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Rodriguez VR, Maffioly JI, Zdanovicz LA, Fabre RM, Barrandeguy ME, García MV, Lagadari M. Genetic diversity of meat quality related genes in Argentinean pigs. Vet Anim Sci 2022; 15:100237. [PMID: 35169654 PMCID: PMC8829130 DOI: 10.1016/j.vas.2022.100237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Duarte DAS, Fortes MRS, Duarte MDS, Guimarães SEF, Verardo LL, Veroneze R, Ribeiro AMF, Lopes PS, de Resende MDV, Fonseca e Silva F. Genome-wide association studies, meta-analyses and derived gene network for meat quality and carcass traits in pigs. Anim Prod Sci 2018. [DOI: 10.1071/an16018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A large number of quantitative trait loci (QTL) for meat quality and carcass traits has been reported in pigs over the past 20 years. However, few QTL have been validated and the biological meaning of the genes associated to these QTL has been underexploited. In this context, a meta-analysis was performed to compare the significant markers with meta-QTL previously reported in literature. Genome association studies were performed for 12 traits, from which 144 SNPs were found out to be significant (P < 0.05). They were validated in the meta-analysis and used to build the Association Weight Matrix, a matrix framework employed to investigate co-association of pairwise SNP across phenotypes enabling to derive a gene network. A total of 45 genes were selected from the Association Weight Matrix analysis, from which 25 significant transcription factors were identified and used to construct the networks associated to meat quality and carcass traits. These networks allowed the identification of key transcription factors, such as SOX5 and NKX2–5, gene–gene interactions (e.g. ATP5A1, JPH1, DPT and NEDD4) and pathways related to the regulation of adipose tissue metabolism and skeletal muscle development. Validated SNPs and knowledge of key genes driving these important industry traits might assist future strategies in pig breeding.
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Barroso LMA, Nascimento M, Nascimento ACC, Silva FF, Serão NVL, Cruz CD, Resende MDV, Silva FL, Azevedo CF, Lopes PS, Guimarães SEF. Regularized quantile regression for SNP marker estimation of pig growth curves. J Anim Sci Biotechnol 2017; 8:59. [PMID: 28702191 PMCID: PMC5504997 DOI: 10.1186/s40104-017-0187-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 11/29/2016] [Accepted: 06/06/2017] [Indexed: 11/14/2022] Open
Abstract
Background Genomic growth curves are generally defined only in terms of population mean; an alternative approach that has not yet been exploited in genomic analyses of growth curves is the Quantile Regression (QR). This methodology allows for the estimation of marker effects at different levels of the variable of interest. We aimed to propose and evaluate a regularized quantile regression for SNP marker effect estimation of pig growth curves, as well as to identify the chromosome regions of the most relevant markers and to estimate the genetic individual weight trajectory over time (genomic growth curve) under different quantiles (levels). Results The regularized quantile regression (RQR) enabled the discovery, at different levels of interest (quantiles), of the most relevant markers allowing for the identification of QTL regions. We found the same relevant markers simultaneously affecting different growth curve parameters (mature weight and maturity rate): two (ALGA0096701 and ALGA0029483) for RQR(0.2), one (ALGA0096701) for RQR(0.5), and one (ALGA0003761) for RQR(0.8). Three average genomic growth curves were obtained and the behavior was explained by the curve in quantile 0.2, which differed from the others. Conclusions RQR allowed for the construction of genomic growth curves, which is the key to identifying and selecting the most desirable animals for breeding purposes. Furthermore, the proposed model enabled us to find, at different levels of interest (quantiles), the most relevant markers for each trait (growth curve parameter estimates) and their respective chromosomal positions (identification of new QTL regions for growth curves in pigs). These markers can be exploited under the context of marker assisted selection while aiming to change the shape of pig growth curves.
