Gene genies

Science is helping breeders to perfect their stock, but how far should they be allowed to go?

Improving the genetic stock of terrestrial farm animals is something that humans have been doing for thousands of years. For fish, that process has only taken place over just a few decades, but already it has had an impact. Farmed fish grow much faster and they have a recognisable genetic signature that marks them out from their wild cousins.

The technology has progressed rapidly. Our understanding of genetics now informs the process of breeding, and the state of the art has progressed a long way. Genetics specialists in aquaculture can operate as breeders – supplying eggs or young fish to producers – or consultants providing expert services, or both. Xelect, based in St Andrews, Scotland started out as a spinout from the academic world and now provides a range of specialist services.

Xelect uses amplicon sequencing, a technique for genotyping that allows the analysis of genetic variation in specific genomic regions. using the company’s proprietorial software.

The team’s expertise includes salmon (Atlantic and chinook), sea bass, barramundi, Tiger prawns, oysters, turbot, tilapia and a range of other species. Their customers are all around the world, and can opt for one of three levels of service: a virtual in-house genetics department (“Elite”); genotyping and genetic services on demand (“Direct”); and quick access to to essential services like triploidy testing (to check that eggs have been correctly processed to create sterile individuals), sex determination and stock control (“Express”).

For a producer looking for help with a

breeding plan, Xelect will use provided �ssue samples and trait data, extrac�ng the gene�c data and analysing it to create a breeding plan to reinforcing the best traits, while maintaining diversity and keeping inbreeding low.

The aim is to enhance natural selec�on, not to replace it. Professor Ian Johnston, Xelect’s CEO, stressed: “Everything we do is natural selec�on – not gene edi�ng.”

Xelect has a close rela�onship with the University of Edinburgh’s Roslin Ins�tute of Animal Breeding, and it is also a par�cipant in Aqua-FAANG, a European project that aims to improve the understanding the genome func�on in the six most important European farmed fish species.

Xelect also provides “Bio-Audit”, a biological due diligence service to help assess the quality of a farmer’s stock. The company is also working on developing low-cost genome selec�on, which can predict how much each parent is likely to contribute to the gene�c makeup of their offspring.

Another project under way involves a scanner, rugged enough to operate in offshore farms, to assess a fish’s fillet yield by quan�fying body shape. That would make it possible to assess fillet yield without actually slaughtering the fish. Since weight alone doesn’t tell you what propor�on the fillet will be – that can vary in salmon by as much as 12%- this will be very useful in breeding stock that can convert feed to fillets in the most efficient way. The project is supported by a grant from the Sco�sh Government and collabora�on with Mowi.

Danish company Aquasearch Ova, in contrast, uses its gene�c exper�se primarily to supply good quality, disease-free trout eggs and young fish. Its self-proclaimed mission is “…to provide superior, customized gene�c material on a compe��ve basis for successful and prosperous trout produc�on worldwide based on supply of superior gene�cs through trout eggs.”

The company produces a number of species including rainbow trout eggs ( or u m ); Arc�c char ( Sal l u al u ); and brown trout ( Salmo Trutta). Its focus is using gene�c exper�se to produce pan-sized trout with good traits – such as fast growth rate and a low feed conversion rate – and high egg quality. For a breeder, however, gene�cs is only half the story. Just as important is biosecurity, to ensure that the stock is disease-free. Aquasearch comes under the health surveillance system of the Danish Veterinary and Food Administra�on (DVFA) of the Ministry of Food, Agriculture and Fisheries and its freshwater site is carefully protected.

Also combining egg produc�on with advanced gene�cs and genomics is Benchmark Gene�cs, one of the biggest players in this field. Bench

mark began in animal gene�cs, and had a fairly diversified range of interests, but more recently it has been focusing on aquaculture.

The company has a large market share in Atlan�c salmon and a growing share in shrimp and �lapia, as well as providing gene�c-related services for other species. As Dr Alan Tinch, technical services director, Benchmark Gene�cs explained: “We use a pedigree structure and high-powered, sta�s�cal analysis to select fast-growing, healthier fish. We use informa�on about the gene�c sequence – genotyping – to predict which individuals will perform best – for example, in resistance to specific diseases.”

Benchmark uses between 50,000 and 60,000 gene�c markers to analyse “difficult” traits such as disease resistance, that are hard to measure in individual animals. The cycle of selec�on, breeding and evalua�on means that it’s possible to keep improving traits with every genera�on.

Tinch says: “We use a broad approach. It’s not just about selec�ng for one characteris�c, like growth. You need a balanced set of characteris�cs, with a pedigree structure that works. So, for example, we also look at mortality rates, risk of deformity and so on. We run tests to assess individual families. Our team collaborates to collect real world data; you can’t do it only from behind a desk!”

