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1. Bayesian inference of genetic parameters for reproductive and performance traits in White Leghorn hens

Author

Jaqueline O. Rosa, Guilherme Costa Venturini, Tatiane Cristina Seleguim Chud, Bruno Carlos Pires, Marcos Eli Buzanskas, Nedenia Bonvino Stafuzza, Gabriel Rezende Furquim, Valdecy Aparecida Mônica Corrêa Ledur, and Danísio Prado Munari

Subjects
egg production, fertility, genetic correlation, hatchability, heritability, Animal culture, SF1-1100
Abstract

This study estimated the genetic parameters for reproductive and performance traits and determined which ones can be used as selection criteria for egg production in laying hens using the Bayesian inference. The data of 1894 animals from three generations of White Leghorn laying hens were analyzed for fertility (FERT), hatchability (HATC), and birth rate measurements at 60 weeks of age (BIRTH), body weight at 16 and 60 weeks of age (BW16 and BW60), age at sexual maturity (ASM), egg height/width ratio, weight, and density at 28, 36, and 40 weeks of age (RHW28, RHW36, RHW40, WEGG28, WEGG36, WEGG40, DENS28, DENS36, and DENS40, respectively) traits. The genetic parameters were estimated by the Bayesian inference method of multi-trait animal model. The model included the additive and residual genetic random effects and the fixed effects of generation. The a posteriori mean distributions of the heritability estimates for reproductive traits ranged from 0.14 ± 0.003 (HATC) to 0.22 ± 0.005 (FERT) and performance from 0.07 ± 0.001 (RHW28) to 0.42 ± 0.001 (WEGG40). The a posteriori mean distributions of the genetic correlation between reproductive traits ranged from 0.18 ± 0.026 (FERT and HACT) to 0.79 ± 0.007 (FERT and BIRTH) and those related to performance ranged from -0.49 ± 0.001 (WEGG36 and DENS36) to 0.75 ± 0.003 (DENS28 and DENS36). Reproductive and performance traits showed enough additive genetic variability to respond to selection, except for RHW28. This trait alone would have little impact on the genetic gain because environmental factors would have a higher impact compared to those from the additive genetic factors. Based on the results of this study, the selection applied on the BIRTH trait can be indicated to improve FERT and HATC of eggs. Furthermore, the use of the WEGG40 could improve egg quality in this population.

Published
2018
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2. Genomic structure of a crossbred Landrace pig population.

Author

Letícia Borges Joaquim, Tatiane Cristina Seleguim Chud, Jorge Augusto Petroli Marchesi, Rodrigo Pelicioni Savegnago, Marcos Eli Buzanskas, Ricardo Zanella, Mauricio Egidio Cantão, Jane Oliveira Peixoto, Mônica Correa Ledur, Renato Irgang, and Danísio Prado Munari

Subjects
Medicine, Science
Abstract

Single nucleotide polymorphism (SNP) markers are used to study population structure and conservation genetics, which permits assessing similarities regarding the linkage disequilibrium and information about the relationship among individuals. To investigate the population genomic structure of 300 females and 25 males from a commercial maternal pig line we analyzed linkage disequilibrium extent, inbreeding coefficients using genomic and conventional pedigree data, and population stratification. The average linkage disequilibrium (r2) was 0.291 ± 0.312 for all adjacent SNPs, distancing less than 100 Kb (kilobase) between markers. The average inbreeding coefficients obtained from runs of homozygosity (ROH) and pedigree analyses were 0.119 and 0.0001, respectively. Low correlation was observed between the inbreeding coefficients possibly as a result of genetic recombination effect accounted for the ROH estimates or caused by pedigree identification errors. A large number of long ROHs might indicate recent inbreeding events in the studied population. A total of 36 homozygous segments were found in more than 30% of the population and these ROH harbor genes associated with reproductive traits. The population stratification analysis indicated that this population was possibly originated from two distinct populations, which is a result from crossings between the eastern and western breeds used in the formation of the line. Our findings provide support to understand the genetic structure of swine populations and may assist breeding companies to avoid a high level of inbreeding coefficients to maintain genetic diversity, showing the effectiveness of using genome-wide SNP information for quantifying inbreeding when the pedigree was incomplete or incorrect.

