• Asian-Australasian Journal of Animal Sciences
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• v.17 no.10
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• pp.1329-1333
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• 2004

To isolate the microsatellites from the chromosomal DNA of the Korean cattle (Hanwoo) and to use those for the genetic selection, four bacteriophage genomic libraries containing the chromosomal DNA of six Hanwoo steers showing the differences in meat quality and quantity were used. Screening of the genomic libraries using $^{32}P-radiolabeled 5'-({CA})_{12}-3$nucleotide as a probe, resulted in isolation of about 3,000 positive candidate bacteriophage clones that contain $(CA)_n$-type dinucleotide microsatellites. After confirming the presence of microsatellite in each positive candidate clone by Southern blot analysis, the DNA fragments that include microsatellite and flanking sequences possessing less than 2 kb in size, were subcloned into plasmid vector. Results from the analysis of microsatellite length polymorphism, using twenty-two PCR primers designed from flanking region of each microsatellite DNA, demonstrated that 208 and 210 alleles of HW-YU-MS#3 were closely related to the economic traits such as marbling score, daily gain, backfat thickness and M. longissimus dorsi area in Hanwoo. Interestingly, HW-YU-MS#3 microsatellite was localized in bovine chromosome 17 on which QTLs related to regulation of the body fat content and muscle ypertrophy locus are previously known to exist. Taken together, the results from the present study suggest the possible use of the two alleles as a DNA marker related to economic trait to select the Hanwoo in the future.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.9
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• pp.1371-1377
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• 2002

During a 5-yr period, 1994-1998, pre-weaning and weaning data were collected on 591 calves produced by mating either straightbred Jersey, straightbred Limousin or $F_1$ (Limousin${\times}$Jersey) bulls to mature purebred Jersey or Limousin cows. Traits recorded included birth and weaning weight, height, length, girth, fat depth and a measure of muscle (ratio of stifle to hip width expressed as a percentage). All traits were analyzed assuming a model with sire and dam random effects that included effects of year and date of birth, sex, breed and year${\times}$sex interaction. Main effects were generally significant with few exceptions. Direct genetic effects were large for weight, height, girth and muscle with a breed trend from purebred Jersey (small) to purebred Limousin (large). At weaning, the maternal effect of the Jersey dam was positive for weight (10.9${\pm}$4.9 kg), girth (3.7${\pm}$1.0 cm) and muscle (6.0${\pm}$0.9%). Heterosis was highly significant and positive only for fat depth (1.5${\pm}$0.2 mm) with the $F_1$ progeny being the fattest, followed by the backcrosses, then purebred Jersey and purebred Limousin. Also, significant (p<0.001) but negative heterosis was observed for weight, girth and muscle. The change in ranking for fat depth relative to other traits is a reflection of the large heterotic effects relative to direct effects on fat depth. Epistatic effects were not significant on any trait at birth or weaning. This study has indicated the possibility of exploiting the positive heterotic and maternal effects for fat depth and muscularity to meet specific meat quality and quantity demand by consumers.

• 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.55 no.6
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• pp.501-508
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• 2013

This study was conducted to determine genetic correlations among carcass traits measured by ultrasound and real carcass measurements and to estimate indirect selection responses for real carcass traits based on ultrasound measurements in Hanwoo cows. To accomplish this, 22,080 ultrasound measurement records from 17,926 cows collected from 2001 to 2012 and 11,907 carcass records obtained from fattened cattle from 2008 to 2012 were used. Genetic parameters were estimated based on eye muscle area (EMA), backfat thickness (BF) and marbling score (MS) measured by ultrasound-scanning of live cows and using the official technique on chilled bovine half-carcasses after slaughtering. Heritability and genetic correlation for carcass traits were estimated using a mixed model equation that consisted of environmental effects as fixed parameters and additive genetic effects and residual effects as random parameters, assuming that traits were different between ultrasound and carcass measurements. This statistical method was applied to the average information restricted maximum likelihood method. The heritability of EMA, BF and MS measured by ultrasound were 0.33, 0.61 and 0.46, respectively, while the heritability estimates of the corresponding traits based on carcass measurements were 0.29, 0.40 and 0.38, respectively and the genetic correlation between ultrasound and carcass traits for EMA, BF and MS were 0.41, 0.78 and 0.67, respectively. The genetic correlation between ultrasound and carcass traits was highly positive. Additionally, the selection response for marbling score was estimated to be 0.42 per generation if the cows were selected based on the ultrasound scan marbling score with an assumed selection intensity of 0.8. Overall, these results indicate that the ultrasound scan technique would be applicable to judging cow selection for genetically improved meat quality.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.7
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• pp.907-911
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• 2017

