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Utilising functional genomic variation for improved disease resistance in Chilean salmon aquaculture

Goal: Research Council UK- CONICYT, Research Partnership Call. (MR/N026144/1)

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Ross Houston
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Breeding for disease resistance has become a highly desirable strategy for mitigating infectious disease problems in aquaculture. However, knowledge of the genetic relationship between resistance and other economically important traits, such as growth, is important to assess prior to including disease resistance into the breeding goal. Our study assessed the genetic correlations between growth and survival traits in a large bacterial infection challenge experiment. A population of 2,606 coho salmon individuals from 107 full-sibling families were challenged with the bacteria Piscirickettsia salmonis. Growth was measured as average daily gain prior (ADG0) and during (ADGi) the experimental infection and as harvest weight (HW). Resistance was measured as Survival time (ST) and binary survival (BS). Furthermore, individual measures of bacterial load (BL) were assessed as new resistance phenotypes and to provide an indication of genetic variation in tolerance in salmonid species. Resistant families showed lower bacterial load than those susceptible to P. salmonis. Furthermore, some surviving fish belonging to resistant families, were considered as bacterial-free because their bacterial load was below the detection threshold. Adding logBL as a covariate into the models for growth under infection and survival indicated significant genetic variation in tolerance. Significant moderate heritabilities were estimated for ADG0 (0.30 ± 0.05), HW (0.38 ± 0.03), and for the survival traits ST (0.16 ± 0.03) and BS (0.18 ± 0.03). In contrast, heritabilities for ADGi and log-transformed BL were low (0.07 ± 0.02 (significant) and 0.04 ± 0.03, respectively), although these increased to moderate significant levels (0.20 ± 0.09 and 0.12 ± 0.05, respectively) when traits were assessed in survivors only. Significant favorable genetic correlations were found between ADG0 and ADGi (0.40 ± 0.16), HW (0.64 ± 0.09), and with resistance as ST (0.43 ± 0.18), indicating that fish with higher genetic growth rate early on and prior to infection not only tend to maintain their genetic growth advantage until harvest, but also tend to grow faster and survive longer during infection. Although a significant unfavorable correlation (-0.50 ± 0.13) between HW and ST was found, this value decreased to -0.35 ± 0.20 using uncensored data from non-survivors only. Similarly, no robust unfavorable genetic correlations between ADG0 and LogBL, or ADG0 and any of the other traits considered in this study, was identified. These results suggest that selective breeding for early growth, in the current coho salmon population, would be expected to simultaneously increase survival time and growth performance during an infection with Piscirickettsia salmonis, without negatively impacting on pathogen burden.
Ross Houston
added a research item
Genomic selection uses genome-wide marker information to predict breeding values for traits of economic interest, and is more accurate than pedigree-based methods. The development of high density SNP arrays for Atlantic salmon has enabled genomic selection in selective breeding programmes, alongside high-resolution association mapping of the genetic basis of complex traits. However, in sibling testing schemes typical of salmon breeding programmes, trait records are available on many thousands of fish with close relationships to the selection candidates. Therefore, routine high density SNP genotyping may be prohibitively expensive. One means to reducing genotyping cost is the use of genotype imputation, where selected key animals (e.g. breeding programme parents) are genotyped at high density, and the majority of individuals (e.g. performance tested fish and selection candidates) are genotyped at much lower density, followed by imputation to high density. The main objectives of the current study were to assess the feasibility and accuracy of genotype imputation in the context of a salmon breeding programme. The specific aims were: (i) to measure the accuracy of genotype imputation using medium (25 K) and high (78 K) density mapped SNP panels, by masking varying proportions of the genotypes and assessing the correlation between the imputed genotypes and the true genotypes; and (ii) to assess the efficacy of imputed genotype data in genomic prediction of key performance traits (sea lice resistance and body weight). Imputation accuracies of up to 0.90 were observed using the simple two-generation pedigree dataset, and moderately high accuracy (0.83) was possible even with very low density SNP data (~250 SNPs). The performance of genomic prediction using imputed genotype data was comparable to using true genotype data, and both were superior to pedigree-based prediction. These results demonstrate that the genotype imputation approach used in this study can provide a cost-effective method for generating robust genome-wide SNP data for genomic prediction in Atlantic salmon. Genotype imputation approaches are likely to form a critical component of cost-efficient genomic selection programmes to improve economically important traits in aquaculture.
José M. Yáñez
added a project goal
Research Council UK- CONICYT, Research Partnership Call. (MR/N026144/1)