Assessing Accuracy of Genomic Predictions for Resistance to Infectious Hematopoietic Necrosis Virus With Progeny Testing of Selection Candidates in a Commercial Rainbow Trout Breeding Population

Vallejo, Roger L.; Fragomeni, B. O.; Cheng, Hao; Gao, Guangtu; Long, Roseanna; Shewbridge, Kristy L.; MacMillan, John R.; Towner, Richard; Palti, Yniv

doi:10.3389/fvets.2020.590048

Cited by 19 publications

(15 citation statements)

References 56 publications

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“…This indicates stronger recent bottlenecks and selection rates in rainbow trout lines than in cattle breeds. Similar long-range LD was independently observed in two US commercial rainbow trout populations (Vallejo et al, 2018, 2020). The pattern of LD decay in rainbow trout commercial lines appears to be more similar to the one observed in conservation flocks of chicken from South Africa (Khanyile et al, 2015), with very similar values reported both at shorter distances than 10 kb, as well as at 500 kb distance where LD values range from 0.15 to 0.24 depending on the conservation flocks and values of 0.21 to 0.25 were derived for LC and LB, respectively.…”

Section: Discussionsupporting

confidence: 78%

“…While a number of studies quantify in salmonids the presence of long-range LD from 50 kb to over 1 Mb either for commercial populations (Kijas et al, 2017; Vallejo et al, 2018; Barría et al, 2019; D’Ambrosio et al, 2019) or wild populations (Kijas et al, 2017), little is known on the LD at very short distances. In rainbow trout farmed populations, the level of strong LD ( r 2 > 0.20) spans over 100 kb (D’Ambrosio et al, 2019) to 1 Mb (Vallejo et al, 2018, 2020).…”

Section: Discussionmentioning

confidence: 99%

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Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Bernard

Dehaullon

Gao

et al. 2022

Preprint

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Single nucleotide polymorphism (SNP) arrays, also named "SNP chips", enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2 kb to 10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50 kb to 100 kb which are usual distances between markers of the medium-density chip.

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Section: Discussionsupporting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Bernard

Dehaullon

Gao

et al. 2022

Preprint

Self Cite

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“…This is the scenario applied in that study. However, in real life, the goal is to improve disease resistance in the next generation, and this can only be tested through progeny testing (Vallejo et al, 2020). In our case, this was not possible as we currently have only one generation of genomically evaluated fish.…”

Section: Discussionmentioning

confidence: 99%

Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, the European Sea Bass (Dicentrarchus labrax) and the Gilthead Sea Bream (Sparus aurata)

et al. 2021

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Disease outbreaks are a major threat to the aquaculture industry, and can be controlled by selective breeding. With the development of high-throughput genotyping technologies, genomic selection may become accessible even in minor species. Training population size and marker density are among the main drivers of the prediction accuracy, which both have a high impact on the cost of genomic selection. In this study, we assessed the impact of training population size as well as marker density on the prediction accuracy of disease resistance traits in European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata). We performed a challenge to nervous necrosis virus (NNV) in two sea bass cohorts, a challenge to Vibrio harveyi in one sea bass cohort and a challenge to Photobacterium damselae subsp. piscicida in one sea bream cohort. Challenged individuals were genotyped on 57K–60K SNP chips. Markers were sampled to design virtual SNP chips of 1K, 3K, 6K, and 10K markers. Similarly, challenged individuals were randomly sampled to vary training population size from 50 to 800 individuals. The accuracy of genomic-based (GBLUP model) and pedigree-based estimated breeding values (EBV) (PBLUP model) was computed for each training population size using Monte-Carlo cross-validation. Genomic-based breeding values were also computed using the virtual chips to study the effect of marker density. For resistance to Viral Nervous Necrosis (VNN), as one major QTL was detected, the opportunity of marker-assisted selection was investigated by adding a QTL effect in both genomic and pedigree prediction models. As training population size increased, accuracy increased to reach values in range of 0.51–0.65 for full density chips. The accuracy could still increase with more individuals in the training population as the accuracy plateau was not reached. When using only the 6K density chip, accuracy reached at least 90% of that obtained with the full density chip. Adding the QTL effect increased the accuracy of the PBLUP model to values higher than the GBLUP model without the QTL effect. This work sets a framework for the practical implementation of genomic selection to improve the resistance to major diseases in European sea bass and gilthead sea bream.

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“…It is mainly directed towards the maximization of growth potential, improvement in fillet quality attributes, or development of resistance to stress and pathogens ( Xu et al, 2015 ). In particular, rainbow trout ( Oncorhynchus mykiss ) has frequently been the object of selective breeding, with current programs being predominantly based on mass selection for growth rates ( Cleveland et al, 2020 ) and resistance to viral or bacterial diseases ( Vallejo et al, 2020 ; Zuo et al, 2020 ). Among all the selective breeding programs carried out to improve the growth potential of rainbow trout, one of the most impactful is related to the efficiency of digesting all-plant protein feeds ( Overturf et al, 2013 ; Lazzarotto et al, 2015 ; Callet et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Efficacy of Utilization of All-Plant-Based and Commercial Low-Fishmeal Feeds in Two Divergently Selected Strains of Rainbow Trout (Oncorhynchus mykiss): Focus on Growth Performance, Whole-Body Proximate Composition, and Intestinal Microbiome

et al. 2022

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The present study aimed to investigate the growth performance, whole-body proximate composition, and intestinal microbiome of rainbow trout strains when selected and non-selected for weight gain on all-plant protein diets. A 2x2 factorial design was applied, where a selected (United States) and a non-selected (ITA) rainbow trout strain were fed using either an all-plant protein (PP) or a commercial low-FM diet (C). Diets were fed to five replicates of 20 (PP) or 25 (C) fish for 105 days. At the end of the trial, growth parameters were assessed, and whole fish (15 pools of three fish/diet) and gut samples (six fish/diet) were collected for whole-body proximate composition and gut microbiome analyses, respectively. Independent of the administered diet, the United States strain showed higher survival, final body weight, weight gain, and specific growth rate when compared to the ITA fish (p < 0.001). Furthermore, decreased whole-body ether extract content was identified in the PP-fed United States rainbow trout when compared to the ITA strain fed the same diet (p < 0.001). Gut microbiome analysis revealed the Cetobacterium probiotic-like genus as clearly associated with the United States rainbow trout, along with the up-regulation of the pathway involved in starch and sucrose metabolism. In summary, the overall improvement in growth performance and, to a lesser extent, whole-body proximate composition observed in the selected rainbow trout strain was accompanied by specific, positive modulation of the intestinal microbiome.

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Assessing Accuracy of Genomic Predictions for Resistance to Infectious Hematopoietic Necrosis Virus With Progeny Testing of Selection Candidates in a Commercial Rainbow Trout Breeding Population

Cited by 19 publications

References 56 publications

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, the European Sea Bass (Dicentrarchus labrax) and the Gilthead Sea Bream (Sparus aurata)

Efficacy of Utilization of All-Plant-Based and Commercial Low-Fishmeal Feeds in Two Divergently Selected Strains of Rainbow Trout (Oncorhynchus mykiss): Focus on Growth Performance, Whole-Body Proximate Composition, and Intestinal Microbiome

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