SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

PICCOLI, M. L.; BRACCINI, J. B.; CARDOSO, F. F.; SARGOLZAEI, M.; LARMER, S. G.; SCHENKEL, F. S..

Article 157.

Accuracy of genotype imputation with different low density panels in Braford and Hereford cattle.

Palavras-chave: Bovino.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1008091

PICCOLI, M. L.; BRACINNI NETO, J.; CARDOSO, F. F.; SARGOLZAEI, M.; SCHENKEL, F. S..

The main objective of this research was to test alternative low density SNP panels to impute Illumina 50K SNP panel genotypes in Braford and Hereford cattle. Genotypes from 3,768 Hereford, Braford and Nellore animals were used for testing imputation from low density SNP panels (3K, 6K, 8K, 15K and 20K) to the Illumina 50K SNP panel, under four different scenarios: including or not Nellore genotypes in the reference population in combination with the use or not of pedigree information. There were no significant differences in imputation accuracy among these four scenarios within each panel. However, significant differences between panels were found. The best accuracy was given by a customized 15K SNP panel, with an overall genotype concordance rate of...

Associações genômicas para perímetro escrotal ao desmame em bovinos da raça Canchim.

Palavras-chave: Seleção genômica; Gado de corte.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/995739

BUZANSKAS, M. E.; GROSSI, D. A.; REGITANO, L. C. de A.; SCHENKEL, F. S.; ALENCAR, M. M. de; MUNARI, D. P..

O objetivo deste trabalho foi estudar a associação entre polimorfismos de base única (SNP) com os valores genéticos do perímetro escrotal mensurado ao desmame (PED) em bovinos de corte de raça sintética. Neste estudo foram utilizados 285 animais da raça Canchim e 114 animais do grupo genético MA (utilizados na formação da raça Canchim), genotipados com o painel de alta densidade (786.799 SNPs). Após o controle de qualidade de informações (genótipos e fenótipos) restaram 672.778 SNPs e 392 animais. Foram observadas associações para PED nos cromossomos 20 e 28. Após a correção para múltiplos testes (?false discovery rate?) ao nível de 10%, 12 SNPs foram significativamente associados, ao longo do cromossomo, com PED. Novos e promissores genes associados com...

Association of apolipoprotein B and adiponectin receptor 1 genes with carcass, bone integrity and performance traits in a paternal broiler Line.

Palavras-chave: Gado de corte; Melhoramento genético; Seleção genômica.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/964251

CRUZ, V. A. R. da; SCHENKEL, F. S.; SAVEGNAGO, R. P.; GRUPIONI, N. V.; STAFUZZA, N. B.; SARGOZAEL, M.; IBELLI, A. M. G.; PEIXOTO, J. de O.; LEDUR, M. C.; MUNARI, D. P..

Apolipoprotein B (APOB) and Adiponectin Receptor 1 (ADIPOR1) are related to the regulation of feed intake, fat metabolism and protein deposition and are candidate genes for genomic studies in birds. In this study, associations of two single nucleotide polymorphisms (SNPs) g.102A>T (APOB) and g.729C>T (ADIPOR1) with carcass, bone integrity and performance traits in broilers were investigated. Genotyping was performed on a paternal line of 1,454 broilers. The SNP detection was carried out by PCR-RFLP technique using the restriction enzymes HhaI for the SNP g.729C>T and MslI for the SNP g.102A>T. The association analyses of the two SNPs with 85 traits were performed using the restricted maximum likelihood (REML) and Generalized Quasi-Likelihood...

Association of polymorphisms in the IGF1, GH and PIT1 genes with growth and reproductive traits in Canchim cattle

Palavras-chave: Frango de corte; Carcaça; Genética animal.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1025860

GROSSI, D. A.; GRUPIONI, N. V.; BUZANSKAS, M. E.; SCHENKEL, F. S.; REGITANO, L. C. de A.; PAZ, C. C. P.; ALENCAR, M. M. de; MUNARI, D..