Published
2019
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3. Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds.

Author

Nedenia Bonvino Stafuzza, Adhemar Zerlotini, Francisco Pereira Lobo, Michel Eduardo Beleza Yamagishi, Tatiane Cristina Seleguim Chud, Alexandre Rodrigues Caetano, Danísio Prado Munari, Dorian J Garrick, Marco Antonio Machado, Marta Fonseca Martins, Maria Raquel Carvalho, John Bruce Cole, and Marcos Vinicius Gualberto Barbosa da Silva

Subjects
Medicine, Science
Abstract

Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs.

Published
2017
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4. Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers.

Author

Marcos Eli Buzanskas, Ricardo Vieira Ventura, Tatiane Cristina Seleguim Chud, Priscila Arrigucci Bernardes, Daniel Jordan de Abreu Santos, Luciana Correia de Almeida Regitano, Maurício Mello de Alencar, Maurício de Alvarenga Mudadu, Ricardo Zanella, Marcos Vinícius Gualberto Barbosa da Silva, Changxi Li, Flavio Schramm Schenkel, and Danísio Prado Munari

Subjects
Medicine, Science
Abstract

The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle.

Published
2017
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5. Selection signatures in Canchim beef cattle

Author

R. H. Higa, Marcos T. Oliveira, Ismael Urbinati, Luciana Correia de Almeida Regitano, Nedenia Bonvino Stafuzza, Maurício Mello de Alencar, Danísio Prado Munari, T.C.S. Chud, Marcos Eli Buzanskas, ISMAEL URBINATI, UNESP, NEDENIA BONVINO STAFUZZA, UNESP, MARCOS TÚLIO OLIVEIRA, UNESP, TATIANE CRISTINA SELEGUIM CHUD, UNESP, ROBERTO HIROSHI HIGA, CNPTIA, LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE, MAURICIO MELLO DE ALENCAR, CPPSE, MARCOS ELI BUZANSKAS, UNESP, DANÍSIO PRADO MUNARI, UNESP., Universidade Estadual Paulista (Unesp), Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), ISMAEL URBINATI, Unesp Jaboticabal, NEDENIA BONVINO STAFUZZA, Unesp Jaboticabal, MARCOS TÚLIO OLIVEIRA, Unesp Jaboticabal, TATIANE CRISTINA SELEGUIM CHUD, Unesp Jaboticabal, MARCOS ELI BUZANSKAS, Unesp Jaboticabal, and DANÍSIO PRADO MUNARI, Unesp Jaboticabal.

Subjects
0301 basic medicine, Quantitative trait loci, Genótipo, Gado de corte, Composite breed, SNP, Cruzamento, Genomics, Single-nucleotide polymorphism, Biology, Biochemistry, Genome, 03 medical and health sciences, Genotype, Genômica, Extended haplotype homozygosity, Genotyping, Selection (genetic algorithm), Polimorfismo de nucleotídeo único, Genetics, Research, Haplotype, Beef cattle, Single nucleotide polymorphism, 030104 developmental biology, Cruzamento Animal, Animal Science and Zoology, Composite breeds, Food Science, Biotechnology
Abstract

Made available in DSpace on 2018-12-11T17:02:41Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-05-05 Background: Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel. Results: A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS > 5, with 39 and nine statistically significant SNPs (P < 0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development. Conclusions: The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization. Univ Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias Departamento de Ciências Exatas UNESP - Univ Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias Departamento de Tecnologia Embrapa Agricultural Informatics Embrapa Southeast Livestock Univ Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias Departamento de Ciências Exatas UNESP - Univ Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias Departamento de Tecnologia

