Kyu-Ho Cho

A genome-wide scan for signatures of directional selection in domesticated pigs

BackgroundAnimal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication.ResultsWhole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an FST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness.ConclusionsWe show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.

Estimation of Genetic Parameters for Economic Traits in Swine

This study was conducted to estimate genetic parameter of Duroc, Landrace and Yorkshire breeds based on the on-farm performance tested records of 57,316 pigs under the supervision of Korean Animal Improvement Association from 1992 to 1999. Genetic parameters were estimated with a multiple trait animal model by using DF - REML. The result obtained in this study was summarized as follow ; The estimated heritabilities of Duroc, Landrace and Yorkshire were 0.460.65 for the average backfat thickness, 0.280.31 for loin depth, 0.50～0.60 for percent lean, 0.450.55 for the average daily gain, 0.380.50 for age at 90kg, respectively. Phenotypic correlation of average backfat thickness with loin depth, percent lean, average daily gain and age at 90㎏ for the three breeds were -0.12-0.01, -0.81-0.76, 0.340.46, and -0.41-0.33, respectively. Phenotypic correlation of loin depth with percent lean, average daily gain and age at 90kg were 0.120.23, 0.030.21, and -0.17-0.03, respectively. Phenotypic correlation of percent lean with average daily gain and age at 90kg were -0.37-0.26 and 0.26～0.35, respectively. Phenotypic correlation of average daily gain with age at 90kg was -0.97-0.95. The estimated genetic correlation coefficients of average backfat thickness with loin depth, percent lean, average daily gain and age at 90kg estimated for the three breeds were -0.170.03, -0.79-0.69, 0.240.45 and -0.41-0.19, respectively. The estimated genetic correlation coefficients of loin depth with percent lean, average daily gain and age at 90kg were 0.11～0.19, 0.23 and -0.30～-0.20, respectively. The estimated correlation coefficients of percent lean with average daily gain and age at 90kg were -0.36-0.13 and 0.10～0.34, respectively. The estimated genetic correlation coefficients of average daily gain with age at 90㎏ was -0.96-0.95.

Length polymorphism in OGT between Korean native pig, Chinese Meishan, and the Western pig breeds

BackgroundThe Korean native pig (KNP) is generally thought to have come from northern China to the Korean peninsula approximately 2000xa0years ago. KNP pigs were at the brink of extinction in the 1980s, since then efforts have been made to restore the breed by bringing together the remaining stocks in South Korea. As a result, KNP was registered as a breed in 2006. To find additional breed-specific markers that are distinct among pig breeds, variations in O-linked N-acetylglucosamine transferase (OGT) were investigated. OGT is located on chromosome X and catalyzes the post-translational addition of a single O-linked-β-N-acetylglucosamine to target proteins.FindingsLength polymorphism in the intron 20 of OGT was identified. The intron 20 of OGT from Duroc, Landrace, and Yorkshire breeds was 281-bp longer than that from either KNP or Chinese Meishan pigs. The difference between the Western pig breeds (BB genotype) and KNP or Meishan pigs (AA genotype) was due to an inserted 276-bp element and the 5-bp ACTTG.ConclusionsThe polymorphism in OGT identified in this study may be used as an additional marker for determining the breed of origin among Meishan and the Western pig breeds. The length polymorphism suggests that the locus near OGT is not fixed in KNP. This marker would be relevant in determining the breed of origin in crossbred pigs between KNP pigs with known genotypes and the Western pig breeds with BB genotypes, thus confirming the contribution of the X chromosome from each breed.

Characterization of Bacteria and Their Antibiotic Sensitivities in Porcine Liquid Semen

The semen collection process in the porcine is far from being a sterile procedure. Consequently, porcine ejaculates commonly contain bacterial contaminants. The aim of this study is to identify the bacteria in porcine semen and to find the antibiotics resistance of bacteria. Twelve porcine originating from four AI center were used to collect semen. Bacteria were identified by automated instrument for rapid organism identification system and bacterial sensitivities of 8 antibiotics were tested. The Bacterial contaminants of Staphylococcus genus(37.8%), Proteus genus(7.0%), Bacillus genus (6.1%), Pasteulla genus(5.7%), Acinetobacte genus(5.2%), Serratia genus(4.3%) and others(33.9%) were frequently isolated. However, amikacin showed higher antibiotic sensitivity than other antibiotics. General sanitation protocols can contribute partly to inhibit the bacterial contamination, with monitoring boar housing, semen collection areas and the extended semen. But, proper selection of preservative antibiotics by microbial sensitivities can minimize the influence of bacteria.

