| Literature DB >> 31249593 |
Christos Palaiokostas1,2, Tomas Vesely3, Martin Kocour4, Martin Prchal4, Dagmar Pokorova3, Veronika Piackova4, Lubomir Pojezdal3, Ross D Houston1.
Abstract
Genomic selection (GS) is increasingly applied in breeding programs of major aquaculture species, enabling improved prediction accuracy and genetic gain compared to pedigree-based approaches. Koi Herpesvirus disease (KHVD) is notifiable by the World Organization for Animal Health and the European Union, causing major economic losses to carp production. GS has potential to breed carp with improved resistance to KHVD, thereby contributing to disease control. In the current study, Restriction-site Associated DNA sequencing (RAD-seq) was applied on a population of 1,425 common carp juveniles which had been challenged with Koi herpes virus, followed by sampling of survivors and mortalities. GS was tested on a wide range of scenarios by varying both SNP densities and the genetic relationships between training and validation sets. The accuracy of correctly identifying KHVD resistant animals using GS was between 8 and 18% higher than pedigree best linear unbiased predictor (pBLUP) depending on the tested scenario. Furthermore, minor decreases in prediction accuracy were observed with decreased SNP density. However, the genetic relationship between the training and validation sets was a key factor in the efficacy of genomic prediction of KHVD resistance in carp, with substantially lower prediction accuracy when the relationships between the training and validation sets did not contain close relatives.Entities:
Keywords: KHVD; RAD-seq; aquaculture breeding; carp; genomic selection
Year: 2019 PMID: 31249593 PMCID: PMC6582704 DOI: 10.3389/fgene.2019.00543
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
FIGURE 1Mean weight and survival for all assigned full-sib families.
Mean survival accuracy for D11 (5-fold cross validation; 5 replicates).
| Reps | pBLUP | rrBLUP | BayesA | BayesB | BayesC |
|---|---|---|---|---|---|
| 1st | 0.47 | 0.51 | 0.52 | 0.52 | 0.52 |
| 2nd | 0.49 | 0.54 | 0.55 | 0.55 | 0.54 |
| 3rd | 0.48 | 0.52 | 0.53 | 0.54 | 0.53 |
| 4th | 0.50 | 0.54 | 0.54 | 0.55 | 0.55 |
| 5th | 0.49 | 0.52 | 0.53 | 0.54 | 0.52 |
| Mean | 0.49 | 0.53 | 0.53 | 0.54 | 0.53 |
FIGURE 2Relative accuracy of genomic prediction models compared to pedigree BLUP for varying SNP densities. (A) SNP filtering based on minor allele frequency and (B) SNP filtering based on linkage disequilibrium.
Prediction metrics for varying genetic relationships in the validation set.
| Scenario | pBLUP | rrBLUP | BayesA | BayesB | BayesC | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Acc1 | AUC2 | Acc1 | AUC2 | Acc1 | AUC2 | Acc1 | AUC2 | Acc1 | AUC2 | |
| S1 | 0.52 | 0.72 | 0.56 | 0.74 | 0.57 | 0.74 | 0.57 | 0.74 | 0.56 | 0.74 |
| S2 | 0.45 | 0.69 | 0.53 | 0.72 | 0.52 | 0.72 | 0.52 | 0.72 | 0.52 | 0.72 |
| S3 | N/A | N/A | 0.17 | 0.57 | 0.16 | 0.57 | 0.18 | 0.58 | 0.20 | 0.57 |
| S4 | 0.49 | 0.71 | 0.52 | 0.72 | 0.53 | 0.74 | 0.54 | 0.74 | 0.52 | 0.72 |
FIGURE 3The ROC curve and corresponding AUC metrics for BayesB-based predictions of KHV survival. The plot was obtained from aggregation of a 5-fold cross validation scheme when full sibs existed in the training set for every animal of the validation set.