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

Genetics, Selection, Evolution : GSE
Rafael M O SilvaDaniela A L Lourenco

Abstract

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. 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 fish from NCCCWA and TLUM, respectively. SNP effects 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 fivefold cross-validation scheme...Continue Reading

References

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Citations

Apr 18, 2020·Nature Reviews. Genetics·Ross D HoustonDiego Robledo
Jan 16, 2021·Frontiers in Genetics·Asma M KaramiKurt Buchmann
Jul 21, 2021·Journal of Animal Science·Natália Galoro LeiteDaniela Lourenco
Sep 28, 2021·Genetics, Selection, Evolution : GSE·Pâmela A AlexandreAntonio Reverter

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Methods Mentioned

BETA
chip
genotyping

Software Mentioned

wssGBLUP
Omy
THRGIBBS1F90
ssGBLUP
GBLUP
THRGIBBSF90
POSTGSF90
mathop

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