ArticleEvolutionary applications2022
Strategies to improve the accuracy and reduce costs of genomic prediction in aquaculture species.
Article in Evolutionary applications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-ancestry genome-wide association meta-analysis identifies candidate genes for computed tomography-based carcass composition traits in pigs.Genetics, selection, evolution : GSE · 2025Pooled it
- From linear models to deep learning: statistical advances in genomic selection for animal breeding.Journal of animal science and biotechnology · 2026Review
- Local Enrichment of Multi-SNP Markers Improves Genomic Prediction from Low-Density Genotyping in Pacific White Shrimp.International journal of molecular sciences · 2026Article
- Enhancing genomic prediction for key production traits in chickens through ultrasound phenotyping and multi-model comparative analysis.Journal of animal science and biotechnology · 2026Article
- Genetic Parameter Estimates for Growth, Meat Yield and Foot Color Traits of Pacific AbaloneAnimals : an open access journal from MDPI · 2026Article
- Genomic Selection for Economic Traits in Inner Mongolia Cashmere Goats by Integrating GWAS Prior Information.Veterinary sciences · 2025Article
- Genomic Prediction for Growth-Related Traits in Golden Pompano (Evolutionary applications · 2025Article
- Prioritized SNP Selection from Whole-Genome Sequencing Improves Genomic Prediction Accuracy in Sturgeons Using Linear and Machine Learning Models.International journal of molecular sciences · 2025Article
- A novel approach for DNA extraction of white spot syndrome virus detection in penaeid shrimp.Scientific reports · 2025Article
- Weighted GBLUP in Simulated Beef Cattle Populations: Impact of Reference Population, Marker Density, and Heritability.Animals : an open access journal from MDPI · 2025Article
- Advancing genetic improvement in the omics era: status and priorities for United States aquaculture.BMC genomics · 2025Review
- Performance of weighted genomic BLUP and Bayesian methods for Hanwoo carcass traits.Tropical animal health and production · 2025Article
- Estimation of ryegrass (Frontiers in plant science · 2025Article
- Caprine and Ovine Genomic Selection-Progress and Application.Animals : an open access journal from MDPI · 2024Review
- GWAS Enhances Genomic Prediction Accuracy of Caviar Yield, Caviar Color and Body Weight Traits in Sturgeons Using Whole-Genome Sequencing Data.International journal of molecular sciences · 2024Article
- Impacts of reference population size and methods on the accuracy of genomic prediction for fleece traits in Inner Mongolia Cashmere Goats.Frontiers in veterinary science · 2024Article
- Increased Accuracy of Genomic Prediction Using Preselected SNPs from GWAS with Imputed Whole-Genome Sequence Data in Pigs.Animals : an open access journal from MDPI · 2023Article
- Potential of low-density genotype imputation for cost-efficient genomic selection for resistance to Flavobacterium columnare in rainbow trout (Oncorhynchus mykiss).Genetics, selection, evolution : GSE · 2023Article
- Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs.Journal of animal science and biotechnology · 2023Article
- Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.Frontiers in genetics · 2023Article
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Abstract
Genomic selection (GS) has great potential to increase genetic gain in aquaculture breeding; however, its implementation is hindered owing to high genotyping cost and the large number of individuals to genotype. This study investigated the efficiency of genomic prediction in four aquaculture species. In total, 749 to 1481 individuals with records for disease resistance and growth traits were genotyped using SNP arrays ranging from 12K to 40K. We compared the prediction accuracies and bias of breeding values obtained from BLUP, genomic BLUP (GBLUP), Bayesian mixture (BayesR), weighted GBLUP (WGBLUP), and genomic feature BLUP (GFBLUP). For GFBLUP, the genomic feature matrix was constructed based on prior information from genome-wide association studies. Fivefold cross-validation was performed with 20 replicates. Moreover, to reduce the cost of GS, we reduced the SNP density based on linkage disequilibrium as well as the reference population size. The results showed that the methods with marker information produced more accurate predictions than the pedigree-based BLUP method. For the genomic model, BayesR performed prediction with a similar or higher accuracy compared to GBLUP. For the four traits, WGBLUP yielded an average of 1.5% higher accuracy than GBLUP. However, the accuracy of genomic prediction decreased by an average of 6.2% for GFBLUP compared to GBLUP. When the density of SNP panels was reduced to 3K, which was sufficient to obtain accuracies similar to those using the whole dataset in the four species, the cost of GS was estimated to be 50% lower than that of genotyping all animals with high-density panels. In addition, when the reference population size was reduced by 10%, evenly from full-sib family, the accuracy of genomic prediction was almost unchanged, and the cost reduction was 8% in the four populations. Our results have important implications for translating the benefits of GS to most aquaculture species.
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