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Title: Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations

Abstract

Background: Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of the additive genetic variance for resistance to CD in two rainbow trout (Oncorhynchus mykiss) populations; and (2) estimate the gains in prediction accuracy when genomic information is used to evaluate the genetic potential of survival to columnaris infection in each population. Methods: Two aquaculture populations were investigated: the National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population. Fish that survived to 21 days post-immersion challenge were recorded as resistant. Single nucleotide polymorphism (SNP) genotypes were available for 1185 and 1137 fsh from NCCCWA and TLUM, respectively. SNP efects and variances were estimated using the weighted single-step genomic best linear unbiased prediction (BLUP) for genome-wide association. Genomic regions that explained more than 1% of the additive genetic variance were considered to be associated with resistance to CD. Predictive ability was calculated in a fvefold cross-validation scheme and using a linear regression method. Results: Validation on adjusted phenotypes provided a prediction accuracy close to zero,more » due to the binary nature of the trait. Using breeding values computed from the complete data as benchmark improved prediction accuracy of genomic models by about 40% compared to the pedigree-based BLUP. Fourteen windows located on six chromosomes were associated with resistance to CD in the NCCCWA population, of which two windows on chromosome Omy 17 jointly explained more than 10% of the additive genetic variance. Twenty-six windows located on 13 chromosomes were associated with resistance to CD in the TLUM population. Only four associated genomic regions overlapped with quantitative trait loci (QTL) between both populations. Conclusions: Our results suggest that genome-wide selection for resistance to CD in rainbow trout has greater potential than selection for a few target genomic regions that were found to be associated to resistance to CD due to the polygenic architecture of this trait, and because the QTL associated with resistance to CD are not sufciently informative for selection decisions across populations.« less

Authors:
; ; ; ; ; ; ORCiD logo;
Publication Date:
Research Org.:
Oak Ridge Associated Univ., Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1618934
Alternate Identifier(s):
OSTI ID: 1626755
Grant/Contract Number:  
AC05-06OR23100; USDA CRIS [8082-32000-006, 8082-31000-012]
Resource Type:
Published Article
Journal Name:
Genetics Selection Evolution (Online)
Additional Journal Information:
Journal Name: Genetics Selection Evolution (Online) Journal Volume: 51 Journal Issue: 1; Journal ID: ISSN 1297-9686
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Agriculture; Genetics & Heredity

Citation Formats

Silva, Rafael M. O., Evenhuis, Jason P., Vallejo, Roger L., Gao, Guangtu, Martin, Kyle E., Leeds, Tim D., Palti, Yniv, and Lourenco, Daniela A. L. Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations. United Kingdom: N. p., 2019. Web. https://doi.org/10.1186/s12711-019-0484-4.
Silva, Rafael M. O., Evenhuis, Jason P., Vallejo, Roger L., Gao, Guangtu, Martin, Kyle E., Leeds, Tim D., Palti, Yniv, & Lourenco, Daniela A. L. Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations. United Kingdom. https://doi.org/10.1186/s12711-019-0484-4
Silva, Rafael M. O., Evenhuis, Jason P., Vallejo, Roger L., Gao, Guangtu, Martin, Kyle E., Leeds, Tim D., Palti, Yniv, and Lourenco, Daniela A. L. Tue . "Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations". United Kingdom. https://doi.org/10.1186/s12711-019-0484-4.
@article{osti_1618934,
title = {Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations},
author = {Silva, Rafael M. O. and Evenhuis, Jason P. and Vallejo, Roger L. and Gao, Guangtu and Martin, Kyle E. and Leeds, Tim D. and Palti, Yniv and Lourenco, Daniela A. L.},
abstractNote = {Background: Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of the additive genetic variance for resistance to CD in two rainbow trout (Oncorhynchus mykiss) populations; and (2) estimate the gains in prediction accuracy when genomic information is used to evaluate the genetic potential of survival to columnaris infection in each population. Methods: Two aquaculture populations were investigated: the National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population. Fish that survived to 21 days post-immersion challenge were recorded as resistant. Single nucleotide polymorphism (SNP) genotypes were available for 1185 and 1137 fsh from NCCCWA and TLUM, respectively. SNP efects and variances were estimated using the weighted single-step genomic best linear unbiased prediction (BLUP) for genome-wide association. Genomic regions that explained more than 1% of the additive genetic variance were considered to be associated with resistance to CD. Predictive ability was calculated in a fvefold cross-validation scheme and using a linear regression method. Results: Validation on adjusted phenotypes provided a prediction accuracy close to zero, due to the binary nature of the trait. Using breeding values computed from the complete data as benchmark improved prediction accuracy of genomic models by about 40% compared to the pedigree-based BLUP. Fourteen windows located on six chromosomes were associated with resistance to CD in the NCCCWA population, of which two windows on chromosome Omy 17 jointly explained more than 10% of the additive genetic variance. Twenty-six windows located on 13 chromosomes were associated with resistance to CD in the TLUM population. Only four associated genomic regions overlapped with quantitative trait loci (QTL) between both populations. Conclusions: Our results suggest that genome-wide selection for resistance to CD in rainbow trout has greater potential than selection for a few target genomic regions that were found to be associated to resistance to CD due to the polygenic architecture of this trait, and because the QTL associated with resistance to CD are not sufciently informative for selection decisions across populations.},
doi = {10.1186/s12711-019-0484-4},
journal = {Genetics Selection Evolution (Online)},
number = 1,
volume = 51,
place = {United Kingdom},
year = {2019},
month = {8}
}

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https://doi.org/10.1186/s12711-019-0484-4

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