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Van Goor A, Pasternak A, Walugembe M, Chehab N, Hamonic G, Dekkers JCM, Harding JCS, Lunney JK. Genome wide association study of thyroid hormone levels following challenge with porcine reproductive and respiratory syndrome virus. Front Genet 2023; 14:1110463. [PMID: 36845393 PMCID: PMC9947478 DOI: 10.3389/fgene.2023.1110463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction: Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to Porcine reproductive and respiratory syndrome virus infection. However, the genetic control of T3 and T4 levels during infection is not completely understood. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with Porcine reproductive and respiratory syndrome virus. Methods: Sera from 5-week-old pigs (N = 1792) at 11 days post inoculation (DPI) with Porcine reproductive and respiratory syndrome virus were assayed for T3 levels (piglet_T3). Sera from fetuses (N = 1,267) at 12 or 21 days post maternal inoculation (DPMI) with Porcine reproductive and respiratory syndrome virus of sows (N = 145) in late gestation were assayed for T3 (fetal_T3) and T4 (fetal_T4) levels. Animals were genotyped using 60 K Illumina or 650 K Affymetrix single nucleotide polymorphism (SNP) panels. Heritabilities, phenotypic correlations, and genetic correlations were estimated using ASREML; genome wide association studies were performed for each trait separately using Julia for Whole-genome Analysis Software (JWAS). Results: All three traits were low to moderately heritable (10%-16%). Phenotypic and genetic correlations of piglet_T3 levels with weight gain (0-42 DPI) were 0.26 ± 0.03 and 0.67 ± 0.14, respectively. Nine significant quantitative trait loci were identified for piglet_T3, on Sus scrofa chromosomes (SSC) 3, 4, 5, 6, 7, 14, 15, and 17, and collectively explaining 30% of the genetic variation (GV), with the largest quantitative trait loci identified on SSC5, explaining 15% of the genetic variation. Three significant quantitative trait loci were identified for fetal_T3 on SSC1 and SSC4, which collectively explained 10% of the genetic variation. Five significant quantitative trait loci were identified for fetal_T4 on SSC1, 6, 10, 13, and 15, which collectively explained 14% of the genetic variation. Several putative immune-related candidate genes were identified, including CD247, IRF8, and MAPK8. Discussion: Thyroid hormone levels following Porcine reproductive and respiratory syndrome virus infection were heritable and had positive genetic correlations with growth rate. Multiple quantitative trait loci with moderate effects were identified for T3 and T4 levels during challenge with Porcine reproductive and respiratory syndrome virus and candidate genes were identified, including several immune-related genes. These results advance our understanding of growth effects of both piglet and fetal response to Porcine reproductive and respiratory syndrome virus infection, revealing factors associated with genomic control of host resilience.
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Affiliation(s)
- Angelica Van Goor
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Alex Pasternak
- Department of Animal Science, Purdue University, West Lafayette, IN, United States
| | - Muhammed Walugembe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Nadya Chehab
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Glenn Hamonic
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jack C. M. Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - John C. S. Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joan K. Lunney
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States,*Correspondence: Joan K. Lunney,
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Whole-genome sequence-based association study for immune cells in an eight-breed pig heterogeneous population. J Genet Genomics 2022; 49:1068-1071. [PMID: 34601119 DOI: 10.1016/j.jgg.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/29/2022]
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Crespo-Piazuelo D, Ramayo-Caldas Y, González-Rodríguez O, Pascual M, Quintanilla R, Ballester M. A Co-Association Network Analysis Reveals Putative Regulators for Health-Related Traits in Pigs. Front Immunol 2021; 12:784978. [PMID: 34899750 PMCID: PMC8662732 DOI: 10.3389/fimmu.2021.784978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022] Open
Abstract
In recent years, the increase in awareness of antimicrobial resistance together with the societal demand of healthier meat products have driven attention to health-related traits in livestock production. Previous studies have reported medium to high heritabilities for these traits and described genomic regions associated with them. Despite its genetic component, health- and immunity-related traits are complex and its study by association analysis with genomic markers may be missing some information. To analyse multiple phenotypes and gene-by-gene interactions, systems biology approaches, such as the association weight matrix (AWM), allows combining genome wide association study results with network inference algorithms. The present study aimed to identify gene networks, key regulators and candidate genes associated to