This approach essen�ally speeds up and directs the process of natural selec�on, but the technology exists to do much more than that. It is possible to intervene directly in an animal’s gene�c make-up and manipulate it. Possible, that is, but not – in Europe – lawful.

The US is another story, however. GMO (gene�cally modified organisms) are already rela�vely common for plants like soya, and one company is applying the GMO approach to farmed salmon. AquaBounty Technologies plans to farm its “AquAdvantage” Atlan�c salmon commercially in Kentucky, having developed a strain modified for fast growth in its hatchery on Prince Edward Island, Canada.

AquaBounty claims its salmon can grow twice as fast as conven�onally farmed Atlan�c salmon, reaching adult size in 18 months as compared to 30 months. The product also requires 25 per cent less feed to grow to the size of wild salmon, and could have a carbon footprint of up to 25 �mes less, the company has said.

The process of approval has been a long one and it is not over yet. In 2019 the US Food and Drug Administra�on finally decided that the rules preven�ng GM organisms from being imported into the country could be waived. In November, however, a court in California ordered the FDA to re-examine the risks of allowing gene�cally modified salmon to be grown in the US.

AquaBounty has since started harves�ng conven�onal – that is, non-GM salmon – in Indiana in order to test its RAS (recircula�ng aquaculture system) technology. The GM fish are now planned to be grown in Kentucky once the system is rolled out at scale.

Although GMO salmon has not been banned in the US, some retailers – for example Costco – have said they would not stock it. Research carried out for AquaBounty, however, suggests that 70% of US consumers would eat GMO salmon. ARK Invest, a New York-based investment firm focused solely on “disrup�ve innova�ons,” does not seem to be worried. It bought a 10.21 percent stake in AquaBounty technologies last month.

Will we see GMO fish in Europe, one day? Benchmark’s Alan Tinch said: “The technology

for gene edi�ng will probably be ready to be used before the regulatory framework is ready. There are already salmon and �lapia alive now that have had genes edited to demonstrate the technology. But will consumers eat GMO fish? And when will there be a regulatory regime that’s workable?”

He noted that, for AquaBounty, the regulatory process has taken so long that its product relies on technology – transgenics, where a desired gene is inserted into the genome – that has since been superseded by a more subtle “gene edi�ng” approach.

Even so, regulators and consumers in Europe are wary. It would be cri�cal that gene-modified fish are prevented from escaping and breeding with their wild counterparts. They would almost certainly need to be grown in land-based farms to prevent this, and probably would need to be sterile too. AquaBounty is required to do both of these things with their GMO salmon in the US.

If regulators were prepared to take a more flexible view, however, there are less controversial alterna�ves to AquaBounty’s approach. Tinch said: “One thing you could do is to use naturally occurring gene�c changes – such as those that confer disease resistance – and introduce them more widely, more precisely. That would be similar to the normal breeding process, but with an addi�onal step.”

Ian Johnston agrees: “Gene edi�ng is a powerful research tool for valida�ng func�onal gene�c varia�ons. At its simplest you could fix gene�c varia�ons that have occurred naturally with poten�ally substan�al benefits for animal welfare, for example, by strengthening resistance to certain diseases that are controlled by just a few genes. However, the adop�on of such technologies in aquaculture is a ma�er for society at large and regulators are likely to take a precau�onary approach balancing the benefits against any perceived risks”.”

Johnston’s colleague, Dr Tom Ashton – Xelect’s opera�ons director – concurred poin�ng out that with tradi�onal gene�c approaches care is taken to ensure that selec�on for one trait does not produce adverse effects on another: “With gene edi�ng there is always the possibility of non-target effects which need to be thoroughly inves�gated.”

So far, European regulators appear to believe we should leave well alone, but is there a case for change? As Alan Tinch put it: “Imagine if we did not already have vaccina�on, and then we discovered it and planned to take to the market, would we go through the same precau�ous analy�c process we are applying to gene edi�ng? We should be asking, how can we use this technology as a force for good?”’.

As this issue goes to press, haulage firms and their customers are waiting to see what the outcome of the UK’s fractious trade talks with the European Union will be. Whatever is or is not agreed, however, as from 1 January big changes will be coming in, affecting anyone importing or exporting to and from continental Europe.

It is very likely that even a no-tariff trade deal will still involve considerably more paperwork than under the current transition period. For seafood exporters, one issue is the requirement for Export Health Certificates (EHCs). Up until now, the certificates have not been required for UK exporters because of free movement of goods within the EU. If EHCs are introduced, the cost for Scottish farmed salmon, which is the UK’s biggest food export, will be between £1.3 million and £8.7 million per year, depending on the amount charged by councils for each EHC and the number of EHCs required per lorry load.

