SNP in exon 2 and G13917A SNP in exon 4, were observed. Moreover, in the coding region, 2 missense mutations, T (Cys) ${\rightarrow}$ G (Trp) mutation at 1570 bp and G (Arg) ${\rightarrow}$ A (Gln) mutation at 13917 bp, were observed. These mutations were subjected to the PCR-RFLP for typing 198 Hanwoo animals. The observed genotype frequency for T1570G was 0.135 (TT), 0.860 (TG) and 0.005 (GG), respectively. Also, 0.900 (GG) and 0.100 (GA) were observed for the G13917A mutation. The association of these SNPs with four economic traits, CW (Carcass Weight), BF (Backfat Thickness), LMA (Longissimus Muscle Area), MS (Marbling Score), were also observed. The results indicated that no significant results were observed in all four traits (P>0.05). This might indicate that further studies are ultimately needed to use the SNPs in ACADS gene in lager populations for effectively used for the marker assisted selection.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.10
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• pp.1404-1408
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• 2006

In order to investigate the genetic marker associated with economic performance in Hanwoo (Korean Brown Cattle), proteomic approach was used. Breeding values were estimated from performance tested steers. The top 20 and bottom 19 steers based on carcass weight (CW), eye muscle area (EMA), backfat thickness (BF) and marbling score (MS) evaluation for one progeny testing period was used. Meat samples dissected from longissimus dorsi muscles were taken from the slaughter house and analyzed for two-dimensional gel electrophoresis. A total of 102 significant spots out of total 146 on each gel were detected and compared with the reference gel (synthetic gel) to be evaluated. Four candidate spots for marbling score were identified: 205, 84, 204 and 198. The study confirmed the relationship between breeding values of economic traits of Hanwoo cattle and spot intensity.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.10
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• pp.1371-1379
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• 2015

Undoubtedly livestock is one of the major contributors to the economy of any country. The economic value of livestock includes meat, dairy products, fiber, fertilizer etc. Understanding and identifying the associations of quantitative trait loci (QTL) with the economically important traits is believed to substantially benefit the livestock industry. The past two decades have seen a flurry of interest in mapping the QTL associated with traits of economic importance on the genome. With the availability of single nucleotide polymorphism chip of various densities it is possible to identify regions, QTL and genes on the genome that explain the association and its effect on the phenotype under consideration. Remarkable advancement has been seen in genome wide association studies (GWAS) since its inception till the present day. In this review we describe the progress and challenges of GWAS in various livestock species.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.9
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• pp.1353-1362
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• 2016

Hanwoo, a Korean native cattle (Bos taurus coreana), has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generation sequencing technologies and the availability of an appropriate reference genome were applied to discover a large amount of single nucleotide polymorphisms (SNPs) in ten Hanwoo bulls. Analysis of whole-genome resequencing generated a total of 26.5 Gb data, of which 594,716,859 and 592,990,750 reads covered 98.73% and 93.79% of the bovine reference genomes of UMD 3.1 and Btau 4.6.1, respectively. In total, 2,473,884 and 2,402,997 putative SNPs were discovered, of which 1,095,922 (44.3%) and 982,674 (40.9%) novel SNPs were discovered against UMD3.1 and Btau 4.6.1, respectively. Among the SNPs, the 46,301 (UMD 3.1) and 28,613 SNPs (Btau 4.6.1) that were identified as Hanwoo-specific SNPs were included in the functional genes that may be involved in the mechanisms of milk production, tenderness, juiciness, marbling of Hanwoo beef and yellow hair. Most of the Hanwoo-specific SNPs were identified in the promoter region, suggesting that the SNPs influence differential expression of the regulated genes relative to the relevant traits. In particular, the non-synonymous (ns) SNPs found in CORIN, which is a negative regulator of Agouti, might be a causal variant to determine yellow hair of Hanwoo. Our results will provide abundant genetic sources of variation to characterize Hanwoo genetics and for subsequent breeding.

