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Lago LV, Nery da Silva A, Zanella EL, Groke Marques M, Peixoto JO, da Silva MVGB, Ledur MC, Zanella R. Identification of Genetic Regions Associated with Scrotal Hernias in a Commercial Swine Herd. Vet Sci 2018; 5:vetsci5010015. [PMID: 29382056 PMCID: PMC5876567 DOI: 10.3390/vetsci5010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 01/17/2023] Open
Abstract
In this paper, we have used two approaches to detect genetic associations with scrotal hernias in commercial pigs. Firstly, we have investigated the effects of runs of homozygosity (ROH) with the appearance of scrotal hernias, followed by a Genome Wide Association Study (GWAS). The phenotype classification was based on visual appearance of scrotal hernias. Each affected animal was matched to a healthy control from the same pen. In the total, 68 animals were genotyped using the Porcine SNP60 Beadchip, out of those, 41 animals had the presence of hernias and 27 were healthy animals. Fifteen animals were removed from the analysis due to differences in genetic background, leaving 18 healthy animals and 35 piglets with scrotal hernia. Further, the detection of extended haplotypes shared ROH were conducted for health (control) and affected (case) animals and a permutation test was used to test whether the ROH segments were more frequent in case/case pairs than non-case/case pairs. Using the ROH, we have identified an association (p = 0.019) on chromosome 2(SSC2) being segregated on animals with the presence of scrotal hernias. Using a GWAS, a region composed by 3 SNPs on the sexual chromosome X (SSCX) were associated with scrotal hernias (p < 1.6 × 10-5), this region harbors the Androgen Receptor Gene (AR).
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Affiliation(s)
- Luisa Vitória Lago
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
| | - Arthur Nery da Silva
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
| | - Eraldo L Zanella
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
- Docentes do Programa de Pós-Graduação em Bioexperimentação-UPF, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
| | | | - Jane O Peixoto
- Embrapa Suínos e Aves, Rodovia BR-153, Km110, Concórdia, SC 89715-899, Brazil.
| | - Marcos V G B da Silva
- Embrapa Gado de Leite, Rua Eugênio do Nascimento, 610, Juiz de Fora, MG 36038-330, Brazil.
| | - Mônica C Ledur
- Embrapa Suínos e Aves, Rodovia BR-153, Km110, Concórdia, SC 89715-899, Brazil.
| | - Ricardo Zanella
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
- Docentes do Programa de Pós-Graduação em Bioexperimentação-UPF, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
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Utsunomiya ATH, Santos DJA, Boison SA, Utsunomiya YT, Milanesi M, Bickhart DM, Ajmone-Marsan P, Sölkner J, Garcia JF, da Fonseca R, da Silva MVGB. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. BMC Genomics 2016; 17:705. [PMID: 27595709 PMCID: PMC5011828 DOI: 10.1186/s12864-016-3049-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/27/2016] [Indexed: 11/21/2022] Open
Abstract
Background Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be detected by the unexpected behavior of marker linkage disequilibrium (LD) decay. We developed a heuristic process to identify misassembly signatures, applied it to the bovine reference genome assembly (UMDv3.1) and presented the consequences of misassemblies in two case studies. Results We identified 2,906 single nucleotide polymorphism (SNP) markers presenting unexpected LD decay behavior in 626 putative misassembled contigs, which comprised less than 1 % of the whole genome. Although this represents a small fraction of the reference sequence, these poorly assembled segments can lead to severe implications to local genome context. For instance, we showed that one of the misassembled regions mapped to the POLL locus, which affected the annotation of positional candidate genes in a GWAS case study for polledness in Nellore (Bos indicus beef cattle). Additionally, we found that poorly performing markers in imputation mapped to putative misassembled regions, and that correction of marker positions based on LD was capable to recover imputation accuracy. Conclusions This heuristic approach can be useful to cross validate reference assemblies and to filter out markers located at low confidence genomic regions before conducting downstream analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3049-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam T H Utsunomiya
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Campus de Jaboticabal, São Paulo, Brasil.