A variance component approach for quantitative trait loci (QTL) mapping was proposed by George et al. (2000), which assumes a mixed inheritance model (polygenes and QTL effects). This approach allows for mapping QTL in general pedigrees from outbreed populations. In this method, besides the use of an additive relationship matrix to estimate the additive polygenic effects, an identical-by-descent (IBD) matrix is used to estimate the QTL effect and its variance. Analyses of the association of genetic markers with economic traits in beef cattle have been mainly reported in developed countries. In the Brazilian Canchim breed, studies found association of polymorphism in the insulin-like growth factor 1 (IGF1), growth hormone (GH) and specific pituitary...

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

Palavras-chave: Polymorphisms; Crescimento; Reprodução; Gado de corte.

Ano: 2010

URL: http://www.alice.cnptia.embrapa.br/handle/doc/862938

BUZANSKAS, M. E.; GROSSI, D. do A.; VENTURA, R. V.; SCHENKEL, F. S.; CHUD, T. C. S.; STAFUZZA, N. B.; ROLA, L. D.; MEIRELLES, S. L. C.; MOKRY, F. B.; MUDADU, M. de A.; HIGA, R. H.; SILVA, M. V. G. B.; ALENCAR, M. M. de; REGITANO, L. C. de A.; MUNARI, D. P..

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 animals. Results: 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...

Estudo de associações genômicas para idade ao primeiro e segundo parto em bovinos da raça Canchim.

Palavras-chave: Polimorfismo de nucleotídeo único; Gado de corte; Gado Canchim; Beef cattle; Genome-wide association study; Single nucleotide polymorphism; Quantitative trait loci.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1074373

BUZANSKAS, M. E.; VENTURA, R. V.; REGITANO, L. C. de A.; SCHENKEL, F. S.; ALENCAR, M. M. de; MUNARI, D. P..

Recentemente, programas de melhoramento genético de bovinos de corte têm dado maior ênfase para características reprodutivas de fêmeas devido à sua importância econômica para o sistema de produção. O objetivo deste trabalho foi estudar a associação entre polimorfismos de base única (SNP) com os valores genéticos das características idade ao primeiro (IPP) e segundo (ISP) parto em bovinos de corte de raça sintética. Neste estudo foram utilizados 285 animais da raça Canchim e 114 animais do grupo genético MA (utilizados na formação da raça Canchim), genotipados com o painel de alta densidade (786.799 SNPs). Após o controle de qualidade de informações (genótipos e fenótipos) restaram 672.778 SNPs e 392 animais. Foram observadas associações para IPP nos...

Genome-wide association for growth traits in Canchim beef cattle.

Palavras-chave: Gado de corte; Melhoramento genético; Seleção genômica.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/964254

BUZANSKAS, M. E.; GROSSI, D. A.; VENTURA, R. V.; SCHENKEL, F. S.; SARGOLZAEI, M.; MEIRELLES, S. L. C.; MOKRY, F. B.; HIGA, R. H.; MUDADU, M. A.; SILVA, M. V. G. B.; NICIURA, S. C. M.; TORRES JÚNIOR, R. A. de A.; ALENCAR, M. M.; REGITANO, L. C. A.; MUNARI, D. P..

Abstract. Studies are being conducted on the applicability of genomic data to improve the accuracy of the selection process in livestock, and genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to identify genomic regions and genes that play roles in birth weight (BW), weaning weight adjusted for 210 days of age (WW), and long-yearling weight adjusted for 420 days of age (LYW) in Canchim cattle. GWAS were performed by means of the Generalized Quasi-Likelihood Score (GQLS) method using genotypes from the BovineHD BeadChip and estimated breeding values for BW, WW, and LYW. Data consisted of 285 animals from the Canchim breed and 114 from the MA genetic...

Genome-wide association for growth traits in Canchim beef cattle.

