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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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2
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Corredor FA, Sanglard LP, Leach RJ, Ross JW, Keating AF, Serão NVL. Genetic and genomic characterization of vulva size traits in Yorkshire and Landrace gilts. BMC Genet 2020; 21:28. [PMID: 32164558 PMCID: PMC7068987 DOI: 10.1186/s12863-020-0834-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/26/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Reproductive performance is critical for efficient swine production. Recent results indicated that vulva size (VS) may be predictive of reproductive performance in sows. Study objectives were to estimate genetic parameters, identify genomic regions associated, and estimate genomic prediction accuracies (GPA) for VS traits. RESULTS Heritability estimates of VS traits, vulva area (VA), height (VH), and width (VW) measurements, were moderately to highly heritable in Yorkshire, with 0.46 ± 0.10, 0.55 ± 0.10, 0.31 ± 0.09, respectively, whereas these estimates were low to moderate in Landrace, with 0.16 ± 0.09, 0.24 ± 0.11, and 0.08 ± 0.06, respectively. Genetic correlations within VS traits were very high for both breeds, with the lowest of 0.67 ± 0.29 for VH and VW for Landrace. Genome-wide association studies (GWAS) for Landrace, reveled genomic region associated with VS traits on Sus scrofa chromosome (SSC) 2 (154-157 Mb), 7 (107-110 Mb), 8 (4-6 Mb), and 10 (8-19 Mb). For Yorkshire, genomic regions on SSC 1 (87-91 and 282-287 Mb) and 5 (67 Mb) were identified. All regions explained at least 3.4% of the genetic variance. Accuracies of genomic prediction were moderate in Landrace, ranging from 0.30 (VH) to 0.61 (VA), and lower for Yorkshire, with 0.07 (VW) to 0.11 (VH). Between-breed and multi-breed genomic prediction accuracies were low. CONCLUSIONS Our findings suggest that VS traits are heritable in Landrace and Yorkshire gilts. Genomic analyses show that major QTL control these traits, and they differ between breed. Genomic information can be used to increase genetic gains for these traits in gilts. Additional research must be done to validate the GWAS and genomic prediction results reported in our study.
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Affiliation(s)
| | | | | | - Jason W. Ross
- Department of Animal Science, Iowa State University, IA50010, Ames, USA
- Iowa Pork Industry Center, Iowa State University, Ames, IA 50010 USA
| | - Aileen F. Keating
- Department of Animal Science, Iowa State University, IA50010, Ames, USA
| | - Nick V. L. Serão
- Department of Animal Science, Iowa State University, IA50010, Ames, USA
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Metodiev S, Thekkoot D, Young J, Onteru S, Rothschild M, Dekkers J. A whole-genome association study for litter size and litter weight traits in pigs. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Alexopoulos JG, Lines DS, Hallett S, Plush KJ. A Review of Success Factors for Piglet Fostering in Lactation. Animals (Basel) 2018. [PMID: 29522470 PMCID: PMC5867526 DOI: 10.3390/ani8030038] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Simple Summary An understanding of behavioural and physiological mechanisms responsible for piglet survival and growth will assist in developing the best recommendations in which to manage piglet movements in the farrowing house. This review has identified six key principles that should underpin successful piglet fostering. These fostering principles will improve productivity and welfare of sows and piglets in commercial pig production. Abstract Piglet movement from one sow to another, or fostering, is required in modern pig farming but there is little available literature on the most effective strategy. In this review, we focus on the behavioural and physiological mechanisms responsible for piglet survival and growth, and have identified six key principles. (1) Colostrum provides piglets with warmth, energy and immunity. It is most accessible during the first 12 h from the birth sow, therefore no piglet should be moved before this; (2) To ensure even intake of birth sow colostrum, techniques such as split suckling prior to piglet movement should be implemented; (3) Udder assessment for functional teats should occur at farrowing, with number of fostered piglets not exceeding teat number; (4) Primiparous sows should receive as many piglets as the udder allows to maximise mammary stimulation, although older parities should be assessed for rearing ability; (5) Piglet fostering should occur between 12 and 24 h and movement kept to a minimum to prevent transfer of disease; Litter outliers should be moved and relocated to a litter of similar size; (6) Piglet movement after 24 h should be minimised. When required, strategies such as nurse usage should be employed. These principles will result in improved farrowing house performance by increasing the litter weight weaned per sow.