| | - Daniel J A Santos
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Campus de Jaboticabal, São Paulo, Brasil
| | | | - Yuri T Utsunomiya
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Campus de Jaboticabal, São Paulo, Brasil
| | - Marco Milanesi
- Faculdade de Medicina Veterinária de Araçatuba, Universidade Estadual Paulista - UNESP, Campus de Araçatuba, São Paulo, Brasil
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD, USA
| | - Paolo Ajmone-Marsan
- Institute of Zootechnics and Biodiversity and Ancient DNA Research Center, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - José F Garcia
- Faculdade de Medicina Veterinária de Araçatuba, Universidade Estadual Paulista - UNESP, Campus de Araçatuba, São Paulo, Brasil.,International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brasil
| | - Ricardo da Fonseca
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Campus de Jaboticabal, São Paulo, Brasil.,Faculdade de Ciências Agrárias e Tecnológicas, Universidade Estadual Paulista - UNESP, Campus de Dracena, São Paulo, Brasil
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Kim ES, Sonstegard TS, da Silva MVGB, Gasbarre LC, Van Tassell CP. Genome-wide scan of gastrointestinal nematode resistance in closed Angus population selected for minimized influence of MHC. PLoS One 2015; 10:e0119380. [PMID: 25803687 PMCID: PMC4372334 DOI: 10.1371/journal.pone.0119380] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/30/2015] [Indexed: 12/03/2022] Open
Abstract
Genetic markers associated with parasite indicator traits are ideal targets for study of marker assisted selection aimed at controlling infections that reduce herd use of anthelminthics. For this study, we collected gastrointestinal (GI) nematode fecal egg count (FEC) data from post-weaning animals of an Angus resource population challenged to a 26 week natural exposure on pasture. In all, data from 487 animals was collected over a 16 year period between 1992 and 2007, most of which were selected for a specific DRB1 allele to reduce the influence of potential allelic variant effects of the MHC locus. A genome-wide association study (GWAS) based on BovineSNP50 genotypes revealed six genomic regions located on bovine Chromosomes 3, 5, 8, 15 and 27; which were significantly associated (-log10 p=4.3) with Box-Cox transformed mean FEC (BC-MFEC). DAVID analysis of the genes within the significant genomic regions suggested a correlation between our results and annotation for genes involved in inflammatory response to infection. Furthermore, ROH and selection signature analyses provided strong evidence that the genomic regions associated BC-MFEC have not been affected by local autozygosity or recent experimental selection. These findings provide useful information for parasite resistance prediction for young grazing cattle and suggest new candidate gene targets for development of disease-modifying therapies or future studies of host response to GI parasite infection.
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Affiliation(s)
- Eui-Soo Kim
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Tad S. Sonstegard
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
- * E-mail:
| | | | - Louis C. Gasbarre
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
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Zavarez LB, Utsunomiya YT, Carmo AS, Neves HHR, Carvalheiro R, Ferenčaković M, Pérez O'Brien AM, Curik I, Cole JB, Van Tassell CP, da Silva MVGB, Sonstegard TS, Sölkner J, Garcia JF. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Front Genet 2015; 6:5. [PMID: 25688258 PMCID: PMC4310349 DOI: 10.3389/fgene.2015.00005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/07/2015] [Indexed: 11/18/2022] Open
Abstract
The use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (>1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation.