Palavras-chave: Genome-wide association study; Gado de corte; Beef cattle.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1003481

BUZANSKAS, M. E.; GROSSI, D. A.; VENTURA, R. V.; SCHENKEL, F. S.; SARGOLZAEI, M.; MEIRELLES, S. L. C.; MOKRY, F. B.; HIGA, R. H.; MUDADU, M. de A.; SILVA, M. V. G. B.; NICIURA, S. C. M.; TORRES JUNIOR, R. A. de A.; ALENCAR, M. M. de; REGITANO, L. C. de A.; MUNARI, D. P..

bitstream/item/101136/1/PROCI-2014.00012.pdf

Genome-wide association study on long-yearling scrotal circumference in Canchim cattle.

Palavras-chave: Genome-wide; Growth trait; Race Canchim; Raça Canchim; Gado de corte.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/984641

BUZANSKAS, M. E.; GROSSI, D. A.; VENTURA, R. V.; CHUD, T. C. S.; URBINATI, I.; MEIRELLES, S. L. C.; MOKRY, F. B.; SCHENKEL, F. S.; REGITANO, L. C. de A.; MUNARI, D. P..

Genome-wide association studies provide valuable information for understanding the genetic control of complex traits in livestock. The goal of this study was to investigate the association of the BovineHD BeadChip SNP genotypes with estimated breeding values for long-yearling scrotal circumference adjusted to 420 days (SC420) in Canchim beef cattle. A total 435 SNPs were significantly associated with SC420 (10% chromosome-wise FDR), of which 30 were located in genes on chromosomes 5, 13, and 14, including HEY1, PLCG1, PAG1, ZFHX4, PEX2, FABP5, FABP12, MED30, and TRHR genes. These genes play a role in biological processes related to reproduction, fat deposition, and hormonal systems development. Future studies targeting these regions and genes could provide...

Genomic predictions for economically important traits in Brazilian Braford and Hereford beef cattle using true and imputed genotypes.

Palavras-chave: Animal breeding; Candidate gene; Canchim breed.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/993744

PICCOLI, M. L.; BRITO, L. F.; BRACCINI, J.; CARDOSO, F. F.; SARGOLZAEI, M.; SCHENKEL, F. S..

Genomic selection (GS) has played an important role in cattle breeding programs. However, genotyping prices are still a challenge for implementation of GS in beef cattle and there is still a lack of information about the use of low-density Single Nucleotide Polymorphisms (SNP) chip panels for genomic predictions in breeds such as Brazilian Braford and Hereford. Therefore, this study investigated the effect of using imputed genotypes in the accuracy of genomic predictions for twenty economically important traits in Brazilian Braford and Hereford beef cattle. Various scenarios composed by different percentages of animals with imputed genotypes and different sizes of the training population were compared.

Linkage disequilibrium and haplotype block structure in a composite beef cattle breed.

Palavras-chave: Genotipagem; Gado de corte; Seleção genótipa.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1073847

MOKRY, F. B.; BUZANSKAS, M. E.; MUDADU, M. de A.; GROSSI, D. do A.; HIGA, R. H.; VENTURA, R. V.; LIMA, A. O. de; SARGOLZAEI, M.; MEIRELLES, S. L. C.; SCHENKEL, F. S.; SILVA, M. V. G. B. da; NICIURA, S. C. M.; ALENCAR, M. M. de; MINARI, D. P.; REGITANO, L. C. de A..

Abstract. Background: The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies. Results: The maximum average LD, measured by r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances...

Linkage disequilibrium and haplotype block structure in a composite beef cattle breed.

Palavras-chave: Polimorfismo de nucleotídeo único; Genome wide association studies; Desequilíbrio de ligação; Gado de corte; Beef cattle; Single nucleotide polymorphism; Linkage disequilibrium.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1003463

MOKRY, F. B.; BUZANSKAS, M. E.; MUDADU, M. de A.; GROSSI, D. do A.; HIGA, R. H.; VENTURA, R. V.; LIMA, A. O. de; SARGOLZAEI, M.; MEIRELLES, S. L. C.; SCHENKEL, F. S.; SILVA, M. V. G. B.; NICIURA, S. C. M.; ALENCAR, M. M. de; MINARI, D. P.; REGITANO, L. C. de A..