Estimation of breeding values using different densities of SNP to inform kinship in broiler chickens

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Salvian, Mayara ; Monteiro Moreira, Gabriel Costa ; Freitas Silveira, Robson Mateus ; Reis, Andrea Plotzki ; D'auria, Brayan Dias ; Pilonetto, Fabricio ; Gervasio, Izally Carvalho ; Ledur, Monica Corre ; Coutinho, Luiz Lehmann ; Spangler, Matthew Lee ; Moura, Gerson Barreto

• Tipo de documento: Artigo Científico
• Fonte: LIVESTOCK SCIENCE; v. 267, p. 8-pg., 2022-11-29.

Resumo

Traditionally, breeding values are estimated based on phenotypic and pedigree information using the numerator relationship (A) matrix. With the availability of genomic information, genome-wide markers can be included in the estimation of breeding values through genomic kinship. Genomic information allows a more accurate estimation of breeding values compared to the breeding values estimated by phenotypic and pedigree information. However, the density of genomic information used can impact the cost of implementation. The aim of this study was to compare the rank, accuracy, and bias of estimated breeding values (EBV) for organs [heart (HRT), liver (LIV), gizzard (GIZ), lungs (LUN)] and carcass [breast (BRST), drumstick (DRM) and thigh (THG)] weight traits in a broiler population using pedigree-based BLUP (PBLUP) and single-step genomic BLUP (ssGBLUP) methods using various densities of SNP and variants imputed from whole-genome sequence (WGS). For both PBLUP and ssGBLUP, heritability estimates varied from low (LUN) to high (HRT, LIV, GIZ, BRST, DRM and THG). Regression coefficient values of EBV on genomic estimated breeding values (GEBV) were similar for both the high density (HD) and WGS sets of SNPs, ranging from 0.87 to 0.99 across scenarios. Results show no benefit of using WGS data compared to HD array data using an unweighted ssGBLUP. Our results suggest that 10% of the content of the HD array can yield unbiased and accurate EBV. (AU)

• Processo FAPESP: 14/08704-0 - Identificação de locos de interesse zootécnico na galinha doméstica
• Beneficiário: Luiz Lehmann Coutinho
• Modalidade de apoio: Auxílio à Pesquisa - Temático
• Processo FAPESP: 14/21380-9 - Estudo de associação ampla do genoma para deposição de gordura e rendimento de carcaça em galinhas
• Beneficiário: Gabriel Costa Monteiro Moreira
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 16/00569-1 - Imputação e associação genômica ampla utilizando haplótipos para gordura abdominal em galinhas.
• Beneficiário: Gabriel Costa Monteiro Moreira
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Doutorado