• Animal Bioscience
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• v.37 no.3
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• pp.461-470
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• 2024

Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, F_st, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, F_st, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

• Korean Journal of Poultry Science
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• v.30 no.4
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• pp.235-244
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• 2003

This study was carried out to estimate the effects of strain and generation on the major production performances of Korean native chicken. The data were collected from 11,583 birds of the 7 generations over the year 1995 through 2001 at National Livestock Research Institute, Korea. Results obtained were summarized as follows: The body weights at 150 and 270 days of age were 1,557.7 and 1880.7, 1,471.7 and 1,738.2, 1,393.5 and 1,694.9, 1,591.2 and 1,910.0, 1,545.6 and 1,763.6g in Red Brown, Yellow Brown, Gray Brown, Black, and White strains, respectively. The Coefficient of Variations (CVs) of the body weights at 150 and 270 days of age were 9.65~13.79% and 13.29~15.16%. The ages at first egg were 150.0, 148.3, 149.5, 152,8 and 147.7 days in Red Brown, Yellow Brown, Gray Brown, Black and White strains, respectively and the CVs were between 9.33 and 10.11%. The egg weights at the first egg and 270 days of age were 33.2 and 50.8, 32.2 and 49.2, 32.2 and 49.1, 33.0 and 50.0, 30.7 and 47.8g respectively. The CVs of the egg weights of the first egg and at 270 days of age were 13.54~15.27% and 6.93~7.36%. The numbers of eggs produced by 270 days of age were 77.0, 79.3, 77.3, 73,7, 75.4, respectively, and observed CVs were between 29.98~36.99%. The significant strain effects were investigated in all the major economic traits in Korean native chicken. The significant strain effects were investigated in all the major economic traits in Korean native chicken. The highest least square (LS) means of the body weights at 150 and 270 days of age were observed in Black strain as 1,594.38 and 1,911.57g. The earliest LS mean of the ages at first egg was 146.88days in White strain. The heaviest LS means of egg weights at the first egg and 270 days of age were observed in Red Brown strain as 32.20 and 50.74g. The LS mean of the largest number of egg production was 79.50 eggs in Yellow Brown strain. Also, The significant generation effects were investigated in all the major economic traits. The highest LS means of the body weights at 150 and 270 days of age were observed in the generation 3 as 1,599.74 and 1,905.01g. The earliest LS mean of the age at first egg was 143.31 days in 4th generation. The heaviest LS means of egg weights at the first egg and 270 days of age were observed in 7th and 5th generation as 35.68 and 50.42g. The LS means of the largest number of egg production was 78.53 eggs in generation 6. In general, light body weight, short time for the age at first egg, heavy egg weight, and large number of egg production were observed as the generation proceeded.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1689-1695
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• 2008

Leptin, the hormone product of the obese gene, is secreted predominately from white adipose tissue and regulates feed intake, energy metabolism and body composition. It has been considered a candidate gene for performance, carcass and meat quality traits in beef cattle. The objective of this study was to identify SNPs in the promoter region of the leptin gene and to evaluate the possible association of the SNP genotypes with carcass and meat quality traits in Korean cattle. We identified a total of 25 SNPs in the promoter region (1,208-3,049 bp upstream from the transcription start site) of the leptin gene, eleven (g.1508C>G, g.1540G>A, g.1545G>A, g.1551C>T, g.1746T>G, g.1798ins(G), g.1932del(T), g.1933del(T), g.1934del(T), g.1993C>T and g.2033C>T) of which have not been reported previously. Their sequences were deposited in GenBank database with accession number DQ202319. Genotyping of the SNPs located at positions g.2418C>G and g.2423G>A within the promoter region was performed by direct sequencing and PCR-SSCP method to investigate the effects of SNP genotypes on carcass and meat quality traits in Korean cattle. The SNP and SSCP genotypes from the two mutations of the leptin promoter were shown to be associated with the BF trait. The average BF value of animals with heterozygous SNP genotype was significantly greater than that of animals with the homozygous SNP genotypes for the g.2418C>G and g.2423G>A SNPs (p<0.05). Analysis of the combined genotype effect in both SNPs showed that animals with the AC SSCP genotype had higher BF value than animals with BB or AA SSCP genotypes (p<0.05). These results suggest that SNP of the leptin promoter region may be useful markers for selection of economic traits in Korean cattle.

