• Asian-Australasian Journal of Animal Sciences
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• v.20 no.3
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• pp.328-333
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• 2007

Carboxypeptidase E (CPE) plays an important role in the regulation of the body fat content. Therefore, it has been suggested as candidate gene for traits related to meat quality in beef cattle. This study was conducted to identify single nucleotide polymorphisms (SNPs) in the CPE gene and to investigate association of SNP marker with carcass and meat quality traits in Korean cattle. Three SNPs were identified in the intron 4 (A309G SNP and C445T SNP) and exon 5 (C601T SNP) of the CPE gene by sequence analyses of CPE cDNA and genomic DNA samples. The sequences have been deposited in GenBank database with accession numbers AY970664 and AY970663. Genotyping of the gene-specific SNP marker was carried out using the PCR-RFLP with restriction enzymes DdeI for C445T SNP and NlaIII for C601T SNP. The frequencies of C and T alleles were 0.43 and 0.57 for C445T SNP and 0.42 and 0.58 for C601T SNP, respectively. Statistical analysis indicated that the C445T SNP showed a significant effect (p<0.05) on marbling score (MS) and breeding value of backfat thickness (BF-EBV), respectively. Animals with the CT genotype showed higher marbling score and backfat thickness than those with the TT genotype. This marker also showed a significant dominance effect for the MS and BF-EBV (p<0.05). However, no significant associations were observed between C601T SNP genotypes and all traits examined. The results suggest that the CPE gene may be used as a marker for carcass traits in Korean cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.58-62
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• 2019

Objective: The oxidized low density lipoprotein receptor 1 (OLR1) gene plays an important role in the degradation of oxidized low-density lipoprotein and adipocyte proliferation in mammals. For this reason, we aimed at investigating the association of OLR1 gene polymorphisms with carcass quality traits in Chinese Qinchuan cattle. Methods: The single nucleotide polymorphism (SNP) was identified in the 3' untranslated region of bovine OLR1 gene by DNA sequencing. In addition, the haplotype frequency and linkage disequilibrium estimates of three SNPs were evaluated in 520 individuals. Results: Results indicated that the studied three SNPs were within the range of moderate genetic diversity (0.25< polymorphism information content<0.5). Haplotype analysis of three SNPs showed that ten different haplotypes were identified, but only five haplotypes were listed as those with a frequency of <0.05 were excluded. The Hap3 ($-G_1T_2C_3-$) had the highest haplotype frequency (42.10%). Linkage disequilibrium analysis showed that the three SNPs had a low linkage ($r^2<0.001$). The T10588C and C10647T were significantly associated with backfat thickness and intramuscular fat content in Qinchuan cattle. Conclusion: Based on our results, we believe that the OLR1 gene could be a strong candidate gene for influencing carcass quality traits in Qinchuan cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.1
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• pp.8-19
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• 2017

Objective: A whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs) with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo. Methods: The data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant. Results: A total of 18 (0), 15 (3), 12 (8), 15 (18), 11 (7), and 21 (1) SNPs were detected at the 5% chromosome (genome) - wise level for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA) and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL) regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29) were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA). Conclusion: The application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.

• Food Science of Animal Resources
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• v.31 no.4
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• pp.537-542
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• 2011

Biological or physiological genes that regulate metabolism and energy partitioning have the potential to influence economically important traits such as carcass and meat quality traits in beef cattle. The neuropeptide Y (NPY) functions as a central appetite stimulator and plays a major role in feed intake and energy-balance control. Therefore, the NPY gene is an excellent biological and physiological candidate gene for body weight, feeding, fatness or growth related traits in beef cattle. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in the NPY gene and to evaluate the association of NPY SNP markers with carcass and meat quality traits in Korean cattle. The genomic region (711 bp) including intron 2 of NPY gene was amplified and sequenced, and five SNPs, g.4389 Del(C), g.4371Del(C), g.4271T>C, g.1899A>G and g.1517A>C, were identified. The PCR-RFLP method was then developed to genotype the individuals examined. The g.4271T>C SNP was significantly associated with M. Longissimus dori area (LDA) value (p<0.027). Animals with the TT ($78.144{\pm}0.950\;cm^2$) genotype had higher LDA than those with the CC ($72.266{\pm}2.039\;cm^2$), and animals with TC genotype showed intermediate value. This SNP genotype also showed a highly significant additive genetic effect for the LDA (p<0.01). No significant associations, however, was detected between any of the SNP genotype and other carcass traits measured in this study. In conclusion, SNP genotype of the NPY gene may be used as DNA markers to select animals that have a higher meat yield.

