Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon.

A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.

Altrenogest affects expression of galectin-3 and fibroblast growth factor 9 in the reproductive tract of sows.

A synthetic progestin altrenogest (ALT) is used to synchronize the estrus cycle of swine for fixed-time artificial insemination (AI) and has been shown to improve follicular development and reproductive performances in post-weaning sows. However, the effects of ALT treatment on reproductive tracts, including the ovaries, oviducts and uterus have not been yet clarified. In this study, we examined the expression of genes involved in endometrial responses in ALT-treated sows. ALT did not significantly alter luteinizing hormone (LH), follicle-stimulating hormone (FSH) and estradiol profiles in blood compared to untreated control. Quantitative RT-polymerase chain reaction (qRT-PCR) analysis showed that the expression of genes encoding galectin-3 (LGALS3) and fibroblast growth factor 9 (FGF9) was upregulated in the reproductive tracts of ALT-treated sows, including the ovaries, oviducts and uteri. Moreover, ALT treatment induced the expression of FGF9 and galectin-3 proteins, and promoted their localization to the luminal epithelium of the oviducts and uterus. Our findings suggest that the enhancement of reproductive performance shown by ALT-treated sows is associated with the upregulation of galectin-3 and FGF9, which are essential for endometrial receptivity, successful implantation, and pregnancy.

Genome-wide investigation of a Korean synthetic breed, Woori-Heukdon using the Illumina PorcineSNP60K BeadChip.

BACKGROUND: Woori-Heukdon (KWH) is a Korean synthetic pig breed generated using Chookjin-Duroc (KCD), Chookjin-Chamdon (KCC), and their crossbreds. Currently, there is a severe lack of studies investigating the Korean breed populations including wild boars (KWB) throughout the genome. OBJECTIVE: This study was performed to investigate the genetic characteristics of Korean pig populations at the genome-wide level. METHODS: Using the SNP dataset derived from genotyped and downloaded datasets using the Illumina PorcineSNP60K BeadChip, we compared the genomes of 532 individuals derived from 23 pig breeds to assess the genetic diversity, inbreeding coefficient, genetic differentiation, and population structure. RESULTS: KWB showed the lowest average expected heterozygosity (HE = 0.1904), while KWH showed the highest genetic diversity (HE = 0.02859) among Korean populations. We verified that the genetic composition of KWH, showing USD of 74.8% and KCC of 25.2% in ADMIXTURE analysis. In population structure analyses, KCC was consistently shown to be separated from other pig populations. In addition, we observed gene flow from Western pigs to a part of Chinese populations. CONCLUSION: This study showed that Korean native pigs, KCC have genetic differences in comparison with Chinese and Western pigs; despite some historical records and recent genetic studies, we could not find any clear evidence that KCC was significantly influenced by Chinese or Western breeds in this study. We also verified the theoretical genomic composition of KWH at the molecular level in structure analyses. To our knowledge, this is the first genomic study to investigate the genomic characteristics of KWH and KCC.

Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs.

In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects of an individual on its own phenotype) on average daily gain (ADG) in Landrace pigs, and to conduct single-step genome-wide association study using SGE and DGE as dependent variables to identify quantitative trait loci (QTLs) and their positional candidate genes. A total of 1,041 Landrace pigs were genotyped using the Porcine SNP 60K BeadChip. Estimates of the two effects were obtained using an extended animal model. The SGE contributed 16% of the total heritable variation of ADG. The total heritability estimated by the extended animal model including both SGE and DGE was 0.52. The single-step genome-wide association study identified a total of 23 QTL windows for the SGE on ADG distributed across three chromosomes (i.e., SSC1, SSC2, and SSC6). Positional candidate genes within these QTL regions included PRDM13, MAP3K7, CNR1, HTR1E, IL4, IL5, IL13, KIF3A, EFHD2, SLC38A7, mTOR, CNOT1, PLCB2, GABRR1, and GABRR2, which have biological roles in neuropsychiatric processes. The results of biological pathway and gene network analyses also support the association of the neuropsychiatric processes with SGE on ADG in pigs. Additionally, a total of 11 QTL windows for DGE on ADG in SSC2, 3, 6, 9, 10, 12, 14, 16, and 17 were detected with positional candidate genes such as ARL15. We found a putative pleotropic QTL for both SGE and DGE on ADG on SSC6. Our results in this study provide important insights that can help facilitate a better understanding of the molecular basis of SGE for socially affected traits.

Genomic Analysis Using Bayesian Methods under Different Genotyping Platforms in Korean Duroc Pigs.

Genomic evaluation has been widely applied to several species using commercial single nucleotide polymorphism (SNP) genotyping platforms. This study investigated the informative genomic regions and the efficiency of genomic prediction by using two Bayesian approaches (BayesB and BayesC) under two moderate-density SNP genotyping panels in Korean Duroc pigs. Growth and production records of 1026 individuals were genotyped using two medium-density, SNP genotyping platforms: Illumina60K and GeneSeek80K. These platforms consisted of 61,565 and 68,528 SNP markers, respectively. The deregressed estimated breeding values (DEBVs) derived from estimated breeding values (EBVs) and their reliabilities were taken as response variables. Two Bayesian approaches were implemented to perform the genome-wide association study (GWAS) and genomic prediction. Multiple significant regions for days to 90 kg (DAYS), lean muscle area (LMA), and lean percent (PCL) were detected. The most significant SNP marker, located near the MC4R gene, was detected using GeneSeek80K. Accuracy of genomic predictions was higher using the GeneSeek80K SNP panel for DAYS (Δ2%) and LMA (Δ2-3%) with two response variables, with no gains in accuracy by the Bayesian approaches in four growth and production-related traits. Genomic prediction is best derived from DEBVs including parental information as a response variable between two DEBVs regardless of the genotyping platform and the Bayesian method for genomic prediction accuracy in Korean Duroc pig breeding.

