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Park J, Do KT, Park KD, Lee HK. Genome-wide association study using a single-step approach for teat number in Duroc, Landrace and Yorkshire pigs in Korea. Anim Genet 2023; 54:743-751. [PMID: 37814452 DOI: 10.1111/age.13357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 07/25/2023] [Accepted: 09/01/2023] [Indexed: 10/11/2023]
Abstract
We investigated the genetic basis of teat number in sows, which is an important factor in their reproductive performance. We collected genotyping data from 20 353 pigs of three breeds (Duroc, Landrace and Yorkshire) using the Porcine SNP60K Bead Chip, and analyzed phenotypic data from 240 603 pigs. The heritability values of total teat number were 0.33 ± 0.02, 0.51 ± 0.01 and 0.50 ± 0.01 in Duroc, Landrace and Yorkshire pigs, respectively. A genome-wide association study was used to identify significant chromosomal regions associated with teat number in SSC7 and SSC9 in Duroc pig, SSC3, SSC7 and SSC18 in Landrace pig, and SSC7, SSC8 and SSC10 in Yorkshire pig. Among the markers, MARC0038565, located between the vertnin (VRTN) and synapse differentiation-inducing 1-like (SYNDIG1L) genes, showed the strongest association in the Duroc pig and was significant in all breeds. In Landrace and Yorkshire pigs, the most significant markers were located within the apoptosis resistant E3 ubiquitin protein ligase 1 (AREL1) and latent transforming growth factor beta-binding protein 2 (LTBP2) genes in SSC7, respectively. VRTN is a candidate gene regulating the teat number. Most markers were located in SSC7, indicating their significance in determining teat number and their potential as valuable genomic selection targets for improving this trait. Extensive linkage disequilibrium blocks were identified in SSC7, supporting their use in genomic selection strategies. Our study provides valuable insights into the genetic architecture of teat numbers in pigs, and helps identify candidate genes and genomic regions that may contribute to this economically important trait.
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Affiliation(s)
- Jun Park
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Korea
| | - Kyoung-Tag Do
- Department of Animal Biotechnology, Jeju National University, Jeju, Korea
| | - Kyung-Do Park
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Korea
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Korea
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2
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Roth K, Pröll-Cornelissen MJ, Henne H, Appel AK, Schellander K, Tholen E, Große-Brinkhaus C. Multivariate genome-wide associations for immune traits in two maternal pig lines. BMC Genomics 2023; 24:492. [PMID: 37641029 PMCID: PMC10463314 DOI: 10.1186/s12864-023-09594-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Immune traits are considered to serve as potential biomarkers for pig's health. Medium to high heritabilities have been observed for some of the immune traits suggesting genetic variability of these phenotypes. Consideration of previously established genetic correlations between immune traits can be used to identify pleiotropic genetic markers. Therefore, genome-wide association study (GWAS) approaches are required to explore the joint genetic foundation for health biomarkers. Usually, GWAS explores phenotypes in a univariate (uv), trait-by-trait manner. Besides two uv GWAS methods, four multivariate (mv) GWAS approaches were applied on combinations out of 22 immune traits for Landrace (LR) and Large White (LW) pig lines. RESULTS In total 433 (LR: 351, LW: 82) associations were identified with the uv approach implemented in PLINK and a Bayesian linear regression uv approach (BIMBAM) software. Single Nucleotide Polymorphisms (SNPs) that were identified with both uv approaches (n = 32) were mostly associated with immune traits such as haptoglobin, red blood cell characteristics and cytokines, and were located in protein-coding genes. Mv GWAS approaches detected 647 associations for different mv immune trait combinations which were summarized to 133 Quantitative Trait Loci (QTL). SNPs for different trait combinations (n = 66) were detected with more than one mv method. Most of these SNPs are associated with red blood cell related immune trait combinations. Functional annotation of these QTL revealed 453 immune-relevant protein-coding genes. With uv methods shared markers were not observed between the breeds, whereas mv approaches were able to detect two conjoint SNPs for LR and LW. Due to unmapped positions for these markers, their functional annotation was not clarified. CONCLUSIONS This study evaluated the joint genetic background of immune traits in LR and LW piglets through the application of various uv and mv GWAS approaches. In comparison to uv methods, mv methodologies identified more significant associations, which might reflect the pleiotropic background of the immune system more accurately. In genetic research of complex traits, the SNP effects are generally small. Furthermore, one genetic variant can affect several correlated immune traits at the same time, termed pleiotropy. As mv GWAS methods consider strong dependencies among traits, the power to detect SNPs can be boosted. Both methods revealed immune-relevant potential candidate genes. Our results indicate that one single test is not able to detect all the different types of genetic effects in the most powerful manner and therefore, the methods should be applied complementary.