immunocompetence in pigs by integrating multiple health-related traits, enriched for innate immune phenotypes, using the AWM approach. The co-association network analysis unveiled a network comprised of 3,636 nodes (genes) and 451,407 edges (interactions), including a total of 246 regulators. From these, five genes (ARNT2, BRMS1L, MED12L, SUPT3H and TRIM25) were selected as key regulators as they were associated with the maximum number of genes with the minimum overlapping (1,827 genes in total). The five regulators were involved in pathways related to immunity such as lymphocyte differentiation and activation, platelet activation and degranulation, megakaryocyte differentiation, FcγR-mediated phagocytosis and response to nitric oxide, among others, but also in immunometabolism. Furthermore, we identified genes co-associated with the key regulators previously reported as candidate genes (e.g., ANGPT1, CD4, CD36, DOCK1, PDE4B, PRKCE, PTPRC and SH2B3) for immunity traits in humans and pigs, but also new candidate ones (e.g., ACSL3, CXADR, HBB, MMP12, PTPN6, WLS) that were not previously described. The co-association analysis revealed new regulators associated with health-related traits in pigs. This approach also identified gene-by-gene interactions and candidate genes involved in pathways related to cell fate and metabolic and immune functions. Our results shed new light in the regulatory mechanisms involved in pig immunity and reinforce the use of the pig as biomedical model.
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Affiliation(s)
- Daniel Crespo-Piazuelo
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Olga González-Rodríguez
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Mariam Pascual
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
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Genetic parameters and associated genomic regions for global immunocompetence and other health-related traits in pigs. Sci Rep 2020; 10:18462. [PMID: 33116177 PMCID: PMC7595139 DOI: 10.1038/s41598-020-75417-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022] Open
Abstract
The inclusion of health-related traits, or functionally associated genetic markers, in pig breeding programs could contribute to produce more robust and disease resistant animals. The aim of the present work was to study the genetic determinism and genomic regions associated to global immunocompetence and health in a Duroc pig population. For this purpose, a set of 30 health-related traits covering immune (mainly innate), haematological, and stress parameters were measured in 432 healthy Duroc piglets aged 8 weeks. Moderate to high heritabilities were obtained for most traits and significant genetic correlations among them were observed. A genome wide association study pointed out 31 significantly associated SNPs at whole-genome level, located in six chromosomal regions on pig chromosomes SSC4, SSC6, SSC17 and SSCX, for IgG, γδ T-cells, C-reactive protein, lymphocytes phagocytic capacity, total number of lymphocytes, mean corpuscular volume and mean corpuscular haemoglobin. A total of 16 promising functionally-related candidate genes, including CRP, NFATC2, PRDX1, SLA, ST3GAL1, and VPS4A, have been proposed to explain the variation of immune and haematological traits. Our results enhance the knowledge of the genetic control of traits related with immunity and support the possibility of applying effective selection programs to improve immunocompetence in pigs.
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Bovo S, Mazzoni G, Bertolini F, Schiavo G, Galimberti G, Gallo M, Dall'Olio S, Fontanesi L. Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes. Sci Rep 2019; 9:7003. [PMID: 31065004 PMCID: PMC6504931 DOI: 10.1038/s41598-019-43297-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/16/2019] [Indexed: 12/20/2022] Open
Abstract
Haematological and clinical-biochemical parameters are considered indicators of the physiological/health status of animals and might serve as intermediate phenotypes to link physiological aspects to production and disease resistance traits. The dissection of the genetic variability affecting these phenotypes might be useful to describe the resilience of the animals and to support the usefulness of the pig as animal model. Here, we analysed 15 haematological and 15 clinical-biochemical traits in 843 Italian Large White pigs, via three genome-wide association scan approaches (single-trait, multi-trait and Bayesian). We identified 52 quantitative trait loci (QTLs) associated with 29 out of 30 analysed blood parameters, with the most significant QTL identified on porcine chromosome 14 for basophil count. Some QTL regions harbour genes that may be the obvious candidates: QTLs for cholesterol parameters identified genes (ADCY8, APOB, ATG5, CDKAL1, PCSK5, PRL and SOX6) that are directly involved in cholesterol metabolism; other QTLs highlighted genes encoding the enzymes being measured [ALT (known also as GPT) and AST (known also as GOT)]. Moreover, the multivariate approach strengthened the association results for several candidate genes. The obtained results can contribute to define new measurable phenotypes that could be applied in breeding programs as proxies for more complex traits.