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Affiliation(s)
- L M A Barroso
- Department of Statistics, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil
| | - M Nascimento
- Department of Statistics, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil
| | - A C C Nascimento
- Department of Statistics, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil
| | - F F Silva
- Department of Animal Science, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil
| | - N V L Serão
- Department of Animal Science, Iowa State University, Kildee Hall 50011 Ames, Iowa, USA
| | - C D Cruz
- Department of General Biology, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil
| | - M D V Resende
- Department of Statistics, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil.,Embrapa Forestry, Estrada da Ribeira, km 111, Colombo, PR Brazil
| | - F L Silva
- Department of Plant Science, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil
| | - C F Azevedo
- Department of Statistics, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil
| | - P S Lopes
- Department of Animal Science, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil
| | - S E F Guimarães
- Department of Animal Science, Federal University of Viçosa, Av. P H Rolfs, s/n, University Campus, Viçosa, MG 36570-000 Brazil
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Lázaro SF, Ibáñez-Escriche N, Varona L, Silva FFE, Brito LC, Guimarães SEF, Lopes PS. Bayesian analysis of pig growth curves combining pedigree and genomic information. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Rossi R, Martins E, Lopes P, Silva F, Marcondes M, Caetano G, Ferreira Júnior H, Knupp L, Ferreira M. Inferência bayesiana da conversão alimentar em diferentes experimentos animais. ARQ BRAS MED VET ZOO 2016. [DOI: 10.1590/1678-4162-8121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
O presente trabalho teve por objetivo avaliar a conversão alimentar (CA) por meio da inferência bayesiana considerando-se análises bivariadas. Foram utilizadas diferentes espécies animais de experimentos conduzidos na Universidade Federal de Viçosa, no estado de Minas Gerais, Brasil. O modelo proposto mostrou ser apropriado, uma vez que possibilitou a detecção de diferenças significativas entre níveis de fatores não detectados por procedimentos frequentistas em ANOVA tradicional, principalmente em pequenas amostras. No experimento com codornas, evidenciou-se que aves cujos níveis de proteína bruta eram de 23% e 29%, respectivamente, para machos e fêmeas, apresentaram uma melhor CA, de 2,83±0,03 e 2,66±0,03, respectivamente. No experimento com frangos, no grupo sem o aditivo antibiótico, a inclusão de 0,02% de extrato de ésteres naturais foi o que promoveu a melhor CA (1,72±0,01), e, de modo geral, o uso de antibiótico e a ausência de ésteres naturais promoveram CA de 1,63±0,02. Em caprinos, verificou-se que o aleitamento, seja com leite de cabra ou de vaca, promove igualmente uma melhor CA, respectivamente, no grupo de 60 e 90 dias, de 1,29±0,14 e 1,79±0,11, sugerindo que o aleitamento seja feito até os 60 dias. Em suínos, a dieta com maior nível de energia metabolizável e aminoácidos foi a que promoveu a melhor CA (2,86±0,07), quando comparada a uma dieta com nível nutricional mais baixo. Já o uso de enzimas na dieta com menor nível energético e de aminoácidos proporcionou resultado intermediário (2,90±007). Em bovinos, observou-se que o uso de 1% de concentrado na dieta promoveria uma melhor CA estimada de 7,33±0,35 entre os Nelores e que essa promoção seria de 7,40±0,58 entre os cruzados com o uso de 2% de concentrado na dieta.
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Affiliation(s)
- R.M. Rossi
- Universidade Estadual de Maringá, Brasil
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Verardo LL, Silva FF, Varona L, Resende MDV, Bastiaansen JWM, Lopes PS, Guimarães SEF. Bayesian GWAS and network analysis revealed new candidate genes for number of teats in pigs. J Appl Genet 2014; 56:123-32. [DOI: 10.1007/s13353-014-0240-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/27/2014] [Accepted: 07/23/2014] [Indexed: 01/01/2023]
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Hidalgo AM, Lopes PS, Paixão DM, Silva FF, Bastiaansen JWM, Paiva SR, Faria DA, Guimarães SEF. Fine mapping and single nucleotide polymorphism effects estimation on pig chromosomes 1, 4, 7, 8, 17 and X. Genet Mol Biol 2014; 36:511-9. [PMID: 24385854 PMCID: PMC3873182 DOI: 10.1590/s1415-47572013000400009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 03/11/2013] [Accepted: 08/26/2013] [Indexed: 11/21/2022] Open
Abstract
Fine mapping of quantitative trait loci (QTL) from previous linkage studies was performed on pig chromosomes 1, 4, 7, 8, 17, and X which were known to harbor QTL. Traits were divided into: growth performance, carcass, internal organs, cut yields, and meat quality. Fifty families were used of a F2 population produced by crossing local Brazilian Piau boars with commercial sows. The linkage map consisted of 237 SNP and 37 microsatellite markers covering 866 centimorgans. QTL were identified by regression interval mapping using GridQTL. Individual marker effects were estimated by Bayesian LASSO regression using R. In total, 32 QTL affecting the evaluated traits were detected along the chromosomes studied. Seven of the QTL were known from previous studies using our F2 population, and 25 novel QTL resulted from the increased marker coverage. Six of the seven QTL that were significant at the 5% genome-wide level had SNPs within their confidence interval whose effects were among the 5% largest effects. The combined use of microsatellites along with SNP markers increased the saturation of the genome map and led to smaller confidence intervals of the QTL. The results showed that the tested models yield similar improvements in QTL mapping accuracy.
