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Selection signatures in Canchim beef cattle

Journal of Animal Science and Biotechnology 2017年第1期8卷 15-23页

作者： Ismael Urbinati nedenia bonvino stafuzza Marcos Túlio Oliveira Tatiane Cristina Seleguim Chud Roberto Hiroshi Higa Luciana Correia de Almeida Regitano Maurício Mello de Alencar Marcos Eli Buzanskas Danísio Prado Munari Departamento de Ciencias Exatas Univ Estadual PaulistaFaculdade de Ciencias Agrairias e VeterinairiasjaboticabalSao Paulo 14884-900Brazil Departamento de Tecnologia UNESP-Univ Estadual PaulistaFaculdade de Ciencias Agrarias e VeterinariasJaboticabalSao Paulo 14884-900Brazil Embrapa Agricultural Informatics CampinasSao Paulo 13083-886Brazil Embrapa Southeast Livestock Sao CarlosSao Paulo 13560-970Brazil

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（i HS）, 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 ***： A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The i HS statistic for each marker was transformed into pi HS for better interpretation of the *** BTA5 and BTA14 showed pi HS 〉 5, with 39 and nine statistically significant SNPs（P 〈 0.00001）,respectively. For the candidate selection regions, i HS 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 ***： 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.

关键词： Composite breed Extended haplotype homozygosity Genomics Single nucleotide polymorphism

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Genomic regions and pathways associated with gastrointestinal parasites resistance in Santa Inês breed adapted to tropical climate

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Journal of Animal Science and Biotechnology 2018年第1期9卷 35-50页

作者： Mariana Piatto Berton Rafael Medeiros de Oliveira Silva Elisa Peripolli nedenia bonvino stafuzza Jesús Fernández Martin Maria Saura álvarez Beatriz Villanueva Gavina Miguel Angel Toro Georgget Banchero Priscila Silva Oliveira Joanir Pereira Eler Fernando Baldi José Bento Sterman Ferraz Departamento de Zootecnia Faculdade de Ciências Agrárias e VeterináriasUniversidade Estadual PaulistaVia de acesso Prof.Paulo Donato Castellane sno Jaboticabal SP CEP 14884 900 Brazil Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA Crta.de la Coruna km75 28040 Madrid Spain Departamento de Producción Agraria School of AgriculturalFood and Byosystems EngineeringUniversisdad Politécnica de MadridCampus Ciudad Universitaria Avda.Complutense 3-Avda.Puerta Hierro 28040 Madrid Spain Instituto Nacional de Investigación Agropecuária(INIA) Ruta 50 Kin. 12 Colonia Uruguay Faculdade de Zootecnia e Engenharia de Alimentos Nucleo de Apoio à Pesquisa em Melhoramento AnimalBiotecnologia e TransgeniaUniversidade de Sao Paulo Rua Duque de Caxias Norte 225 Pirassununga SP CEP 13635 900Brazil

Background： The aim of this study was to estimate variance components and to identify genomic regions and pathways associated with resistance to gastrointestinal parasites, particularly Haemonchus contortus, in a breed of sheep adapted to tropical climate. Phenotypes evaluations were performed to verify resistance to gastrointestinal parasites, and were divided into two categories： i） farm phenotypes, assessing body condition score（BCS）, degree of anemia assessed by the famacha chart（FAM）, fur score（FS） and feces consistency（FC）; and ii） lab phenotypes,comprising blood analyses for hematocrit（HCT）, white blood cell count（WBC）, red blood cell count（RBC）,hemoglobin（HGB）, platelets（PLT） and transformed（log10） egg per gram of feces（EPG_（log））. A total of 576 animals were genotyped with the Ovine SNP12k Bead Chip（Illumina, Inc.）, that contains 12,785 bialleleic SNP markers. The variance components were estimated using a single trait model by single step genomic BLUP ***： The overall linkage disequilibrium（LD） mean between pairs of markers measured by r2 was 0.23. The overall LD mean between markers considering windows up to 10 Mb was 0.07. The mean LD between adjacent SNPs across autosomes ranged from 0.02 to 0.10. Heritability estimates were low for EPG_（log）（0.11）, moderate for RBC（0.18）, PLT（0.17） HCT（0.20）, HGB（0.16） and WBC（0.22）, and high for FAM（0.35）. A total of 22, 21, 23, 20, 26, 25 and 23 windows for EPG_（log）for FAM, WBC, RBC, PLT, HCT and HGB traits were identified, respectively. Among the associated windows, 10 were shown to be common to HCT and HGB traits on OAR1, OAR2, OAR3, OAR5, OAR8 and ***： The traits indicating gastrointestinal parasites resistance presented an adequate genetic variability to respond to selection in Santa Inês breed, and it is expected a higher genetic gain for FAM trait when compared to the others. The level of LD estimated for markers separated by less than 1 Mb indicated that the Ovine SNP12k Bead Chip m

关键词： Gwas Linkage disequilibrium arasites resistance Santa Inês breed

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

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Journal of Animal Science and Biotechnology 2018年第1期9卷 59-68页

作者： Marcos Eli Buzanskas Daniela do Amaral Grossi Ricardo Vieira Ventura Flavio Schramm Schenkel Tatiane Cristina Seleguim Chud nedenia bonvino stafuzza Luciana Diniz Rola Sarah Laguna Conceio Meirelles Fabiana Barichello Mokry Maurício de Alvarenga Mudadu Roberto Hiroshi Higa Marcos Vinícius Gualberto Barbosa da Silva Maurício Mello de Alencar Luciana Correia de Almeida Regitano Danísio Prado Munari Departamento de Zootecnia Universidade Federal da Paraíba(UFPB)AreiaParailba 58397-000Brazil Fast Genetics SaskatoonSK S7K 2K6Canada Beef Improvement Opportunities(BIO) GuelphON N1K 1ESCanada Department of Animal and Poultry Science University of GuelphCentre for Genetic Improvement of Livestock(CGIL)GuelphON N1G 2W1Canada Departamento de Ciencias Exatas Faculdade de Ci6ncias Agrarias e VeterinariasUniversidade Estadual Paulista(Unesp)JaboticabalSao Paulo 14884 900Brazil Departamento de Zootecnia Nucleo de Pesquisa e Conservacao de CervMeosFaculdade de Ciencias Agrarias e VeterinariasUniversidade Estadual Paulista(Unesp)JaboticabalSao Paulo 14884 900Brazil Department of Animal Science Federal University/of Lavras(UFLA)LavrasMinas Gerais 37200 000Brazil Department of Genetics and Evolution Federa University of Sao Carlos(UFSCar)Sao CarlosSao Paulo 13565-905Brazil Embrapa Agricultural Informatics Campinas55o Paulo 13083 886Brazil Embrapa Dairy Cattle Juiz de ForaMinas Gerais 36038 330Brazil Embrapa Southeast Livestock Sao CarlosSao Paulo 13560 970Brazil

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 210 d of age, scrotal circumference at 420 d 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 ***： Associated SNPs were observed for scrotal circumference at 420 d of age（435 SNPs）, followed by scrotal circumference at 210 d 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 ***： Few associations were observed for scrotal circumference at 210 d 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 420 d 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, al 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.

关键词： Animal breeding Composite breed Genome-wide association Genomic data Single nucleotide polymorphism

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