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1.
J Anim Physiol Anim Nutr (Berl) ; 105(5): 952-959, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32772452

RESUMO

Typhoid is a distinct gastrointestinal disease that largely affects the public by consumption of inadequately or partially cooked eggs from contaminated laying hen farms. This has led the research on laying hens to focus on controlling the contamination by an effective anti-Salmonella spp. agent in the intestine. The treatments included, control, without challenge; PC, Salmonella typhimurium challenged (STC); BP5, 5 ppm bacteriophage/kg + STC; BP10, 10 ppm bacteriophage/kg + STC, on Salmonella shedding, body organs inflammatory reactions, and expression of toll-like receptor (TLR), pro-inflammatory cytokines, and heat shock protein (HSP) in the jejunum, liver,and thigh muscle in the STC laying hens. The RT-PCR method was used to enumerate the number of Salmonella typhimurium in the organs. The birds in the STC groups exhibited the increased population of Salmonella spp. in the excreta (p < .01). In the STC groups, the BP5 and BP10 laying hens exhibited a lower (p < .01) population of Salmonella spp. in the excreta at d 7 after STC. Supplementation of bacteriophage significantly decreased (p < .01) the colonization of S. Typhimurium in the spleen, oviduct, caecum and excreta. Among the STC treatments, the BP10 laying hens showed lower (p < .01) mRNA expression of interferon-γ (IFNγ) and TLR-4 in the jejunum compared with the PC treatment. After the STC, dietary supplementation with BP5 or BP10 decreased (p < .01) the mRNA expressions of IFNγ, HSP-27 and tumour necrosis factor-α in the liver compared with the PC treatment. These results suggest that bacteriophage can be used as an effective agent to decrease S. Typhimurium contamination in laying hens and possibly lower S. Typhimurium transfer to foods.


Assuntos
Bacteriófagos , Microbioma Gastrointestinal , Doenças das Aves Domésticas , Salmonelose Animal , Animais , Galinhas , Feminino , Óvulo , Doenças das Aves Domésticas/prevenção & controle , Salmonelose Animal/prevenção & controle , Salmonella typhimurium
2.
Asian-Australas J Anim Sci ; 31(4): 473-479, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29059723

RESUMO

OBJECTIVE: The study was designed to perform a genome-wide association (GWA) and partitioning of genome using Illumina's PorcineSNP60 Beadchip in order to identify variants and determine the explained heritability for the total number of teats in Yorkshire pig. METHODS: After screening with the following criteria: minor allele frequency, MAF≤0.01; Hardy-Weinberg equilibrium, HWE≤0.000001, a pair-wise genomic relationship matrix was produced using 42,953 single nucleotide polymorphisms (SNPs). A genome-wide mixed linear model-based association analysis (MLMA) was conducted. And for estimating the explained heritability with genome- or chromosome-wide SNPs the genetic relatedness estimation through maximum likelihood approach was used in our study. RESULTS: The MLMA analysis and false discovery rate p-values identified three significant SNPs on two different chromosomes (rs81476910 and rs81405825 on SSC8; rs81332615 on SSC13) for total number of teats. Besides, we estimated that 30% of variance could be explained by all of the common SNPs on the autosomal chromosomes for the trait. The maximum amount of heritability obtained by partitioning the genome were 0.22±0.05, 0.16±0.05, 0.10±0.03 and 0.08±0.03 on SSC7, SSC13, SSC1, and SSC8, respectively. Of them, SSC7 explained the amount of estimated heritability along with a SNP (rs80805264) identified by genome-wide association studies at the empirical p value significance level of 2.35E-05 in our study. Interestingly, rs80805264 was found in a nearby quantitative trait loci (QTL) on SSC7 for the teat number trait as identified in a recent study. Moreover, all other significant SNPs were found within and/or close to some QTLs related to ovary weight, total number of born alive and age at puberty in pigs. CONCLUSION: The SNPs we identified unquestionably represent some of the important QTL regions as well as genes of interest in the genome for various physiological functions responsible for reproduction in pigs.

