How Genetics is Leveling The Aquaculture Playing Field

Genetics-breeding programs are no longer limited only to\r\naffluent fish farming behemoths; there’s an increasing number of cost-effective\r\nservices coming on-stream to help get small and medium sized operations on the\r\nright track.

The rapid growth of the aquaculture sector has seen two\r\ndifferent producer models come to the fore. First, there are those operations\r\nthat will source their eggs from a centralized breeding program and grow them\r\nout to market size. Many companies follow this strategy, particularly in the\r\nAtlantic salmon and other salmonid sectors. In the other camp, there are those\r\ncompanies that have their own breeding programs in place and manage them\r\nin-house.

For those with a program, genetics is essential. Without it,\r\nand thereby making parent fish selections on appearance only, farms run the\r\nrisk of mating siblings, Xelect CEO, Ian Johnston told SeafoodSource.

“If you’re mating brothers and sisters for any length of\r\ntime then you will suffer a loss of vigor, of fecundity, and other things that\r\nwill make your business unsustainable,” he said.

Established in 2012, St Andrews, Scotland-based Xelect\r\nprovides genetic services to aquaculture operations all over the world. Its\r\ncore business is focused on managing breeding selection services. To this end,\r\nit has built up a team comprising a broad range of skillsets – incorporating\r\naquaculture specialists, fish biologists, physiologists, quantitative\r\ngeneticists, computer scientists and more. Indeed, a dozen of Xelect’s current\r\nteam of 15 have doctoral degrees.

“It is a big data science and it’s at the cutting-edge of\r\nmany developments in life sciences, driven by genomics,” Johnston said, adding\r\nthat aquaculture’s use of genetics is gradually closing the gap in its\r\napplications in both plant and terrestrial animal farming.

Shared expertise

To have such a team to maintain a genetics-based breeding\r\nprogram in-house would be an expensive undertaking for even the largest\r\nproducer. But Xelect’s business model means companies that it works with\r\nessentially have a “fractional” but “very cost-effective” share in its team,\r\nwho will then enable them to manage their own breeding program to a very high\r\nlevel, Johnston said.

“Having your own program, but one managed by a genetics\r\nprovider like us, means you don’t run into issues with egg suppliers and\r\navailability. It also allows you to differentiate your product. Many of our\r\ncustomers are high-end producers that have distinct brands which are associated\r\nwith quality. Genetics is part of that story and their branding,” he said.\r\n“Beyond that, there’s the ability with a trait selection program to drive\r\nimprovements in performance like growth – salmonids can achieve up to 10\r\npercent improvement per generation – that’s widely achieved in the industry.\r\nThen there’s FCR, robustness, disease resistance, resistance to specific\r\npathogens. There are lots of things you can do to improve the performance of\r\nyour stock.”

Another benefit is having the ability to genetically select\r\nstock that’s particularly suited to local environmental conditions, he said.

“We are managing the salmonid breeding programs for some very\r\nwell-known companies in the southern hemisphere. These producers are beginning\r\nto experience problems with high temperatures, due to climate change,” Johnston\r\nsaid. “If you’re just buying a standard egg then there’s no scope to do\r\nanything about that, but if you are running your own breeding program, then you\r\ncan select fish that have a better performance in warmer summer temperatures.”

Differentiated\r\noffering

Xelect’s business has grown a lot in the eight years since\r\nlaunching out of the University of St Andrews. It’s also not alone in the\r\nmarketplace, with two similarly-sized genetics service providers – one in\r\nNorway and one in North America.

There are, however, some key differences.

“We have set Xelect up in such a way that we can do\r\neverything in-house,” Johnston said. “We have our own laboratories, we do our\r\nown genomic sequencing, while at least one of our competitors is outsourcing\r\nthings like that. And for breeding programs where things are time critical,\r\nit’s really good to have that under your control rather than sending off\r\nsamples and then waiting for the results.”

Johnston said this “self-sustaining philosophy” led Xelect’s\r\nto launch a new rapid response suite of services in February. Called “Xelect\r\nExpress,” it provides quick access to the laboratory’s expertise for\r\ngenotyping, pedigree assignment, gene expression, ploidy and sex determination.

Xelect Express is a standalone offering, positioned between\r\nthe company’s comprehensive Xelect Elite breeding program and its basic Xelect\r\nDirect services. The former includes full genetic analysis of a client’s\r\navailable bloodstock, operational evaluations, the development of a bespoke\r\nbreeding program, and all the tools and databases needed to meet its commercial\r\nobjectives.

“Xelect Elite is a big task in data management and project\r\nmanagement. We are also now starting to roll-out a very user-friendly front-end\r\nfor our clients so they can enter data a way that doesn’t cause mistakes and\r\nwhich makes it easily useable for us,” Johnston said. “Our Xelect Direct is a\r\nlower level of support, but it’s still extremely useful. It utilizes the same\r\nhighly skilled staff, the same level of expertise, but it comes without the\r\ndedicated account management, and it’s on a pay-as-you-go basis. For every big\r\ncompany out there, there’s probably 10 wanting a little bit of steer on\r\ngenetics – that’s what our Xelect Direct service does.”

The Xelect Direct service, Johnston said, is for companies\r\nthat aren’t quite at the level of doing a large breeding program, but still\r\nwant access to proper genetic support.  

“In the new Direct [service], we have recognized that most\r\nof our customers are medium-sized companies and it takes quite a bit of\r\nresource to have a full-blown breeding program management service,” he said.\r\n“Nevertheless, there are lots and lots of companies that really want to do some\r\ngenetics.”

Emerging technologies

With regards to where aquaculture genetics is heading,\r\nJohnston explained that in the past five years, there has been a strong uptake\r\nof genomic selection. This involves the use of tens of thousands of markers to\r\nestimate the breeding value of parent fish.

While genomic selection remains very expensive, Xelect is\r\ninvolved in ongoing projects aimed at addressing this barrier. Among these, it\r\nis an industrial partner in both the E.U.-led AquaFaang project – which is run\r\nfrom the Norwegian University of Life Science – and the U.K. Research\r\nCouncils-funded AquaLeap project – coordinated by the Roslin Institute at the\r\nUniversity of Edinburgh.

“In both of these projects, which have different objectives,\r\nwe are devising much, much more cost-effective ways of doing genomic selection.\r\nThey will be a fraction of the current price,” Johnston said.

To do this genotyping, marker panels are being used that can\r\ndetermine parent assignment, genomic selection, and also marker-assisted\r\nselection (MAS), which is where functional markers locate a particular genetic\r\nvariant that can have a significant effect on fish traits.

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“There’s a whole range of new ‘precision breeding’ tests\r\nthat’s coming. These are based around sequencing and they will be\r\nrevolutionary, and I think we are pretty much at the forefront of that,”\r\nJohnston said. “Establishing low-cost genomic selection means that in the\r\nfuture it won’t be just the preserve of the few; it will be brought down to a\r\nprice that it can be used by the many.” 

Source: Seafood Source