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Affiliation(s)
| | - David S Lines
- SunPork Farms, PO Box 92, Wasleys 5400, South Australia, Australia.
| | - Suzanne Hallett
- SunPork Farms, PO Box 92, Wasleys 5400, South Australia, Australia.
| | - Kate J Plush
- SunPork Farms, PO Box 92, Wasleys 5400, South Australia, Australia.
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5
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Wang Y, Ding X, Tan Z, Ning C, Xing K, Yang T, Pan Y, Sun D, Wang C. Genome-Wide Association Study of Piglet Uniformity and Farrowing Interval. Front Genet 2017; 8:194. [PMID: 29234349 PMCID: PMC5712316 DOI: 10.3389/fgene.2017.00194] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 11/15/2017] [Indexed: 02/04/2023] Open
Abstract
Piglet uniformity (PU) and farrowing interval (FI) are important reproductive traits related to production and economic profits in the pig industry. However, the genetic architecture of the longitudinal trends of reproductive traits still remains elusive. Herein, we performed a genome-wide association study (GWAS) to detect potential genetic variation and candidate genes underlying the phenotypic records at different parities for PU and FI in a population of 884 Large White pigs. In total, 12 significant SNPs were detected on SSC1, 3, 4, 9, and 14, which collectively explained 1–1.79% of the phenotypic variance for PU from parity 1 to 4, and 2.58–4.11% for FI at different stages. Of these, seven SNPs were located within 16 QTL regions related to swine reproductive traits. One QTL region was associated with birth body weight (related to PU) and contained the peak SNP MARC0040730, and another was associated with plasma FSH concentration (related to FI) and contained the SNP MARC0031325. Finally, some positional candidate genes for PU and FI were identified because of their roles in prenatal skeletal muscle development, fetal energy substrate, pre-implantation, and the expression of mammary gland epithelium. Identification of novel variants and candidate genes will greatly advance our understanding of the genetic mechanisms of PU and FI, and suggest a specific opportunity for improving marker assisted selection or genomic selection in pigs.
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Affiliation(s)
- Yuan Wang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhen Tan
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chao Ning
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Xing
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ting Yang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yongjie Pan
- Beijing Shunxin Agriculture Co., Ltd., Beijing, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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6
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Genome-wide association study for sow lifetime productivity related traits in a Landrace purebred population. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Peng WF, Xu SS, Ren X, Lv FH, Xie XL, Zhao YX, Zhang M, Shen ZQ, Ren YL, Gao L, Shen M, Kantanen J, Li MH. A genome-wide association study reveals candidate genes for the supernumerary nipple phenotype in sheep (Ovis aries). Anim Genet 2017; 48:570-579. [PMID: 28703336 DOI: 10.1111/age.12575] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2017] [Indexed: 01/20/2023]
Abstract
Genome-wide association studies (GWASs) have been widely applied in livestock to identify genes associated with traits of economic interest. Here, we conducted the first GWAS of the supernumerary nipple phenotype in Wadi sheep, a native Chinese sheep breed, based on Ovine Infinium HD SNP BeadChip genotypes in a total of 144 ewes (75 cases with four teats, including two normal and two supernumerary teats, and 69 control cases with two teats). We detected 63 significant SNPs at the chromosome-wise threshold. Additionally, one candidate region (chr1: 170.723-170.734 Mb) was identified by haplotype-based association tests, with one SNP (rs413490006) surrounding functional genes BBX and CD47 on chromosome 1 being commonly identified as significant by the two mentioned analyses. Moreover, Gene Ontology enrichment for the significant SNPs identified by the GWAS analysis was functionally clustered into the categories of receptor activity and synaptic membrane. In addition, pathway mapping revealed four promising pathways (Wnt, oxytocin, MAPK and axon guidance) involved in the development of the supernumerary nipple phenotype. Our results provide novel and important insights into the genetic mechanisms underlying the phenotype of supernumerary nipples in mammals, including humans. These findings may be useful for future breeding and genetics in sheep and other livestock.