It is expected that an extra 50,000 to 100,000 EHCs would need to be processed every year, each one of which has to be signed by either an environmental health officer or a vet.

Based on pre-pandemic figures, it is estimated that 300 orders of Scottish salmon are sent to Europe each day from DFDS alone, in about 35 lorry loads. The annual £8.7 million figure is based on 300 orders per day, each one needing an EHC at a cost of £80 per certificate. The £1.3 million figure is based on 300 orders a day but with each EHC costing £12 per order – if only one certificate per lorry load is demanded. The cost of an EHC varies from council to council, from £15 to £92.

Fortunately, transport and logistics professionals have already put a lot of effort into ensuring they are as ready as they can be, given the uncertainty that exists. DFDS, which runs the important hub at Larkhall, offers customers a “Brexit readiness check” to find out if they are all set for the new UK-EU relationship. The company can also act as a customs broker.

Laurence O’Toole is managing director with O’Toole Transport, which is headquartered in the Republic of Ireland – still in the EU – but

also runs routes between the UK and con�nental Europe, working with supermarkets, food manufacturers, growers and importers.

He said “ e have a full customs team in place for import/export declara�ons, which will be necessary whether or not there is a trade deal. Up to now we have only had to do this for wit erland.”

For seafood exports from cotland, O’Toole explained, the border control will effec�vely be at Boulogne, the key fish market for UK exports.

RAINBOW trout is produced under highly diverse environmental conditions, and harvested in many different sizes with a wide array of tissue pigment levels, ranging from white-fleshed pan-size trout produced in 6-10 fresh water to large 4 kg-plus steelhead trout in 18-20oC seawater!

Such variation in conditions and production cycle, obviously calls for different genetics, and no single breeding line would serve all.

AquaSearch is now addressing the consequence of this and expanding its already comprehensive product program with the option to have individual batches of eggs custom produced by marker-assisted selection and improved genetics-related specific disease resistance, age of maturation and more.

AQUATURU A/S is a Danish technology company which has developed groundbreaking, innovative and environmentally friendly water treatment solutions that can help secure sustainable landbased fish farming.

The company has introduced a new and revolutionary method to reduce bacteria, viruses, parasites and algae in freshwater fish farming facilities, challenging the traditional solutions used for disinfection of process water in the aquaculture industry. It even works in brown water.

The company is ready to supply units from Q2 2021, and is looking for distributors and pre-IPO investors for its upcoming 2021 IPO.

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O’TOOLE Transport in Bellshill has become an approved hub for creating export health certificates, and we can offer this service to any Scottish seafood company that will require the service in January. We recently became BRC AA approved and have grown our management team to help us with the creation of customs export declarations in Scotland and import declarations in France. We can now offer the complete package to our clients: customs, health certificates and, most of all, our unrivalled logistics service, delivered by our own new fleet.

BORIS Nets – one of the UK’s oldest aquaculture net supply companies – and Fibras Industriales SA (FISA) a leading volume supplier in the Americas are happy to confirm they have formed a partnership to serve the UK and Irish markets.

John Howard,

Managing Director at Boris Nets, said:

“The relationship brings together the joint experience of two well established manufacturing companies with many years in aquaculture throughout the world’s fish farming markets, and allows us to take advantage of volume production and range to suit some of today’s large requirements whilst giving me the ability to meet the more immediate requirements of local markets in the UK and Ireland.

“We are currently working exclusively with FISA’s premium brand of “Supra® Advanced Fibers HDPE, a knotted braided net with or without a stainless steel core ideal for seal protection. This product has performed exceptionally well and repeat orders have already been gained. We are also working on a large project for full cages where we will be able to meet the strict delivery dates required.” John Howard added: “I hate it when delivery dates are not met and I will never accept an order where I know I cannot meet it.“

IN-SITU has introduced RDO Blue, the latest innovation in Optical Rugged Dissolved Oxygen technology, specifically designed for the aquaculture industry. RDO Blue uses patented technology, an EPA-approved dissolved oxygen measurement method ideal for measuring DO and temperature in even the harshest environments. Suitable for handheld use or long-term deployment in fresh water or saltwater, this low-maintenance and cost-effective probe requires no calibration or conditioning prior to deployment. The replaceable RDO Smart Sensor Cap stores calibration coefficients for error-free setup. Also, a Modbus/RS485 communication protocol supports easy integration with PLC systems and telemetry.

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