Journal Article

Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture

Leeds, Timothy D., Martin, Kyle E., Fragomeni, Breno O., Wiens, Gregory D., Palti, Yniv, Vallejo, Roger L., Parsons, James E., Evenhuis, Jason P., Gao, Guangtu

2017

Overview

Background Previously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative that enables exploitation of within-family genetic variation. Methods We compared three GS models [single-step genomic best linear unbiased prediction (ssGBLUP), weighted ssGBLUP (wssGBLUP), and BayesB] to predict genomic-enabled breeding values (GEBV) for BCWD resistance in a commercial rainbow trout population, and compared the accuracy of GEBV to traditional estimates of breeding values (EBV) from a pedigree-based BLUP (P-BLUP) model. We also assessed the impact of sampling design on the accuracy of GEBV predictions. For these comparisons, we used BCWD survival phenotypes recorded on 7893 fish from 102 families, of which 1473 fish from 50 families had genotypes [57 K single nucleotide polymorphism (SNP) array]. Naïve siblings of the training fish ( n  = 930 testing fish) were genotyped to predict their GEBV and mated to produce 138 progeny testing families. In the following generation, 9968 progeny were phenotyped to empirically assess the accuracy of GEBV predictions made on their non-phenotyped parents. Results The accuracy of GEBV from all tested GS models were substantially higher than the P-BLUP model EBV. The highest increase in accuracy relative to the P-BLUP model was achieved with BayesB (97.2 to 108.8%), followed by wssGBLUP at iteration 2 (94.4 to 97.1%) and 3 (88.9 to 91.2%) and ssGBLUP (83.3 to 85.3%). Reducing the training sample size to n  = ~1000 had no negative impact on the accuracy (0.67 to 0.72), but with n  = ~500 the accuracy dropped to 0.53 to 0.61 if the training and testing fish were full-sibs, and even substantially lower, to 0.22 to 0.25, when they were not full-sibs. Conclusions Using progeny performance data, we showed that the accuracy of genomic predictions is substantially higher than estimates obtained from the traditional pedigree-based BLUP model for BCWD resistance. Overall, we found that using a much smaller training sample size compared to similar studies in livestock, GS can substantially improve the selection accuracy and genetic gains for this trait in a commercial rainbow trout breeding population.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Accuracy / Agriculture / Animal Genetics and Genomics / Animal husbandry / Animals / Aquaculture / bacterial cold-water disease / Bacterial infections / Bacterial Infections - genetics / Bacterial Infections - microbiology / Bayes Theorem / Biomedical and Life Sciences / Breeding / breeding value / Cold / Cold Temperature / Cold water / Disease resistance / Disease Resistance - genetics / Diseases / Estimates / Evolutionary Biology / Fish / Fish Diseases - genetics / Fish Diseases - microbiology / Fish populations / Gene polymorphism / Genetic aspects / Genetic diversity / Genetic improvement / Genetic Markers / genetic variation / Genomics / Genomics - methods / genotype / Genotypes / genotyping / Iterative methods / Life Sciences / Livestock / Low temperature resistance / Marker assisted selection / Methods / Models, Genetic / Nucleotides / Offspring / Oncorhynchus mykiss / Oncorhynchus mykiss - genetics / parents / Pedigree / Phenotype / Phenotypes / Polymorphism / Polymorphism, Single Nucleotide / Population / prediction / Predictions / Progeny / progeny testing / Quantitative Trait Loci / Rainbow trout / Reproducibility of Results / Research Article / Sample size / sampling / Sampling designs / Selection, Genetic / siblings / Single-nucleotide polymorphism / Training / Trout