• Journal of Animal Science and Technology
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• v.53 no.1
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• pp.15-22
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• 2011

The purpose of this study was to analyse of association between growth traits and single nucleotide polymorphisms (SNPs) polymorphism of phosphoglycerate kinase 2 (PGK 2) gene in pigs. The birth weight of piglet influences on weaning weight and survival rate that are import economic traits in pig industry. Also, these growth traits are representative factor to decrease a period getting to marketing weight as well as growth rate in pig. The PGK 2 is an isozyme that catalyzes the first ATP-generating step in the glycolytic pathwayand important enzyme related with energy metabolism. Twenty of SNPs were discoveredby genome structure analysis that compares the sequence on promoter and transcription region of PGK 2 gene in porcine chromosome 7. An association between PGK 2 SNPs and growth traits was analyzed in $F_2$ reciprocal-crossbred population between korean native pig (KNP) and Landrace. Association analysis indicated that polymorphism of the PGK 2 gene promoter region has significant effects on weight at birth (p<0.01) and weight at 3 weeks of age (p<0.0001). These results suggest that PGK 2 gene polymorphism was associated with energy metabolism and physiological function of growth in pig.

• Journal of Animal Science and Technology
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• v.48 no.1
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• pp.9-14
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• 2006

Milk yield and its quality traits determine the dairy enterprise profitability and sustainability. Milk quality traits including somatic cell counts (SCC) is an upcoming economic challenge for dairy farming community in Korea. This study estimated the effect of parity, stage of lactation (early, mid and late lactation) on SCC, stress (blood cortisol) and immunity (blood IgG, lymphocyte and neutrophil) traits, their heritabilities and genetic correlations between them. SCS and blood neutrophil count were significantly affected by both parity and stage of lactation, however; IgG was affected by only stage of lactation, and blood cortisol and lymphocyte were not affected by both factors. The SCS has shown increasing trend with the parity, however; the difference between first and second parity, second and third parity were not significant. The SCS in early (≤90 days) and late lactation (181≤days) were higher than that of mid lactation (91～180 days). Cortisol concentration in blood was lowest in fourth parity, however; the differences among the first three parties were not significant. The IgG was higher in fourth parity compare with first parity however; all other comparisons were noted non-significant. The IgG concentration was significantly higher in early lactation than those of mid and late lactation. The blood lymphocytes were decreased with increasing parity however the differences beyond second parity were not significant. The neutrophils were increased with the increasing lactation stage however; the difference between early and mid lactation was not significant. Although heritability of SCS was still lower, but it was meaningful value (0.09) and may be considered to improve milk quality. The genetic correlations between SCS and cortisol (-0.96), and lymphocyte (-0.76) were highly negative. Heritability of cortisol was low, however genetic correlations between cortisol and lymphocyte (0.79) was highly positive. IgG with medium heritability was correlated negatively with lymphocyte (-0.88) and neutrophil (-0.98). Lymphocyte was lowly heritable and highly correlated with neutrophil concentration (0.87).This study suggested that cortisol, IgG, lymphocyte and neutrophil being positively genetically correlation with somatic cell score could be used as alternative traits to enhance milk quality in Holstein cattle. Further studies are warranted to estimate genetic relationships between immunological and production traits to increase the genetic merit of Holstein cows for milk yield, to improve animal health and economic viability under intensive management system.

• Korean Journal of Agricultural Science
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• v.42 no.2
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• pp.141-149
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• 2015

