• Journal of Animal Science and Technology
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• v.55 no.1
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• pp.13-18
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• 2013

This study was conducted to estimate the Genomic Estimated Breeding Value (GEBV) using Genomic Best Linear Unbiased Prediction (GBLUP) method in Hanwoo (Korean native cattle) population. The result is expected to adapt genomic selection onto the national Hanwoo evaluation system. Carcass weight (CW), eye muscle area (EMA), backfat thickness (BT), and marbling score (MS) were investigated in 552 Hanwoo progeny-tested steers at Livestock Improvement Main Center. Animals were genotyped with Illumina BovineHD BeadChip (777K SNPs). For statistical analysis, Genetic Relationship Matrix (GRM) was formulated on the basis of genotypes and the accuracy of GEBV was estimated with 10-fold Cross-validation method. The accuracies estimated with cross-validation method were between 0.915~0.957. In 534 progeny-tested steers, the maximum difference of GEBV accuracy compared to conventional EBV for CW, EMA, BT, and MS traits were 9.56%, 5.78%, 5.78%, and 4.18% respectively. In 3,674 pedigree traced bulls, maximum increased difference of GEBV for CW, EMA, BT, and MS traits were increased as 13.54%, 6.50%, 6.50%, and 4.31% respectively. This showed that the implementation of genomic pre-selection for candidate calves to test on meat production traits could improve the genetic gain by increasing accuracy and reducing generation interval in Hanwoo genetic evaluation system to select proven bulls.

• Journal of the Korean Data and Information Science Society
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• v.23 no.3
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• pp.467-474
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• 2012

Human diseases and livestock economic traits are not typically the result of variation of a single genetic locus, but are rather the result of interplay between interactions among multiple genes and a variety of environmental exposures. We have used linear regression model for adjusted environmental effects and multifactor dimensionality reduction (MDR) method to identify gene-gene interaction effect of statistical model in general. Of course, we use 5 SNPs (single uncleotide polymorphism) which were studied recently by Oh et al. (2011). We apply the MDR (multifactor demensionality reduction) method on the identify major interaction effects of single nucleotide polymorphisms responsible for economic traits in a Korean cattle population.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.222-227
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• 2009

The seasonal variation of bacterial populations in the Korean cattle (Hanwoo) feedlots dispersed in the 20 cities of Gyeongsangbuk-do, Korea, was monitored for two years (2006 and 2007) to provide quantitative criteria for good agricultural management. Outside the feedlots, the average falling bacterial populations of the air were $3{\pm}1$ CFU/$cm^2\cdot15$ min (n=63) in a year. Inside the feedlots, the average falling bacterial populations of the air were $8{\pm}1$ CFU/$cm^2\cdot15$ min (n=63) in the spring, $16{\pm}2$ CFU/$cm^2\cdot15$ min (n=69) in the summer, $7{\pm}2$ CFU/$cm^2\cdot15$ min (n=69) in the autumn, and $6{\pm}1$ CFU/$cm^2\cdot15$ min (n=70) in the winter. Without using the summer data, the average falling bacterial population of the air was $7{\pm}1$ CFU/$cm^2\cdot15$ min, which was not statistically significant (P=0.37). The average bacterial populations in the cattle drinking water of the cattle feedlots were $4,710{\pm}780$ CFU/ml (n=65) in the spring, $10,430{\pm}1170$ CFU/ml (n=65) in the summer, $4,820{\pm}700$ CFU/ml (n=64) in the autumn, and $2,510{\pm}530$ CFU/ml (n=64) in the winter. Without using the summer data, the average bacterial population of the drinking water was $4,000{\pm}400$ CFU/ml, which was statistically significant (P=0.027). The average frequency of Escherichia coli O157 inside the feedlots was 5% (n=65) in the spring, 72% (n=65) in the summer, 67% (n=66) in the autumn, and 29% (n=66) in the winter on the basis of soil samples of the year 2007. The results indicate that most of the Escherichia coli O157 strains distributed in the summer and autumn was disappeared in the spring through the cold weather of the winter.