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Affiliation(s)
- W-F Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - S-S Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - X Ren
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - F-H Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - X-L Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Y-X Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - M Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Z-Q Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - Y-L Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - L Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - M Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - J Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - M-H Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
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8
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Chalkias H, Jonas E, Andersson LS, Jacobson M, de Koning DJ, Lundeheim N, Lindgren G. Identification of novel candidate genes for the inverted teat defect in sows using a genome-wide marker panel. J Appl Genet 2017; 58:249-259. [PMID: 28050760 PMCID: PMC5391382 DOI: 10.1007/s13353-016-0382-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 11/24/2016] [Indexed: 11/29/2022]
Abstract
The number of functional teats is an important selection criterion in pig breeding. Inherited defects of the udder, such as the inverted teat, do have a considerable negative impact on the nursing ability of the sow. To investigate the genetic background of this defect and the number of functional teats in Swedish maternal lines, samples from 230 Yorkshire pigs were selected for genotyping using the PorcineSNP60K BeadChip (Illumina Inc.), each pig with at least one inverted teat was matched with one non-affected pig (fullsib or pairs with matching herd and gender). A genome-wide association study on these 230 pigs was performed using the two-step approach implemented in GenABEL using 46,652 single nucleotide polymorphisms across all autosomes and the X chromosome. A number of significant regions were identified for the inverted teat defect on chromosomes 2, 10, and 18. Many of the regions associated with the number of functional teats were located in the same or close regions, except two associated markers on the X chromosome and one on chromosome 3. We identified some of the regions on chromosomes previously reported in one linkage and one gene expression study. We conclude, despite being able to suggest new candidate genes, that further studies are needed to better understand the biologic background of the teat development. Despite the in-depth comparison of identified regions for the inverted teat defect done here, more studies are required to allow a clear identification of genetic regions relevant for this defect across many pig populations.
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Affiliation(s)
- Helena Chalkias
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Elisabeth Jonas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden.
| | - Lisa S Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Magdalena Jacobson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-750 07, Uppsala, Sweden
| | - Dirk Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Nils Lundeheim
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden.,Capilet Genetics AB, SE-725 93, Västerås, Sweden
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9
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Cao J, Wei C, Zhang S, Capellini TD, Zhang L, Zhao F, Li L, Zhong T, Wang L, Du L, Zhang H. Screening of reproduction-related single-nucleotide variations from MeDIP-seq data in sheep. Mol Reprod Dev 2016; 83:958-967. [DOI: 10.1002/mrd.22734] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/29/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province; Sichuan Agricultural University; Chengdu China
- Chengdu JDK Biotechnology LTD; Chengdu China
| | - Caihong Wei
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - Shuzhen Zhang
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - Terence D. Capellini
- Department of Human Evolutionary Biology; Harvard University; Cambridge Massachusetts
| | - Li Zhang
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - Fuping Zhao
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province; Sichuan Agricultural University; Chengdu China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province; Sichuan Agricultural University; Chengdu China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province; Sichuan Agricultural University; Chengdu China
| | - Lixin Du
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province; Sichuan Agricultural University; Chengdu China
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10
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Guo X, Su G, Christensen OF, Janss L, Lund MS. Genome-wide association analyses using a Bayesian approach for litter size and piglet mortality in Danish Landrace and Yorkshire pigs. BMC Genomics 2016; 17:468. [PMID: 27317562 PMCID: PMC4912826 DOI: 10.1186/s12864-016-2806-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 05/27/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Litter size and piglet mortality are important traits in pig production. The study aimed to identify quantitative trait loci (QTL) for litter size and mortality traits, including total number of piglets born (TNB), litter size at day 5 (LS5) and mortality rate before day 5 (MORT) in Danish Landrace and Yorkshire pigs by genome-wide association studies (GWAS). METHODS The phenotypic records and genotypes were available in 5,977 Landrace pigs and 6,000 Yorkshire pigs born from 1998 to 2014. A linear mixed model (LM) with a single SNP regression and a Bayesian mixture model (BM) including effects of all SNPs simultaneously were used for GWAS to detect significant QTL association. The response variable used in the GWAS was corrected phenotypic value which was obtained by adjusting original observations for non-genetic effects. For BM, the QTL region was determined by using a novel post-Gibbs analysis based on the posterior mixture probability. RESULTS The detected association patterns from LM and BM models were generally similar. However, BM gave more distinct detection signals than LM. The clearer peaks from BM indicated that the BM model has an advantage in respect of identifying and distinguishing regions of putative QTL. Using BM and QTL region analysis, for the three traits and two breeds a total of 15 QTL regions were identified on SSC1, 2, 3, 6, 7, 9, 13 and 14. Among these QTL regions, 6 regions located on SSC2, 3, 6, 7 and 13 were associated with more than one trait. CONCLUSION This study detected QTL regions associated with litter size and piglet mortality traits in Danish pigs using a novel approach of post-Gibbs analysis based on posterior mixture probability. All of the detected QTL regions overlapped with regions previously reported for reproduction traits. The regions commonly detected in different traits and breeds could be resources for multi-trait and across-bred selection. The proposed novel QTL region analysis method would be a good alternative to detect and define QTL regions.
