Effect of single nucleotide polymorphism on the total number of piglets born per parity of three different pig breeds

Do, Kyoung-Tag,Jung, Soon-Woo,Park, Kyung-Do,Na, Chong-Sam Asian Australasian Association of Animal Productio 2018 Animal Bioscience Vol.31 No.5

Objective: To determine the effects of genomic breeding values (GBV) and single nucleotide polymorphisms (SNP) on the total number of piglets born (TNB) in 3 pig breeds (Berkshire, Landrace, and Yorkshire). Methods: After collecting genomic information (Porcine SNP BeadChip) and phenotypic TNB records for each breed, the effects of GBV and SNP were estimated by using single step best linear unbiased prediction (ssBLUP) method. Results: The heritability estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were 0.078, 0.107, and 0.121, respectively. The breeding value estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were in the range of -1.34 to 1.47 heads, -1.79 to 1.87 heads, and -2.60 to 2.94 heads, respectively. Of sows having records for TNB, the reliability of breeding value for individuals with SNP information was higher than that for individuals without SNP information. Distributions of the SNP effects on TNB did not follow gamma distribution. Most SNP effects were near zero. Only a few SNPs had large effects. The numbers of SNPs with absolute value of more than 4 standard deviations in Berkshire, Landrace, and Yorkshire breeds were 11, 8, and 19, respectively. There was no SNP with absolute value of more than 5 standard deviations in Berkshire or Landrace. However, in Yorkshire, four SNPs (ASGA 0089457, ASGA0103374, ALGA0111816, and ALGA0098882) had absolute values of more than 5 standard deviations. Conclusion: There was no common SNP with large effect among breeds. This might be due to the large genetic composition differences and the small size of reference population. For the precise evaluation of genetic performance of individuals using a genomic selection method, it may be necessary to establish the appropriate size of reference population.

RESEARCH : Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse

( Kyoung Tag Do ),( Joon Ho Lee ),( Hak Kyo Lee ),( Jun Kim ),( Kyung Do Park ) 한국동물자원과학회(구 한국축산학회) 2014 한국축산학회지 Vol.56 No.28

This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that had raced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missing genotype rate of >10%, minor allele frequency of <0.05 and Hardy?Weinberg equilibrium test P-value of <10?6) were excluded after quality control processes. SNPs on the X and Y chromosomes and genotyped individuals with missing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used for the analysis. The measures of the LD, square of correlation coefficient (r2) between SNP pairs, were calculated for each allele and the effective population size was determined based on r2 measures. The polymorphism information contents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline was observed over the first 1 Mb. But r2 decreased more slowly with increasing distance and was constant after 2 Mb of distance and the decline was almost linear with log-transformed distance. The average r2 between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average r2 between all SNP pairs was 0.02. We observed an initial pattern of decreasing Ne and estimated values were closer to 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be large considering Jeju horse`s population size (about 2,000 heads), but it should be interpreted with caution because of the technical limitations of the methods and sample size.

An Approach to Identify Single Nucleotide Polymorphisms in the Period Circadian Clock 3 (PER3) Gene and Proposed Functional Associations with Exercise Training in a Thoroughbred Horse

Kyoung-Tag Do(도경탁),Byung-Wook Cho(조병욱) 한국생명과학회 2015 생명과학회지 Vol.25 No.11

주기성 시계 유전자 3(period circadian clock gene 3, PER3)는 포유류에서 생물학적 주기 타이밍 시스템의 역할을 수행 한다. 이 유전자는 규칙적인 운동 체계에 의해 근육에서 전사 개시 되는 것으로 알려져 있다. 인간과 마우스에서는 본 유전자에 대해 잘 알려져 있지만, 주기 및 연주기 동안 낮의 길이에 영향을 많이 받는 말에서 운동연관 연구는 존재하지 않는다. 운동 시 근육의 기능에 중요한 역할을 하는 PER3 유전자에 대해 대표적인 경주마인 국내산 더러브렛 품종의 운동 전과 운동 후 유전자 발현을 분석하기 위해 본 연구를 수행하였다. 그 결과, 골격근에서 PER3 유전자의 발현은 운동 전에 비해 운동 후에 유의적으로 증가하는 것으로 나타났다. 또한, 인실리코상에서 4개의 비동의성 단일 염기 변이(non-synonymous single nucleotide polymorphism, nsSNP) 분석과 이러한 nsSNP의 단백질 구조 및 기능 분석 결과, 전체 자유 에너지와 RMSD 값은 돌연변이의 원인이 될 수 있음으로 나타났다. 이 중, nsSNP–s395916798 (G72R)은 구조적 기능적 측면에서 중요한 잔기의 안정화 효과와 연관된 것을 알 수 있었다. 본 연구는 운동에 따라 더러브렛 골격근 내 PER3 발현 차이는 운동이라는 표현형에 대표될 수 있음을 확인하였다. 또한, SNP의 조합을 활용하여 운동 후 경주마의 조기 회복의 평가 지표로써 유용한 바이오마커가 될 수 있음을 시사한다. The period circadian clock gene 3 (PER3) plays a role in the mammalian circadian clocksystem. A regular exercise regime may affect the PER3 transcription in skeletal muscle. Although the effects of day length on circadian and circannual processes are well established in humans and mice, the influence of exercise on these processes in the horse has not been investigated. The present study investigated the expression of the PER3 gene following exercise in a thoroughbred breed of Korean horse. In addition, a comprehensive in silico nonsynonymous single nucleotide polymorphism (nsSNP) analysis of the horse PER3 gene and predicted effects of nsSNPs on proteins were examined. The expression of PER3 in skeletal muscle was significantly upregulated after exercise. Four nsSNPs were functionally annotated and analyzed by computational prediction. The total free energy and RMSD values of PER3 gene showed causative mutations. The results showed that nsSNP s395916798 (G72R) was associated with residues that have stabilizing effects on structure and function of PER3 gene. This study documented role of PER3 gene in phenotypic adaptation related to exercise in skeletal muscle. Further, the SNPs in PER3 could serve as useful biomarkers of early recovery after exercise in racehorses.

Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse

Do, Kyoung-Tag,Lee, Joon-Ho,Lee, Hak-Kyo,Kim, Jun,Park, Kyung-Do Korean Society of Animal Sciences and Technology 2014 한국축산학회지 Vol.56 No.8

This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that had raced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missing genotype rate of >10%, minor allele frequency of <0.05 and Hardy-Weinberg equilibrium test P-value of < $10^{-6}$) were excluded after quality control processes. SNPs on the X and Y chromosomes and genotyped individuals with missing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used for the analysis. The measures of the LD, square of correlation coefficient ($r^2$) between SNP pairs, were calculated for each allele and the effective population size was determined based on $r^2$ measures. The polymorphism information contents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline was observed over the first 1 Mb. But $r^2$ decreased more slowly with increasing distance and was constant after 2 Mb of distance and the decline was almost linear with log-transformed distance. The average $r^2$ between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average $r^2$ between all SNP pairs was 0.02. We observed an initial pattern of decreasing $N_e$ and estimated values were closer to 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be large considering Jeju horse's population size (about 2,000 heads), but it should be interpreted with caution because of the technical limitations of the methods and sample size.

Copy Number Deletion Has Little Impact on Gene Expression Levels in Racehorses

Park, Kyung-Do,Kim, Hyeongmin,Hwang, Jae Yeon,Lee, Chang-Kyu,Do, Kyoung-Tag,Kim, Heui-Soo,Yang, Young-Mok,Kwon, Young-Jun,Kim, Jaemin,Kim, Hyeon Jeong,Song, Ki-Duk,Oh, Jae-Don,Kim, Heebal,Cho, Byung-W Asian Australasian Association of Animal Productio 2014 Animal Bioscience Vol.27 No.9

Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

Complete genome of Halomonas aestuarii Hb3, isolated from tidal flat

Kim, So-Jeong,Do, Kyoung-Tag,Park, Soo-Je Elsevier Science B.V. Amsterdam 2018 MARINE GENOMICS Vol.37 No.-

단일염기다형성 정보를 이용한 국내 홀스타인 젖소의 유효집단 크기 추정

조광현,도경탁,박경도,Cho, Kwang-Hyun,Do, Kyoung-Tag,Park, Kyung-Do 한국데이터정보과학회 2017 한국데이터정보과학회지 Vol.28 No.3

본 연구는 홀스타인 젖소, 923두에 대한 단일염기다형성 (SNP) 42,201개를 이용하여 국내 젖소집단의 유전적 특성 및 유효집단크기를 조사하고자 실시하였다. 염색체별 인접 단일염기다형성간의 평균 연관불평형 ($r^2$)은 0.22로 추정되었으며, 14번 염색체 (0.26)에서 가장 높은 반면, 27번 염색체 (0.17)에서 가장 낮게 나타났다. SNP간의 물리적 거리가 25Kb 미만인 경우에서 $r^2$은 $0.31{\pm}0.33$으로 추정되었으며, SNP간 물리적 거리가 증가할수록 $r^2$은 현저히 감소하였다. SNP간 물리적 거리가 2.5Mb 이상에서의 $r^2$은 0.04로 25Kb 미만인 경우와 비교할 때 0.27 (87.1%) 감소하였다. 국내 홀스타인 젖소의 유효집단크기는 세대수와 비례하여 감소하는 경향을 나타내었으며, 1~5세대에서 110두로 추정되었다. In this study, we investigated the genetic characteristics and the effective population size of domestic dairy cattle using 42,201 SNPs for 923 heads of Holstein cattle. The estimate for the average linkage disequilibrium ($r^2$) among the adjacent SNPs by chromosome was 0.22, and it was highest (0.26) in chromosome 14 and lowest (0.17) in chromosome 27. When the physical distance among SNPs was less than 25Kb, the estimate for the average $r^2$ was $0.31{\pm}0.33$ and it was markedly decreased as the physical distance increased. When the physical distance among SNPs was larger than 25Mb, the estimate for the average $r^2$ was 0.04, and it decreased by 0.27 (87.1%) compared with case of physical distance of less than 25Kb. There was a trend that the effective population size in Holstein dairy cattle decreased over generations and the estimate for the effective population size in the first 5 generations (1~5th generation) was 110 heads.

