ArticleGenetics, selection, evolution : GSE2020
Prediction of genomic breeding values based on pre-selected SNPs using ssGBLUP, WssGBLUP and BayesB for Edwardsiellosis resistance in Japanese flounder.
Article in Genetics, selection, evolution : GSE, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 49 citations in OpenAlex.
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- A genomic estimated breeding value-assisted reduction method of single nucleotide polymorphism sets: a novel approach for determining the cutoff thresholds in genome-wide association studies and best linear unbiased prediction.Animal cells and systems · 2023Article
- The prediction accuracies of linear-type traits in Czech Holstein cattle when using ssGBLUP or wssGBLUP.Journal of animal science · 2022Article
- Weighted Single-Step Genomic Best Linear Unbiased Prediction Method Application for Assessing Pigs on Meat Productivity and Reproduction Traits.Animals : an open access journal from MDPI · 2022Article
- Increased accuracy of genomic predictions for growth under chronic thermal stress in rainbow trout by prioritizing variants from GWAS using imputed sequence data.Evolutionary applications · 2022Article
- Strategies to improve the accuracy and reduce costs of genomic prediction in aquaculture species.Evolutionary applications · 2022Article
- Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus).G3 (Bethesda, Md.) · 2022Article
- Article
- Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia (Frontiers in genetics · 2021Article
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Authors and funding
11 authors at 2 institutions in 3 countries.
Funding
Abstract
backgroundEdwardsiella tarda causes acute symptoms with ascites in Japanese flounder (Paralichthys olivaceus) and is a major problem for China's aquaculture sector. Genomic selection (GS) has been widely adopted in breeding industries because it shortens generation intervals and results in the selection of individuals that have great breeding potential with high accuracy. Based on an artificial challenge test and re-sequenced data of 1099 flounders, the aims of this study were to estimate the genetic parameters of resistance to E. tarda in Japanese flounder and to evaluate the accuracy of single-step GBLUP (ssGBLUP), weighted ssGBLUP (WssGBLUP), and BayesB for improving resistance to E. tarda by using three subsets of pre-selected single nucleotide polymorphisms (SNPs). In addition, SNPs that are associated with this trait were identified using a single-SNP genome-wide association study (GWAS) and WssGBLUP.
resultsWe estimated a heritability of 0.13 ± 0.02 for resistance to E. tarda in Japanese flounder. One million SNPs at fixed intervals were selected from 4,978,724 SNPs that passed quality controls. GWAS identified significant SNPs on chromosomes 14 and 24. WssGBLUP revealed that the putative quantitative trait loci on chromosomes 1 and 14 contained SNPs that explained more than 1% of the genetic variance. Three 50 k-SNP subsets were pre-selected based on different criteria. Compared with pedigree-based prediction (ABLUP), the three genomic methods evaluated resulted in at least 7.7% greater accuracy of predictions. The accuracy of these genomic prediction methods was almost unchanged when pre-selected trait-related SNPs were used for prediction.
conclusionsResistance to E. tarda in Japanese flounder has a low heritability. GWAS and WssGBLUP revealed that the genetic architecture of this trait is polygenic. Genomic prediction of breeding values performed better than ABLUP. It is feasible to implement genomic selection to increase resistance to E. tarda in Japanese flounder with 50 k SNPs. Based on the criteria used here, pre-selection of SNPs was not beneficial and other criteria for pre-selection should be considered.
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