Effective lice control through breeding and genetics

Nr. 1 / August 2016

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The battle against salmon lice can only be won by using a combination of preventative and treatment methods.  Breeding and genetics is one of the few methods that increase the resistance of fish to lice throughout the whole production cycle. Reduced risk of lice infection, robust fish that tolerate handling and a short production time in the sea are important contributors, the potential of which can be opened up with the use of new breeding technology.

AquaGen has developed the world’s most powerful search-tools that give the ability to identify brood fish with the genes that make them suitable to meet the biological challenges the salmon industry faces.  This so-called SNP-chip can analyse up to 930,000 genetic markers per fish that directly correlate with desirable and undesirable attributes.  The size and quality of SNP-chips is crucial to what can be achieved by using QTL’s and genomic selection is now at full-speed in the most professional breeding programmes related to agriculture and aquaculture.

Three strategies for reducing the lice problem

AquaGen has focussed on three key traits, that are important contributors individually, but which in combination will result in a very considerable impact in the battle against salmon lice:

  • Genetic resistance against lice will reduce lice infection by 30-40 percent
  • Genetic resistance against CMS and AGD will contribute to high tolerance to handling
  • Increased growth potential will reduce production time in the sea by 1-2 months

Figure 1. Challenge trial with lice in tanks where fish with one copy of the lice-susceptibility-QTL have more lice than the average for all fish in the population.

QTL for lice susceptibility

QTL for lice susceptibility
Based on the genetic testing of more than 4000 lice challenged fish in controlled trials, a genetic marker has been found for lice susceptibility.

This marker is over-represented in fish with high lice numbers, those we could call “lice-magnets” (Figure 1). If we remove these lice susceptible fish from breeding and egg production, the result will be a reduction in the proportion of very susceptible fish in the cages. Removing these fish that act as a “gateway” for lice infection in the population, increases population resistance, which in turn gives a reduced infection pressure on the overall population and susceptible wild fish in the area.

Figure 2. Results from the field validation of QTL for lice susceptibility. Amount of lice for fish that had the adverse marker (QQ) is set to 100 percent. When the 11 locations were evaluated together, we found that fish with one copy of the adverse marker had 11 percent more lice, while fish that had two copies (qq) of the adverse marker had 28 percent more lice.

Understanding the significance of the QTL for lice susceptibility, in typical farming conditions

Based on field material comprising 625 fish from 11 different locations in central and western Norway, it was documented that fish with the unfavourable gene marker did in fact have a higher lice number under field conditions. Fish with one copy of the unfavourable marker had 11 percent more lice than fish without the marker, but fish with two copies of the marker had 28 percent more lice than those without it (Figure 2).

The impact of lice susceptible fish varies greatly and can be up to 40 percent in some populations. These populations will be pre-disposed to serious lice problems, and it will be extremely important to control the frequency of the unfavourable marker. An example that we can use is a location where fish with the marker had 1.9 lice on average, whereas for fish without the marker the average was just 1.0 lice. In this instance the proportion with the marker was 33 percent of the fish.

Figure 3. Average number of lice per fish after one day with a lice challenge (acute infection) for fish groups selected for respectively high and low genomic resistance against lice in two separate trials.

Genomic selection for lice resistance

Genomic selection is a method that utilises advanced technology and statistics to increase the reliability and accuracy of selection of animals used in breeding work. By studying almost all of the genetic information of an individual salmon, it is possible with a high degree of security, to pick out the top-candidates for further use. Based on data from challenge trials it has been documented that genomic selection is much more effective than classic selection for lice-resistance. Since 2013 AquaGen has been using genomic selection to increase lice resistance in breeding work.

After only one generation using genomic selection, by using a challenge test it was possible to demonstrate a 20-25 percent difference in lice numbers between fish selected for high or low resistance. The more rounds we go through using genomic selection for a single trait, the stronger will be the effect. Two generations of genomic selection provide a higher resistance against lice than one generation of genomic selection.

AquaGen has, in collaboration with the Sea Lice Research Centre (The University of Bergen) and the University of Life sciences recently conducted research using fish groups with two generations of genomic selection for lice resistance. Two separate lice challenge trials were carried out. In these trials it was recorded that there were 50 percent less lice the first day following lice challenge for fish groups selected for high resistance (Figure 3). 18 days post challenge, the groups that were selected for high resistance had over 30 percent less lice compared with lower resistant fish.

From autumn 2016 AquaGen will for the first time deliver eggs with 2nd generation genomic selection for resistance to salmon lice. Meanwhile, genomic selection for AGD-resistance (1st generation) and growth (2nd generation) will also be available.

High handling tolerance

The capacities related to heart, blood circulation and respiration are essential for how each animal copes with physical challenges.  For salmon a strong heart combined with effective respiration via it’s gills provides an improved ability to withstand handling events such as sorting, transport and treatment.  For fish as in other species of animals, some diseases are often the cause of reduced organ function and detrimental health effects, and therefore improved resistance against the diseases CMS and AGD are important traits.

Resistance against CMS and AGD

Breeding for resistance is a well documented preventative method against CMS. Fish with the CMS-QTL rid themselves of the virus and reduce heart damage more effectively than fish without the genetic marker. In field outbreaks it has been recorded around 20 percent less mortality for fish that had the CMS-QTL.

AGD resistance has been shown to be a trait with a high breeding value. A challenge trial carried out with AGD showed large differences for both mortality and gill-score between families. For survival we found a breeding value of 55-58 percent, and for gill score a breeding value of 25-28 percent. In Tasmania, by using traditional breeding, a reduction was achieved in the number of bath treatments for AGD from five to two per year-class in the period from 2005 to 2013. The potential for improvement is therefore even greater by using genomic selection.



Growth has throughout 45 years of selection been one of the most important traits in the breeding programme. Growth is a relatively simple trait to breed for, and progress in the region of 300-500gm per generation for sea-weight has been recorded. Experience from other species also shows a significant improvement in growth when traditional breeding is supplemented with genomic selection.

Since 2013 AquaGen has carried out comparative growth studies between fish groups bred with and without genomic selection. Fish bred with genomic selection had approximately 20 percent higher weight than comparable fish bred without genomic selection, at the same point in time. This extra growth potential opens up the possibility for a 1-2 months shorter production time from sea transfer to harvest, depending on the time of the year the smolt transfer takes place. Reduced time to harvest contributes to a reduced risk of diseases and parasites, and fallowing of sites and management areas can start earlier.

Facts about genetics/genomics


Heritable material (genome) of an individual. It consists of different bases, and the order of these will create different genes. Genes dictate which traits will be expressed.

Genetic variation:

Variation among individuals in a population due to differences in genetic composition.

QTL and QTL selection:

A QTL is an area of the genome that is involved in controlling a particular trait. Using genetic markers, it is possible to keep track of the inheritance of this QTL and thus the trait that it controls.

Genomic selection:

Fish are selected based on their genome-based index that is calculated from the information contained in the fish’s DNA.

Genetic marker (SNP):

Single base changes in a DNA region where there is variation between individuals in the population. Markers can be used to find the degree of similarity / dissimilarity between individuals.

Breeding value:

Measure of the proportion of the total variation in a trait in a population due to genetics.


A tool to analyse many genetic markers simultaneously. The information is used in genomic selection for specific characteristics of individuals.