The new genetic tools will produce better farmed fish, oysters and shrimp
Two years ago, off the coast of Norway, the blue-hulled Ro Fjell approached Ocean Farm 1, a steel-netted pen the size of an apple. Connecting a heavy vacuum hose to the pen, the ship's crew began pumping muscular adult salmon out of the water and into a tank below deck. Later, they unloaded the fish at an onshore processing facility owned by SalMar, a major salmon aquaculture company.
The 2018 harvest marked the debut of the world's largest offshore fish pen at 110 meters wide. SalMar's flagship facilities, dwarfing typical pens kept in calmer coastal waters, can house 1.5 million fish, with 22,000 sensors monitoring their environment and behavior, which are eventually shipped around the world. The fish in Ocean Farm 1 were 10% larger than average, thanks to stable and favorable temperatures. And the deep water and strong currents meant they were free of parasitic sea lice.
Just half a century ago, the Atlantic salmon trade was primarily a regional affair based solely on wild-caught fish. Now, salmon farming has grown into a global business generating $ 18 billion in annual sales. Farming has been key to the boom in aquaculture. The silver inhabitants of Ocean Farm 1 grow roughly twice as fast as their wild ancestors and have been bred to resist disease and other traits that make them well suited for farm life. Those improvements in salmon are just the beginning: Advances in genomics are poised to dramatically reshape aquaculture by helping to improve a multitude of species and traits.
Genetic engineering has been slow to take hold in aquaculture; only one genetically modified species, a transgenic salmon, has been commercialized. But companies and research institutions are bolstering traditional breeding with genomic knowledge and tools, such as gene chips, that speed up the identification of fish and shellfish that have the desired traits. The main objectives include increasing growth rates and resistance to diseases and parasites. Breeders are also improving the resistance of some species, which could help farmers adapt to a changing climate. And many hope to improve the traits that consumers like, by raising fish for higher quality fillets, bold colors or higher levels of nutrients. "There is a paradigm shift in adopting new technologies that can more effectively improve complex traits," says Morten Rye, director of genetics at Benchmark Genetics, an aquaculture farming company.
Farmed fish farmers can tap into a rich trove of genetic material; Most fish and shellfish have undergone little systematic genetic enhancement for agriculture, compared to the selective breeding that chickens, cattle and other domestic animals have undergone. "There is a lot of genetic potential in aquaculture species that has yet to be realized," says geneticist Ross Houston of the Roslin Institute.
However, amid the enthusiasm for the future of aquaculture, there are concerns. It is not clear, for example, whether consumers will accept fish and shellfish that have been altered using technologies that rewrite genes or move them between species. And some observers worry that genomic breeding efforts are neglecting species important to food for people in the developing world. Still, expectations are high. "The technology is amazing, it's moving so fast, the costs are coming down," says Ximing Guo, a geneticist at Rutgers University, New Brunswick. "Everyone on the field is excited."
FISH FARMING may not have roots as old as agriculture, but it goes back millennia. About 3,500 years ago, the Egyptians raised gilthead bream in a large lagoon. The Romans grew oysters. And carp has been selectively cultivated and bred in China for thousands of years. However, few aquaculture species experienced systematic scientific improvement until the 20th century.
One species that has received extensive attention from breeders is Atlantic salmon, which has relatively high prices. Farming started in the late 1960s in Norway. In 10 years, the breeding had helped drive growth rates and crop weight. Each new generation of fish (it takes 3 to 4 years for salmon to mature) grows 10-15% faster than their ancestors. "My colleagues in the poultry industry can only dream of these kinds of percentages," says Robbert Blonk, director of aquaculture R&D at Hendrix Genetics, an animal husbandry company. During the 1990s, breeders also began selecting for disease resistance, fillet quality, delayed sexual maturation (which increases yields), and other characteristics.
Another success story involves tilapia, a large group of freshwater species that do not typically command high prices, but play a key role in the developing world. An international research center in Malaysia, now known as WorldFish, started a breeding program in the 1980s that quickly doubled the growth rate of a commonly farmed species, the Nile tilapia. The breeders also improved their resistance to disease, a task that continues due to the appearance of new pathogens, such as the tilapia lake virus.
Genetically improved farmed tilapia "was a revolution in terms of tilapia production," says Alexandre Hilsdorf, a fish geneticist at the University of Mogi das Cruzes in Brazil. China, a world leader in aquaculture production, has capitalized on the strain and built the world's largest tilapia hatchery. Raise billions of young fish a year.
Aquaculture now supplies nearly half of the fish and shellfish consumed worldwide (see chart below), and production has grown by nearly 4.5% annually over the past decade, faster than most. of the cultivated food sector sectors. That expansion has come with some collateral damage, including contamination from farm waste, large catches of wild fish to feed locked salmon and other species, and destruction of coastal wetlands to build shrimp ponds. However, aquaculture is now poised for further acceleration, thanks in large part to genomics.
A rising tide
Aquaculture rivals catches from wild fisheries and is expected to increase. Much of the growth comes from freshwater fish in Asia, such as grass carp, but most research has focused on Atlantic salmon and other high-value species. Genomic technology is now being extended to shrimp and tilapia.
Breeders are most excited about a technique called genomic selection. To understand why, it is helpful to understand how farmers typically improve aquaculture species. They start by crossing two parents and then, among hundreds or thousands of their descendants, they select individuals to evaluate the traits they want to improve. Advanced programs make hundreds of crosses in each generation and choose from the best performing families for breeding. But some evidence indicates that the animal cannot be used later for reproduction; Measuring fillet quality is lethal, for example, and detecting disease resistance means that the infected individual must remain in quarantine. As a result, when researchers identify a promising animal, they must choose a sibling to use in breeding and hope it performs just as well. "It is not known whether they are the best or the worst in the family," says Dean Jerry, an aquaculture geneticist at James Cook University, Townsville, who works with shrimp, oyster and fish farmers.