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Affiliation(s)
- André M Hidalgo
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Paulo S Lopes
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Débora M Paixão
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fabyano F Silva
- Departamento de Estatística, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - John W M Bastiaansen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - Samuel R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Danielle A Faria
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
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Silva FFE, de Resende MDV, Rocha GS, Duarte DAS, Lopes PS, Brustolini OJB, Thus S, Viana JMS, Guimarães SEF. Genomic growth curves of an outbred pig population. Genet Mol Biol 2013; 36:520-7. [PMID: 24385855 PMCID: PMC3873183 DOI: 10.1590/s1415-47572013005000042] [Citation(s) in RCA: 9] [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: 12/21/2012] [Accepted: 07/07/2013] [Indexed: 11/23/2022] Open
Abstract
In the current post-genomic era, the genetic basis of pig growth can be understood by assessing SNP marker effects and genomic breeding values (GEBV) based on estimates of these growth curve parameters as phenotypes. Although various statistical methods, such as random regression (RR-BLUP) and Bayesian LASSO (BL), have been applied to genomic selection (GS), none of these has yet been used in a growth curve approach. In this work, we compared the accuracies of RR-BLUP and BL using empirical weight-age data from an outbred F2 (Brazilian Piau X commercial) population. The phenotypes were determined by parameter estimates using a nonlinear logistic regression model and the halothane gene was considered as a marker for evaluating the assumptions of the GS methods in relation to the genetic variation explained by each locus. BL yielded more accurate values for all of the phenotypes evaluated and was used to estimate SNP effects and GEBV vectors. The latter allowed the construction of genomic growth curves, which showed substantial genetic discrimination among animals in the final growth phase. The SNP effect estimates allowed identification of the most relevant markers for each phenotype, the positions of which were coincident with reported QTL regions for growth traits.
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Affiliation(s)
| | | | | | - Darlene Ana S Duarte
- Departamento de Estatística, Universidade Federal de Viçosa, Viçosa, MG, Brazil . ; Departamento de Ciência Animal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Paulo Sávio Lopes
- Departamento de Ciência Animal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Otávio J B Brustolini
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Sander Thus
- Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - José Marcelo S Viana
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Simone E F Guimarães
- Departamento de Ciência Animal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Paixão D, Carneiro P, Paiva S, Sousa K, Verardo L, Braccini Neto J, Pinto A, Hidalgo A, Nascimento CSD, Périssé I, Lopes P, Guimarães S. Mapeamento de QTL nos cromossomos 1, 2, 3, 12, 14, 15 e X em suínos: características de carcaça e qualidade de carne. ARQ BRAS MED VET ZOO 2012. [DOI: 10.1590/s0102-09352012000400026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A realização do presente estudo teve como objetivo mapear Quantitative Trait Loci (QTL) de carcaça e qualidade de carne em uma população F2 de suínos desenvolvida pelo cruzamento de dois reprodutores da raça brasileira Piau com 18 fêmeas comerciais (Landrace x Large White x Pietrain). O mapa de ligação para essa população foi construído após a genotipagem de 684 animais para 35 marcadores microssatélites. Os dados foram analisados pelo mapeamento por intervalo usando-se sexo, lote e genótipo halotano como efeitos fixos e peso de carcaça ao abate, peso da carcaça direita e idade ao abate como covariáveis. Um total de 18 QTLs foi encontrado; os QTLs para maior espessura de toucinho na região da copa, na linha dorsolombar, e a perda por cozimento foram significativos em nível de 5% genômico. A característica espessura de toucinho foi essencialmente associada aos alelos da raça Piau, conhecido como porco tipo banha. As informações dos QTLs significativos encontrados servem para futuros estudos de mapeamento fino para identificação de genes a serem usados em conjunto com os métodos tradicionais de seleção, para melhorar a eficiência dos programas de melhoramento, assim como prover informação acerca da fisiologia envolvida no desenvolvimento das características quantitativas dos suínos.
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Affiliation(s)
| | | | - S.R. Paiva
- Empresa Brasileira de Pesquisa Agropecuária
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Silva FF, Rosa GJ, Guimarães SE, Lopes PS, de los Campos G. Three-step Bayesian factor analysis applied to QTL detection in crosses between outbred pig populations. Livest Sci 2011; 142:210-5. [DOI: 10.1016/j.livsci.2011.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Paixão DM, Silva Filho MID, Pereira MS, Lopes MS, Barbosa L, Souza KRS, Lopes PS, Guimarães SE. Quantitative trait loci for carcass, internal organ and meat quality traits on porcine chromosomes 16, 17 and 18. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000500016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Rojas JE, Wilches MA, Cepeda LA, Garcés MF, Suarez MA, Baldrich RM, Vélez CA, Guerrero MF, García MR, Moreno IH, Bravo SB, Omelka R, Caminos § JE. Molecular Diagnostics of Porcine Stress Syndrome Susceptibility Associated with the Arg615Cys Mutation Using Real-Time PCR with Fluorescent Hybridization Probes. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0120-3347(08)61003-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Silva KDM, Paixão DM, Silva PV, Solero BP, Pereira MS, Lopes PS, Guimarães SEF. Mapping of quantitative trait loci and confirmation of the FAT1 region on chromosome 4 in an F2 population of pigs. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000300013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Faria DAD, Guimarães SEF, Lopes PS, Pires AV, Paiva SR, Sollero BP, Wenceslau AA. Association between G316A growth hormone polymorphism and economic traits in pigs. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000400010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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