Performing Department
(N/A)
Non Technical Summary
Infectious hematopoietic necrosis virus (IHNV) is a widespread problem for the rainbow trout (Oncorhynchus mykiss) aquaculture industry, resulting in large scale production losses and economic hardship. Selective breeding of fish for resistance to IHNV offers a powerful option for management of this devastating pathogen and mitigation of its impacts. In particular, selective breeding for fish that are resistant to infection and transmission is likely to be the most effective strategy, because it has the potential to facilitate virus eradication from production facilities. In this project, we plan to quantify variation in IHNV transmission resistance across rainbow trout genetic lineages (families) and estimate the heritability of the trait. We will the determine if transmission resistance is linked to other farm performance traits such as resistance to clinical disease, growth, yield, and fillet quality. This will lay the foundation for future campaigns to selective breed rainbow trout for IHNV transmission resistance. The project will involve a partnership between a leading expert in IHNV biology, Andrew Wargo, PhD at the Virginia Institute of Marine Science, and the Chief Science Officer, Jesse Trushenski, PhD at a large rainbow trout aquaculture company, Riverence Holdings. Results will be disseminated across the salmonid aquaculture and disease management communities through presentations at professional associations, industry forums, and scientific meetings; as well as through publications in trade and scientific journals for dissemination to the larger community. Collectively, this project will not only bolster IHNV management in salmonid aquaculture, but provide a framework for selective breeding of transmission resistance that could be applied to a variety of aquaculture systems.
Animal Health Component
100%
Research Effort Categories
Basic
50%
Applied
30%
Developmental
20%
Goals / Objectives
The goal of the proposed work is to identify a new collection of broad-based traits that can be used in conjunction to breed healthier, more robust livestock and enhance the long-range genetic potential of intensively cultured salmonids. Our long-term goal is to develop a selection regimen that produces stocks with high resilience and vigor that are genetically equipped to thrive. In particular, we will focus on elucidating if IHNV transmission resistance (e.g., reduced viral shedding) is linked with clinical disease (e.g. morbidity and mortality) resistance as well as other performance traits. We focus primarily on IHNV resistance because it remains one of the most problematic infectious disease issues in salmonid aquaculture and we believe large gains can be made by rethinking IHNV management and refocusing genetic improvement strategies on IHNV transmission resistance and multi-trait selection [53]. We will achieve this through a partnership between Riverence Holdings LLC and the Virginia Institute of Marine Science (VIMS), leading institutions in aquaculture, aquatic health, virology, and selective breeding.
Project Methods
Obj. 1: Quantify disease resistance of trout families against infectious hematopoietic necrosis virusApproximately 80-100 trout families will be produced by single dam/sire pairings in each year of the project in the course of Riverence's ongoing selective breeding program. Families will be hatched and reared in segregation until they reach 2 months of age, in a biosecure facility. Juvenile fish will then undergo a standard IHNV virulence challenge using established protocols at Riverence. This will involve exposing duplicate tanks of 50 fish per family to a controlled dosage of IHNV (locally isolated strain; 2 x 105 pfu/ml) through static immersion in water for 1 hour. Fish will be reared according to routine practices and mortality will be tracked for 21 days. Survival analysis will be conducted to elucidate differences in IHNV disease resistance between families. These studies will be repeated in year 1 and 2 of the project, to allow for investigation of a larger number of trout families and increase replication. Combining this with data from previous generations of broodstock at Riverence, including molecular pedigrees and relatedness, will enable us to estimate heritability for IHNV disease resistance.Obj. 2: Quantify IHNV transmission resistance capacity of trout familiesTo get an initial assessment of viral shedding at a family level, we will sample water from all tanks in the family-based IHNV challenge studies (Obj. 1) at two time points (2-4 days post-challenge) to capture the peak in viral shedding. We will then process samples for IHNV using quantitative PCR to get a preliminary assessment of which families differ in shedding. A subset of 50 trout families (~20 from a IHNV resistance-selected line, ~20 from an unselected line, and ~10 resistance-selected × unselected crosses to generate families of half-siblings to the other families) undergoing virulence challenges in Obj. 1 will then be randomly selected for further IHNV transmission resistance quantification, using established protocols. Groups of 20 fish per family will be exposed to a controlled dosage of IHNV (same locally isolated strain used by Riverence; 2 x 105 pfu/ml) in a 1-hr static immersion challenge. Each fish will then be separated into individual 0.8L tanks on a tower rack system (Aquaneering) to track viral shedding at individual fish level