• Journal of Animal Science and Technology
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• v.62 no.3
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• pp.293-305
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• 2020

The difference in the breeding programs and population history may have diversely shaped the genomes of Korean native cattle breeds. In the absence of phenotypic data, comparisons of breeds that have been subjected to different selective pressures can aid to identify genomic regions and genes controlling qualitative and complex traits. In this study to decipher genetic variation and identify evidence of divergent selection, 3 Korean cattle breeds were genotyped using the recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array. The three Korean cattle breeds clustered according to their coat color phenotypes and breeding programs. The Heugu breed reliably showed smaller effective population size at all generations considered. Across the autosomal chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the two pairwise comparisons. The most important signals of selection were detected on bovine chromosomes 14 (24.39-25.13 Mb) and 18 (13.34-15.07 Mb), containing genes related to body size, and coat color (XKR4, LYN, PLAG1, SDR16C5, TMEM68, CDH15, MC1R, and GALNS). Some of the candidate genes are also associated with meat quality traits (ACSF3, EIF2B1, BANP, APCDD1, and GALM) and harbor quantitative trait locus (QTL) for beef production traits. Further functional analysis revealed that the candidate genes (DBI, ACSF3, HINT2, GBA2, AGPAT5, SCAP, ELP6, APOB, and RBL1) were involved in gene ontology (GO) terms relevant to meat quality including fatty acid oxidation, biosynthesis, and lipid storage. Candidate genes previously known to affect beef production and quality traits could be used in the beef cattle selection strategies.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.6
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• pp.862-869
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• 2015

The current study was designed to estimate the pork quality traits using metabolites from exsanguination blood and postmortem muscle simultaneously under the Korean standard pre- and post-slaughter conditions. A total of 111 Yorkshire (pure breed and castrated male) pigs were evaluated under the Korean standard conditions. Measurements were taken of the levels of blood glucose and lactate at exsanguination, and muscle glycogen and lactate content at 45 min and 24 h postmortem. Certain pork quality traits were also evaluated. Correlation analysis and multiple regression analysis including stepwise regression were performed. Exsanguination blood glucose and lactate levels were positively correlated with each other, negatively related to postmortem muscle glycogen content and positively associated with postmortem muscle lactate content. A rapid and extended postmortem glycolysis was associated with high levels of blood glucose and lactate, with high muscle lactate content, and with low muscle glycogen content during postmortem. In addition, these were also correlated with paler meat color and reduced water holding capacity. The results of multiple regression analyses also showed that metabolites in exsanguination blood and postmortem muscle explained variations in pork quality traits. Especially, levels of blood glucose and lactate and content of muscle glycogen at early postmortem were significantly associated with an elevated early glycolytic rate. Furthermore, muscle lactate content at 24 h postmortem alone accounted for a considerable portion of the variation in pork quality traits. Based on these results, the current study confirmed that the main factor influencing pork quality traits is the ultimate lactate content in muscle via postmortem glycolysis, and that levels of blood glucose and lactate at exsanguination and contents of muscle glycogen and lactate at postmortem can explain a large portion of the variation in pork quality even under the standard slaughter conditions.

• Animal Bioscience
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• v.37 no.4
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• pp.555-566
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• 2024

Objective: This study aimed to assess the genetic parameters and accuracy of genomic predictions for twenty-four linear body conformation traits and overall conformation scores in Korean Holstein dairy cows. Methods: A dataset of 2,206 Korean Holsteins was collected, and genotyping was performed using the Illumina Bovine 50K single nucleotide polymorphism (SNP) chip. The traits investigated included body traits (stature, height at front end, chest width, body depth, angularity, body condition score, and locomotion), rump traits (rump angle, rump width, and loin strength), feet and leg traits (rear leg set, rear leg rear view, foot angle, heel depth, and bone quality), udder traits (udder depth, udder texture, udder support, fore udder attachment, front teat placement, front teat length, rear udder height, rear udder width, and rear teat placement), and overall conformation score. Accuracy of genomic predictions was assessed using the single-trait animal model genomic best linear unbiased prediction method implemented in the ASReml-SA v4.2 software. Results: Heritability estimates ranged from 0.10 to 0.50 for body traits, 0.21 to 0.35 for rump traits, 0.13 to 0.29 for feet and leg traits, and 0.05 to 0.46 for udder traits. Rump traits exhibited the highest average heritability (0.29), while feet and leg traits had the lowest estimates (0.21). Accuracy of genomic predictions varied among the twenty-four linear body conformation traits, ranging from 0.26 to 0.49. The heritability and prediction accuracy of genomic estimated breeding value (GEBV) for the overall conformation score were 0.45 and 0.46, respectively. The GEBVs for body conformation traits in Korean Holstein cows had low accuracy, falling below the 50% threshold. Conclusion: The limited response to selection for body conformation traits in Korean Holsteins may be attributed to both the low heritability of these traits and the lower accuracy estimates for GEBVs. Further research is needed to enhance the accuracy of GEBVs and improve the selection response for these traits.