Published
2015

6. Candidate genes for male and female reproductive traits in Canchim beef cattle

Author

Ricardo Vieira Ventura, Marcos Vinícius Gualberto Barbosa da Silva, D. A. Grossi, Flavio S Schenkel, Danísio Prado Munari, Nedenia Bonvino Stafuzza, Marcos Eli Buzanskas, Fabiana Barichello Mokry, Sarah Laguna Conceição Meirelles, Maurício Mello de Alencar, T.C.S. Chud, R. H. Higa, Luciana Correia de Almeida Regitano, Maurício A. Mudadu, Luciana Diniz Rola, Universidade Federal da Paraíba (UFPB), Fast Genetics, Beef Improvement Opportunities (BIO), Centre for Genetic Improvement of Livestock (CGIL), Universidade Estadual Paulista (Unesp), Universidade Federal de Lavras (UFLA), Universidade Federal de São Carlos (UFSCar), Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), MARCOS ELI BUZANSKAS, UFPB, FLAVIO SCHRAMM SCHENKEL, University of Guelph, TATIANE CRISTINA SELEGUIM CHUD, FCAV/Unesp, NEDENIA BONVINO STAFUZZA, FCAV/Unesp, LUCIANA DINIZ ROLA, FCAV/Unesp, SARAH LAGUNA CONCEIÇÃO MEIRELLES, Ufla, FABIANA BARICHELLO MOKRY, UFSCar, MAURICIO DE ALVARENGA MUDADU, CNPTIA, ROBERTO HIROSHI HIGA, CNPTIA, MARCOS VINICIUS GUALBERTO B SILVA, CNPGL, MAURICIO MELLO DE ALENCAR, CPPSE, LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE, DANÍSIO PRADO MUNARI, FCAV/Unesp., DANIELA DO AMARAL GROSSI, Fast Genetics, Saskatoon, and RICARDO VIEIRA VENTURA, Beef Improvement Opportunities, Guelph

Subjects
0301 basic medicine, Candidate gene, Genome-wide association study, Quantitative trait loci, Breeding program, Biological adhesion, Gado de corte, Composite breed, Single-nucleotide polymorphism, Biology, Quantitative trait locus, Beef cattle, Biochemistry, 03 medical and health sciences, Genomic data, Multicellular organismal process, Polimorfismo de nucleotídeo único, Animal breeding, Genetics, Gado Canchim, Genome-wide association, Research, 0402 animal and dairy science, 04 agricultural and veterinary sciences, 040201 dairy & animal science, Single nucleotide polymorphism, Cellular component organization, 030104 developmental biology, Animal Science and Zoology, Food Science, Biotechnology
Abstract

Made available in DSpace on 2018-12-11T17:14:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-08-23 Background: Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210d of age, scrotal circumference at 420d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals. Results: Associated SNPs were observed for scrotal circumference at 420d of age (435 SNPs), followed by scrotal circumference at 210d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction. Conclusions: Few associations were observed for scrotal circumference at 210d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program. Universidade Federal da Paraíba (UFPB) Departamento de Zootecnia Fast Genetics Beef Improvement Opportunities (BIO) University of Guelph Centre for Genetic Improvement of Livestock (CGIL) Department of Animal and Poultry Science Universidade Estadual Paulista (Unesp) Departamento de Ciências Exatas Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp) Departamento de Zootecnia Núcleo de Pesquisa e Conservação de Cervídeos Faculdade de Ciências Agrárias e Veterinárias Federal University of Lavras (UFLA) Department of Animal Science Federal University of São Carlos (UFSCar) Department of Genetics and Evolution Embrapa Agricultural Informatics Embrapa Dairy Cattle Embrapa Southeast Livestock Universidade Estadual Paulista (Unesp) Departamento de Ciências Exatas Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp) Departamento de Zootecnia Núcleo de Pesquisa e Conservação de Cervídeos Faculdade de Ciências Agrárias e Veterinárias

