AquaTrace: assessing the genetic impact of aquaculture on native populations

The aims of the project The overarching aim of AquaTrace is to contribute to a prosperous and sustainable future for European aquaculture. This ambitious goal has been pursued through state-of-the art genetic and genomic approaches, leading to new valuable knowledge of the target species Atlantic salmon, European sea bass, turbot, sea bream and brown trout. This will eventually lead to the development of novel analytical tools with benefits for aquaculture breeding and management. Related to this, we attempt to assess and contain potential risks associated with aquaculture, as escapes or releases of domesticated aquaculture fish can have adverse effects on native fish gene pools. Thus, the development of tools for identifying wild and farmed fish, interbreeding between them and effects on key fitness traits (survival and reproduction) is essential. AquaTrace is developing innovative molecular genetic tools, which will vastly improve the ability for tracing marine farmed fish in the wild (European sea bass, gilthead sea bream and turbot) and for documentation of their potential effects on wild conspecifics with Atlantic salmon and brown trout as model species. Importantly, if properly integrated, these tools and insights can also be used by the industry in order to reach their breeding goals faster and more efficiently, thus assisting productivity and welfare across the sector.

Previous information on target species Much progress has been made since the start of the project in November 2012. When starting a large project like AquaTrace, it is important to make use of information from previous projects on the species. This includes published information from previous international research projects, but also information from national projects, which are rarely available to a wider community. So, we have collated biological information such as life-history traits, genetic and genomic characteristics for our target species and published them as specific species leaflets for turbot, European sea bass and sea bream released at our website (https://aquatrace.eu/species_leaflets).

Survey on breeding practices Related to this we have concluded a large survey on breeding practices in European aquaculture. The rationale was to investigate how intensively selective breeding and genetic methods are actually applied in the industry. The survey was based on the answers from 29 major fish breeding companies and has provided an excellent overview of the status of fish breeding in Europe. Among many other insights the survey has revealed that the implementation of selective breeding programs is an ongoing process for all target species in Europe and many new programs have been initiated over the last 3 years. In most cases precautions are taken by the breeding companies to monitor the increase of inbreeding at each new generation. Across Europe, the number of programs using molecular tools has more than doubled since the previous survey three years ago. Growth is the most popular selected trait, followed by morphology and disease resistance. Feed efficiency is now present in seven programs encompassing all target species. We expect that our full data will be ready for publication soon.

Sampling of target species One of the most daunting tasks in relation to taking on a project like this is the collection of tissue samples for DNA analysis of wild and aquaculture specimens of the three marine species. Therefore, we’re very happy to say that – due to the committed collective action of the consortium – we completed the sampling of new and archived samples during the first 1½ years of the project. We have, to a very large extent, been able to achieve the geographical and production coverage initially planned. For sea bream we have more than 3200 samples covering the wild distribution of the species as well as a very significant part of the major producers in aquaculture. For European sea bass and turbot we have similar coverage with around 2000 and 1800 samples respectively. These highly prized samples will assure both an optimal geographical coverage and unique information on potential temporal genetic changes in both wild and aquaculture populations.

Development of genetic markers We have also made significant scientific progress in relation to the development of genetic markers, Single Nucleotide Polymorphisms (SNPs) for the targeted marine species. Reference genomic sequences have been generated for all three species in order to be able to genetically map the variation subsequently identified in individuals. As the project also entails genetic analysis of archived samples of turbot, sea bass and sea bream, and the DNA from such samples is partly degraded, we could not use the standard methods for identification of SNPs (“RAD” sequencing, Restriction site associated DNA). Accordingly, to make full use of the samples available, we have shifted from a two-step to a one-step marker development and genotyping strategy. We are now using ddRAD (double digest RAD) sequencing and simultaneous genotyping of all samples. This method is faster, more robust to DNA quality and allow more specimens to be genotyped than originally foreseen. This means that we are very close to completion of the DNA sequencing of all individuals and can move on to the the process of translating the raw DNA data into biologically meaningful insights. This will eventually not only lead to an understanding of population structure and the level of domestication in the targeted species, but also release a wealth of DNA markers and tools, which can readily be implemented by the industry and lead to faster attainment of breeding goals.

Model species As explained initially the project also comprises an investigation with Atlantic salmon and brown trout as model species in order to elucidate the effects of interbreeding between wild and farmed fish. Fish of wild and farmed origin were crossed, and juveniles from different families subjected to a variety of treatments and important life-history traits were measured. This was done in order to investigate differences in key traits, such as growth and reproduction. The experiments were all conducted under controlled conditions at Matre Research Station in Norway, which holds excellent facilities for keeping fish at various environmental settings. However, we experienced truly anxious moments when the Danish trout eggs were transported to Norway by car and ferry in the middle of a snowstorm in early spring. Fortunately, everything went well. For both species the first round of experiments has been successfully terminated. Tissue samples have been taken and are now being genotyped in order to identify the parental origin and investigate the genetic background of the observed trait differences.

Differences among salmon families For the model species, most of the data analysis is in progress, but we would like to reveal a few of our initial insights generated by one of our dedicated PhD students, Alison Harvey from University of Bangor, Wales, and her collaborators. The main aim of Alison’s work is to elucidate and quantify the genetic differences between wild, hybrid and farmed Atlantic salmon in key life-history traits. In her experiments she examined the differences in growth at low (7°C), medium (12°C) and high (16°C) temperatures for two farmed, five wild and two first generation (F1) hybrid strains/populations. Her data shows that, farmed fish (on average) outgrew the wild fish in all treatments, with hybrids displaying intermediate growth, although there were subtle differences in growth between all the strains/populations. Variation increased at the extreme temperatures. This data strongly indicates that growth differences at varied temperatures are strain/population specific. We think that these new findings have already contributed to a broader understanding of the effects of introgression between farmed and wild conspecifics, which will be very valuable for the final risk-assessment of the impact of European aquaculture on wild fish populations; a key deliverable of AquaTrace.

The future of AquaTrace We have already come a long way with the project over the first two years. We’re very happy to say that most of the nerve-wracking tasks in relation to collection of sufficient samples, experiments with live fish and the DNA genotyping have been completed. So, overall, most of the primary data has already been generated. Over the next two years we will engage in analyzing the primary data in order to develop and refine high powered tools for tracing fish of different origin and the interbreeding between wild and farmed fish for our target species. We will continue our analysis with our model species, Atlantic salmon and brown trout, in order to elucidate the fitness differences between wild and farmed fish and their hybrids. Furthermore we will attempt to identify where in their genomes these differences are situated. Eventually, this will all end up in a risk assessment and a series of recommendations for a future sustainable and prosperous European aquaculture industry.