• Proceedings of the Korean Society of Crop Science Conference
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• 2018.10a
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• pp.231-231
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• 2018

• Proceedings of the Korean Society of Crop Science Conference
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• 2019.09a
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• pp.198-198
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• 2019

• Proceedings of the Korean Society of Crop Science Conference
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• 2023.04a
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• pp.21-21
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• 2023

• Proceedings of the Korean Society of Crop Science Conference
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• 2021.04a
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• pp.97-97
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• 2021

• 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.26 no.1
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• pp.1-7
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• 2016

Fatness is one of the most important economic traits in pigs. The leptin receptor (LEPR) gene may be a potential candidate for the fatness quantitative trait locus (QTL) on porcine chromosome 6, due to its position and physiological role. Thus, this study was carried out to evaluate the associations between structural variants in the LEPR gene and economic traits in pigs. We obtained an approximately 114-kb sequence containing the complete genomic DNA of the porcine LEPR gene, using shotgun sequencing of a bacterial artificial chromosome clone. We report the complete genomic structure of the porcine LEPR gene. Dozens of transcription factor-binding sites were found in the 1.2 kb upstream region from the transcription start point. An association study was performed with 550 Duroc pigs for 24 single-nucleotide polymorphisms (SNPs), including 6 SNPs within exons and 18 SNPs within the putative 5‘ regulatory region of the porcine LEPR gene. Among them, one SNP (−790C/G) was significantly associated with backfat thickness and lean meat percentage, whereas the others, including two SNPs with missense polymorphisms, had no effect on any phenotype. These results suggest that SNP −790C/G may be a useful marker for genetic improvements of fatness and leanness in Duroc pigs.

• Journal of agriculture & life science
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• v.50 no.3
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• pp.99-117
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• 2016

Data on primal cuts were collected from 1,829 steers of Hanwoo progeny testing programs, between 2010 and 2015 for the ssGWAS. SNP data were analyzed by using Illumina Bovine 50K Beadchip. The SNP data that matches with phenotype data was 674 animals. As a first step, the genomic estimated breeding value(GEBV) of the loin and rib cuts were estimated, which was used in the estimation of SNP marker effects and their variances related to the traits. Then, the estimated variance explained by each marker was expressed as a proportion to the total genetic variance. Finally, the SNP loci and their significance to any possible QTL were examined. Among the 20 best SNP loci explaining a larger proportion of SNP variance to the total genetic variance for tender loin yield, the region between 12,812,193 ~ 12,922,313bp on BTA 10 harbored a cluster of SNPs that explained about 7.32 to 7.34% of the total genetic variance. For strip loin yield, a peak for higher effects for multiple SNPs was found in BTA24, between 38,158,543 and 38,347,278bp distances, which explained about 8.36 to 8.56% of the observed variance for this trait. For loin yield had relatively smaller effects in terms of the total genetic variance. Therefore, loin yield might be affected by a few loci with moderate effects and many other loci with smaller effects across the genome.

• Korean Journal of Agricultural Science
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• v.40 no.2
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• pp.155-162
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• 2013

Genome-wide association study was performed on data from 266 Hanwoo steers derived from 66 sire using bovine 10K mapping chip in Hanwoo (Korean Cattle). SNPs were excluded from the analysis if they failed in over 5% of the genotypes, had median GC scores below 0.6, had GC scores under 0.6 in less than 90% of the samples, deviated in heterozygosity more than 3 standard deviations from the other SNPs and were out of Hardy-Weinberg equilibrium for a cutoff p-value of $1^{-15}$. Unmapped and SNPs on sex chromosomes were also excluded. A total of 4,522 SNPs were included in the analysis. To test an association between SNP and QTL, GWAS for five genetic mode (additive, dominant, overdominant, recessive and codominant) was implemented in this study. Three SNPs (rs29018694, ss46526851 and rs29018222) at a threshold p< $1.11{\times}10^{-5}$ were detected on BTA12 and BTA21 for dressing percentages in codominant and recessive genetic mode. The G allele for rs29018694 has 4.9% higher dressing percentage than A allele, while the T allele for ss46526851 has 2.57 % higher dressing percentage than C allele. Therefore, rs29018694 SNP showed a bigger effect than the other two SNPs (ss46526851 and rs29018222) in this study. In conclusion, this study identifies three loci with moderate effects and many loci with infinitesimally small effect across genome in Hanwoo.

• Journal of the Korean Data and Information Science Society
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• v.21 no.3
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• pp.387-395
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• 2010

It is important to identify the interaction of genes about human disease and characteristic value. Many studies as like logistic analysis, have associated being pursued, but, previous methods did not consider the sub-group of the genotypes. So, QTL interactions and the GMM (genotype matrix mapping) have been developed. In this study, we detect the superior genotype combination to have an impact on economic traits of Korean cattle based on the study over GMM method. Thus, we identified interaction effects of single nucleotide polymorphisms (SNPs) responsible for average daily gain(ADG), marbling score (MS), carcass cold weight (CWT), longissimus muscle dorsiarea (LMA) using GMM method. In addition, we examine significance of the major genotype combination selected by implementing permutation test of the F-measure which was not obtained by Sachiko et al.

• Journal of Animal Science and Technology
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• v.46 no.3
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• pp.301-306
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• 2004

This study was conducted to develop new markers at the region that was related to QTL affecting intramuscular fat and backfat thickness on chromosome 6q28 - 6q32 in pigs. Dozens of repeated sequences were founded using shotgun sequencing of several BAC clones corresponding to that region, of which five new microstellite markers that identified polymorphism were discovered. The mean number of alleles at each locus observed 2.13(KP0290F2), 4.63(KP0248Cll), 7.38(KP1231C91), 2.75(KPI23IC92) and 6.2S(KP1231C93) in 8 breeds(Landrace, Korean native pig, Duroc, Yorkshire, Berkshire, Wuzhishan pig, Xiang pig, Min pig). The average estimated heterozygosity values at each locus varied from 0.2100(KP0290F2) to 0.8304(KPI23IC91) in all populations. In other hand, the average allele of all loci WlL'I within range of 0.4517(Berkshire) and 0.6957 (Yorkshire). Of these markers, KP0248C11, KP1231C91 and KP1231C93 were identified to have optimal number of alleles, high heterozygosity values and low standard deviation values. Especially, KPI23IC91 and KPI231C93 might be considered as a useful marker for genetic mapping and diversity study.