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Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Gianluca Mazzoni
- Department of Health Technology, Technical University of Denmark (DTU), Lyngby, 2800, Denmark
| | - Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), Lyngby, 2800, Denmark
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Giuliano Galimberti
- Department of Statistical Sciences "Paolo Fortunati", University of Bologna, Via delle Belle Arti 41, 40126, Bologna, Italy
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Roma, Italy
| | - Stefania Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.
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Hu Z, Li H, Xie R, Wang S, Yin Z, Liu Y. Genomic variant in porcine TNFRSF1A gene and its effects on TNF signaling pathway in vitro. Gene 2019; 700:105-109. [PMID: 30914326 DOI: 10.1016/j.gene.2019.03.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 12/31/2022]
Abstract
Our initial genome-wide association study (GWAS) revealed the presence of single nucleotide polymorphisms (SNPs) related to immune traits in the tumor necrosis factor receptor superfamily member 1A (TNFRSF1A) gene, suggesting the association of this gene with immune function in pigs. To better understand the immune functions of the TNFRSF1A gene, SNPs within the TNFRSF1A gene were detected by sequencing. One SNP (c.1394C > T) in exon 6 of TNFRSF1A was identified, and association analysis in two pig populations was subsequently performed. The results showed that this SNP was significantly associated with CD4-CD8-CD3-, CD4+CD8-CD3+, and CD4+/CD8+ (P = 0.0038, P = 0.0007, and P = 0.0076, respectively). Based on quantitative real-time polymerase chain reaction (RT-qPCR), the TNFRSF1A mRNA was shown to be widely expressed in six different tissues. Finally, functional verification of the TNFRSF1A gene was performed in vitro to better understand its role. RNAi was used to generate a porcine PK15 cell line with a silenced TNFRSF1A gene, and a vector was also constructed to assess overexpression of TNFRSF1A. RT-qPCR was then used to detect changes in the expression levels of five critical genes. Our results indicated that TNFRSF1A activated the TNF signaling pathway and inhibited the NFκB signaling pathway in vitro. These findings provide evidence for an immune-related regulatory function for porcine TNFRSF1A.
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Affiliation(s)
- Zhengzheng Hu
- Department of Animal Genetics, Breeding and Reproduction, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hejun Li
- Shanghai Animal Disease Control Center, Shanghai 201103, China
| | - Rui Xie
- Department of Animal Genetics, Breeding and Reproduction, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shiwei Wang
- Department of Animal Genetics, Breeding and Reproduction, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yang Liu
- Department of Animal Genetics, Breeding and Reproduction, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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7
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Gao X, Guo D, Kou M, Xing G, Zha A, Yang X, Wang X, Di S, Cai J, Niu B. Identification of porcine CTLA4 gene polymorphism and their association with piglet diarrhea and performance traits. Mol Biol Rep 2018; 46:813-822. [PMID: 30515696 DOI: 10.1007/s11033-018-4536-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 11/28/2018] [Indexed: 11/29/2022]
Abstract
The objective of this study was to evaluate the association between the cytotoxic T-lymphocyte-associated antigen 4 (CTLA4) gene and piglet diarrhea. In this study, the mRNA expression of the CTLA4 gene increased significantly in IPEC-J2 cells after Escherichia coli K88 infection. Single nucleotide polymorphisms (SNPs) located in the 5' flanking region (SNPs g.107281989C>T) and 3'-untranslated region (3'-UTR; SNPs g.107288753C>A) were identified, and they were in linkage disequilibrium in both Min pigs and the Landrace population. Association analysis showed that Landrace piglets with a TT or AA genotype had a lower diarrhea index, and AA animals had higher average daily gain when compared to CC pigs, respectively (p < 0.05). However, the relationship between SNPs and diarrhea and performance traits in the Min population was not significant. Haplotype analysis indicated that the TC haplotype had the lowest diarrhea index. The 5' flanking deletion assay suggested that SNP g.107281989C>T was a molecular marker instead of the functional marker. This research demonstrated that genetic variances in the CTLA4 gene had significant effects on Landrace piglet diarrhea resistance.