• Animal Bioscience
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• v.36 no.6
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• pp.840-850
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• 2023

Objective: This study aimed to investigate the polymorphisms of the dopa decarboxylase (DDC) gene and association analysis with lamb quality and expression quantification of the DDC gene in phenotypically divergent Indonesian sheep. Methods: The totals of 189 rams with an average body weight of 24.12 kg at 10 to 12 months were used to identify DDC gene polymorphism using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Among 189 rams, several rams representing various sheep genotypes were used for an association study between genotypes and phenotypic traits with proc general linear model (GLM) analysis. In addition, the gene expression analysis of the DDC mRNA in the phenotypically divergent sheep population was analyzed using quantitative reverse-transcription PCR. Results: The DDC gene (g. 5377439 G>A) showed polymorphisms that indicated three genotypes: AA, AG, and GG. The DDC gene polymorphism was significantly associated (p≤0.05) with carcass characteristics including carcass percentage, carcass length, hot and cold carcass; physical properties of lamb quality including pH value; retail cut carcass; fatty acid composition such as fat content, pentadecanoic acid (C15:0), tricosylic acid (C23:0), lignoceric acid (C24:0), oleic acid (C18:1n9c), elaidic acid (C18:1n9t), nervonic acid (C24:1), linoleic acid (C18:2n6c), arachidonic acid (C20:4n6), cervonic acid (C22:6n3); and mineral content including potassium (K). The GG genotype of the DDC gene had the best association with lamb quality traits. The DDC gene expression analysis mRNA showed no significant difference (p≥0.05) between lamb quality traits. Conclusion: The DDC gene could be used as a potential candidate gene to improve lamb quality.

• Korean Journal of Agricultural Science
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• v.45 no.1
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• pp.50-57
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• 2018

Meat comes from the skeletal muscles of farm animals, such as pigs, chickens, and cows. Skeletal muscles are composed of many muscle fibers. Muscle fibers are categorized into three types, fiber type I, IIA, and IIB, based on their contractile speed and metabolic properties. Different muscle fiber types have different biochemical, physiological, and biophysical characteristics. Especially, the characteristics of muscle fiber type I and IIB are opposite to each other. Muscle fiber type I has a relatively strong oxidative metabolic trait and a higher content of lipids. In contrast to fiber type I, muscle fiber type IIB has a strong glycolytic metabolic trait and a relatively lower content of lipids and a higher content of glycogen. Muscle fiber type IIA has intermediate properties between fiber type I and IIB. Thus, muscles with different fiber type compositions exhibit different ante- and post-mortem muscle characteristics. In particular, the different metabolic traits of muscles due to the different compositions of the fiber types strongly affect the biochemical and physiological processes during the conversion of muscle to meat and subsequently influence the quality of the meat. Therefore, understating muscle metabolism and muscle fiber characteristics is very important when discussing the traits of meat quality. This review is an overview on basic muscle metabolism, muscle fiber characteristics, and their influence on meat quality and finally provides a comprehensive understanding about the fundamental traits of muscles and meat quality.

• Food Science of Animal Resources
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• v.39 no.2
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• pp.197-208
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• 2019

The aim of this study was to investigate the relation of sensory quality traits of cooked beef to fresh meat quality and histochemical characteristics, especially muscle bundle traits, in the longissimus thoracis muscle of Hanwoo steers. Cooking loss negatively correlated with softness, initial tenderness, chewiness, rate of breakdown (RB), and amount of perceptible residue (AR) after chewing (p<0.05), and drip loss showed negative correlation with RB and AR (p<0.05). All the attributes of tenderness exhibited negative correlation with the Warner-Bratzler shear force value (p<0.05). Marbling score and the intramuscular fat (IMF) content showed positive correlation with all the organoleptic characteristics, including tenderness attributes, juiciness, and flavor (p<0.05). Regarding histochemical characteristics, muscle fiber size did not have a significant correlation with all the sensory quality traits, although the area percentage of type I fiber was related with softness, initial tenderness, and chewiness (p<0.05). On the contrary, the characteristics of muscle bundle were related to all the sensory tenderness attributes (p<0.05), and the sensory tenderness increased with smaller muscle bundle size (p<0.05). These results suggest that the IMF content and bundle characteristics can be used as indicators for explaining the variations in sensory tenderness in well-marbled beef.