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Affiliation(s)
- Ludmilla B Zavarez
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Adriana S Carmo
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Haroldo H R Neves
- GenSys Consultores Associados Porto Alegre, Rio Grande do Sul, Brazil ; Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - John B Cole
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Marcos V G B da Silva
- Bioinformatics and Animal Genomics Laboratory, Embrapa Dairy Cattle Juiz de Fora, Minas Gerais, Brazil
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria
| | - José F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil ; Laboratório de Bioquímica e Biologia Molecular Animal, Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista Araçatuba, São Paulo, Brazil
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Neves HHR, Carvalheiro R, O'Brien AMP, Utsunomiya YT, do Carmo AS, Schenkel FS, Sölkner J, McEwan JC, Van Tassell CP, Cole JB, da Silva MVGB, Queiroz SA, Sonstegard TS, Garcia JF. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Genet Sel Evol 2014; 46:17. [PMID: 24575732 PMCID: PMC4014866 DOI: 10.1186/1297-9686-46-17] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 02/18/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Nellore cattle play an important role in beef production in tropical systems and there is great interest in determining if genomic selection can contribute to accelerate genetic improvement of production and fertility in this breed. We present the first results of the implementation of genomic prediction in a Bos indicus (Nellore) population. METHODS Influential bulls were genotyped with the Illumina Bovine HD chip in order to assess genomic predictive ability for weight and carcass traits, gestation length, scrotal circumference and two selection indices. 685 samples and 320 238 single nucleotide polymorphisms (SNPs) were used in the analyses. A forward-prediction scheme was adopted to predict the genomic breeding values (DGV). In the training step, the estimated breeding values (EBV) of bulls were deregressed (dEBV) and used as pseudo-phenotypes to estimate marker effects using four methods: genomic BLUP with or without a residual polygenic effect (GBLUP20 and GBLUP0, respectively), a mixture model (Bayes C) and Bayesian LASSO (BLASSO). Empirical accuracies of the resulting genomic predictions were assessed based on the correlation between DGV and dEBV for the testing group. RESULTS Accuracies of genomic predictions ranged from 0.17 (navel at weaning) to 0.74 (finishing precocity). Across traits, Bayesian regression models (Bayes C and BLASSO) were more accurate than GBLUP. The average empirical accuracies were 0.39 (GBLUP0), 0.40 (GBLUP20) and 0.44 (Bayes C and BLASSO). Bayes C and BLASSO tended to produce deflated predictions (i.e. slope of the regression of dEBV on DGV greater than 1). Further analyses suggested that higher-than-expected accuracies were observed for traits for which EBV means differed significantly between two breeding subgroups that were identified in a principal component analysis based on genomic relationships. CONCLUSIONS Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions. Recurrent updates of the training population would be required to enable accurate prediction of the genetic merit of young animals. The technical feasibility of applying genomic prediction in a Bos indicus (Nellore) population was demonstrated. Further research is needed to permit cost-effective selection decisions using genomic information.
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Affiliation(s)
- Haroldo H R Neves
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900, Brazil.
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Utsunomiya YT, do Carmo AS, Carvalheiro R, Neves HHR, Matos MC, Zavarez LB, Pérez O'Brien AM, Sölkner J, McEwan JC, Cole JB, Van Tassell CP, Schenkel FS, da Silva MVGB, Porto Neto LR, Sonstegard TS, Garcia JF. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genet 2013; 14:52. [PMID: 23758625 PMCID: PMC3683327 DOI: 10.1186/1471-2156-14-52] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 06/05/2013] [Indexed: 12/30/2022] Open
Abstract
Background Birth weight (BW) is an economically important trait in beef cattle, and is associated with growth- and stature-related traits and calving difficulty. One region of the cattle genome, located on Bos primigenius taurus chromosome 14 (BTA14), has been previously shown to be associated with stature by multiple independent studies, and contains orthologous genes affecting human height. A genome-wide association study (GWAS) for BW in Brazilian Nellore cattle (Bos primigenius indicus) was performed using estimated breeding values (EBVs) of 654 progeny-tested bulls genotyped for over 777,000 single nucleotide polymorphisms (SNPs). Results The most significant SNP (rs133012258, PGC = 1.34 × 10-9), located at BTA14:25376827, explained 4.62% of the variance in BW EBVs. The surrounding 1 Mb region presented high identity with human, pig and mouse autosomes 8, 4 and 4, respectively, and contains the orthologous height genes PLAG1, CHCHD7, MOS, RPS20, LYN, RDHE2 (SDR16C5) and PENK. The region also overlapped 28 quantitative trait loci (QTLs) previously reported in literature by linkage mapping studies in cattle, including QTLs for birth weight, mature height, carcass weight, stature, pre-weaning average daily gain, calving ease, and gestation length. Conclusions This study presents the first GWAS applying a high-density SNP panel to identify putative chromosome regions affecting birth weight in Nellore cattle. These results suggest that the QTLs on BTA14 associated with body size in taurine cattle (Bos primigenius taurus) also affect birth weight and size in zebu cattle (Bos primigenius indicus).
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Affiliation(s)
- Yuri T Utsunomiya
- Faculdade de Medicina Veterinária de Araçatuba, Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
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