Published
2017

7. Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds

Author

John B. Cole, Nedenia Bonvino Stafuzza, Dorian J. Garrick, Maria Raquel Santos Carvalho, T.C.S. Chud, Alexandre Rodrigues Caetano, Marco Antonio Machado, Danísio Prado Munari, Marta Fonseca Martins, Francisco Pereira Lobo, Michel Eduardo Beleza Yamagishi, Adhemar Zerlotini, Marcos Vinícius Gualberto Barbosa da Silva, NEDENIA BONVINO STAFUZZA, FCAV/Unesp, ADHEMAR ZERLOTINI NETO, CNPTIA, FRANCISCO PEREIRA LOBO, CNPTIA, MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA, TATIANE CRISTINA SELEGUIM CHUD, FCAV/Unesp, ALEXANDRE RODRIGUES CAETANO, Cenargen, DANÍSIO PRADO MUNARI, FCAV/Unesp, DORIAN J. GARRICK, Iowa State University, MARCO ANTONIO MACHADO, CNPGL, MARTA FONSECA MARTINS, CNPGL, MARIA RAQUEL CARVALHO, UFMG, JOHN BRUCE COLE, Agricultural Research Service, MARCOS VINICIUS GUALBERTO B SILVA, CNPGL., Universidade Estadual Paulista (Unesp), Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Iowa State Univ, Universidade Federal de Minas Gerais (UFMG), and ARS

Subjects
Male, 0301 basic medicine, Genetic variants, Sensory Receptors, Social Sciences, lcsh:Medicine, Breeding, Genome, Database and Informatics Methods, INDEL Mutation, Cell Signaling, Genotype, Psychology, Membrane Receptor Signaling, lcsh:Science, Oligonucleotide Array Sequence Analysis, Polimorfismo de nucleotídeo único, Mammals, Genetics, Multidisciplinary, Gene Ontologies, High-Throughput Nucleotide Sequencing, food and beverages, Agriculture, Genomics, Ruminants, 04 agricultural and veterinary sciences, Genomic Databases, Important traits, Breed, Molecular Sequence Annotation, Vertebrates, Female, Sensory Perception, Brazil, Research Article, Signal Transduction, Livestock, dbSNP, Sequence analysis, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, Variação genética, Frameshift mutation, Single nucleotide variations, 03 medical and health sciences, Species Specificity, Bovines, Animals, Indel, Sequence Assembly Tools, lcsh:R, Organisms, 0402 animal and dairy science, Biology and Life Sciences, Computational Biology, Sequence Analysis, DNA, Cell Biology, Genome Analysis, 040201 dairy & animal science, Single nucleotide polymorphism, Cattle breeds, Biological Databases, 030104 developmental biology, Amniotes, Cattle, lcsh:Q, Gado, Neuroscience
Abstract

Made available in DSpace on 2018-11-28T07:23:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-03-21 Embrapa (Brazil) Genomic Selection in Dairy Cattle in Brazil Embrapa (Brazil) National network for development of innovative genomic strategies applied to animal breeding, conservation and production (PI - ARC) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs. Univ Estadual Paulista, Dept Ciencias Exatas, Fac Ciencias Agrarias & Vet, Sao Paulo, Brazil Embrapa Informat Agr, Campinas, SP, Brazil Embrapa Recursos Genet & Biotecnol, Brasilia, DF, Brazil Iowa State Univ, Dept Anim Sci, Ames, IA USA Embrapa Gado Leite, Juiz De Fora, MG, Brazil Univ Fed Minas Gerais, Dept Biol Geral, Belo Horizonte, MG, Brazil ARS, USDA, Anim Genom & Improvement Lab, Beltsville, MD USA Univ Estadual Paulista, Dept Ciencias Exatas, Fac Ciencias Agrarias & Vet, Sao Paulo, Brazil Embrapa (Brazil) Genomic Selection in Dairy Cattle in Brazil: SEG 02.09.07.008.00.00 Embrapa (Brazil) National network for development of innovative genomic strategies applied to animal breeding, conservation and production (PI - ARC): SEG 01.11.07.002.00.00 CNPq: PVE 407246/2013-4 FAPEMIG: CVZ PPM 00395/14 FAPESP: 15/08939-0

