Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski’s horse

성하승,김남영,김대철,황남현,손다혜,신종서,이준희,정원형,최정우 한국유전학회 2019 Genes & Genomics Vol.41 No.6

Background The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds. Objective The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski’s horse). Results Using the equine reference genome assembly (EquCab 2.0), more than ~ 6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of which 73.7% were found to be novel. All the detected SNPs were deeply annotated to retrieve SNPs in gene regions using the RefSeq and Ensemble gene sets. Approximately 27% of the total SNPs were located within genes, whereas the remaining 73% were found in intergenic regions. Using 129,776 coding SNPs, we retrieved a total of 49,171 nonsynonymous SNPs in 12,351 genes. Furthermore, we identified a total of 10,770 deleterious nonsynonymous SNPs which are predicted to affect protein structure or function. Conclusion We showed numerous genomic variants from domestic and wild horse breeds. These results provide a valuable resource for further studies on functions of SNP-containing genes, and can aid in determining the molecular basis underlying variation in economically important traits of horses.

Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array

김남영,성하승,김대철,박남건,양병철,손준규,신상민,우재훈,신문철,유지현,최정우 한국유전학회 2018 Genes & Genomics Vol.40 No.11

The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju × Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas r2 values were lowest in Jeju horse. Expected heterozygosity was the highest in Jeju crossbred (0.351), followed by the Thoroughbred (0.337) and Jeju horse (0.311). The level of inbreeding was slightly higher in Thoroughbred (− 0.009) than in Jeju crossbred (− 0.035) and Jeju horse (− 0.038). FST value was the highest between Jeju horse and Thoroughbred (0.113), whereas Jeju crossbred and Thoroughbred showed the lowest value (0.031). The genetic relationship was further assessed by principal component analysis, suggesting that Jeju crossbred is more genetically similar to Thoroughbred than Jeju horse population. Additionally, we detected potential selection signatures, for example, in loci located on LCORL/NCAPG and PROP1 genes that are known to influence body. Genome-wide analyses of the three horse populations showed that all the breeds had somewhat a low level of inbreeding within each population. In the population structure analysis, we found that Jeju crossbred was genetically closer to Thoroughbred than Jeju horse. Furthermore, we identified several signatures of selection which might be associated with traits of interest. To our current knowledge, this study is the first genomic research, analyzing genetic relationships of Jeju horse, Thoroughbred and Jeju crossbred.

Genome-wide analysis of Hanwoo and Chikso populations using the BovineSNP50 genotyping array

송준석,성하승,최봉환,이창우,황남현,임다정,이준희,김진수,김정대,박연수,최정우,김종복 한국유전학회 2018 Genes & Genomics Vol.40 No.12

Hanwoo and Chikso are classified as Korean native cattle breeds that are currently registered with the Food and Agriculture Organization. However, there is still a lack of genomic studies to compare Hanwoo to Chikso populations. The objective of this study was to perform genome-wide analysis of Hanwoo and Chikso populations, investigating the genetic relationships between these two populations. We genotyped a total of 319 cattle including 214 Hanwoo and 105 Chikso sampled from Gangwon Province Livestock Technology Research Institute, using the Illumina Bovine SNP50K Beadchip. After performing quality control on the initially generated datasets, we assessed linkage disequilibrium patterns for all the possible SNP pairs within 1 Mb apart. Overall, average r2 values in Hanwoo (0.048) were lower than Chikso (0.074) population. The genetic relationship between the populations was further assured by the principal component analysis, exhibiting clear clusters in each of the Hanwoo and Chikso populations, respectively. Overall heterozygosity for Hanwoo (0.359) was slightly higher than Chikso (0.345) and inbreeding coefficient was also a bit higher in Hanwoo (− 0.015) than Chikso (− 0.035). The average FST value was 0.036 between Hanwoo and Chikso, indicating little genetic differentiation between those two breeds. Furthermore, we found potential selection signatures including LRP1B and NTRK2 genes that might be implicated with meat and reproductive traits in cattle. In this study, the results showed that both Hanwoo and Chikso populations were not under severe level of inbreeding. Although the principal component analysis exhibited clear clusters in each of the populations, we did not see any clear evidence that those two populations are highly differentiated each other.