3.
Sensors (Basel) ; 17(10)2017 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-29053623

RESUMO

Face routing has been adopted in wireless sensor networks (WSNs) where topological changes occur frequently or maintaining full network information is difficult. For message forwarding in networks, a planar graph is used to prevent looping, and because long edges are removed by planarization and the resulting planar graph is composed of short edges, and messages are forwarded along multiple nodes connected by them even though they can be forwarded directly. To solve this, face routing using information on all nodes within 2-hop range was adopted to forward messages directly to the farthest node within radio range. However, as the density of the nodes increases, network performance plunges because message transfer nodes receive and process increased node information. To deal with this problem, we propose a new face routing using the planar graphs of neighboring nodes to improve transfer efficiency. It forwards a message directly to the farthest neighbor and reduces loads and processing time by distributing network graph construction and planarization to the neighbors. It also decreases the amount of location information to be transmitted by sending information on the planar graph nodes rather than on all neighboring nodes. Simulation results show that it significantly improves transfer efficiency.

5.
Asian-Australas J Anim Sci ; 27(12): 1678-83, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25358359

RESUMO

This study considers a problem of genomic selection (GS) for adjacent genetic markers of Yorkshire pigs which are typically correlated. The GS has been widely used to efficiently estimate target variables such as molecular breeding values using markers across the entire genome. Recently, GS has been applied to animals as well as plants, especially to pigs. For efficient selection of variables with specific traits in pig breeding, it is required that any such variable selection retains some properties: i) it produces a simple model by identifying insignificant variables; ii) it improves the accuracy of the prediction of future data; and iii) it is feasible to handle high-dimensional data in which the number of variables is larger than the number of observations. In this paper, we applied several variable selection methods including least absolute shrinkage and selection operator (LASSO), fused LASSO and elastic net to data with 47K single nucleotide polymorphisms and litter size for 519 observed sows. Based on experiments, we observed that the fused LASSO outperforms other approaches.

6.
J Vet Sci ; 25(1): e4, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38311319

RESUMO

BACKGROUND: Lawsonia intracellularis is the causative agent of proliferative enteropathy and is associated with several outbreaks, causing substantial economic loss to the porcine industry. OBJECTIVES: In this study, we focused on demonstrating the protective effect in the mouse model through the immunological bases of two vaccine strains against porcine proliferative enteritis. METHODS: We used live-attenuated Salmonella Typhimurium (ST) secreting two selected immunogenic LI antigens (Lawsonia autotransporter A epitopes and flagellin [FliC]-peptidoglycan-associated lipoprotein-FliC) as the vaccine carrier. The constructs were cloned into a Salmonella expression vector (pJHL65) and transformed into the ST strain (JOL912). The expression of immunogenic proteins within Salmonella was evaluated via immunoblotting. RESULTS: Immunizing BALB/c mice orally and subcutaneously induced high levels of LI-specific systemic immunoglobulin G and mucosal secretory immunoglobulin A. In immunized mice, there was significant upregulation of interferon-γ and interleukin-4 cytokine mRNA and an increase in the subpopulations of cluster of differentiation (CD) 4+ and CD 8+ T lymphocytes upon splenocytes re-stimulation with LI antigens. We observed significant protection in C57BL/6 mice against challenge with 106.9 times the median tissue culture infectious dose of LI or 2 × 109 colony-forming units of the virulent ST strain. Immunizing mice with either individual vaccine strains or co-mixture inhibited bacterial proliferation, with a marked reduction in the percentage of mice shedding Lawsonia in their feces. CONCLUSIONS: Salmonella-mediated LI gene delivery induces robust humoral and cellular immune reactions, leading to significant protection against LI and salmonellosis.