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Affiliation(s)
- Xiaowen Gao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Dongchun Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150001, China
| | - Mingxing Kou
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Guiling Xing
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Andong Zha
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Xiuqin Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Xibiao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Shengwei Di
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | | | - Buyue Niu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China.
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Effects of Acremonium terricola culture on growth performance, antioxidant status and immune functions in weaned calves. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Xu J, Cai Z, Liu Y, Wang C, Fu W, Wang H, Wang W, Zhang Q. Expression Profile and PorcinDQB1Gene Association Analysis of the with Peripheral Blood T Lymphocyte Subsets. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2015.3864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Yang T, Wilkinson J, Wang Z, Ladinig A, Harding J, Plastow G. A genome-wide association study of fetal response to type 2 porcine reproductive and respiratory syndrome virus challenge. Sci Rep 2016; 6:20305. [PMID: 26846722 PMCID: PMC4742883 DOI: 10.1038/srep20305] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/30/2015] [Indexed: 01/22/2023] Open
Abstract
Control of porcine reproductive and respiratory syndrome (PRRS) is economically important for the swine industry worldwide. As current PRRS vaccines do not completely protect against heterologous challenge, alternative means of control, including enhanced genetic resilience, are needed. For reproductive PRRS, the genetic basis of fetal response to PRRS virus (PRRSV) infection is poorly understood. Genome-wide association studies (GWAS) were done here using data from 928 fetuses from pregnant gilts experimentally challenged with type 2 PRRSV. Fetuses were assessed for viral load in thymus (VLT), viral load in endometrium (VLE), fetal death (FD) and fetal viability (FV), and genotyped at a medium density. Collectively, 21 candidate genomic regions were found associated with these traits, seven of which overlap with previously reported QTLs for pig health and reproduction. A comparison with ongoing and related transcriptomic analyses of fetal response to PRRSV infection found differentially expressed genes within 18 candidate regions. Some of these genes have immune system functions, and have been reported to contribute to host response to PRRSV infection. The results provide new evidence about the genetic basis of fetal response to PRRSV challenge, and may ultimately lead to alternative control strategies to reduce the impact of reproductive PRRS.
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Affiliation(s)
- Tianfu Yang
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - James Wilkinson
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Zhiquan Wang
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Andrea Ladinig
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - John Harding
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Graham Plastow
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Single-nucleotide polymorphisms in CD8A and their associations with T lymphocyte subpopulations in pig. Mol Genet Genomics 2015; 290:1447-56. [PMID: 25690570 DOI: 10.1007/s00438-015-1008-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 02/07/2015] [Indexed: 10/24/2022]
Abstract
Findings from previous studies suggested that the cluster of the differentiation 8 alpha (CD8A) gene plays a prominent role in human T lymphocyte subpopulations. However, the evidence from pig population is still rare. To determine whether the important role of the CD8A gene is conserved in pig, a candidate gene analysis was performed herein through genotype-phenotype associations. Five single-nucleotide polymorphisms (SNPs) locating in the regulatory region of porcine CD8A gene were detected and tested for association analysis with seven T lymphocyte subpopulations (proportion of CD4(-)CD8(-), CD4(+)CD8(+), CD4(+)CD8(-), CD4(-)CD8(+), CD4(+), CD8(+), and the ratio of CD4(+) to CD8(+) T cells in peripheral blood) in 382 Large White piglets. After Bonferroni correction for multiple testing, four SNPs were significantly associated with some or all of the seven T lymphocyte subpopulations. Analyses of pairwise D' measures of linkage disequilibrium between all SNPs were also explored. Two haplotype blocks was inferred and the association study on haplotype level revealed similar effects on T lymphocyte subpopulations. In addition, the tissue-specific RNA expression pattern and electrophoretic mobility shift assay offered further explanation of the link between the CD8A gene with porcine T lymphocyte subpopulations. The findings presented here provide strong evidence for associations of CD8A variants with T lymphocyte subpopulations and may be applied in porcine breeding programs.