Association of Single Nucleotide Polymorphism (SNP) in the PGK 2 Gene with Growth Traits in Pigs

The purpose of this study was to analyse of association between growth traits and single nucleotide polymorphisms (SNPs) polymorphism of phosphoglycerate kinase 2 (PGK 2) gene in pigs. The birth weight of piglet influences on weaning weight and survival rate that are import economic traits in pig industry. Also, these growth traits are representative factor to decrease a period getting to marketing weight as well as growth rate in pig. The PGK 2 is an isozyme that catalyzes the first ATP-generating step in the glycolytic pathwayand important enzyme related with energy metabolism. Twenty of SNPs were discoveredby genome structure analysis that compares the sequence on promoter and transcription region of PGK 2 gene in porcine chromosome 7. An association between PGK 2 SNPs and growth traits was analyzed in F2 reciprocal-crossbred population between korean native pig (KNP) and Landrace. Association analysis indicated that polymorphism of the PGK 2 gene promoter region has significant effects on weight at birth (p<0.01) and weight at 3 weeks of age (p<0.0001). These results suggest that PGK 2 gene polymorphism was associated with energy metabolism and physiological function of growth in pig. (Key words : PGK 2, SNP, Pig, Birth weight, 3 weeks weight)

Estimation of Genetic Parameters via Gibbs Sampler using Animal Model for Economic Traits in Pigs

ABSTRACT Heritability and genetic correlation for growth traits in Duroc pig breed were estimated using Bayesian method via Gibbs sampling. The data set consisted of 3,526 performance records at National Institute of Animal Science. For estimating those parameters using Gibbs sampling, 5,000 cycles of ‘burn-in’ period were discarded among a total of 55,000 samples. Out of the remaining 50,000 samples, 5,000 estimates by each parameter were retained and used for analyses to avoid any correlation among adjacent samples. The growth traits considered in this study were average daily gain at 30kg (ADG1), average daily gain at 90kg(ADG2), backfat thickness (BF), days to 90 kg (D90) and feed conversion ratio (FC). The estimated heritabilities and their standard deviation using Gibbs sampler were 0.43±0.04, 0.49±0.038, 0.31±0.040, 0.48±0.039 and 0.62±0.086, respectively. Genetic correlations were 0.02, 0.13, 0.55 and 0.15 between ADG1 with ADG2, BF, D90 and FC, respectively, 0.16, 0.73, 0.32 between ADG2 with BF, D90 and FC respectively, 0.01, 0.08 between BF with D90, FC, respectively, and 0.23 between D90 with FC.(

Associations of the Porcine Melanocortin-4 Receptor (MC4R) Gene with Growth Traits in Duroc Pigs

본 연구는 축산과학원에서 보유중인 듀록 품종내에서 MC4R 유전자의 SNP 발현 특성과 육종가에 의한 선발 후 MC4R 유전자 빈도의 변화 및 경제형질에 대한 유전자형간 육종가의 차이를 구명하고자 수행하였다. 1999년부터 2005년까지 검정된 검정성적을 바탕으로 일당증체량, 등지방두께, 90kg 도달일령 및 사료요구율에 대하여 유전력과 유전상관 및 육종가를 추정하였으며, 2003년과 2004년에 출생한 660두에 대한 혈액을 채취하여 MC4R 유전자에 대한 유전자형 및 대립유전자 분석을 실시하였다. 또한 육종가에 의한 선발 후 유전자의 빈도변화를 세대별 그리고 선발군 및 도태군에 대하여 분석하였으며, 육종가의 분석결과를 이용하여 MC4R의 유전자형 효과를 보았다. 분석결과 육종가를 근거하여 선발한 MC4R 유전자형은 세대당 그리고 선발군과 도태군에서 차이를 보였으며, 각 형질별 육종가의 분산분석결과 사료요구율을 제외한 기타 경제형질에서 유의적으로 MC4R 유전자의 효과가 있는 것으로 나타났다. MC4R 유전자의 효과에 대한 보고는 상이한 부분도 있지만 자체 축군에 대한 다형성 분석 및 경제형질과의 연관성 분석에 의하여 축군 및 개량하고자 하는 경제형질에 따라 표지 유전인자로 활용하여 선발반응 및 정확도를 높일 수 있을 것으로 사료된다. 【The melanocortin-4 receptor(MC4R) is virtually expressed in all brain regions and plays an important role in energy homeostasis in mammals. MC4R has been intensively studied as a trait gene controlling economically important traits, such as growth and feed conversion, etc. Six hundreds and sixty Duroc pigs were genotyped for the MC4R locus and analyzed their relationships with breeding values for average daily gain(ADG), backfat thickness(BF), days to 90kg(D90) and feed conversion(FC). The estimated genotype frequencies for the all Duroc pigs were: 30.8%, 45.2%, 24.1% for AA, AB and BB genotypes, respectively. The mutant A allele was significantly associated with ADG, D90 and BF whereas no significant relationship was found with FC. The change of gene frequencies by generation was shown in both selected and culled groups. These results indicate that the MC4R polymorphism could be integrated in the present selection program to realize a marker-assisted selection for the growth traits of the Duroc population.】

Effect of Administration of Gonadotropin and Scheduled Fixed-time Insemination on Onset of Estrus and Reproductive Performance in Lactating Sows

This study was to investigate the effectiveness of pre-weaning injection of gonadotropin and scheduled fixed-time insemination on sow fertility. Sows were randomly assigned to receive gonadotropin 2 days before weaning, 1 day after weaning or none as control. In gonadotropin treated groups, half of sows were inseminated twice at 24 and 36 hours after onset estrus and half of sows were inseminated twice at scheduled fixed-time. Weaning to onset of estrus was the shortest in lactating sows injected with gonadotropin prior to weaning. Liter size was significantly higher in AI groups after detection of estrus, compared to fixed-time AI group. Results of these experiments indicated that injection of gonadotropin in lactating sows could initiate the final follicular development, and has potential to enhance the reintegration of estrus. Further researches are needed to define the relationship between reduced interval of wean to onset estrus and enhanced fertility in lactating sows.