Assuntos
Lawsonia (Bactéria) , Doenças dos Roedores , Doenças dos Suínos , Vacinas , Camundongos , Animais , Suínos , Modelos Animais de Doenças , Camundongos Endogâmicos C57BL , Salmonella typhimurium , Camundongos Endogâmicos BALB C , Doenças dos Suínos/prevenção & controle
7.
Anim Biosci ; 37(4): 622-630, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38228129

RESUMO

OBJECTIVE: Pig breeders cannot obtain phenotypic information at the time of selection for sow lifetime productivity (SLP). They would benefit from obtaining genetic information of candidate sows. Genomic data interpreted using deep learning (DL) techniques could contribute to the genetic improvement of SLP to maximize farm profitability because DL models capture nonlinear genetic effects such as dominance and epistasis more efficiently than conventional genomic prediction methods based on linear models. This study aimed to investigate the usefulness of DL for the genomic prediction of two SLP-related traits; lifetime number of litters (LNL) and lifetime pig production (LPP). METHODS: Two bivariate DL models, convolutional neural network (CNN) and local convolutional neural network (LCNN), were compared with conventional bivariate linear models (i.e., genomic best linear unbiased prediction, Bayesian ridge regression, Bayes A, and Bayes B). Phenotype and pedigree data were collected from 40,011 sows that had husbandry records. Among these, 3,652 pigs were genotyped using the PorcineSNP60K BeadChip. RESULTS: The best predictive correlation for LNL was obtained with CNN (0.28), followed by LCNN (0.26) and conventional linear models (approximately 0.21). For LPP, the best predictive correlation was also obtained with CNN (0.29), followed by LCNN (0.27) and conventional linear models (approximately 0.25). A similar trend was observed with the mean squared error of prediction for the SLP traits. CONCLUSION: This study provides an example of a CNN that can outperform against the linear model-based genomic prediction approaches when the nonlinear interaction components are important because LNL and LPP exhibited strong epistatic interaction components. Additionally, our results suggest that applying bivariate DL models could also contribute to the prediction accuracy by utilizing the genetic correlation between LNL and LPP.

8.
Sci Rep ; 13(1): 18668, 2023 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-37907519

RESUMO

Understanding the influence of genetic variations in olfactory receptor (OR) genes on the olfaction-influenced phenotypes such as behaviors, reproduction, and feeding is important in animal biology. However, our understanding of the complexity of the OR subgenome is limited. In this study, we analyzed 1120 typing results of 20 representative OR genes belonging to 13 OR families on 14 pig chromosomes from 56 individuals belonging to seven different breeds using a sequence-based OR typing method. We showed that the presence of copy number variations, conservation of locus-specific diversity, abundance of breed-specific alleles, presence of a loss-of-function allele, and low-level purifying selection in pig OR genes could be common characteristics of OR genes in mammals. The observed nucleotide sequence diversity of pig ORs was higher than that of dogs. To the best of our knowledge, this is the first report on the individual- or population-level characterization of a large number of OR family genes in livestock species.


Assuntos
Receptores Odorantes , Humanos , Suínos/genética , Animais , Cães , Receptores Odorantes/genética , Variações do Número de Cópias de DNA/genética , Cruzamento , Sequência de Bases , Gado/genética , Variação Genética , Mamíferos/genética
9.
J Anim Sci Technol ; 65(2): 401-411, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37093902

RESUMO

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.

10.
J Anim Sci Technol ; 65(2): 365-376, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37093914

RESUMO

Pig breeding management directly contributes to the profitability of pig farms, and pregnancy diagnosis is an important factor in breeding management. Therefore, the need to diagnose pregnancy in sows is emphasized, and various studies have been conducted in this area. We propose a computer-aided diagnosis system to assist livestock farmers to diagnose sow pregnancy through ultrasound. Methods for diagnosing pregnancy in sows through ultrasound include the Doppler method, which measures the heart rate and pulse status, and the echo method, which diagnoses by amplitude depth technique. We propose a method that uses deep learning algorithms on ultrasonography, which is part of the echo method. As deep learning-based classification algorithms, Inception-v4, Xception, and EfficientNetV2 were used and compared to find the optimal algorithm for pregnancy diagnosis in sows. Gaussian and speckle noises were added to the ultrasound images according to the characteristics of the ultrasonography, which is easily affected by noise from the surrounding environments. Both the original and noise added ultrasound images of sows were tested together to determine the suitability of the proposed method on farms. The pregnancy diagnosis performance on the original ultrasound images achieved 0.99 in accuracy in the highest case and on the ultrasound images with noises, the performance achieved 0.98 in accuracy. The diagnosis performance achieved 0.96 in accuracy even when the intensity of noise was strong, proving its robustness against noise.