• Journal of the Korean Society of Food Science and Nutrition
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• v.45 no.2
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• pp.230-238
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• 2016

This study examined the effects of freezing and thawing conditions on quality of Hanwoo bottom round. The beef samples were frozen by air blast freezing at $-20^{\circ}C$ or ethanol immersion freezing at $-70^{\circ}C$ and then stored at $-20^{\circ}C$ for 10 days. After 10 days of storage, the frozen samples were thawed with air blast thawing at $4^{\circ}C$ or water immersion thawing at $4^{\circ}C$ and subjected to subsequent analyses of drip loss, water holding capacity, thiobarbituric acid reactive substance (TBARS), volatile basic nitrogen (VBN), total aerobic bacteria, and microstructure. Drip loss significantly increased in samples treated with air blast freezing compared to ethanol immersion freezing, whereas freezing and thawing processes had no significant impact on water holding capacity of the samples. Thawing conditions had a much stronger influence on the TBARS and VBN of the samples than freezing conditions. There was no significant difference in the population of total aerobic bacteria among the four samples subjected to one freeze-thaw cycle. In addition, to analyze the effects of freeze-thaw cycle on the quality of beef, three freeze-thaw cycles were performed during storage. Multiple freeze-thaw cycles increased drip loss, TBARS, and VBN and decreased water holding capacity, accelerating microstructural damage. These data indicate that Hanwoo bottom round can be rapidly frozen and thawed by using ethanol immersion freezing and water immersion thawing methods with minimal impact on meat quality.

• Journal of Animal Science and Technology
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• v.50 no.5
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• pp.613-620
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• 2008

The genetic parameters used in National Hanwoo Genetic Evaluation(NHGE) were needed to be monitored and updated periodically for accounting any possible changes in population parameters due to selection and environmental changes. Genetic parameters were estimated with single and two-trait models with MTDFREML package using 2,791 carcass records of steers collected from Hanwoo Progeny Test Program(HPTP). Single and two-trait models gave similar parameter estimates for all traits. The heritability estimates from single and two-trait models for carcass weight(CW), dressing percentage(DP), eye muscle area(EMA), back fat thickness(BFT) and marbling score(MS) were 0.30, 0.30, 0.37, 0.44 and 0.44, respectively. The heritability estimates for all the traits except BFT were slightly lower than those used in NHGE but seemed to be within the acceptable ranges. However, further monitoring is needed because the data might not have fully reflected the changes such as carcass grading standards in performance testing program. In order to shift statistical model of NHGE from single trait model to multiple-trait model, the genetic correlations between carcass traits were estimated with pairwise two-trait models. The genetic correlation coefficients between CW and DP, between CW and EMA, between CW and BFT and between CW and MS were 0.44, 0.63, 0.17 and 0.06, respectively. Those between DP and EMA, between DP and BFT and between DP and MS were 0.29, 0.40 and 0.20. Those between EMA and BFT and between EMA and MS were －0.24 and 0.15, respectively. The genetic correlation coefficient between BFT and MS was 0.03.

• Journal of Animal Science and Technology
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• v.49 no.6
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• pp.699-710
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• 2007

This study was conducted to estimate the genetic parameters and their relationships with weight traits of the steers and bulls in the Hanwoo population. The data used were weights and weight gain of performance and progeny test from 6,024 heads of Hanwoo. Data of performance test consisted of total 3,737 heads raised from August, 1989 to September, 2005. The number of the records of progeny test was total 2,287 heads from August, 1996 to June, 2004. The heritabilities and correlations for the body weights at the ages of 6 months, 12 months and 24 months and average daily gain were estimated by DFREML. Overall means and standard deviations of body weights at 6 and 12 months of age and average daily gain(ADG) from the data of performance test were 181.72±30.22kg, 351.48±40.24kg, 998.07±153.84g, respectively. Overall means and standard deviations of body weights at 6, 12, and 24 month of age and ADG from the data of progeny test were 169.18±32.82kg, 229.37±44.57kg, 570.45±64.36kg and 739.41± 172.14g, respectively. The heritability estimates of the body weight at 6, 12 month and ADG from the performance test were 0.54±0.06, 0.60±0.06 and 0.23±0.04, respectively. The heritability estimates of the body weight at 6, 12, 24 month and ADG from the progeny test were 0.80±0.08, 0.50±0.07, 0.46±0.07 and 0.07±0.03, respectively.

