Three statistical approaches for genetic analysis of disease resistance to vibriosis in Atlantic cod (Gadus morhua L.)1

Abstract

The objective of this study was to estimate and compare variance components and sire breeding values for disease resistance to vibriosis in Atlantic cod (Gadus morhua L.) using 3 statistical approaches. A total of 3,576 individually tagged juvenile cod from 50 full-sib families were infected with Vibrio anguillarum, which causes vibriosis, a frequently reported disease in cod aquaculture. The experimental fish were progeny of captured wild cod from populations of southern coastal cod (POP1), and northern coastal cod and northeast Arctic cod (combined as POP2 in the genetic analyses). Fish were randomly assigned to 1 of 3 test tanks, and daily mortality was recorded until the termination of the experiment at d 31 postinfection. Variance components were estimated separately for the 2 populations using a Cox regression model, univariate linear model, and a linear model that accounted for censoring. With all approaches, the additive genetic sire variance estimated from POP1 was greater than for POP2. Heritability estimates across populations varied from 0.08 to 0.17 depending on the method used. The Cox regression model and univariate linear model resulted in greater heritability estimates for POP1 (0.10 and 0.16) than for POP2 (0.08 and 0.13), whereas the contrary was true with a linear model that accounted for censoring (0.17 vs. 0.14). The predicted breeding values for the sires from the 3 approaches were highly correlated (0.97 to 0.99). This is likely due to the fact that censoring only occurred at the end of the test; i.e., observations of the most resistant fish were censored. The considerable genetic variation found in this study suggests that vibriosis resistance may be improved through selective breeding. The univariate linear model, even without censoring of the data, was robust for the estimation of breeding values using the present data. Therefore, inclusion of vibriosis resistance in the multivariate linear estimation of breeding values for the traits of economic importance in Atlantic cod seems appropriate.

Genetic analysis of vibriosis and viral nervous necrosis resistance in Atlantic cod (Gadus morhua L.) using a cure model1

“…Additive genetic variation exists for both the diseases, and the estimated underlying heritability for end survival using the SIMPLE model were moderate for vibriosis (0.19 ± 0.03) and extremely high for VNN (0.76 ± 0.08). These estimates are in line with previously reported heritability estimates for survival to vibriosis and VNN challenge (Kettunen et al, 2007;0degârd et al, 2010b;Bangera et al, 2011). Analyzing survival as binary trait using SIMPLE model considered early and late mortalities as belonging to the same class.…”

“…In addition, we wanted to test whether choice of model (SIMPLE, NAÏVE, or CURE) or selection criteria within model (CURE) would give substantial reranking of predicted breeding values among families. Parts of this dataset, including data until YC 2009, has previously been analyzed using conventional statistical models treating disease resistance either as a linear or as a threshold binary trait (Kettunen and Fjalestad, 2006;Kettunen et al, 2007;0degârd et al, 2010b;Bangera et al, 2011). In the current study, the 3 applied models used different trait definitions for genetic analysis and were thus difficult to compare directly.…”

“…Water quality variables, fish density, and test environments were standardized across YC and test tanks. More details about the challenge test protocol and fish populations can be found in Kettunen et al (2007Kettunen et al ( ), 0degârd et al (2010b, and Bangera et al (2011).…”

The nature of fisheries‐ and farming‐induced evolution

“…For instance, many aquaculture breeding programmes now aim to improve the (Fj?lestad et al . 1993; Gjoen & Bentsen 1997; Kettunen et al 2007) which might confer a fitness advantage to wild fishes if they are naturally exposed to the same pathogens. We are unaware of any empirical study on fishes that has examined such a possibility in the wild.…”

Spatiotemporal distribution of coastal and oceanic Atlantic cod Gadus morhua sub-groups after escape from a farm

“…The farmed cod were hatched during spring 2003 and were transferred to sea cages in Grøt-sund, located 80 km from the field site in Balsfjord, during February 2004. The sub-groups were cultured in an identical way in the same sea cage, since they were a part of a breeding programme aimed at selection of cod strains with optimal properties for farming (Delghandi et al 2003, Kettunen et al 2007). The fish were tagged with passive integrated transponder (PIT) tags before they were transferred to common ongrowing tanks and later sea cages to allow individual identification.…”