12.
Animals (Basel) ; 12(17)2022 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-36078021

RESUMO

Average daily gain (ADG) is an important growth trait in the pig industry. The direct genetic effect (DGE) has been studied mainly to assess the association between genetic information and economic traits. The social genetic effect (SGE) has been shown to affect ADG simultaneously with the DGE because of group housing systems. We conducted this study to elucidate the genetic characteristics and relationships of the DGE and SGE of purebred Korean Duroc and crossbred pigs by single-step genomic best linear unbiased prediction and a genome-wide association study. We used the genotype, phenotype, and pedigree data of 1779, 6022, and 7904 animals, respectively. Total heritabilities on ADG were 0.19 ± 0.04 and 0.39 ± 0.08 for purebred and crossbred pigs, respectively. The genetic correlation was the greatest (0.77 ± 0.12) between the SGE of purebred and DGE of crossbred pigs. We found candidate genes located in the quantitative trait loci (QTLs) for the SGE that were associated with behavior and neurodegenerative diseases, and candidate genes in the QTLs for DGE that were related to body mass, size of muscle fiber, and muscle hypertrophy. These results suggest that the genomic selection of purebred animals could be applied for crossbred performance.

13.
Front Genet ; 13: 779152, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35186025

RESUMO

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.

14.
J Anim Sci ; 100(12)2022 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-36074647

RESUMO

Fat is involved in synthesizing fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. The samples were collected from the porcine abdominal fat of different developmental stages (10 and 26 weeks of age). Then, the samples were sequenced using MBD-seq and RNA-seq for profiling DNA methylation and RNA expression. In 26 weeks of age pigs, differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified as 2,251 and 5,768, compared with 10 weeks of age pigs, respectively. Gene functional analysis was performed using GO and KEGG databases. In functional analysis results of DMGs and DEGs, immune responses such as chemokine signaling pathways, B cell receptor signaling pathways, and lipid metabolism terms such as PPAR signaling pathways and fatty acid degradation were identified. It is thought that there is an influence between DNA methylation and gene expression through changes in genes with similar functions. The effects of DNA methylation on gene expression were investigated using cis-regulation and trans-regulation analysis to integrate and interpret different molecular layers. In the cis-regulation analysis using 629 overlapping genes between DEGs and DMGs, immune response functions were identified, while in trans-regulation analysis through the TF-target gene network, the co-expression network of lipid metabolism-related functions was distinguished. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging.


Fat is involved in the synthesis of new fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. Modifications in DNA methylation and expression values were confirmed epigenetically with growth. Changed genes in each DNA and RNA showed identical trends in the function of immune response and lipid metabolism. The effects of DNA methylation on gene expression were investigated using cis-regulation (functional enrichment analysis of overlapping genes) and trans-regulation (transcription factor and target gene networking) analysis to integrate and interpret different molecular layers. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging.


