• Asian-Australasian Journal of Animal Sciences
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• 제27권9호
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• pp.1219-1227
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• 2014

A whole genome association (WGA) study was carried out to find quantitative trait loci (QTL) for sensory evaluation traits in Hanwoo. Carcass samples of 250 Hanwoo steers were collected from National Agricultural Cooperative Livestock Research Institute, Ansung, Gyeonggi province, Korea, between 2011 and 2012 and genotyped with the Affymetrix Bovine Axiom Array 640K single nucleotide polymorphism (SNP) chip. Among the SNPs in the chip, a total of 322,160 SNPs were chosen after quality control tests. After adjusting for the effects of age, slaughter-year-season, and polygenic effects using genome relationship matrix, the corrected phenotypes for the sensory evaluation measurements were regressed on each SNP using a simple linear regression additive based model. A total of 1,631 SNPs were detected for color, aroma, tenderness, juiciness and palatability at 0.1% comparison-wise level. Among the significant SNPs, the best set of 52 SNP markers were chosen using a forward regression procedure at 0.05 level, among which the sets of 8, 14, 11, 10, and 9 SNPs were determined for the respectively sensory evaluation traits. The sets of significant SNPs explained 18% to 31% of phenotypic variance. Three SNPs were pleiotropic, i.e. AX-26703353 and AX-26742891 that were located at 101 and 110 Mb of BTA6, respectively, influencing tenderness, juiciness and palatability, while AX-18624743 at 3 Mb of BTA10 affected tenderness and palatability. Our results suggest that some QTL for sensory measures are segregating in a Hanwoo steer population. Additional WGA studies on fatty acid and nutritional components as well as the sensory panels are in process to characterize genetic architecture of meat quality and palatability in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
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• 제23권11호
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• pp.1510-1518
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• 2010

The study was conducted to evaluate the effect of lighting schedule and nutrient density on growth performance, carcass traits and meat quality of broiler chickens. A total of 576 day old Arbor Acre male chickens was used with a $4{\times}2$ factorial arrangement. The four lighting schedules were continuous (23 L:1 D, CL), 20 L:4 D (12 L:2 D:8 L:2 D), 16 L:8 D (12 L:3 D:2 L:3 D: 2 L:2 D) and 12 L:12 D (9 L:3 D:1 L:3 D:1 L:3 D:1 L:3 D) and provided by incandescent bulbs. The two nutrient densities were high (H, starter diet: 13.39 MJ/kg apparent metabolisable energy (AME), 23.00% crude protein (CP); finisher diet: 13.39 MJ AME/kg, 19.70% CP) and low energy and protein level (L, starter diet: 12.03 MJ AME/kg, 20.80% CP; finisher diet: 12.14 MJ AME/kg, 18.30% CP). Houses with dark curtains and solid sidewalls were used. Chickens were randomly allocated to the 8 treatments with each treatment comprising 6 replicates of 12 chickens. Feed and water were available ad libitum. Lighting schedules showed no difference (p>0.05) in growth performance at the end of the experiment. 12 L:12 D significantly reduced (p<0.05) the concentration of malondialdehyde (MDA) compared to 23 L:1 D treatment. Intermittent lighting (IL) schedules produced higher protein content (p<0.001) in breast meat. Birds on high density diets had higher body weight (BW), feed intake (FI) (p<0.001), and feed conversion ratio (FCR) (p<0.001) throughout the experiment with the exception of 36 to 42 d. High nutrient density increased (p<0.05) abdominal fat, decreased (p<0.05) the moisture loss of meat, and reduced percentage of wings and legs. There was a significant lighting schedule${\times}$diet interaction (p<0.001) on FCR for days 8 to 14 and 15 to 21. Results indicated that IL can give similar growth performance in comparison with CL, meanwhile with positive effects on meat quality by increasing protein content and decreasing the concentration of MDA. High nutrient density resulted in greater growth performance.