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Lee YM, Alam M, Choi BH, Kim KS, Kim JJ. A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and Yorkshire. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 25:1674-80. [PMID: 25049532 PMCID: PMC4094150 DOI: 10.5713/ajas.2012.12503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/20/2012] [Accepted: 09/19/2012] [Indexed: 01/06/2023]
Abstract
The purpose of this study was to detect significant SNPs for blood components that were related to immunity using high single nucleotide polymorphism (SNP) density panels in a Korean native pig (KNP)×Yorkshire (YK) cross population. A reciprocal design of KNP×YK produced 249 F2 individuals that were genotyped for a total of 46,865 available SNPs in the Illumina porcine 60K beadchip. To perform whole genome association analysis (WGA), phenotypes were regressed on each SNP under a simple linear regression model after adjustment for sex and slaughter age. To set up a significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were determined using a stepwise regression procedure with the rates of inclusion and exclusion of each SNP out of the model at 0.001 level. A total of 54 SNPs were detected; 10, 6, 4, 4, 5, 4, 5, 10, and 6 SNPs for neutrophil, lymphocyte, monocyte, eosinophil, basophil, atypical lymph, immunoglobulin, insulin, and insulin-like growth factor-I, respectively. Each set of significant SNPs per trait explained 24 to 42% of phenotypic variance. Several pleiotropic SNPs were detected on SSCs 4, 13, 14 and 15.
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Affiliation(s)
- Y-M Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - M Alam
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - B H Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - K-S Kim
- Department of Animal Science, Chungbuk National University, Cheongju, Korea
| | - J-J Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
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Xu J, Liu Y, Fu W, Wang J, Wang W, Wang H, Liu J, Ding X, Zhang Q. Association of the porcine cluster of differentiation 4 gene with T lymphocyte subpopulations and its expression in immune tissues. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:463-9. [PMID: 25049810 PMCID: PMC4093383 DOI: 10.5713/ajas.2012.12576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/04/2013] [Accepted: 12/17/2012] [Indexed: 02/03/2023]
Abstract
Cluster of differentiation 4 (CD4) is mainly expressed on CD4+ T cells, which plays an important role in immune response. The aim of this study was to detect the association between polymorphisms of the CD4 gene and T lymphocyte subpopulations in pigs, and to investigate the effects of genetic variation on the CD4 gene expression level in immune tissues. Five missense mutations in the CD4 gene were identified using DNA pooling sequencing assays, and two main haplotypes (CCTCC and AGCTG) in strong linkage disequilibrium (with frequencies of 50.26% and 46.34%, respectively) were detected in the population of Large White pigs. Our results indicated that the five SNPs and the two haplotypes were significantly associated with the proportions of CD4−CD8−, CD4+CD8+, CD4+CD8−, CD4+ and CD4+/CD8+ in peripheral blood (p<0.05). Gene expression analysis showed the mRNA level of the CD4 gene in thymus was significantly higher than that in lymph node and spleen (p<0.05). However, no significant difference was observed between animals with CCTCC/CCTCC genotype and animals with AGCTG/AGCTG genotype in the three immune tissues (p>0.05). These results indicate that the CD4 gene may influence T lymphocyte subpopulations and can be considered as a candidate gene affecting immunity in pigs.
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Affiliation(s)
- Jingen Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Weixuan Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jiying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haifei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianfeng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Lu X, Liu J, Fu W, Zhou J, Luo Y, Ding X, Liu Y, Zhang Q. Genome-wide association study for cytokines and immunoglobulin G in swine. PLoS One 2013; 8:e74846. [PMID: 24098351 PMCID: PMC3788770 DOI: 10.1371/journal.pone.0074846] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 08/08/2013] [Indexed: 12/31/2022] Open
Abstract
Increased disease resistance through improved immune capacity would be beneficial for the welfare and productivity of farm animals. To identify genomic regions responsible for immune capacity traits in swine, a genome-wide association study was conducted. In total, 675 pigs were included. At 21 days of age, all piglets were vaccinated with modified live classical swine fever vaccine. Blood samples were sampled when the piglets were 20 and 35 days of age, respectively. Four traits, including Interferon-gamma (IFN-γ) and Interleukin 10 (IL-10) levels, the ratio of IFN-γ to IL-10 and Immunoglobulin G (IgG) blocking percentage to CSFV in serum were measured. All the samples were genotyped for 62,163 single nucleotide polymorphisms (SNP) using the Illumina porcineSNP60k BeadChip. After quality control, 46,079 SNPs were selected for association tests based on a single-locus regression model. To tackle the issue of multiple testing, 10,000 permutations were performed to determine the chromosome-wise and genome-wise significance level. In total, 32 SNPs with chromosome-wise significance level (including 4 SNPs with genome-wise significance level) were identified. These SNPs account for 3.23% to 13.81% of the total phenotypic variance individually. For the four traits, the numbers of significant SNPs range from 5 to 15, which jointly account for 37.52%, 82.94%, 26.74% and 24.16% of the total phenotypic variance of IFN-γ, IL-10, IFN-γ/IL-10, and IgG, respectively. Several significant SNPs are located within the QTL regions reported in previous studies. Furthermore, several significant SNPs fall into the regions which harbour a number of known immunity-related genes. Results herein lay a preliminary foundation for further identifying the causal mutations affecting swine immune capacity in follow-up studies.