Objective: Intramuscular fat is one of the meat quality traits that is considered in the selection strategies for Hanwoo (Korean cattle). Different methods are used to estimate the breeding value of selection candidates. In the present work we focused on accuracy of different genotype relationship matrices as described by forni and pedigree based relationship matrix. Methods: The data set included a total of 778 animals that were genotyped for BovineSNP50 BeadChip. Among these 778 animals, 72 animals were sires for 706 reference animals and were used as a validation dataset. Single trait animal model (best linear unbiased prediction and genomic best linear unbiased prediction) was used to estimate the breeding values from genomic and pedigree information. Results: The diagonal elements for the pedigree based coefficients were slightly higher for the genomic relationship matrices (GRM) based coefficients while off diagonal elements were considerably low for GRM based coefficients. The accuracy of breeding value for the pedigree based relationship matrix (A) was 13% while for GRM (GOF, G05, and Yang) it was 0.37, 0.45, and 0.38, respectively. Conclusion: Accuracy of GRM was 1.5 times higher than A in this study. Therefore, genomic information will be more beneficial than pedigree information in the Hanwoo breeding program.

• Korean Journal of Poultry Science
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• v.45 no.4
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• pp.291-298
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• 2018

TBC1D1 gene has known functional effects on body energy homeostasis and glucose uptake pathway in skeletal muscle tissue. This biological function is reported to have significant effects on traits of growth and meat quality in chicken. In this study, we focused on two single nucleotide polymorphisms (SNPs) (g.70179137A>G and g.70175861T>C) identified through SNP annotation information of Korean native chicken and previous literature for TBC1D1 in chicken. Association of SNPs in TBC1D1 with growth and serum clinical-chemical traits were evaluated. A total of 584 male and female birds from five Korean native chicken lines were used in the study. The SNP1 (g.70179137A>G) is located in intron 11 and SNP2 (g.70175861T>C) is a non-synonymous missense mutation in exon 10, responsible for the amino acid change from Methionine to Valine. The A allele of SNP1 and T allele of SNP2 had the highest allele frequencies. Both SNPs indicated moderate polymorphism information content values (0.25

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.5
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• pp.607-613
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• 2019

Objective: Intramuscular fat (IMF) content plays an important role in meat quality. Identification of single nucleotide polymorphisms (SNPs) and genes related to pig IMF, especially using pig populations with high IMF content variation, can help to establish novel molecular breeding tools for optimizing IMF in pork and unveil the mechanisms that underlie fat metabolism. Methods: We collected muscle samples of 453 Chinese Lulai black pigs, measured IMF content by Soxhlet petroleum-ether extraction method, and genotyped genome-wide SNPs using GeneSeek Genomic Profiler Porcine HD BeadChip. Then a genome-wide association study was performed using a linear mixed model implemented in the GEMMA software. Results: A total of 43 SNPs were identified to be significantly associated with IMF content by the cutoff p<0.001. Among these significant SNPs, the greatest number of SNPs (n = 19) were detected on Chr.9, and two linkage disequilibrium blocks were formed among them. Additionally, 17 significant SNPs are mapped to previously reported quantitative trait loci (QTLs) of IMF and confirmed previous QTLs studies. Forty-two annotated genes centering these significant SNPs were obtained from Ensembl database. Overrepresentation test of pathways and gene ontology (GO) terms revealed some enriched reactome pathways and GO terms, which mainly involved regulation of basic material transport, energy metabolic process and signaling pathway. Conclusion: These findings improve our understanding of the genetic architecture of IMF content in pork and facilitate the follow-up study of fine-mapping genes that influence fat deposition in muscle.

