• Korean Journal of Food Science and Technology
• /
• v.50 no.5
• /
• pp.480-485
• /
• 2018

In this study, to identify single nucleotide polymorphisms (SNPs) associated with meat quality in Berkshire pigs, we performed RNA sequencing. A non-synonymous SNP (nsSNP) in the Complement component 9 (C9) gene was identified, and the association between meat quality traits and the C9 genotype was analyzed. The nsSNP in the C9 gene was located at c.942 G>T. In the dominant model, significant associations were observed between the SNP and meat quality traits such as CIE L, collagen content, moisture level, and $pH_{24h}$, whereas in the co-dominant model, significant associations were observed between the SNP and CIE L, collagen content, and protein content. In the recessive model, a significant association between the C9 genotype and the collagen content was observed. In addition, we identified the significant relationship between the C9 genotype and meat quality according to sex. These results indicate that the C9 SNP can be used as a genetic marker for improving pork quality.

• Korean Journal of Poultry Science
• /
• v.34 no.2
• /
• pp.151-156
• /
• 2007

The Function of the calcium sensing receptor (CaSR) is to control calcium levels by altering PTH (parathyroid hormone) secretion and renal calcium resorption. The influence of calcium on the basal and stimulated release of several hormones from chicken pituitary glands has been determined in vitro. The objective of this study was to identify SNP in chicken CaSR gene and to investigate the effect of the SNP on economic traits. The sequencing analysis method was used to identify nucleotide polymorphisms within chicken CaSR gene. This study identified SNP at position 1949 bp(Genebank accession No : XM_416491) in the exon 1. The SNP changed the amino acid to alanine(GCC) from serine(TCC). This SNP showed three genotypes, AA, AS and SS by digestion with the restriction enzyme NcoⅠ using the PCR-RFLP method. The A963S showed significant effect only on the first lay day (P<0.05) in Leghorn population. Leghorn with the genotype AA had significantly faster the first lay day(137.6) than the genotype AS(143.0, P<0.05). Also, the A963S showed significant effect only on the first lay day(P<0.05) and mean of egg weight(P<0.05) in KNC population. KNC with the genotypes AA ans AS had significantly faster the first lay day (151.0 and 152.6, respectively) than the genotype SS(159.4, P<0.05). And the genotypes SS had significantly heavier the mean of egg weight(50.4 kg, P<0.05) than the genotype AA ans AS (47.5 and 47.8 kg, respectively). According to result of this study, an a allele of the A963S was found to have a significant effect on the first lay day. It will be possible to use this SNP marker on selecting chicken to improve the first lay day.

• Asian-Australasian Journal of Animal Sciences
• /
• v.31 no.6
• /
• pp.784-790
• /
• 2018

Objective: The genetic effects of an individual on the phenotypes of its social partners, such as its pen mates, are known as social genetic effects. This study aims to identify the candidate genes for social (pen-mates') average daily gain (ADG) in pigs by using the genome-wide association approach. Methods: Social ADG (sADG) was the average ADG of unrelated pen-mates (strangers). We used the phenotype data (16,802 records) after correcting for batch (week), sex, pen, number of strangers (1 to 7 pigs) in the pen, full-sib rate (0% to 80%) within pen, and age at the end of the test. A total of 1,041 pigs from Landrace breeds were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel, which comprised 61,565 single nucleotide polymorphism (SNP) markers. After quality control, 909 individuals and 39,837 markers remained for sADG in genome-wide association study. Results: We detected five new SNPs, all on chromosome 6, which have not been associated with social ADG or other growth traits to date. One SNP was inside the prostaglandin $F2{\alpha}$ receptor (PTGFR) gene, another SNP was located 22 kb upstream of gene interferon-induced protein 44 (IFI44), and the last three SNPs were between 161 kb and 191 kb upstream of the EGF latrophilin and seven transmembrane domain-containing protein 1 (ELTD1) gene. PTGFR, IFI44, and ELTD1 were never associated with social interaction and social genetic effects in any of the previous studies. Conclusion: The identification of several genomic regions, and candidate genes associated with social genetic effects reported here, could contribute to a better understanding of the genetic basis of interaction traits for ADG. In conclusion, we suggest that the PTGFR, IFI44, and ELTD1 may be used as a molecular marker for sADG, although their functional effect was not defined yet. Thus, it will be of interest to execute association studies in those genes.