The data of Duroc swine species that were born from 2000 to 2014 excluding missing ones collected by Korea National Institute of Animal Science were used in the present study. After removing missing data we used 9756 of productions data and 1728 of reproductive reference of breeding research to study the level of inbreeding and to investigate the impact on the reproductive traits, production traits. The correlation of reproductive traits and inbreeding coefficient are -0.07, -0.08 for total number pigs born, number of pigs born alive respectively and birth weight per litter is -0.10, number of pigs born alive per litter to 21days is -0.06 and body weight per litter to 21days is -0.09. The correlation coefficients of the inbreeding coefficients of reproductive traits are shown within 10% with negative correlation (P < 0.05). Days of 90kg and Backfat in the correlation coefficient and inbreeding coefficient production traits were not observed significant correlations, Average daily gain was investigated by the positive correlation of 0.05. According to the above results, the inbreeding level gave a negative effect on the improvement of the breed traits, investigating a relatively high compared to a negative effect on other traits. But overall correlation degree is less than 10% was observed. This inbreeding coefficient has not been clearly observed due to degeneration of the average inbreeding coefficients of these generations was maintained within 10% of the population. The scale of the experimental group was about 150 degree pig husbandry is very small compared to the advanced countries. However, the level of inbreeding in the population group with the appropriate mating combinations is maintained below 10% of population is thought to be small and can minimize the effects of inbreeding degeneration. further testing utilizing this selection is constantly considered to be necessary.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.2
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• pp.187-196
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• 2020

Objective: Porcine respiratory disease is one of the most important health problems causing significant economic losses. To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 single nucleotide polymorphisms in a total of 249 individuals based on genome-wide sequencing data. Methods: Genome comparison of susceptibility to swine EP in three pig breeds (Jinhua, Erhualian, and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using cross-population extended haplotype homozygosity and F-statistic (F_ST) statistical approaches identified 691 positively selected genes. Based on quantitative trait loci, gene ontology terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma. Results: Most of these genes were tested by several methods including transcription analysis and candidate genes association study. Among these genes: cytochrome P450 1A1 and catenin beta 1 (CTNNB1) are involved in fertility; transforming growth factor beta receptor 3 plays a role in meat quality traits; Wnt family member 2, CTNNB1 and transcription factor 7 take part in adipogenesis and fat deposition simultaneously; plasminogen activator, urokinase receptor (completely linked to AXL receptor tyrosine kinase, r² = 1) plays an essential role in the successful ovulation of matured oocytes in pigs; colipase like 2 (strongly linked to SAM pointed domain containing ETS transcription factor, r² = 0.848) is involved in male fertility. Conclusion: These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provides insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

• Journal of Life Science
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• v.18 no.6
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• pp.770-775
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• 2008

Several studies reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2. For application of the chromosomal information to pig industry through using DNA technology, single nucleotide polymorphism (SNP) markers are developed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes. A total of 34 SNPs were identified in 11 PCR products, an average of one SNP in every 296 bp.PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to genotype four commercial pig populations in Korea. The SNP markers were used to map candidate genes in QTL and to clarify the relevance of SNP and quantitative traits.

• Journal of Life Science
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• v.17 no.11
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• pp.1505-1510
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• 2007

We found 8 single nucleotide polymorphisms (SNPs) in adipocyte fatty acid bonding protein (FABP4) gene as candidate gene of FAT1 locus on pig chromosome 4. With over 800 heads of major commercial pig breeds including Duroc, Landrace, Berkshire and Yorkshire, we analyzed SNPs of FABP4 gene to determine possible effects of FABP4 genotype to economically important traits. $400{\sim}800\;bp$ amplicons in FABP4 gene were used PCR-RFLP for each SNPs and we found that the frequency of some SNPs of this gene was different among the breeds. According to the statistical analyses to determine possible associations of each genotype with economic traits, it was found that subgroup with different genotypes showed significant differences in daily gain, backfat thickness, lean percentage and feed conversion ratio (P<0.05). Thus, as a Part of enhancing the selection competence related to swine growth rate and lean percentage, it is expected that FABP4 gene markers verified in this study will be useful to use for Korean commercial pig industry.

• Journal of Life Science
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• v.15 no.6 s.73
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• pp.968-971
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• 2005

The Melanocortin-4 receptor gene (MC4R) regulates the energy balance and the genetic basis of obesity. A polymorphism in the porcine melanocortin-4 receptor has previously shown to be associated with growth, fat deposition and feed intake. In this study, the polymorphism of the gene was studied in several pig breeds of Duroc, Landrace, Berkshire, and Yorkshire. The results showed that the frequencies of MC4R genotype varied among those breeds. Association analyses were also performed between the MC4R polymorphism and average daily gain, feed conversion ratio, backfat thickness and lean percentage phenotypes. The results strongly support that the MC4R polymorphism can be used DNA marker selection indicator for economically important traits for pig breeding program in Korea.