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Affiliation(s)
- Xiangyu Guo
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark.
| | - Ole Fredslund Christensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
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Abstract
The aim of this study was to develop a methodology to measure sow udder conformation to use in studying the correlation between udder traits and piglet survival, health and performance. The steps in the investigation were (i) to assess the repeatability of measures, (ii) to determine if there was an important difference between the two sides of the udder, (iii) to assess the extent of variation between sows, and finally (iv) to verify if the measures differ in a systematic way over the days shortly before farrowing. A total of 24 sows were scored for six conformation traits of the udder measured twice a day, every day from the sows' entrance into the farrowing crates until farrowing (1 to 4 days later). The data were recorded from both sides when the sow was lying and when she was standing. The measurements taken were: inter-teat distance within the same row (SAMER; mm between the adjacent teat bases); distance from the base of the teats to the abdominal midline, recorded only in a lying posture (B); distance between the teat base and the adjacent teat on the opposite row, recorded only in a standing posture (OPPR), distance from the base of the teats to the ground (FLOOR); teat length (LEN) measured from the tip to the base, and diameter (DIA) measured at the tip of the teat. Intraclass correlation coefficients (ICC) revealed that most udder conformation traits were highly repeatable (ICC>0.8); only DIA and FLOOR had lower repeatability (ICC=0.7). Measurements did not differ by side. In general, the greatest proportion of variance occurred at the sow level. Traits changed little in the days before farrowing, except for a change 1 day before farrowing in DIA, FLOOR and OPPR. Measures which used anatomical landmarks as the reference point were more reliable than those using the floor of the pen. Udder conformation measures can be used as a reliable phenotype for further study. They can be collected on any day shortly before farrowing, and only from one side and in one posture to save time.
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Xu RX, Wei N, Wang Y, Wang GQ, Yang GS, Pang WJ. Association of Novel Polymorphisms in Lymphoid Enhancer Binding Factor 1 (LEF-1) Gene with Number of Teats in Different Breeds of Pig. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:1254-62. [PMID: 25178368 PMCID: PMC4150191 DOI: 10.5713/ajas.2013.13772] [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: 11/29/2013] [Revised: 02/14/2014] [Accepted: 04/14/2014] [Indexed: 11/27/2022]
Abstract
Lymphoid enhancer binding factor 1 (LEF-1) is a member of the T-cell specific factor (TCF) family, which plays a key role in the development of breast endothelial cells. Moreover, LEF-1 gene has been identified as a candidate gene for teat number trait. In the present study, we detected two novel mutations (NC_010450.3:g. 99514A>G, 119846C>T) by DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism in exon 4 and intron 9 of LEF-1 in Guanzhong Black, Hanjiang Black, Bamei and Large White pigs. Furthermore, we analyzed the association between the genetic variations with teat number trait in these breeds. The 99514A>G mutation showed an extremely significant statistical relevance between different genotypes and teat number trait in Guanzhong (p<0.001) and Large White (p = 0.002), and significant relevance in Hanjiang (p = 0.017); the 119846C>T mutation suggested significant association in Guanzhong Black pigs (p = 0.042) and Large White pigs (p = 0.003). The individuals with “AG” or “GG” genotype displayed more teat numbers than those with “AA”; the individuals with “TC” or “CC” genotype showed more teat numbers than those with “TT”. Our findings suggested that the 99514A>G and 119846C>T mutations of LEF-1 affected porcine teat number trait and could be used in breeding strategies to accelerate porcine teat number trait improvement of indigenous pigs breeds through molecular marker assisted selection.