• Journal of Animal Science and Technology
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• v.49 no.2
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• pp.161-170
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• 2007

A submerged biofilm sequencing batch reactor (SBSBR) process, which liquor was internally circulated through sandfilter, was designed, and performances in swine wastewater treatment was evaluated under a condition of no external carbon source addition. Denitrification of NOx-N with loading rate in vertical and slope type of sandfilter was 19% and 3.8%, respectively, showing approximately 5 times difference, and so vertical type sandfilter was chosen for the combination with SBSBR. When the process was operated under 15 days HRT, 105L/hr.m3 of internal circulation rate and 54g/m3.d of NH4-N loading rate, treatment efficiencies of STOC, NH4-N and TN (as NH4-N plus NOx-N) was 75%, 97% and 85%, respectively. By conducting internal circulation through sandfilter, removal performances of TN were enhanced by 14%, and the elevation of nitrogen removal was mainly attributed to occurrence of denitrification in sandfilter. Also, approximately 57% of phosphorus was removed with the conduction of internal circulation through sandfilter, meanwhile phosphorus concentration in final effluent rather increased when the internal circulation was not performed. Therefore, It was quite sure that the continuous internal circulation of liquor through sandfilter could contribute to enhancement of biological nutrient removal. Under 60g/m3.d of NH4-N loading rate, the NH4-N level in final effluent was relatively low and constant(below 20mg/L) and over 80% of nitrogen removal was maintained in spite of loading rate increase up to 100g/m3.d. However, the treatment efficiency of nitrogen was deteriorated with further increase of loading rate. Based on this result, an optimum loading rate of nitrogen for the process would be 100g/m3.d.

• Journal of Animal Science and Technology
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• v.45 no.6
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• pp.939-948
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• 2003

The objective of this study was to identify the quantitative traits loci(QTL) for economically important traits such as growth, carcass and meat quality on pig chromosome 6. A three generation resource population was constructed from cross between Korean native boars and Landrace sows. A total of 240 F$_2$ animals were produced using intercross between 10 boars and 31 sows of F$_1$ animals. Phenotypic data including body weight at 3 weeks, backfat thickness, muscle pH, shear force and crude protein level were collected from F$_2$ animals. Animals including grandparents(F$_0$), parents(F$_1$) and offspring(F$_2$) were genotyped for 29 microsatellite markers and PCR-RFLP marker on chromosome 6. The linkage analysis was performed using CRI-MAP software version 2.4(Green et al., 1990) with FIXED option to obtain the map distances. The total length of SSC6 linkage map estimated in this study was 169.3cM. The average distance between adjacent markers was 6.05cM. For mapping of QTL, we used F$_2$ QTL Analysis Servlet of QTL express, a web-based QTL mapping tool(http://qtl.cap.ed.ac.uk). Five QTLs were detected at 5% chromosome-wide level for body weight of 3 weeks of age, shear force, meat pH at 24 hours after slaughtering, backfat thickness and crude protein level on SSC6.

• Journal of Animal Science and Technology
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• v.50 no.3
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• pp.301-308
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• 2008

DNA variation of MYL2 intron 5 A345G and ADCYAP1R1 intron 2 A337G were investigated for carcass trait association in finished pigs. Three genotypes(two homozygotes and their heterozygote) were found at 10.6% AA, 45.6% AG and 43.8% GG in MYL2 and 60.5% AA, 34.6% AG, and 22.2% GG for ADCYAP1R1. In finished pig population, individuals containing genotype G- of MYL2 had significantly heavier carcass weight by more than 2.4 kg and thicker backfat thickness by more than 1.3 mm than those of AA homozygous pigs(p<0.05). No significant difference was found in other traits tested in this study such as marbling score, meat color, texture, moisture and separation score(p>0.05). The ADCYAP1R1 intron 2 377GG homozygotes showed coarse texture, i.e., meat quality was inferior than those of AG and AA genotypes, and the moisture level of homozygote AA was higher than those of AG and GG genotypes(p<0.05). The other carcass traits were not significantly associated with ADCYAP1R1 genotypes(p>0.05). The genetic polymorphism of MYL2 and ADCYAP1R1 genes affected the carcass traits in finished pig population. Further studies to explain the association between genetic variations and their phenotypic effects including economic traits in pigs are required including critical mutation in both genes through molecular approaches.