Published
2017

8. Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers

Author

Luciana Correia de Almeida Regitano, Changxi Li, Flavio S Schenkel, D.J.A. Santos, Priscila Arrigucci Bernardes, T.C.S. Chud, Maur�cio Mello De Alencar, Ricardo Vieira Ventura, Marcos Vinícius Gualberto Barbosa da Silva, Ricardo Zanella, Maurício A. Mudadu, Marcos Eli Buzanskas, Dan�sio Prado Munari, Universidade Estadual Paulista (Unesp), Beef Improvement Opportunities (BIO), Universidade de São Paulo (USP), Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Universidade de Passo Fundo, University of Alberta, Agriculture and Agri-Food Canada, Centre for Genetic Improvement of Livestock (CGIL), Marcos Eli Buzanskas, Unesp, Ricardo Vieira Ventura, USP, Tatiane Cristina Seleguim Chud, Unesp, Priscila Arrigucci Bernardes, Unesp, Daniel Jordan de Abreu Santos, Unesp, LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE, MAURICIO MELLO DE ALENCAR, CPPSE, MAURICIO DE ALVARENGA MUDADU, CNPTIA, Ricardo Zanella, UPF, MARCOS VINICIUS GUALBERTO B SILVA, CNPGL, Changxi Li, University of Alberta, Flavio Schramm Schenke, University of Guelph, and Danísio Prado Munari, Unesp.

Subjects
0301 basic medicine, Male, Linkage disequilibrium, Heredity, Heterosis, Introgression, lcsh:Medicine, Breeding, Linkage Disequilibrium, polymorphism, beef cattle, Mathematical and Statistical Techniques, lcsh:Science, Genetics, Mammals, Principal Component Analysis, Multidisciplinary, Heterozygosity, Agriculture, Ruminants, Zebu, Breed, Genetic Mapping, Vertebrates, Physical Sciences, Body Composition, Female, Statistics (Mathematics), Research Article, Evolutionary Processes, Livestock, Single-nucleotide polymorphism, Variant Genotypes, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, 03 medical and health sciences, Quantitative Trait, Heritable, Bovines, Genetic model, Hybrid Vigor, Animals, Statistical Methods, Genetic Association Studies, Evolutionary Biology, Population Biology, lcsh:R, Organisms, Biology and Life Sciences, Red Meat, Canchim cattle, 030104 developmental biology, Amniotes, Multivariate Analysis, Hybridization, Genetic, lcsh:Q, Cattle, Purebred, Zebus, Mathematics, Population Genetics
Abstract

Made available in DSpace on 2018-12-11T17:31:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-02-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine 50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle. Departamento de Ci�ncias Exatas Universidade Estadual Paulista (Unesp) Faculdade de Ci�ncias Agrarias e Veterinarias Beef Improvement Opportunities (BIO) Departamento de Ci�ncias Basicas Universidade de S�o Paulo (USP) Faculdade de Zootecnia e Engenharia de Alimentos (FZEA) Departamento de Zootecnia Universidade Estadual Paulista (Unesp) Faculdade de Ci�ncias Agrarias e Veterinarias Embrapa Southeast Livestock Embrapa Agricultural Informatics Faculdade de Agronomia e Medicina Veterin�ria Universidade de Passo Fundo Embrapa Dairy Cattle Department of Agricultural Food and Nutritional Science University of Alberta Lacombe Research and Development Centre Agriculture and Agri-Food Canada, 6000 C and E Trail Department of Animal and Poultry Science University of Guelph Centre for Genetic Improvement of Livestock (CGIL) Departamento de Ci�ncias Exatas Universidade Estadual Paulista (Unesp) Faculdade de Ci�ncias Agrarias e Veterinarias Departamento de Zootecnia Universidade Estadual Paulista (Unesp) Faculdade de Ci�ncias Agrarias e Veterinarias CAPES: 02663/09-0 CNPq: 449564/2014-2

Published
2016

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