• Asian-Australasian Journal of Animal Sciences
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• 제21권12호
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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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• 제62권3호
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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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• 제24권9호
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• pp.1184-1191
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• 2011

We attempted to generate a linkage map using Illumina Porcine 60K SNP Beadchip genotypes of the $F_2$ offspring from Korean native pig (KNP) crossed with Yorkshire (YS) pig, and to identify quantitative trait loci (QTL) using the line-cross model. Among the genotype information of the 62,136 SNPs obtained from the high-density SNP analysis, 45,308 SNPs were used to select informative markers with allelic frequencies >0.7 between the KNP (n = 16) and YS (n = 8) F0 animals. Of the selected SNP markers, a final set of 500 SNPs with polymorphic information contents (PIC) values of >0.300 in the $F_2$ groups (n = 252) was used for detection of thirty meat quality-related QTL on chromosomes at the 5% significance level and 10 QTL at the 1% significance level. The QTL for crude protein were detected on SSC2, SSC3, SSC6, SSC9 and SSC12; for intramuscular fat and marbling on SSC2, SSC8, SSC12, SSC14 and SSC18; meat color measurements on SSC1, SSC3, SSC4, SSC5, SSC6, SSC10, SSC11, SSC12, SSC16 and SSC18; water content related measurements in pork were detected on SSC4, SSC6, SSC7, SSC10, SSC12 and SSC14. Additional QTL of pork quality traits such as texture, tenderness and pH were detected on SSC6, SSC12, SSC13 and SSC16. The most important chromosomal region of superior pork quality in KNP compared to YS was identified on SSC12. Our results demonstrated that a QTL linkage map of the $F_2$ design in the pig breed can be generated with a selected data set of high density SNP genotypes. The QTL regions detected in this study will provide useful information for identifying genetic factors related to better pork quality in KNP.

• Asian-Australasian Journal of Animal Sciences
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• 제18권11호
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• pp.1524-1528
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• 2005

Molecular genetic markers were used to detect chromosomal regions which contain economically important traits such as growth, carcass, and meat quality traits in pigs. A three generation resource population was constructed from a cross between Korean native boars and Landrace sows. A total of 240 F2 animals from intercross of F1 was produced. Phenotypic data on 17 traits, birth weight, body weights at 3, 5, 12, and 30 weeks of age, teat number, carcass weight, backfat thickness, body fat, backbone number, muscle pH, meat color, drip loss, cooking loss, water holding capacity, shear force, and intramuscular fat content were collected for F2 animals. Animals including grandparents (F0), parents (F1), and offspring (F2) were genotyped for 80 microsatellite markers covering from chromosome 1 to 10. Least squares regression interval mapping was used for quantitative trait loci (QTL) identification. Significance thresholds were determined by permutation tests. A total of 10 QTL were detected at 5% chromosome-wide significance levels for growth traits on SSCs 2, 4, 5, 6, and 8.

• Asian-Australasian Journal of Animal Sciences
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• 제30권8호
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• pp.1061-1065
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• 2017

Objective: This study was conducted to locate quantitative trait loci (QTL) influencing fatty acid (FA) composition in a large $F_2$ intercross between Landrace and Korean native pigs. Methods: Eighteen FA composition traits were measured in more than 960 $F_2$ progeny. All experimental animals were genotyped with 165 microsatellite markers located throughout the pig autosomes. Results: We detected 112 QTLs for the FA composition; Forty seven QTLs reached the genome-wide significant threshold. In particular, we identified a cluster of highly significant QTLs for FA composition on SSC12. QTL for polyunsaturated fatty acid on pig chromosome 12 (F-value = 97.2 under additive and dominance model, nominal p-value $3.6{\times}10^{-39}$) accounted for 16.9% of phenotypic variance. In addition, four more QTLs for C18:1, C18:2, C20:4, and monounsaturated fatty acids on the similar position explained more than 10% of phenotypic variance. Conclusion: Our findings of a major QTL for FA composition presented here could provide helpful information to locate causative variants to improve meat quality traits in pigs.