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Affiliation(s)
- Katharina Roth
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | | | - Hubert Henne
- BHZP GmbH, An der Wassermühle 8, 21368, Dahlenburg-Ellringen, Germany
| | | | - Karl Schellander
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Ernst Tholen
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
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3
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Wu Y, Zhang Y, Liu H, Gao Y, Liu Y, Chen L, Liu L, Irwin DM, Hou C, Zhou Z, Zhang Y. Genome-wide identification of functional enhancers and their potential roles in pig breeding. J Anim Sci Biotechnol 2022; 13:75. [PMID: 35781353 PMCID: PMC9252078 DOI: 10.1186/s40104-022-00726-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/04/2022] [Indexed: 01/04/2023] Open
Abstract
Background The pig is an economically important livestock species and is a widely applied large animal model in medical research. Enhancers are critical regulatory elements that have fundamental functions in evolution, development and disease. Genome-wide quantification of functional enhancers in the pig is needed. Results We performed self-transcribing active regulatory region sequencing (STARR-seq) in the porcine kidney epithelial PK15 and testicular ST cell lines, and reliably identified 2576 functional enhancers. Most of these enhancers were located in repetitive sequences and were enriched within silent and lowly expressed genes. Enhancers poorly overlapped with chromatin accessibility regions and were highly enriched in chromatin with the repressive histone modification H3K9me3, which is different from predicted pig enhancers detected using ChIP-seq for H3K27ac or/and H3K4me1 modified histones. This suggests that most pig enhancers identified with STARR-seq are endogenously repressed at the chromatin level and may function during cell type-specific development or at specific developmental stages. Additionally, the PPP3CA gene is associated with the loin muscle area trait and the QKI gene is associated with alkaline phosphatase activity that may be regulated by distal functional enhancers. Conclusions In summary, we generated the first functional enhancer map in PK15 and ST cells for the pig genome and highlight its potential roles in pig breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00726-y.