• Asian-Australasian Journal of Animal Sciences
• /
• v.25 no.11
• /
• pp.1529-1539
• /
• 2012

A whole genome association (WGA) study was performed to detect significant polymorphisms for meat quality traits in an $F_2$ cross population (N = 478) that were generated with Korean native pig sires and Landrace dams in National Livestock Research Institute, Songwhan, Korea. The animals were genotyped using Illumina porcine 60k SNP beadchips, in which a set of 46,865 SNPs were available for the WGA analyses on ten carcass quality traits; live weight, crude protein, crude lipids, crude ash, water holding capacity, drip loss, shear force, CIE L, CIE a and CIE b. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model, after adjusting for sex, sire and slaughter stage as fixed effects. With the significant SNPs for each trait (p<0.001), a stepwise regression procedure was applied to determine the best set of SNPs with the additive and/or dominance effects. A total of 106 SNPs, or quantitative trait loci (QTL) were detected, and about 32 to 66% of the total phenotypic variation was explained by the significant SNPs for each trait. The QTL were identified in most porcine chromosomes (SSCs), in which majority of the QTL were detected in SSCs 1, 2, 12, 13, 14 and 16. Several QTL clusters were identified on SSCs 12, 16 and 17, and a cluster of QTL influencing crude protein, crude lipid, drip loss, shear force, CIE a and CIE b were located between 20 and 29 Mb of SSC12. A pleiotropic QTL for drip loss, CIE L and CIE b was also detected on SSC16. These QTL need to be validated in commercial pig populations for genetic improvement in meat quality via marker-assisted selection.

• Asian-Australasian Journal of Animal Sciences
• /
• v.24 no.3
• /
• pp.322-329
• /
• 2011

A whole genome association (WGA) study was conducted to identify quantitative trait loci (QTL) for body conformation traits in Hanwoo cattle. The phenotypes of 497 steers were recorded from the Hanwoo Improvement Center of National Agricultural Cooperative Federation, Seosan, Korea, and analyzed using the Illumina Bovine 50 k SNP chip. A set of 35,987 SNPs that were available in the Hanwoo population was selected from the chip. After adjustments for the effects of year-season of birth, region and sire, phenotypes were regressed on each SNP using a linear regression model. Three hundred nineteen SNPs were detected for the ten conformation traits (p<0.003). For the significant SNPs, stepwise regression procedures were applied to determine best sets of markers. A total of 72 SNPs were selected (p<0.001), for which the sets of 5, 9, 10, 9, 8, 11, 4, 6, 3 and 7 SNPs were determined for height at withers, rump height, body length, chest depth, chest width, rump length, hip width, thurl width, pinbone width and heart girth, respectively. About 7-26% of the total phenotypic variation was explained by the set of SNPs for each trait. QTL for the conformation traits were harbored on most bovine chromosomes (BTAs). Four SNPs with pleiotropic effects on height at withers and rump height were detected on BTAs 3, 4, 6 and 16. A SNP with pleiotropic effects on chest width and rump length was also detected on BTA10. Two QTL regions, i.e. between 87 and 97 Mb in BTA3 and between 41 and 44 Mb in BTA7, were found, in which SNPs were detected for the five and three conformation traits, respectively. The detected SNPs need to be validated in other Hanwoo populations for commercial application to the genetic improvement of conformation characteristics in Hanwoo via marker-assisted selection (MAS).