Effects of Fermented Milk Supplements on the Growth Performance and Gut Conditions in Piglets during the Pre-and Post-Weaning Periods

Yong-Dae Jeong(정용대),Kang Min Seo(서강민),Ha-Seung Seong(성하승),Yo-Han Choi(최요한),Ye-Jin Min(민예진),Jo-Eun Kim(김조은),Doo-Wan Kim(김두완),Eun-Seok Cho(조은석),Hyun-Ju Jin(진현주),Ki-Hyun Kim(김기현),Ki-Taeg Nam(남기택) 한국산학기술학회 2022 한국산학기술학회논문지 Vol.23 No.4

본 연구는 발효유 급여가 포유 및 이유자돈의 성장 및 장관 환경에 미치는 영향을 구명하고자 실시하였다. 공시동물은 총 100마리의 포유자돈을 준비하였고 대조구 및 발효유 급여구에 임의로 50두씩 배치하여 처리구당 5반복, 반복당 10두씩 할당하였으며 이유 후에는 동일 처리구 내에서 공시돈을 처리구당 3반복, 반복당 16두씩 재배치하였다. 사양시험은 포유기(생후 10~27일) 및 이유기(생후 27-64일)동안 실시하였다. 발효유 급여는 포유기에 top-dressing법(2리터/일)로 공급하였으며 이유기에는 별도의 급여기를 이용하여 20리터/일씩 공급하였다. 포유기간동안 증체량은 처리구간 차이는 없었다. 반면에 이유기간동안 증체량 및 사료섭취량은 대조구 대비 발효유 급여구에서 통계적으로 증가하였고 사료요구율은 대조구보다 발효유 급여구에서 유의한 개선을 나타냈다. 분변 내 Echerichia coli 및 Lactobacillus spp.는 발효유 급여구에서 대조구보다 각각 통계적으로 감소 및 증가하였다. 또한, 분변 유래 황화수소 및 총메르캅탄은 발효유 급여에 따라 유의하게 감소하였다. 게다가 장 융모 발달은 대조구보다 발효유 급여구에서 형태학적으로 조밀한 상태가 확인되었다. 그러나 혈중 혈구세포 및 영양대사지표들은 처리구간 차이를 나타내지 않았다. 이러한 결과는 발효유의 급여는 성장 및 장 내 환경을 개선시켜 이유 전 · 후 자돈의 생산성 향상에 기여할 것으로 사료된다. This study investigated the effects of fermented milk (FM) supplementation on the growth performance and gut conditions of weaning piglets. A total of one hundred 10-day-old piglets were assigned to the control and FM treatment groups during the pre-weaning (10-27 day-old) and post-weaning (27-64 day-old) periods. The FM was provided daily in the form of two l/replication/d for the pre-weaning and twenty l/replication/d for the post-weaning periods. There was no difference observed in the growth performance between the two experimental groups during pre-weaning. However, during post-weaning, the daily gain and feed intake were higher in the FM group than in the control, and the feed conversion ratio decreased in the treatment group compared with the control. The blood corpuscles and physiological indexes showed no difference between the control and FM groups. Fecal Escherichia coli was lower in the FM group compared to the control, while Lactobacillus spp. was higher. Emissions of fecal hydrogen sulfide and total mercaptans were reduced by the FM supplementation. The intestinal villi in piglets fed with the FM were morphologically denser than in the control. Therefore, these results suggest that the growth performance, noxious fecal emission, and intestinal environment would be improved by FM supplementation.

Profiling of differentially expressed proteins between fresh and frozen-thawed Duroc boar semen using Protein- Chip CM10

Yong-Min Kim,Sung-Woo Park,Mi-Jin Lee,Da-Yeon Jeon,Su-Jin Sa,Yongdae Jeong,성하승,최정우,Shinichi Hochi,Eun-Seok Cho,Hak-Jae Chung 한국축산학회 2023 한국축산학회지 Vol.65 No.2

Many studies have been conducted to improve technology for semen cryopreservation in pigs. However, computer-assisted analysis of sperm motility and morphology is insufficient to predict the molecular function of frozen-thawed semen. More accurate expression patterns of boar sperm proteins may be derived using the isobaric tags for relative and absolute quantification (iTRAQ) technique. In this study, the iTRAQ-labeling system was coupled with liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis to identify differentially expressed CM10-fractionated proteins between fresh and frozen-thawed boar semen. A total of 76 protein types were identified to be differentially expressed, among which 9 and 67 proteins showed higher and lower expression in frozen-thawed than in fresh sperm samples, respectively. The classified functions of these proteins included oxidative phosphorylation, mitochondrial inner membrane and matrix, and pyruvate metabolic processes, which are involved in adenosine triphosphate (ATP) synthesis; and sperm flagellum and motile cilium, which are involved in sperm tail structure. These results suggest a possible network of biomarkers associated with survival after the cryopreservation of Duroc boar semen.