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Rymen D, Jaeken J. Skin manifestations in CDG. J Inherit Metab Dis 2014; 37:699-708. [PMID: 24554337 DOI: 10.1007/s10545-014-9678-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/01/2013] [Accepted: 01/20/2014] [Indexed: 10/25/2022]
Abstract
The group of congenital disorders of glycosylation (CDG) has expanded tremendously since its first description in 1980, with around 70 distinct disorders described to date. A great phenotypic variability exists, ranging from multisystem disease to single organ involvement. Skin manifestations, although inconsistently present, are part of this broad clinical spectrum. Indeed, the presence of inverted nipples, fat pads and orange peel skin in a patient with developmental delay are considered as a hallmark of CDG, particularly seen in PMM2 deficiency. However, over the years many more dermatological findings have been observed (e.g., ichthyosis, cutis laxa, tumoral calcinosis…). In this review we will discuss the variety of skin manifestations reported in CDG. Moreover, we will explore the possible mechanisms that link a certain glycosylation deficiency to its skin phenotype.
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Affiliation(s)
- D Rymen
- Center for Human Genetics, University of Leuven, Leuven, Belgium,
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Chalkias H, Ekman E, Lundeheim N, Rydhmer L, Jacobson M. Inverted teats (Mammillae invertitae) in gilts – Effect on piglet survival and growth rate. J Anim Sci 2014; 92:2587-94. [DOI: 10.2527/jas.2013-7387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- H. Chalkias
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala, Sweden
| | - E. Ekman
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, SE-750 07 Uppsala, Sweden
| | - N. Lundeheim
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala, Sweden
| | - L. Rydhmer
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala, Sweden
| | - M. Jacobson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-750 07 Uppsala, Sweden
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Preissler R, Tetens J, Reiners K, Looft H, Kemper N. A genome-wide association study to detect genetic variation for postpartum dysgalactia syndrome in five commercial pig breeding lines. Anim Genet 2013; 44:502-8. [DOI: 10.1111/age.12047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Regine Preissler
- Institute of Agricultural and Nutritional Sciences; Martin-Luther-University Halle-Wittenberg; Theodor-Lieser-Straße 11; D-06120; Halle (Saale); Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry; Christian-Albrechts-University; Olshausenstraße 40; D-24098; Kiel; Germany
| | | | - Holger Looft
- PIC Germany; Ratsteich 31; D-24837; Schleswig; Germany
| | - Nicole Kemper
- Institute of Agricultural and Nutritional Sciences; Martin-Luther-University Halle-Wittenberg; Theodor-Lieser-Straße 11; D-06120; Halle (Saale); Germany
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Chalkias H, Rydhmer L, Lundeheim N. Genetic analysis of functional and non-functional teats in a population of Yorkshire pigs. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Growth and development of the mammary glands of livestock: A veritable barnyard of opportunities. Semin Cell Dev Biol 2012; 23:557-66. [DOI: 10.1016/j.semcdb.2012.03.018] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 03/21/2012] [Accepted: 03/22/2012] [Indexed: 01/27/2023]
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Chomwisarutkun K, Murani E, Brunner R, Ponsuksili S, Wimmers K. QTL region-specific microarrays reveal differential expression of positional candidate genes of signaling pathways associated with the liability for the inverted teat defect. Anim Genet 2012; 44:139-48. [PMID: 22690698 DOI: 10.1111/j.1365-2052.2012.02378.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2012] [Indexed: 01/23/2023]
Abstract
The inverted teat defect is the most common disorder of the mammary complex in pigs. It is characterized by the failure of teats to protrude from the udder surface, preventing normal milk flow and thus limiting the rearing capacity and increasing the risk of mastitis. The inverted teat defect is a liability trait with a complex mode of inheritance. We previously identified QTL for inverted teats. As a complementary approach that integrates map-based efforts to identify candidate genes for the inverted teat defect with function-driven expression analysis, application-specific microarrays were constructed that cover 1525 transcripts mapping in QTL regions on pig chromosomes 2, 3, 4, 6 and 11. About 950 transcripts were expressed in epithelial and mesenchymal teat tissue. The expression of three categories of teats was compared: normal teats of both non-affected and affected animals and inverted teats of affected animals. In epithelium and mesenchyme, 62 and 24 genes respectively were significantly differentially expressed (DE). The majority of biofunctions to which a significant number of DE genes were assigned are related to the following: (1) cell maintenance, proliferation, differentiation and replacement; (2) organismal, organ and tissue development; or (3) genetic information and nucleic acid processing. Moreover, the DE genes belong almost exclusively to canonical pathways related to signaling rather than metabolic pathways. This is in line with findings obtained by genome-wide catalogue microarrays. This study adds another piece to the puzzle of the etiology of inverted teats by indicating that causal genetic variation leading to the disorder is likely among the genes encoding for members of the signaling cascades of growth factors.