• Journal of Life Science
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• v.22 no.12
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• pp.1644-1650
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• 2012

The aim of this study was to screen the polymorphisms and distribution of each genotype of insertion/ deletion (indel) markers which were found in a preliminary comparative study of bovine genomic sequence databases. Comparative bioinformatic analyses were first performed between the nucleotide sequences of Bovine Genome Project and those of expressed sequence tag (EST) database, and a total of fifty-one species of indel markers were screened. Of these, forty-two indel markers were evaluated, and nine informative indel markers were ultimately selected for population analysis. Nucleotide sequences of each marker were re-sequenced and their polymorphic patterns were typed in six cattle breeds: Holstein, Angus, Charolais, Hereford, and two Korean native cattle breeds (Hanwoo and Jeju Black cattle). Cattle breeds tested in this study showed polymorphic patterns in eight indel markers but not in the Indel-15 marker in Charolais and Holstein. The results of analysis for Jeju Black cattle (JBC) population indicated an observed heterozygosity (Ho) that was highest in HW_G1 (0.600) and the lowest in Indel_29 (0.274). The PIC value was the highest in HW_G4 (0.373) and lowest in Indel_6 (0.305). These polymorphic indel markers will be useful in supplying genetic information for parentage tests and traceability and to develop a molecular breeding system for improvement of animal production in cattle breeds as well as in the JBC population.

• Korean Journal of Poultry Science
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• v.18 no.3
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• pp.151-159
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• 1991

As a part of investigation on causes of drop in egg production in domestic chicken breeding farm, bacteriological contamination on air, feed, drinking water and artificial insemination instruments of randomly selected three farms was surveyed. Total bacterial population in the air was very high in all of the chicken houses tested and was not significantly different among these farms . However, total bacterial counts in the air of the problem house having egg drop problem and colibacillosis was higher than normal house within the problem farm. Bacterial population in the assorted feed was low before or after administration on the normal farm while it was much more increased after administration than before administration on the problem farm. Bacterial population of the drinking water in the source of water supply was very low and has no differences among farms tested. Also, bacterial population in the normal farm was not significantly different between source of water supply and after administration. However, population of total bacteria and coliform bacteria after administration was increased. Bacterial population was much higher in the artificial insemination instrument of problem farm than normal farm. However, this bacterial population in the problem farm was decreased to those of normal farm after these instruments were sanitized.

• Journal of Life Science
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• v.28 no.11
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• pp.1255-1261
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• 2018

Whole genome analysis have been made possible with the development of DNA sequencing technologies and discovery of many single nucleotide polymorphisms (SNPs). Large number of SNP can be analyzed with SNP chips, since SNPs of human as well as livestock genomes are available. Among the various missing nucleotide imputation programs, Minimac3 software is suggested to be highly accurate, with a simplified workflow and relatively fast. In the present study, we used Minimac3 program to perform genomic missing value substitution 1,226 animals 770K SNP chip and imputing missing SNPs with next generation sequencing data from 311 animals. The accuracy on each chromosome was about 94~96%, and individual sample accuracy was about 92~98%. After imputation of the genotypes, SNPs with R Square ($R^2$) values for three conditions were 0.4, 0.6, and 0.8 and the percentage of SNPs were 91%, 84%, and 70% respectively. The differences in the Minor Allele Frequency gave $R^2$ values corresponding to seven intervals (0, 0.025), (0.025, 0.05), (0.05, 0.1), (0.1, 0.2), (0.2, 0.3). (0.3, 0.4) and (0.4, 0.5) of 64~88%. The total analysis time was about 12 hr. In future SNP chip studies, as the size and complexity of the genomic datasets increase, we expect that genomic imputation using Minimac3 can improve the reliability of chip data for Hanwoo discrimination.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.12
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• pp.1637-1643
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• 2011

Korean native chickens are a very valuable chicken population in Korea and their prices are higher than that of commercial broilers. In order to discriminate two commercial Korean native chicken populations (CCP1 and CCP2), single nucleotide polymorphisms (SNPs) from mitochondrial (mt) DNA D-loop sequences and LEI0258 marker polymorphisms in the major histocompatibility complex (MHC) region were investigated. A total of 718 birds from nine populations were sampled and 432 mtDNA sequences were obtained. Of these, two commercial Korean native chicken populations (363 birds) were used for investigation of their genetic relationship and breed differentiation. The sequence data classified the chickens into 20 clades, with the largest number of birds represented in clade 1. Analysis of the clade distribution indicated the genetic diversity and relation among the populations. Based on the mtDNA sequence analysis, three selected SNPs from mtDNA polymorphisms were used for the breed identification. The combination of identification probability (Pi) between CCP1 and CCP2 using SNPs from mtDNA and LEI0258 marker polymorphisms was 86.9% and 86.1%, respectively, indicating the utility of these markers for breed identification. The results will be applicable in designing breeding and conservation strategies for the Korean native chicken populations and also used for the development of breed identification markers.