Gene Expression Patterns Associated with Peroxisome Proliferator-activated Receptor (PPAR) Signaling in the Longissimus dorsi of Hanwoo (Korean Cattle)

임다정,최한하,이승환,조영민,최정우,김남국 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.8

Adipose tissue deposited within muscle fibers, known as intramuscular fat (IMF or marbling), is a major determinant of meat quality and thereby affects its economic value. The biological mechanisms that determine IMF content are therefore of interest. In this study, 48 genes involved in the bovine peroxisome proliferator-activated receptor signaling pathway, which is involved in lipid metabolism, were investigated to identify candidate genes associated with IMF in the longissimus dorsi of Hanwoo (Korean cattle). Ten genes, retinoid X receptor alpha, peroxisome proliferator-activated receptor gamma (PPARG), phospholipid transfer protein, stearoylCoA desaturase, nuclear receptor subfamily 1 group H member 3, fatty acid binding protein 3 (FABP3), carnitine palmitoyltransferase II, acyl-Coenzyme A dehydrogenase long chain (ACADL), acyl-Coenzyme A oxidase 2 branched chain, and fatty acid binding protein 4, showed significant effects with regard to IMF and were differentially expressed between the low- and high-marbled groups (p<0.05). Analysis of the gene co-expression network based on Pearson’s correlation coefficients identified 10 up-regulated genes in the highmarbled group that formed a major cluster. Among these genes, the PPARG-FABP4 gene pair exhibited the strongest correlation in the network. Glycerol kinase was found to play a role in mediating activation of the differentially expressed genes. We categorized the 10 significantly differentially expressed genes into the corresponding downstream pathways and investigated the direct interactive relationships among these genes. We suggest that fatty acid oxidation is the major downstream pathway affecting IMF content. The PPARG/RXRA complex triggers activation of target genes involved in fatty acid oxidation resulting in increased triglyceride formation by ATP production. Our findings highlight candidate genes associated with the IMF content of the loin muscle of Korean cattle and provide insight into the biological mechanisms that determine adipose deposition within muscle.

Demographic Trends in Korean Native Cattle Explained Using Bovine SNP50 Beadchip

Aditi Sharma,임다정,최한하,조용민 한국유전체학회 2016 Genomics & informatics Vol.14 No.4

Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ∼29,000 single nucleotide polymorphisms (SNPs) for which r2 value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average r2 between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on r2 varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.

Genomic Polymorphism Analysis using Microsatellite Markers in Gyeongju Donggyeong Dogs

김승창,김이경,최승규,박창민,박선애,조용민,임다정,최한하,이승환,이지웅,선상수,최봉환 사단법인 한국동물생명공학회 2013 Reproductive & developmental biology Vol.36 No.4

This study was conducted to find a useful marker for gene polymorphism analysis using Microsatellite marker (MS marker) in Gyeongju Donggyeong dog. Twenty three MS marker analyzed the genetic features of DNA using 100Gyeongju Donggyeong dogs in Gyeongju area. It was performed multiplex PCR with 3 set primer divided 9, 10 and 4 by analysis of conditions among MS markers. The results were calculated heterozygosity, polymorphic information content (PIC), allele frequency and number of allele at each locus using Microsatellite Toolkit software and Cervus 3.0 program. Total 148 alleles were genotyped to determine and average 6.43 alleles was detected. FH3381 had the highest of 15 alleles and FH2834 had the lowest of 2 alleles. Expected heterozygosity had a wide range from 0.282 to 0.876 and had average value of 0.6496. Also, Observed heterozygosity had a more wide range from 0.200 to 0.950 and had average value of 0.6404. PIC had range from 0.262 to 0.859 and average PIC was calculated 0.606. Especially, FH2998 represented the highest rate of observed heterozygosity of 0.950 and FH3381 represented the highest rate of expected heterozygosity of 0.876 and PIC of 0.859. The use of these markers was considered to be useful to study genetic traits of Gyeongju Donggyeong dog.

Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

최정우,이승환,최봉환,이승수,김형철,유대영,정원형,최한하,이경태,임다정,조영민 한국분자세포생물학회 2015 Molecules and cells Vol.38 No.5

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53- fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea

Aditi Sharma,박종은,박병호,박미나,노승희,정우영,이승환,최한하,조용민,임다정 한국유전체학회 2018 Genomics & informatics Vol.16 No.1

Until now microsatellite (MS) have been a popular choice of markers for parentage verification. Recently many countries have moved or are in process of moving from MS markers to single nucleotide polymorphism (SNP) markers for parentage testing. FAO-ISAG has also come up with a panel of 200 SNPs to replace the use of MS markers in parentage verification. However, in many countries most of the animals were genotyped by MS markers till now and the sudden shift to SNP markers will render the data of those animals useless. As National Institute of Animal Science in South Korea plans to move from standard ISAG recommended MS markers to SNPs, it faces the dilemma of exclusion of old animals that were genotyped by MS markers. Thus to facilitate this shift from MS to SNPs, such that the existing animals with MS data could still be used for parentage verification, this study was performed. In the current study we performed imputation of MS markers from the SNPs in the 500-kb region of the MS marker on either side. This method will provide an easy option for the labs to combine the data from the old and the current set of animals. It will be a cost efficient replacement of genotyping with the additional markers. We used 1,480 Hanwoo animals with both the MS data and SNP data to impute in the validation animals. We also compared the imputation accuracy between BovineSNP50 and BovineHD BeadChip. In our study the genotype concordance of 40% and 43% was observed in the BovineSNP50 and BovineHD BeadChip respectively.

Association of Heat Shock Protein Beta 1 (HSPB1) Gene Expression with Tenderness in Loin Muscle of Korean Cattle (Hanwoo)

Dajeong Lim(임다정),Seung-Hwan Lee(이승환),Yong-Min Cho(조용민),Bong-Hwan Choi(최봉환),Han-Ha Choi(최한하),Hwan-Hoo Seong(성환후),Seong-Koo Hong(홍성구),Nam-Kuk Kim(김남국) 한국생명과학회 2012 생명과학회지 Vol.22 No.11

육질 등급에 차이를 보이는(3등급과 1++등급) 한우 등심육을 대상으로 한 단백체 연구를 통해 heat shock protein beta 1 (HSPB1)의 발현 차이가 관찰되었다. 따라서 본 연구는 HSPB1의 유전자와 단백질 수준에서의 발현이 육질에 중요한 요인으로 작용하는 연도(전단력)에 미치는 영향을 규명하기 위하여 수행하였다. 전단력 값의 차이를 보이는 동기우 집단 20두를 대상으로 유전자 및 단백질의 발현량을 분석하였고, 통계분석을 수행하였다. 유전자 및 단백질 수준에서의 발현량을 분석한 결과 HSPB1은 전단력이 낮은 그룹에서 전단력이 높은 그룹보다 2배 발현이 높은 것으로 확인되었으며(p<0.05), 전단력과의 관련성 분석 결과에서도 유전자와 단백질 발현량 모두에서 통계적 유의성이 확인하였다(p<0.05). 이러한 결과로 볼 때 HSPB1 유전자는 한우 등심육의 연도와 밀접히 관련되어있다고 판단되며, 지속적으로 유전자구조 변이연구 등을 통해 유전자 마커로의 개발이 필요할 것으로 생각된다. In a previous proteomic study, heat shock protein beta 1 (HSPB1) was detected as differentially expressed protein in longissimus thoracis between low (grade 3) and high (grade 1++) meat quality groups by 2DE gel electrophoresis. The present study investigated an association of HSPB1 expression at the level of gene and protein with Warner-Bratzler shear force (WBS) measured in 20 Hanwoo steers. An analysis of variance (ANOVA) between expression values and WBS showed that WBS was affected by HSPB1 expression (p<0.05). The expression (at both gene and protein level) of the HSPB1 was 2 times higher in the low WBS group than that in the high WBS group (p<0.01). This result suggests that the HSPB1 gene may be a candidate gene associated with tenderness in longissimus thoracis of Korean cattle.