<abstract xmlns="http://www.w3.org/1999/xhtml">

Genetic improvement of body weight (BW) traits has received major consideration in the poultry industry due to their economic and environmental implications. With the rapid implementation of genomic selection (GS) in the poultry industry and a decrease in the cost of genotyping, genomic prediction (GP) is a feasible way to increase productivity. Moreover, a pre-selection of SNPs could represent a reasonable option to speed up GP. We used 312 F2 broiler chicken genotyped with 60K Illumina Beadchip to investigate the effect of reduced SNP densities on accuracy and bias of prediction using single-step genomic BLUP (ssGBLUP) for BW at 2-4 weeks of age (488 chickens). To investigate the effect of reduced SNP densities by varying minor allele frequency (MAF), SNPs were grouped into five subgroups with MAF of 0.05-0.1, 0.1-0.2, 0.2-0.3, 0.3-0.4 and 0.4-0.5. The accuracy and bias of genomic predictions from different MAF bins were compared to that using a standard array of 60k SNP genotypes and the traditional BLUP method. Our study showed that using a subset of common SNPs genotypes may increase accuracy of genomic predictions compared to using all SNPs, specifically in the studied F2 population with a limited number of genotyped/phenotyped individuals.
</abstract>

Genetic improvement of body weight (BW) traits has received major consideration in the poultry industry due to their economic and environmental implications. With the rapid implementation of genomic selection (GS) in the poultry industry and a decrease in the cost of genotyping, genomic prediction (GP) is a feasible way to increase productivity. Moreover, a pre-selection of SNPs could represent a reasonable option to speed up GP. We used 312 F2 broiler chicken genotyped with 60K Illumina Beadchip to investigate the effect of reduced SNP densities on accuracy and bias of prediction using single-step genomic BLUP (ssGBLUP) for BW at 2-4 weeks of age (488 chickens). To investigate the effect of reduced SNP densities by varying minor allele frequency (MAF), SNPs were grouped into five subgroups with MAF of 0.05-0.1, 0.1-0.2, 0.2-0.3, 0.3-0.4 and 0.4-0.5. The accuracy and bias of genomic predictions from different MAF bins were compared to that using a standard array of 60k SNP genotypes and the traditional BLUP method. Our study showed that using a subset of common SNPs genotypes may increase accuracy of genomic predictions compared to using all SNPs, specifically in the studied F2 population with a limited number of genotyped/phenotyped individuals.

Genomic evaluation of body weight traits in a F2 mixture of commercial broiler and native chicken

Department of Animal Science, Faculty of Agriculture

Animal Science Papers and Reports

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Genomic evaluation of body weight traits in a F mixture of commercial broiler and native chicken

Genetic improvement of body weight (BW) traits has received major consideration in the poultry industry due to their economic and environmental implications....

Genomic evaluation of body weight traits in a F₂ mixture of commercial broiler and native chicken

Published Online: Jul 26, 2023

Page range: 123 - 137

Accepted: Apr 27, 2023

DOI: https://doi.org/10.2478/aspr-2023-0003

Keywords
SNP, genomic prediction, phylogenetic tree, reciprocal crosses

© 2023 Hamed Asadollahi et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Genomic evaluation of body weight traits in a F2 mixture of commercial broiler and native chicken

Published Online: Jul 26, 2023

Page range: 123 - 137

Accepted: Apr 27, 2023

DOI: https://doi.org/10.2478/aspr-2023-0003

KeywordsSNP, genomic prediction, phylogenetic tree, reciprocal crosses

© 2023 Hamed Asadollahi et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Genomic evaluation of body weight traits in a F₂ mixture of commercial broiler and native chicken

Keywords
SNP, genomic prediction, phylogenetic tree, reciprocal crosses