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Affiliation(s)
- Yinqiao Wu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Yuedong Zhang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China.,State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China.,School of Life Science, Yunnan University, Kunming, 650091, Yunnan, China
| | - Hang Liu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yuyan Liu
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China.,School of Life Science, Yunnan University, Kunming, 650091, Yunnan, China
| | - Ling Chen
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China.,School of Life Science, Yunnan University, Kunming, 650091, Yunnan, China
| | - Lu Liu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Chunhui Hou
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhongyin Zhou
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Yaping Zhang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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Exploiting single-marker and haplotype-based genome-wide association studies to identify QTL for the number of teats in Italian Duroc pigs. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Krayem I, Sohrabi Y, Javorková E, Volkova V, Strnad H, Havelková H, Vojtíšková J, Aidarova A, Holáň V, Demant P, Lipoldová M. Genetic Influence on Frequencies of Myeloid-Derived Cell Subpopulations in Mouse. Front Immunol 2022; 12:760881. [PMID: 35154069 PMCID: PMC8826059 DOI: 10.3389/fimmu.2021.760881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Differences in frequencies of blood cell subpopulations were reported to influence the course of infections, atopic and autoimmune diseases, and cancer. We have discovered a unique mouse strain B10.O20 containing extremely high frequency of myeloid-derived cells (MDC) in spleen. B10.O20 carries 3.6% of genes of the strain O20 on the C57BL/10 genetic background. It contains much higher frequency of CD11b+Gr1+ cells in spleen than both its parents. B10.O20 carries O20-derived segments on chromosomes 1, 15, 17, and 18. Their linkage with frequencies of blood cell subpopulations in spleen was tested in F2 hybrids between B10.O20 and C57BL/10. We found 3 novel loci controlling MDC frequencies: Mydc1, 2, and 3 on chromosomes 1, 15, and 17, respectively, and a locus controlling relative spleen weight (Rsw1) that co-localizes with Mydc3 and also influences proportion of white and red pulp in spleen. Mydc1 controls numbers of CD11b+Gr1+ cells. Interaction of Mydc2 and Mydc3 regulates frequency of CD11b+Gr1+ cells and neutrophils (Gr1+Siglec-F- cells from CD11b+ cells). Interestingly, Mydc3/Rsw1 is orthologous with human segment 6q21 that was shown previously to determine counts of white blood cells. Bioinformatics analysis of genomic sequence of the chromosomal segments bearing these loci revealed polymorphisms between O20 and C57BL/10 that change RNA stability and genes’ functions, and we examined expression of relevant genes. This identified potential candidate genes Smap1, Vps52, Tnxb, and Rab44. Definition of genetic control of MDC can help to personalize therapy of diseases influenced by these cells.
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Affiliation(s)
- Imtissal Krayem
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Yahya Sohrabi
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Eliška Javorková
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czechia.,Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Valeriya Volkova
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Hynek Strnad
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Helena Havelková
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Jarmila Vojtíšková
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Aigerim Aidarova
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Vladimír Holáň
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czechia.,Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Peter Demant
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Marie Lipoldová
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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6
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Sanglard LP, Huang Y, Gray KA, Linhares DCL, Dekkers JCM, Niederwerder MC, Fernando RL, Serão NVL. Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses. Genet Sel Evol 2021; 53:91. [PMID: 34875996 PMCID: PMC8650375 DOI: 10.1186/s12711-021-00676-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Background The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance. Results There was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP. Conclusions Specific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00676-5.
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Affiliation(s)
- Leticia P Sanglard
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Yijian Huang
- Smithfield Premium Genetic, Rose Hill, NC, 28458, USA
| | - Kent A Gray
- Smithfield Premium Genetic, Rose Hill, NC, 28458, USA
| | - Daniel C L Linhares
- Department of Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, 66506, USA
| | - Rohan L Fernando
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Nick V L Serão
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
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Dauben CM, Pröll-Cornelissen MJ, Heuß EM, Appel AK, Henne H, Roth K, Schellander K, Tholen E, Große-Brinkhaus C. Genome-wide associations for immune traits in two maternal pig lines. BMC Genomics 2021; 22:717. [PMID: 34610786 PMCID: PMC8491387 DOI: 10.1186/s12864-021-07997-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Background In recent years, animal welfare and health has become more and more important in pig breeding. So far, numerous parameters have been considered as important biomarkers, especially in the immune reaction and inflammation. Previous studies have shown moderate to high heritabilities in most of these traits. However, the genetic background of health and robustness of pigs needs to be extensively clarified. The objective of this study was to identify genomic regions with a biological relevance for the immunocompetence of piglets. Genome-wide Association Studies (GWAS) in 535 Landrace (LR) and 461 Large White (LW) piglets were performed, investigating 20 immune relevant traits. Besides the health indicators of the complete and differential blood count, eight different cytokines and haptoglobin were recorded in all piglets and their biological dams to capture mediating processes and acute phase reactions. Additionally, all animals were genotyped using the Illumina PorcineSNP60v2 BeadChip. Results In summary, GWAS detected 25 genome-wide and 452 chromosome-wide significant SNPs associated with 17 immune relevant traits in the two maternal pig lines LR and LW. Only small differences were observed considering the maternal immune records as covariate within the statistical model. Furthermore, the study identified across- and within-breed differences as well as relevant candidate genes. In LR more significant associations and related candidate genes were detected, compared with LW. The results detected in LR and LW are partly in accordance with previously identified quantitative trait loci (QTL) regions. In addition, promising novel genomic regions were identified which might be of interest for further detailed analysis. Especially putative pleiotropic regions on SSC5, SSC12, SSC15, SSC16 and SSC17 are of major interest with regard to the interacting structure of the immune system. The comparison with already identified QTL gives indications on interactions with traits affecting piglet survival and also production traits. Conclusion In conclusion, results suggest a polygenic and breed-specific background of immune relevant traits. The current study provides knowledge about regions with biological relevance for health and immune traits. Identified markers and putative pleiotropic regions provide first indications in the context of balancing a breeding-based modification of the porcine immune system. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-07997-1).