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Affiliation(s)
- Xin Lu
- Key Laboratory Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - JianFeng Liu
- Key Laboratory Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - WeiXuan Fu
- Key Laboratory Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America
| | - JiaPeng Zhou
- Key Laboratory Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - YanRu Luo
- Key Laboratory Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - XiangDong Ding
- Key Laboratory Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yang Liu
- Key Laboratory Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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Gao F, Liu Y, Zhang C, Zhang Z, Song S. Effect of intrauterine growth restriction during late pregnancy on the growth performance, blood components, immunity and anti-oxidation capability of ovine fetus. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lu X, Fu WX, Luo YR, Ding XD, Zhou JP, Liu Y, Liu JF, Zhang Q. Genome-wide association study for T lymphocyte subpopulations in swine. BMC Genomics 2012; 13:488. [PMID: 22985182 PMCID: PMC3481476 DOI: 10.1186/1471-2164-13-488] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Accepted: 07/25/2012] [Indexed: 12/21/2022] Open
Abstract
Background Lymphocytes act as a major component of the adaptive immune system, taking very crucial responsibility for immunity. Differences in proportions of T-cell subpopulations in peripheral blood among individuals under same conditions provide evidence of genetic control on these traits, but little is known about the genetic mechanism of them, especially in swine. Identification of the genetic control on these variants may help the genetic improvement of immune capacity through selection. Results To identify genomic regions responsible for these immune traits in swine, a genome-wide association study was conducted. A total of 675 pigs of three breeds were involved in the study. At 21 days of age, all individuals were vaccinated with modified live classical swine fever vaccine. Blood samples were collected when the piglets were 20 and 35 days of age, respectively. Seven traits, including the proportions of CD4+, CD8+, CD4+CD8+, CD4+CD8−, CD4−CD8+, CD4−CD8− and the ratio of CD4+ to CD8+ T cells were measured at the two ages. All the samples were genotyped for 62,163 single nucleotide polymorphisms (SNP) using the Illumina porcineSNP60k BeadChip. 40833 SNPs were selected after quality control for association tests between SNPs and each immune trait considered based on a single-locus regression model. To tackle the issue of multiple testing in GWAS, 10,000 permutations were performed to determine the chromosome-wise and genome-wise significance levels of association tests. In total, 61 SNPs with chromosome-wise significance level and 3 SNPs with genome-wise significance level were identified. 27 significant SNPs were located within the immune-related QTL regions reported in previous studies. Furthermore, several significant SNPs fell into the regions harboring known immunity-related genes, 14 of them fell into the regions which harbor some known T cell-related genes. Conclusions Our study demonstrated that genome-wide association studies would be a feasible way for revealing the potential genetics variants affecting T-cell subpopulations. Results herein lay a preliminary foundation for further identifying the causal mutations underlying swine immune capacity in follow-up studies.
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Affiliation(s)
- Xin Lu
- Key Laboratory Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China.
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Gao F, Liu YC, Zhang ZH, Zhang CZ, Su HW, Li SL. Effect of prepartum maternal energy density on the growth performance, immunity, and antioxidation capability of neonatal calves. J Dairy Sci 2012; 95:4510-8. [DOI: 10.3168/jds.2011-5087] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/26/2012] [Indexed: 11/19/2022]
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