Assuntos
Epigênese Genética , Perfilação da Expressão Gênica , Suínos/genética , Animais , Perfilação da Expressão Gênica/veterinária , Metilação de DNA , Metabolismo dos Lipídeos/genética , Gordura Abdominal , Imunidade , Transcriptoma
15.
J Anim Sci Technol ; 63(5): 977-983, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34796341

RESUMO

Closely correlated expression patterns between ubiquitin specific peptidase 9X-linked (USP9X) and adherens junction formation factor (Afadin) in mouse testis development suggests that Usp9x regulates the deubiquitination of Af-6 (also known as Afadin, AFDN), and subsequently, the cell adhesion dynamics during gametogenesis. However, this relationship has not yet been tested in other domestic animals. The study was examined the temporal and spatial expression patterns of porcine USP9X and AFDN from the pre-pubertal to adult stages using real time-PCR and immunohistochemistry. Furthermore, we detected the transcripts of USP9X and AFDN in the testis of 1-, 6- and 12-months old boar, respectively. USP9X and AFDN were found to have similar expressions patterns, with basal expression after 1 month followed by a significant up-regulation from 6 months (puberty) onwards. In addition, neither the AFDN or USP9X proteins were detected in spermatogenic cells but they were expressed in the leydig cells and sertoli cells. USP9X was detected around the basal lamina during pre-puberty, and predominantly expressed in the leydig cells at puberty. Finally, in adult testis, USP9X was increased at the sertoli cell-cell interface and the sertoli cell-spermatid interface. In summary, closely correlated expression patterns between USP9X and AFDN in boar testis supports the previous findings in mice. Furthermore, the junction connections between the sertoli cells may be regulated by the ubiquitination process mediated via USP9X.

16.
Animals (Basel) ; 10(5)2020 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-32344859

RESUMO

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.

17.
Sci Rep ; 10(1): 14958, 2020 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-32917921

RESUMO

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.


Assuntos
Genótipo , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Suínos , Animais , Estudo de Associação Genômica Ampla , Suínos/genética , Suínos/crescimento & desenvolvimento
18.
Genes Genomics ; 42(3): 263-272, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31833050

RESUMO

BACKGROUND: Miniature pigs have been increasingly used as mammalian model animals for biomedical research because of their similarity to human beings in terms of their metabolic features and proportional organ sizes. However, despite their importance, there is a severe lack of genome-wide studies on miniature pigs. OBJECTIVE: In this study, we performed whole-genome sequencing analysis of 20 Micro-pigs obtained from Medi Kinetics to elucidate their genomic characteristics. RESULTS: Approximately 595 gigabase pairs (Gb) of sequence reads were generated to be mapped to the swine reference genome assembly (Sus scrofa 10.2); on average, the sequence reads covered 99.15% of the reference genome at an average of 9.6-fold coverage. We detected a total of 19,518,548 SNPs, of which 8.7% were found to be novel. With further annotation of all of the SNPs, we retrieved 144,507 nonsynonymous SNPs (nsSNPs); of these, 5968 were found in all 20 individuals used in this study. SIFT prediction for these SNPs identified that 812 nsSNPs in 402 genes were deleterious. Among these 402 genes, we identified some genes that could potentially affect traits of interest in Micro-pigs, such as RHEB and FRAS1. Furthermore, we performed runs of homozygosity analysis to locate potential selection signatures in the genome, detecting several loci that might be involved in phenotypic characteristics in Micro-pigs, such as MSTN, GDF5, and GDF11. CONCLUSION: In this study, we identified numerous nsSNPs that could be used as candidate genetic markers with involvement in traits of interest. Furthermore, we detected putative selection footprints that might be associated with recent selection applied to miniature pigs.


Assuntos
Suínos/genética , Animais , Cruzamento , Mapeamento Cromossômico , Proteínas da Matriz Extracelular/genética , Ontologia Genética , Fator 5 de Diferenciação de Crescimento/genética , Homozigoto , Miostatina/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Proteína Enriquecida em Homólogo de Ras do Encéfalo/genética , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
19.
Genes Genomics ; 42(12): 1443-1453, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33145727

RESUMO

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.


Assuntos
Genômica , Polimorfismo de Nucleotídeo Único , Sus scrofa/genética , Animais , Variação Genética , Genética Populacional , Endogamia , Análise de Sequência de DNA
20.
Saudi J Biol Sci ; 26(2): 373-377, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31485180

RESUMO

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.

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