Abstract
BackgroundColumnaris 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.MethodsTwo 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 and using a linear regression method.ResultsValidation 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.ConclusionsOur 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 sufficiently informative for selection decisions across populations.
Highlights
Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US
The average number of Single nucleotide polymorphism (SNP) per window (± SD) was 27.9 (± 6.2) and 22.2 (± 8.9) for the NCCCWA and TLUM populations, respectively, which means that the genome coverage was better for the NCCCWA population
Columnaris disease in rainbow trout has a complex polygenic inheritance architecture, since it is controlled by several genomic regions that explain a considerable amount of the genetic variance (> 1%)
Summary
Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. Rainbow trout (Oncorhynchus mykiss) is an economically important aquaculture commodity. Columnaris disease (CD) is an emerging problem for rainbow trout aquaculture in the US, which is caused by the gram-negative bacterium Flavobacterium columnare. CD is distributed around the world and infects cultured and wild freshwater fish species, such as rainbow trout, tilapia and channel catfish. It can infect fish of all ages, but it is more frequent in young fish, and it can cause major losses [2, 3]. Transmission occurs often horizontally and indirectly through the water column without fish-to-fish contact, and generally the severity and occurrence are greater at warmer water temperatures [2]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
