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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
Total Authors: 11
Document type: Journal article
Source: LIVESTOCK SCIENCE; v. 267, p. 8-pg., 2022-11-29.
Abstract

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)

FAPESP's process: 14/08704-0 - Identification of loci of interest for poultry production
Grantee:Luiz Lehmann Coutinho
Support Opportunities: Research Projects - Thematic Grants
FAPESP's process: 14/21380-9 - Genome wide association studies for fat deposition and carcass yield in chickens
Grantee:Gabriel Costa Monteiro Moreira
Support Opportunities: Scholarships in Brazil - Doctorate
FAPESP's process: 16/00569-1 - IMPUTATION AND GENOME-WIDE ASSOCIATION ANALYSIS USING HAPLOTYPES FOR ABDOMINAL FAT IN CHICKENS.
Grantee:Gabriel Costa Monteiro Moreira
Support Opportunities: Scholarships abroad - Research Internship - Doctorate