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(Referência obtida automaticamente do Web of Science, por meio da informação sobre o financiamento pela FAPESP e o número do processo correspondente, incluída na publicação pelos autores.)

Comparison between haplotype-based and individual snp-based genomic predictions for beef fatty acid profile in Nelore cattle

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Autor(es):
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Braga Feitosa, Fabieli Loise [1] ; Cravo Pereira, Angelica Simone [2] ; Amorim, Sabrina Thaise [1] ; Peripolli, Elisa [1] ; de Oliveira Silva, Rafael Medeiros [3] ; Braz, Camila Urbano [1] ; Ferrinho, Adrielle Matias [2] ; Schenkel, Flavio Schramm [4] ; Brito, Luiz Fernando [4] ; Espigolan, Rafael [5] ; de Albuquerque, Lucia Galvao [1] ; Baldi, Fernando [1]
Número total de Autores: 12
Afiliação do(s) autor(es):
[1] Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Zootecnia, BR-14884900 Jaboticabal - Brazil
[2] Univ Sao Paulo, Fac Zootecnia & Engn Alimentos, Dept Nutr & Prod Anim, Pirassununga - Brazil
[3] Zoetis, Kalamazoo, MI - USA
[4] Purdue Univ, Dept Anim Sci, W Lafayette, IN 47907 - USA
[5] Univ Sao Paulo, Fac Zootecnia & Engn Alimentos, Dept Med Vet, Pirassununga - Brazil
Número total de Afiliações: 5
Tipo de documento: Artigo Científico
Fonte: JOURNAL OF ANIMAL BREEDING AND GENETICS; v. 137, n. 5, p. 468-476, SEP 2020.
Citações Web of Science: 1
Resumo

The aim of this study was to evaluate the genomic predictions using the single-step genomic best linear unbiased predictor (ssGBLUP) method based on SNPs and haplotype markers associated with beef fatty acids (FAs) profile in Nelore cattle. The data set contained records from 963 Nelore bulls finished in feedlot (+/- 90 days) and slaughtered with approximately 24 months of age. Meat samples from the Longissimus dorsi muscle were taken for FAs profile measurement. FAs were quantified by gas chromatography using a SP-2560 capillary column. Animals were genotyped with the high-density SNP panel (BovineHD BeadChip assay) containing 777,962 markers. SNPs with a minor allele frequency and a call rate lower than 0.05 and 0.90, respectively, monomorphic, located on sex chromosomes, and with unknown position were removed from the data set. After genomic quality control, a total of 469,981 SNPs and 892 samples were available for subsequent analyses. Missing genotypes were imputed and phased using the FImpute software. Haplotype blocks were defined based on linkage disequilibrium using the Haploview software. The model to estimate variance components and genetic parameters and to predict the genomic values included the random genetic additive effects, fixed effects of the contemporary group and the age at slaughter as a linear covariate. Accuracies using the haplotype-based approach ranged from 0.07 to 0.31, and those SNP-based ranged from 0.06 to 0.33. Regression coefficients ranged from 0.07 to 0.74 and from 0.08 to 1.45 using the haplotype- and SNP-based approaches, respectively. Despite the low to moderate accuracies for the genomic values, it is possible to obtain genetic progress trough selection using genomic information based either on SNPs or haplotype markers. The SNP-based approach allows less biased genomic evaluations, and it is more feasible when taking into account the computational and operational cost underlying the haplotypes inference. (AU)

Processo FAPESP: 15/25304-8 - Associação e seleção genômica para perfil de ácidos graxos utilizando haplótipos como marcadores em bovinos nelore
Beneficiário:Fabieli Loise Braga Feitosa
Linha de fomento: Bolsas no Brasil - Doutorado
Processo FAPESP: 09/16118-5 - Ferramentas genômicas no melhoramento genético de características de importância econômica direta em bovinos da raça Nelore
Beneficiário:Lucia Galvão de Albuquerque
Linha de fomento: Auxílio à Pesquisa - Temático
Processo FAPESP: 16/24085-3 - Seleção genômica e vias metabólicas associadas com o perfil de ácidos graxos da carne utilizando haplótipos em bovinos da raça Nelore
Beneficiário:Fabieli Loise Braga Feitosa
Linha de fomento: Bolsas no Exterior - Estágio de Pesquisa - Doutorado