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Accounting for genetic architecture for body weight improves accuracy of predicting breeding values in a commercial line of broilers

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Accounting for genetic architecture for body weight improves accuracy of predicting breeding values in a commercial line of broilers. / Rome, Helene Julie Sophie; Chu, Thinh Tuan; Marois, Danye; Huang, Chyong-Huoy; Madsen, Per; Jensen, Just.

In: Journal of Animal Breeding and Genetics, Vol. 138, No. 5, 528-540, 09.2021.

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@article{a5dd8d89c58b49a7a493abb093664f1b,
title = "Accounting for genetic architecture for body weight improves accuracy of predicting breeding values in a commercial line of broilers",
abstract = "BLUP (best linear unbiased prediction) is the standard for predicting breeding values, where different assumptions can be made on variance–covariance structure, which may influence predictive ability. Herein, we compare accuracy of prediction of four derived‐BLUP models: (a) a pedigree relationship matrix (PBLUP), (b) a genomic relationship matrix (GBLUP), (c) a weighted genomic relationship matrix (WGBLUP) and (d) a relationship matrix based on genomic features that consisted of only a subset of SNP selected on a priori information (GFBLUP). We phenotyped a commercial population of broilers for body weight (BW) in five successive weeks and genotyped them using a 50k SNP array. We compared predictive ability of univariate models using conservative cross‐validation method, where each full‐sib group was divided into two folds. Results from cross‐validation showed, with WGBLUP model, a gain in accuracy from 2% to 7% compared with GBLUP model. Splitting the additive genetic matrix into two matrices, based on significance level of SNP (Gf: estimated with only set of SNP selected on significance level, Gr: estimated with the remaining SNP), led to a gain in accuracy from 1% to 70%, depending on the proportion of SNP used to define Gf. Thus, information from GWAS in models improves predictive ability of breeding values for BW in broilers. Increasing the power of detection of SNP effects, by acquiring more data or improving methods for GWAS, will help improve predictive ability.",
author = "Rome, {Helene Julie Sophie} and Chu, {Thinh Tuan} and Danye Marois and Chyong-Huoy Huang and Per Madsen and Just Jensen",
year = "2021",
month = sep,
doi = "10.1111/jbg.12546",
language = "English",
volume = "138",
journal = "Journal of Animal Breeding and Genetics (Online)",
issn = "1439-0388",
publisher = "Wiley-Blackwell Verlag GmbH",
number = "5",

}

RIS

TY - JOUR

T1 - Accounting for genetic architecture for body weight improves accuracy of predicting breeding values in a commercial line of broilers

AU - Rome, Helene Julie Sophie

AU - Chu, Thinh Tuan

AU - Marois, Danye

AU - Huang, Chyong-Huoy

AU - Madsen, Per

AU - Jensen, Just

PY - 2021/9

Y1 - 2021/9

N2 - BLUP (best linear unbiased prediction) is the standard for predicting breeding values, where different assumptions can be made on variance–covariance structure, which may influence predictive ability. Herein, we compare accuracy of prediction of four derived‐BLUP models: (a) a pedigree relationship matrix (PBLUP), (b) a genomic relationship matrix (GBLUP), (c) a weighted genomic relationship matrix (WGBLUP) and (d) a relationship matrix based on genomic features that consisted of only a subset of SNP selected on a priori information (GFBLUP). We phenotyped a commercial population of broilers for body weight (BW) in five successive weeks and genotyped them using a 50k SNP array. We compared predictive ability of univariate models using conservative cross‐validation method, where each full‐sib group was divided into two folds. Results from cross‐validation showed, with WGBLUP model, a gain in accuracy from 2% to 7% compared with GBLUP model. Splitting the additive genetic matrix into two matrices, based on significance level of SNP (Gf: estimated with only set of SNP selected on significance level, Gr: estimated with the remaining SNP), led to a gain in accuracy from 1% to 70%, depending on the proportion of SNP used to define Gf. Thus, information from GWAS in models improves predictive ability of breeding values for BW in broilers. Increasing the power of detection of SNP effects, by acquiring more data or improving methods for GWAS, will help improve predictive ability.

AB - BLUP (best linear unbiased prediction) is the standard for predicting breeding values, where different assumptions can be made on variance–covariance structure, which may influence predictive ability. Herein, we compare accuracy of prediction of four derived‐BLUP models: (a) a pedigree relationship matrix (PBLUP), (b) a genomic relationship matrix (GBLUP), (c) a weighted genomic relationship matrix (WGBLUP) and (d) a relationship matrix based on genomic features that consisted of only a subset of SNP selected on a priori information (GFBLUP). We phenotyped a commercial population of broilers for body weight (BW) in five successive weeks and genotyped them using a 50k SNP array. We compared predictive ability of univariate models using conservative cross‐validation method, where each full‐sib group was divided into two folds. Results from cross‐validation showed, with WGBLUP model, a gain in accuracy from 2% to 7% compared with GBLUP model. Splitting the additive genetic matrix into two matrices, based on significance level of SNP (Gf: estimated with only set of SNP selected on significance level, Gr: estimated with the remaining SNP), led to a gain in accuracy from 1% to 70%, depending on the proportion of SNP used to define Gf. Thus, information from GWAS in models improves predictive ability of breeding values for BW in broilers. Increasing the power of detection of SNP effects, by acquiring more data or improving methods for GWAS, will help improve predictive ability.

U2 - 10.1111/jbg.12546

DO - 10.1111/jbg.12546

M3 - Journal article

C2 - 33774870

VL - 138

JO - Journal of Animal Breeding and Genetics (Online)

JF - Journal of Animal Breeding and Genetics (Online)

SN - 1439-0388

IS - 5

M1 - 528-540

ER -