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Affiliation(s)
- K Chomwisarutkun
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, Dummerstorf, Germany
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Chomwisarutkun K, Murani E, Ponsuksili S, Wimmers K. Gene expression analysis of mammary tissue during fetal bud formation and growth in two pig breeds--indications of prenatal initiation of postnatal phenotypic differences. BMC DEVELOPMENTAL BIOLOGY 2012; 12:13. [PMID: 22537077 PMCID: PMC3527354 DOI: 10.1186/1471-213x-12-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 04/12/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND The mammary gland is key to all mammal species; in particular in multiparous species like pigs the number and the shape of functional mammary gland complexes are major determinants of fitness. Accordingly, we aimed to catalog the genes relevant to mammogenesis in pigs. Moreover, we aimed to address the hypothesis that the extent and timing of proliferation, differentiation, and maturation processes during prenatal development contribute to postnatal numerical, morphological and functional properties of the mammary gland. Thus we focused on differentially expressed genes and networks relevant to mammary complex development in two breeds that are subject to different selection pressure on number, shape and function of teats and show largely different prevalence of non-functional inverted teats. The expression patterns of fetal mammary complexes obtained at 63 and 91 days post conception (dpc) from German Landrace (GL) and Pietrain (PI) were analyzed by Affymetrix GeneChip Porcine Genome Arrays. RESULTS The expression of 11,731 probe sets was analysed between the two stages within and among breeds. The analysis showed the largest distinction of samples of the breed GL at 63 dpc from all other samples. According to Ingenuity Pathways Analysis transcripts with abundance at the four comparisons made (GL63-GL91, PI63-PI93, GL63-PI63 and GL91-PI91) were predominantly assigned to biofunctions relevant to 'cell maintenance, proliferation, differentiation and replacement', 'organismal, organ and tissue development' and 'genetic information and nucleic acid processing'. Moreover, these transcripts almost exclusively belong to canonical pathways related to signaling rather than metabolic pathways. The accumulation of transcripts that are up-regulated in GL compared to PI indicate a higher proliferating activity in GL, whereas processes related to differentiation, maturation and maintenance of cells are more prominent in PI. Differential expression was validated by quantitative RT-PCR of five genes (GAB1, MAPK9, PIK3C2B, PIK3C3 and PRKCH) that are involved in several relevant signaling pathways. CONCLUSIONS The results indicate that mammary complex development in PI precedes GL. The differential expression between the two breeds at fetal stages likely reflects the prenatal initiation of postnatal phenotypes concerning the number and shape as well as functionality of teats.
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Affiliation(s)
- Kunsuda Chomwisarutkun
- Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
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Chomwisarutkun K, Murani E, Ponsuksili S, Wimmers K. Microarray analysis reveals genes and functional networks relevant to the predisposition to inverted teats in pigs1. J Anim Sci 2012; 90:1-15. [DOI: 10.2527/jas.2011-4269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- K. Chomwisarutkun
- Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - E. Murani
- Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - S. Ponsuksili
- Leibniz Institute for Farm Animal Biology, Research Group Functional Genome Analysis, Dummerstorf, Germany
| | - K. Wimmers
- Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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Tetzlaff S, Murani E, Schellander K, Ponsuksili S, Wimmers K. Differential expression of growth factors and their receptors indicates their involvement in the inverted teat defect in pigs1. J Anim Sci 2009; 87:3451-7. [DOI: 10.2527/jas.2008-1660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Tetzlaff S, Chomdej S, Jonas E, Ponsuksili S, Murani E, Phatsara C, Schellander K, Wimmers K. Association of parathyroid hormone-like hormone (PTHLH) and its receptor (PTHR1) with the number of functional and inverted teats in pigs. J Anim Breed Genet 2009; 126:237-41. [DOI: 10.1111/j.1439-0388.2008.00781.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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