• Korean Journal of Agricultural Science
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• v.45 no.1
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• pp.66-73
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• 2018

Hanwoo is an important livestock resource in Korea. Its genetic improvements of economic traits have mainly focused on the steers in the past. However, there is a great necessity to extend the breed improvement programs to the cows as well. Therefore, the objective of this study was to investigate the effects of various environmental factors (person taking the measurement, region, year of measurement, month of measurement, image interpreter, birth-year and birth-year) on ultrasound measured carcass traits. A total of 27,215 ultrasound measurements of carcass traits were recorded between 2004 and 2012 for 22,620 cows born from 1997 to 2011. The ultrasound measures included backfat thickness (BFT), eye muscle area (EMA), and marbling score (MAR). The mean values for the BFT, EMA and MAR were 4.46 mm, $56.24cm^2$, and 4.12 point, respectively. Seven environmental factors, person taking the measurement, region, year of measurement, month of measurement, image interpreter, birth-year and birth-month, were tested to determine if they had a significant effect on the studied traits using the GLM procedure in SAS. All factors were found to significantly affect all the ultrasound carcass traits in this study. Unlike in previous studies, among the environmental effects, the significant effect of the image interpreter on the ultrasound carcass traits was shown for the first time in this study. These results indicate that future genetic evaluations of ultrasound carcass traits of Hanwoo cows should include all of the above environmental factors as well as the effect from people taking the measurements.

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

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.6
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• pp.784-788
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• 2008

Studies to detect genes responsible for economic traits in farm animals have been performed using parametric linear models. A non-parametric, model-free approach using the 'expanded multifactor-dimensionality reduction (MDR) method' considering high dimensionalities of interaction effects between multiple single nucleotide polymorphisms (SNPs), was applied to identify interaction effects of SNPs responsible for carcass traits in a Hanwoo beef cattle population. Data were obtained from the Hanwoo Improvement Center, National Agricultural Cooperation Federation, Korea, and comprised 299 steers from 16 paternal half-sib proven sires that were delivered in Namwon or Daegwanryong livestock testing stations between spring of 2002 and fall of 2003. For each steer at approximately 722 days of age, the Longssimus dorsi muscle area (LMA) was measured after slaughter. Three functional SNPs (19_1, 18_4, 28_2) near the microsatellite marker ILSTS035 on BTA6, around which the QTL for meat quality were previously detected, were assessed. Application of the expanded MDR method revealed the best model with an interaction effect between the SNPs 19_1 and 28_2, while only one main effect of SNP19_1 was statistically significant for LMA (p<0.01) under a general linear mixed model. Our results suggest that the expanded MDR method better identifies interaction effects between multiple genes that are related to polygenic traits, and that the method is an alternative to the current model choices to find associations of multiple functional SNPs and/or their interaction effects with economic traits in livestock populations.

• Journal of Animal Science and Technology
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• v.64 no.1
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• pp.143-154
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• 2022

This study was conducted to evaluate the relationship among market weight, slaughter age, yield grade, and primal cut yield in Hanwoo. A total of 403 Hanwoo (Korean native cattle) was assessed for carcass traits such as carcass cold weight, backfat thickness, ribeye area, dressing percentage, yield index, and marbling score. The production yield of the individual major primal cuts of Hanwoo beef was also measured. Carcass cold weight, ribeye area, and backfat thickness, which affect meat quality increased with increased market weight (p < 0.05). The production yield of the ten major primal cuts also increased with increased market weight (p < 0.05). In terms of slaughter age, carcass cold weight, ribeye area, and backfat thickness all increased from 25 months to 28-29 months, and the production yield of all prime cuts also increased with increasing slaughter age. According to the meat yield grade, carcass cold weight and backfat thickness increased from grade A to grade C, although the ribeye area was not affected. The combined findings of the study suggest that slaughtering Hanwoo at the weight of 651-700 kg and 701-750 and age of 28.23 and 29.83 months could be desirable to achieve the best quality and quantity grade of Hanwoo beef. However, the positive correlation of carcass cold weight and backfat thickness, and the negative correlation of the yield index according to primal cuts yield indicated that it is necessary to couple the slaughtering management of cattle with improved genetic and breeding method of Hanwoo to increase the production yield of the major prime cuts of Hanwoo beef.