• Proceedings of the Korean Society of Life Science Conference
• /
• 2008.10a
• /
• pp.91.2-91.2
• /
• 2008

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2021.10a
• /
• pp.177-177
• /
• 2021

• Korean Journal of Agricultural Science
• /
• v.38 no.1
• /
• pp.51-63
• /
• 2011

BoLA (bovine leukocyte antigens) have been known as gene complex related with bovine diseases and immunological traits. This study was conducted to find out the characteristics of BoLA-DRB3 gene related to mastitis and BL(bovine leukocyte) from 280 cattle [193 animals of Holstein cattle and 87 animals of Hanwoo]. As a result, five PCR-RFLP types (b, d, e, f and g) using HaeIII restriction enzyme, three BstYI restriction patterns (b, d and e) and eight RsaI restriction types(b, d, f, I, j, n, o and w) were identified. Moreover, we identified new d' type ($197{\rightarrow}175$/22), having one more cutting site by BstYI enzyme than d type allele and n' type ($180{\rightarrow}169$/11) having one more cutting site by RsaI enzyme than n allele was additionally identified. Next, we identified 53 SNPs in BoLA-DRB3 exon2 from 280 cattle. SNP frequency and heterozygosity of Holstein and Hanwoo were investigated in all the SNP genotype. These results might be based on research for identifying marker associated with bovine diseases.

• Genomics & Informatics
• /
• v.10 no.2
• /
• pp.117-122
• /
• 2012

A sample size with sufficient statistical power is critical to the success of genetic association studies to detect causal genes of human complex diseases. Genome-wide association studies require much larger sample sizes to achieve an adequate statistical power. We estimated the statistical power with increasing numbers of markers analyzed and compared the sample sizes that were required in case-control studies and case-parent studies. We computed the effective sample size and statistical power using Genetic Power Calculator. An analysis using a larger number of markers requires a larger sample size. Testing a single-nucleotide polymorphism (SNP) marker requires 248 cases, while testing 500,000 SNPs and 1 million markers requires 1,206 cases and 1,255 cases, respectively, under the assumption of an odds ratio of 2, 5% disease prevalence, 5% minor allele frequency, complete linkage disequilibrium (LD), 1:1 case/control ratio, and a 5% error rate in an allelic test. Under a dominant model, a smaller sample size is required to achieve 80% power than other genetic models. We found that a much lower sample size was required with a strong effect size, common SNP, and increased LD. In addition, studying a common disease in a case-control study of a 1:4 case-control ratio is one way to achieve higher statistical power. We also found that case-parent studies require more samples than case-control studies. Although we have not covered all plausible cases in study design, the estimates of sample size and statistical power computed under various assumptions in this study may be useful to determine the sample size in designing a population-based genetic association study.

• BMB Reports
• /
• v.42 no.4
• /
• pp.200-205
• /
• 2009

Thromboxane A2 (TBXA2) is a potent vasoconstrictor in cerebral circulation and is a known contributor to the pathogenesis of cerebral infarction. Thromboxane A2 synthase 1 (TBXAS1) and thromboxane A2 receptors (TBXA2R) are key components in TBXA2 function. We examined whether genetic variants in TBXA2R and TBXAS1 are risk factors for cerebral infarction by genotyping 453 Korean patients with noncardiogenic cerebral infarction and 260 controls. A few, specific polymorphisms in the TBXA2R (-3372G>C, +4710T>C and 4839T>C) and TBXAS1 (+16184G>T, +141931A>T and +177729G>A) genes were chosen and investigated. Logistic regression showed the frequencies of TBXAS1+16184G>T and TBXAS1-ht3 were significantly more frequent in cerebral infarction (P = 0.002, OR = 2.75 and P = 0.01, OR = 1.57, respectively), specifically in small-artery occlusion (SAO) type of cerebral infarction (P = 0.0003 and 0.005, respectively). These results suggest specific TBXAS1 gene polymorphisms may be a useful marker for development of cerebral infarction, especially SAO type in Korean population.