Journal Article

International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight

Veerkamp, Roel F., Vandenplas, Jérémie, Cromie, Andrew, ten Napel, Jan, Michenet, Alexis, Bonifazi, Renzo, Calus, Mario P. L., Savoia, Simone

2022

Overview

Background Compared to national evaluations, international collaboration projects further improve accuracies of estimated breeding values (EBV) by building larger reference populations or performing a joint evaluation using data (or proxy of them) from different countries. Genomic selection is increasingly adopted in beef cattle, but, to date, the benefits of including genomic information in international evaluations have not been explored. Our objective was to develop an international beef cattle single-step genomic evaluation and investigate its impact on the accuracy and bias of genomic evaluations compared to current pedigree-based evaluations. Methods Weaning weight records were available for 331,593 animals from seven European countries. The pedigree included 519,740 animals. After imputation and quality control, 17,607 genotypes at a density of 57,899 single nucleotide polymorphisms (SNPs) from four countries were available. We implemented two international scenarios where countries were modelled as different correlated traits: an international genomic single-step SNP best linear unbiased prediction (SNPBLUP) evaluation (ssSNPBLUP INT ) and an international pedigree-based BLUP evaluation (PBLUP INT ). Two national scenarios were implemented for pedigree and genomic evaluations using only nationally submitted phenotypes and genotypes. Accuracies, level and dispersion bias of EBV of animals born from 2014 onwards, and increases in population accuracies were estimated using the linear regression method. Results On average across countries, 39 and 17% of sires and maternal-grand-sires with recorded (grand-)offspring across two countries were genotyped. ssSNPBLUP INT showed the highest accuracies of EBV and, compared to PBLUP INT , led to increases in population accuracy of 13.7% for direct EBV, and 25.8% for maternal EBV, on average across countries. Increases in population accuracies when moving from national scenarios to ssSNPBLUP INT were observed for all countries. Overall, ssSNPBLUP INT level and dispersion bias remained similar or slightly reduced compared to PBLUP INT and national scenarios. Conclusions International single-step SNPBLUP evaluations are feasible and lead to higher population accuracies for both large and small countries compared to current international pedigree-based evaluations and national evaluations. These results are likely related to the larger multi-country reference population and the inclusion of phenotypes from relatives recorded in other countries via single-step international evaluations. The proposed international single-step approach can be applied to other traits and breeds.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agriculture / Animal and Dairy Science / Animal Genetics and Genomics / Animals / Beef / Beef cattle / Bias / Biomedical and Life Sciences / Cattle / Comparative analysis / Dairy cattle / Dispersion / Evolutionary Biology / Genetics and Breeding / Genetik och förädling / Genomics / Genotype & phenotype / Genotypes / genotyping / Husdjursvetenskap / International cooperation / Life Sciences / marker-assisted selection / Nucleotides / Offspring / Pedigree / Phenotypes / Population / prediction / progeny / Quality control / regression analysis / Research Article / Single nucleotide polymorphisms / Single-nucleotide polymorphism / Weaning