• Asian-Australasian Journal of Animal Sciences
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• 제25권5호
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• pp.613-620
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• 2012

Marbling from intramuscular fat is an important trait of meat quality and has an economic benefit for the beef industry. Quantitative trait loci (QTL) fine mapping was performed to identify the marbling trait in 266 Hanwoo steers using a 10K single nucleotide polymorphism panel with the combined linkage and linkage disequilibrium method. As a result, we found nine putative QTL regions for marbling: three on BTA6, two on BTA17, two on BTA22, and two on BTA29. We detected candidate genes for marbling within 1 cM of either side of the putative QTL regions. Additionally, to understand the functions of these candidate genes at the molecular level, we conducted a functional categorization using gene ontology and pathway analyses for those genes involved in lipid metabolism or fat deposition. In these putative QTL regions, we found 95 candidate genes for marbling. Using these candidate genes, we found five genes that had a direct interaction with the candidate genes. We also found SCARB1 as a putative candidate gene for marbling that involves fat deposition related to cholesterol transport.

• Asian-Australasian Journal of Animal Sciences
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• 제25권11호
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• pp.1507-1510
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• 2012

Quantitative trait loci (QTL) associated with fat deposition traits in pigs are important gene positions in a chromosome that influence meat quality of pork. For QTL study, a three generation resource population was constructed from a cross between Korean native boars and Landrace sows. A total of 240 F2 animals from intercross of F1 were produced. 80 microsatellite markers covering chromosomes 1 to 10 were selected to genotype the resource population. Intervals between adjacent markers were approximately 19 cM. Linkage analysis was performed using CRIMAP software version 2.4 with a FIXED option to obtain the map distances. For QTL analysis, the public web-based software, QTL express (http://www.qtl.cap.ed.ac.uk) was used. Two significant and two suggestive QTL were identified on SSC 6, 7, and 8 as affecting body fat and IMF traits. For QTL affecting IMF, the most significant association was detected between marker sw71 and sw1881 on SSC 6, and a suggestive QTL was identified between sw268 and sw205 on SSC8. These QTL accounted for 26.58% and 12.31% of the phenotypic variance, respectively. A significant QTL affecting IMF was detected at position 105 cM between markers sw71 and sw1881 on SSC 6.

• 농업과학연구
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• 제45권4호
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• pp.707-713
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• 2018

This study was done to search for positional candidate genes associated with the back fat thickness trait using a Genome-Wide Association Study (GWAS) in purebred Yorkshires (N = 1755). Genotype and phenotype analyses were done for 1,642 samples. As a result of the associations with back fat thickness using the Gemma program (ver. 0.93), when the genome-wide suggestive threshold was determined using the Bonferroni method ($p=1.61{\times}10^{-5}$), the single nucleotide polymorphism (SNP) markers with suggestive significance were identified in 1 SNP marker on chromosome 2 (MARC0053928; $p=3.65{\times}10^{-6}$), 2 SNP markers on chromosome 14 (ALGA0083078; $p=7.85{\times}10^{-6}$, INRA0048453; $p=1.27{\times}10^{-5}$), and 1 SNP marker on chromosome 18 (ALGA0120564; $p=1.44{\times}10^{-5}$). We could select positional candidate genes (KCNQ1, DOCK1, LOC106506151, and LOC110257583), located close to the SNP markers. Among these, we identified a potassium voltage-gated channel subfamily Q member gene (KCNQ1) and the dedicator of cytokinesis 1 (DOCK1) gene associated with obesity and Type-2 diabetes. The SNPs and haplotypes of the KCNQ1 and DOCK1 genes can contribute to understanding the genetic structure of back fat thickness. Additionally, it may provide basic data regarding marker assisted selection for a meat quality trait in pigs.