using quantitative RT-PCR. The fish will be held in static flow for three days with aeration (previous experience indicates water quality is sufficiently maintained when applying this protocol), at which time a water sample will be taken from each tank and processed via quantitative RT-qPCR for IHNV quantification. As for Obj. 1, heritability of transmission resistance will be estimated by comparing variation among families with estimates of relatedness generated as part of Riverence's ongoing selective breeding practices. Further, heritability estimates will be determined on an individual basis by comparisons between full- and half-siblings and unrelated individuals (i.e., if transmission resistance is heritable, shedding rates will be most similar between full-siblings, least similar between unrelated individuals, and intermediate between half-siblings).Obj. 3: Correlate IHNV transmission and disease resistance traits with other performance traits of trout families and on-farm performance in a commercial settingIn addition to its ongoing IHNV viral challenge testing, Riverence has developed a series of indicators of biological fitness related to growth performance and efficiency, health, stress tolerance. Families are assessed relative to these traits in the context of 'sentinel' experiments conducted annually. These are essentially common garden experiments in which representative numbers of individuals from each family group are commingled and reared together according to standard commercial practices. The performance data gathered from the sentinel experiments will be evaluated in conjunction with the IHNV resistance and shedding data described in the preceding objectives to determine whether correlations exist among these traits. Groups of eggs are collected from each of the 50-100 family pairings used in Objs. 1-2 and incubated such that all groups hatch at the same time (eggs that are spawned earlier are reared in colder water to extend the incubation time as needed). After hatch, all groups are commingled and reared as a production lot according to standard commercial practices. Once the fish reach market size, representative individuals are assessed regarding the performance metrics/traits of interest and genotyped to reassign individuals back to family groups. In this manner, families can be evaluated in terms of unbiased, 'real-world' performance and these data can be compared with the aforementioned IHNV resistance and shedding data generated for the same family groups.Obj. 4: Develop combined, multi-trait, performance metric for trout selective breeding to improve fish health outcomesWe will combine data from various performance-based metrics (disease resistance - Obj. 1, transmission resistance - Obj. 2, sentinel field performance - Obj. 3) to develop a selective breeding strategy for higher performance families across multiple traits. The first step of this process will involve determining the positive or negative associations between traits. We will construct appropriate linear models to elucidate overall correlations between various traits across families. Heritability estimates will be calculated for the various metrics based on each family's performance and estimates of relatedness among the families. The possible coheritability of breeding targets, including IHNV disease resistance and transmission resistance, will be examined further by assessing whether these traits co-occur in individuals identified as over-performing ('winners') and under-performers ('losers') in the sentinel experiments. Briefly, as the average size of the sentinel population reaches the desired market weight (e.g., ~500 g or 1.25 lbs), all fish will be graded to determine the approximate size distribution of the population. Those individuals in the top 5-10% will be considered winners, those in the bottom 5-10% will be considered losers. Winners and losers will be evaluated according to Riverence's comprehensive phenotypic assessment, including various morphometric and physiological measurements. Additionally, winners and losers will be subjected to genetic pedigree analysis to determine their family of origin, allowing end-of-trial sentinel metrics (i.e., the aforementioned sentinel phenotypic assessment) to be associated with pre-trial metrics (i.e., results of the IHNV challenges and other biological fitness assessments conducted as part of the Riverence breeding program) and the creation of comprehensive profiles describing the combinations of phenotypes exhibited by over- and underperforming individuals. Although the number of individuals sampled is generally large (1000-2000 individuals are assessed at the end of each sentinel experiment), it is unlikely that all families will be represented among the winners and losers. Nonetheless, the results of this analysis will allow for real-world ground-truthing of coheritability among traits identified by the simple correlation analysis. The benefit to our approach is that it allows us to identify individual families which perform well in multiple traits as targets for future selection. This will allow us to develop an overall scoring system for each family across multiple-traits. We intend to apply this methodology after year 1 of the project to inform breeding for year 2. This will allow us to provide initial estimates of heritability of various traits, in particular, transmission resistance, which has not been previously investigated in this system.