Digestibility of phosphorous in cereals and co-products for animal feed.

Feed ingredients used in swine diets contain various levels and availabilities of nutrients. Nutritional precision evaluation of each ingredient is necessary for formulating diets of pigs. Especially, phosphorous (P) is one of important nutrients for metabolism. However, current data of P digestibility were most apparent digestibility. Therefore, this study was aimed to estimate the coefficient of total tract standardized digestibility (CTTSD) of P in cereals and various co-products used in pig diet. Twelve barrows (initial BW ±â€¯SD, 46.70 ±â€¯3.21 kg) were used in this experiment. The experimental design was a 12 × 8 incomplete Latin square with 12 diets and 8 periods. Experimental diets were consisted of barley, wheat, lupine kernel (LK), soybean meal (SBM), almond meal (AM), corn gluten meal (CGM), corn gluten feed from China (CGF-C), corn gluten feed from Korea (CGF-C), wheat bran (WB), rice bran (RB), lupine hull (LH) and P-free diet. The CTTAD of Ca was higher in AM than RB and CGF-K. The LK and CGM showed greater CTTSD of P than RB and LH. In conclusion, our results indicated that the cereals and co-products as P sources were the ideally used as an ingredient in mixed diets of the growing-finishing pigs.

Potential use of transgenic domestic pigs expressing recombinant human erythropoietin in diabetes translation research.

Recently, diabetes mellitus (DM) has shown rapid global increases with about five million deaths annually. Animal models are imperative to understand disease mechanisms and develop diagnostic, preventive, and therapeutic interventions in translational research. Rodent and mini-pig models have been established and widely used for DM research. However, domestic pig models are limited in spite of advantages such as pharmacokinetic and physiopathological availability. This study examines the potential use of domestic pigs expressing recombinant human erythropoietin (rhEPO) as disease and therapeutic response models for DM. We previously generated transgenic pigs (n = 16, EPO Tg) in which rhEPO was expressed and circulated in all organs. Thirty-two pigs, including 16 controls, were fed high fat (HF) diets for 42 weeks. Subsequently, blood samples for chemical and metabolic analysis were collected after fasting for 24 h and glucose loading for oral glucose tolerance tests (OGTTs). We found increased activation of the PI3 K/Akt signaling pathway under hypoxic conditions after rhEPO treatment, and HF diet-inducible-obesity in the EPO Tg and control pigs. OGTTs showed lower fasting glucose levels in the EPO Tg pigs than in controls before and after the HF diet, suggesting that rhEPO may affect glucose concentrations. Insulin and C-peptide concentrations responded slowly to glucose administration and returned to initial levels after 2 h. The blood test results suggest that EPO might affect metabolic and chemical components such as glucose, high-density lipoprotein, glucagon, triglyceride, and free fatty acid. Our findings support the use of rhEPO transgenic domestic pigs as model animals for translational DM research.

Production of human tissue-type plasminogen activator (htPA) using in vitro cultured transgenic pig mammary gland cells.

Tissue plasminogen activator (tPA) is a protein involved in the breakdown of blood clots. We have previously produced a human tPA (htPA)-overexpressing transgenic pig using a mammary gland-specific promoter. In this study, we have established a transgenic pig mammary gland cell line that produces recombinant htPA. The mammary gland cells grew well and retained their character over long periods of culture. There was no difference in the extent of apoptosis in transgenic cells compared to wild-type mammary gland cells. In addition, the transgenic mammary gland cells expressed and secreted htPA into the conditioned media at a concentration similar to that in milk. This transgenic cell line represents a simple and ethical method for recombinant htPA production.

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

BACKGROUND: The Korean native pig (KNP) is generally thought to have come from northern China to the Korean peninsula approximately 2000 years 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-ß-N-acetylglucosamine to target proteins. FINDINGS: Length 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. CONCLUSIONS: The 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.

Effects of genetic variants for the swine FABP3, HMGA1, MC4R, IGF2, and FABP4 genes on fatty acid composition.

This study aimed to verify genetic relationships between fatty acid composition (FAC) and genotypes of several genes (FABP3, HMGA1, MC4R, IGF2, and FABP4) using pig breeds. The effects of genetic variations on FAC of the longissimus muscle were statistically significant with additive and dominance effects. The polymorphisms of FABP3 and IGF2 had the largest effects on stearic (C18:0, P=0.009) and γ-linoleic (C18:3n6, P=0.039) acids, respectively, whereas HMGA1 and FABP4 did not show significances. The analysis revealed that MC4R was significantly associated with palmitoleic acid (C16:ln7) and MUFA. Allele frequencies of the genes examined in this analysis were significantly skewed or fixed in the Korean native pig (KNP), whereas the allele frequencies of the crossbreds tended to fall between those of the purebreds except that HMGA1 and FABP4 had approximately the same allele frequencies with Duroc and KNP, respectively. The polymorphisms found in this study could be used as genetic markers in breeding programs to simultaneously change proportions of fatty acids in muscle tissues.

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

BACKGROUND: Animal 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. RESULTS: Whole-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 F ST-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. CONCLUSIONS: We 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.

Origin of leakage paths driven by electric fields in Al-doped TiO2 films.

The growth of leakage current paths in Al-doped TiO2 (ATO) films is observed by in situ TEM under negative bias stress. Through systematic HAADF-STEM, STEM-EDS, and STEM-EELS studies, it is confirmed that the electric field-induced growth of the Ru-doped TiO2 phase is the main reason for the ATO film's negative leakage.