노화촉진마우스의 텔로미어 함량 분석

이미랑(Mi-Rang Lee),도경탁(Kyoung-Tag Do),한정주(Jyung-Ju Han),문소현(So-Hyun Moon),강한석(Han-Seok Kang),김선구(Seon-Ku Kim),신택순(Teak-Soon Shin),이홍구(Hong-Goo Lee),황대연(Dae-Yon Hwang),김용균(Yong-Gyun Kim),손시환(Sea-Hwan Soh 한국생명과학회 2009 생명과학회지 Vol.19 No.10

Telomeres, comprised of tandem repeats of TTAGGG sequences, are special nucleoprotein structures that protect and stabilize chromosome ends. These structures form the crux of the telomere concept of aging, senescence and genomic instability. The classic terminal restriction fragment (TRF) analysis to quantify the amount of telomeric DNA is disadvantageous in species containing ultra long telomeres like in mice (100Kb). In this study, we used a more sensitive quantitative fluorescence in situ hybridization (Q FISH) technique to quantify telomeric DNA, and used it as a biological aging marker in mice. 12 litters each of Senescence-Resistant (SAMR1) and ?Prone (SAMP1) known as senescence accelerated mouse strains were purchased from Central Lab, Animal Inc. We quantified the amount of telomeric DNA using telomere specific DNA probes on the two strains of male mice at 8 weeks, 18 weeks and 26 weeks of age. The amount of telomeric DNA correlated with aging and age associated changes in body and organ weight between SAMR1 and SAMP1 strains of mice. These data suggest the usefulness of the amount of telomeric DNA as a biological aging marker in human aging studies.

Objective and Subjective Quality Characteristics of Pork Longissimus Muscle as a Function of the Ultimate pH

Cho, Byung-Wook,Oliveros, Maria Cynthia,Park, Kyoung-Mi,Do, Kyoung-Tag,Lee, Ki-Hwan,Seo, Kang-Seok,Choi, Jae-Gwan,Lee, Moon-Jun,Cho, In-Kyung,Choi, Byoung-Chul,Ryu, Kyeong-Seon,Hwang, In-Ho Korean Society for Food Science of Animal Resource 2009 한국축산식품학회지 Vol.29 No.6

The aim of the present study was to evaluate the variation in ultimate pH of commercial populations of pure-breed (Landrace, Duroc and Yorkshire) pig's longissimus muscles and their effect on objective meat quality traits and sensory characteristics. Fifty boars were sampled from 184 pigs, which were reared at three breeding farms and slaughtered at a commercial abattoir. The selection was determined based on ultimate pH, and animals were segregated into three groups: low pH (pH $\leq$ 5.5, n=13), medium pH (pH 5.5 to 5.6, n=18) and high pH (pH $\geq$ 5.6, n=16). The breeds had no significant effects; however, pigs with a higher ultimate pH had significantly (p<0.05) higher intramuscular fat content, lower level of polyunsaturated fatty acids, lower level of lipid oxidation and higher eating quality compared to those with lower ultimate pH. As the ultimate pH increased, the relative proportion of C14:0, C16:0 and C18:1 increased while C18:2n6 and C20:4n6 decreased. The present study demonstrates that the economic value of pigs can be characterized by the ultimate pH and/or intramuscular fat content. However, these results do not necessarily indicate that a high ultimate pH directly corresponds to high intramuscular fat content and vice versa.

Draft genome sequence of Streptococcus sp. strain NM isolated from head and neck cancer patients

김영석,도경탁,박수제,Kim, Young Suk,Do, Kyoung-Tag,Park, Soo-Je The Microbiological Society of Korea 2019 미생물학회지 Vol.55 No.1

Firmicutes에 속하는 Streptococcus sp. strain NM을 두경부암 환자로부터 분리하였다. 본 연구에서는 약1.90 Mb의 크기와 39.3%의 평균 G+C 함량을 가진 NM 균주의 비완전한 유전체를 보고한다. 유전체는 1,845개의 코딩서열, 12개의 리보솜 RNA 및 58개의 전사 RNA유전자를 포함하였다. 본 유전체로 부터, 항생제내성, 용혈 및 방어시스템과 관련된 유전자들이 확인되었다. Streptococcus sp. strain NM belonging to Firmicutes was isolated from head and neck cancer patients. Here, we report the draft genome sequence of strain NM with a size of approximately 1.90 Mbp and a mean G+C content of 39.3%. The draft genome included 1,845 coding sequences, and 12 ribosomal RNA and 58 transfer RNA genes. In the draft genome, genes involved in the antimicrobial resistance, hemolysis and defense system have been identified.