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Affiliation(s)
- Christina M Dauben
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
| | | | - Esther M Heuß
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
| | - Anne K Appel
- BHZP GmbH, An der Wassermühle 8, Dahlenburg-Ellringen, 21368, Germany
| | - Hubert Henne
- BHZP GmbH, An der Wassermühle 8, Dahlenburg-Ellringen, 21368, Germany
| | - Katharina Roth
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
| | - Karl Schellander
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
| | - Ernst Tholen
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
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8
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Bovo S, Ballan M, Schiavo G, Ribani A, Tinarelli S, Utzeri VJ, Dall'Olio S, Gallo M, Fontanesi L. Single-marker and haplotype-based genome-wide association studies for the number of teats in two heavy pig breeds. Anim Genet 2021; 52:440-450. [PMID: 34096632 PMCID: PMC8362157 DOI: 10.1111/age.13095] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
The number of teats is a reproductive‐related trait of great economic relevance as it affects the mothering ability of the sows and thus the number of properly weaned piglets. Moreover, genetic improvement of this trait is fundamental to parallelly help the selection for increased litter size. We present the results of single‐marker and haplotypes‐based genome‐wide association studies for the number of teats in two large cohorts of heavy pig breeds (Italian Large White and Italian Landrace) including 3990 animals genotyped with the 70K GGP Porcine BeadChip and other 1927 animals genotyped with the Illumina PorcineSNP60 BeadChip. In the Italian Large White population, genome scans identified three genome regions (SSC7, SSC10, and SSC12) that confirmed the involvement of the VRTN gene (as we previously reported) and highlighted additional loci known to affect teat counts, including the FRMD4A and HOXB1 gene regions. A different picture emerged in the Italian Landrace population, with a total of 12 genome regions in eight chromosomes (SSC3, SSC6, SSC8, SSC11, SSC13, SSC14, SSC15, and SSC16) mainly detected via the haplotype‐based genome scan. The most relevant QTL was close to the ARL4C gene on SSC15. Markers in the VRTN gene region were not significant in the Italian Landrace breed. The use of both single‐marker and haplotype‐based genome‐wide association analyses can be helpful to exploit and dissect the genome of the pigs of different populations. Overall, the obtained results supported the polygenic nature of the investigated trait and better elucidated its genetic architecture in Italian heavy pigs.
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Affiliation(s)
- S Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - M Ballan
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - G Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - A Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - S Tinarelli
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy.,Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, Roma, 00198, Italy
| | - V J Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - S Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - M Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, Roma, 00198, Italy
| | - L Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
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Dall'Olio S, Bovo S, Tinarelli S, Schiavo G, Padalino B, Fontanesi L. Association between candidate gene markers and harness racing traits in Italian trotter horses. Livest Sci 2021. [DOI: 10.1016/j.livsci.2020.104351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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