With genomic selection, researchers can identify siblings with high-throughput traits based on genetic markers. All they need is a small tissue sample, such as a fin cutout, that can be pureed and analyzed. The DNA arrays, which detect base pair changes called single nucleotide polymorphisms (SNPs), allow breeders to thoroughly screen many siblings for multiple traits. If the SNP pattern suggests that an individual carries optimal alleles, it can be selected for further reproduction even if it has not been tested. Genomic analyzes also allow breeders to minimize inbreeding.
Cattle breeders were pioneers in genomic selection. Salmon farmers adopted it a few years ago, followed by those who work with shrimp and tilapia. "There is a great industry race to implement this technology," says geneticist José Yáñez from the University of Chile, who adds that even small producers are now interested in genetic improvement. On a rough average, the technique increases selection precision and the amount of genetic improvement by about 25%, Houston says. This and other tools help researchers to pursue goals such as:
This feature improves the bottom line, allowing producers to produce larger and more frequent sets. Growth is highly heritable and easy to measure, so traditional breeding works well. But breeders have other tactics to boost growth, including providing single-sex fish to farmers. Male tilapia, for example, can grow significantly faster than females. Another strategy is to hybridize species. The dominant farmed catfish in the United States, a hybrid of a female channel catfish and a male blue catfish, grows faster and is more resistant.
The induction of sterility also stimulates growth and has helped increase the production of shellfish, particularly oysters. In the 1990s, Guo and Standish Allen, now at the Virginia Institute of Marine Sciences, discovered a new way to create triploid oysters, which are infertile because they have an extra copy of each chromosome. These oysters do not put much energy into reproduction, so they reach harvest size earlier, reducing exposure to disease. (When oysters reproduce, more than half of their body is made up of sperm or eggs, which no one wants to eat.)
Looking ahead, researchers are exploring gene transfer or gene editing to further improve profits. And an American company, AquaBounty, is just beginning to sell the world's first transgenic edible animal, an Atlantic salmon, which it claims is 70% more productive than standard farmed salmon. But fish is controversial and has faced resistance from consumers and regulatory hurdles.
Diseases are often the biggest concern and expense of aquaculture operations. In shrimp, sprouts can reduce overall yield by up to 40% per year and can kill all operations. Vaccines can prevent some diseases in fish, but not in invertebrates, because their adaptive immune system is less developed. So for all species, resistant strains are very desirable.
To improve resistance to disease, researchers need a rigorous way of testing animals. Thanks to a collaboration with fish pathologists at the US Department of Agriculture (USDA), Benchmark Genetics was able to detect the susceptibility of tilapia to two major bacterial diseases by administering a precise dose of the pathogen and then measuring the response. They identified genetic markers correlated with infection and used genomic selection to help develop a more resistant strain. USDA scientists have also worked with Hendrix Genetics to increase the survival of trout exposed to a different bacterial pathogen from 30% to 80% in just three generations.
Perhaps the most famous success has been salmon. After researchers discovered a genetic marker for resistance to infectious pancreatic necrosis, companies quickly created strains that can survive this deadly disease. Meanwhile, oyster farmers have been successful in developing strains resistant to a strain of herpes that devastated the industry in France, Australia and New Zealand.
Parasite resistant salmon
A big problem for Atlantic salmon farmers is sea lice. The tiny parasite attaches itself to the salmon's skin, causing wounds that damage or kill the fish and render their meat useless. Between the loss of fish and the expense of controlling parasites, lice cost producers more than $ 500 million a year in Norway alone. Lice are attracted to fish pens and can jump onto passing wild salmon.
For years, farmers have relied on pesticides to fight lice, but the parasite has become resistant to many chemicals. Other techniques, such as pumping the salmon in hot water, which causes the lice to fall off, can stress the fish.
Researchers have found that some Atlantic salmon are better than others at resisting lice, and breeders have been trying to improve this trait. So far, they have had modest success. A better understanding of why various species of Pacific salmon are immune to certain lice could lead to progress. Scientists are exploring whether sea lice are attracted to certain chemicals released by Atlantic salmon; if so, it is possible that they are modified by gene editing.
There is no sex on the farm. That is a goal with many aquaculture species, because reproduction diverts energy from growth. Additionally, fertile fish that escape aquaculture operations can cause problems for wild relatives. When wild fish breed with their domestic cousins, for example, the young tend to be less successful at reproduction.
Salmon can be sterilized by making them triploid, typically by pressurizing newly fertilized embryos in a steel tank when the chromosomes are replicating. But this can have side effects, such as increased susceptibility to disease. Instead, Anna Wargelius, a molecular physiologist at the Norwegian Institute of Marine Research, and her colleagues altered Atlantic salmon genes to sterilize them, using the CRISPR genome editor to remove a gene called deadend. In 2016, they showed that these fish, although healthy, lack germ cells and do not mature sexually. Now, they are working on developing fertile broodstock that will produce these sterile offspring for hatcheries. Gene-deleted embryos should become fertile adults if they are injected with messenger RNA, according to a paper the group published last month in Scientific Reports. When these fish mature in late December, they will try to breed them. "It looks very promising," says Wargelius.
Another approach would not involve genetic modifications. Fish reproductive physiologists Yonathan Zohar and Ten-Tsao Wong of the University of Maryland, Baltimore County, are using small molecule drugs to disrupt early reproductive development so that fish mature without sperm or eggs.
Cooks and diners hate bones. Almost half of the main aquaculture species are carp species or their relatives, which are known for the small bones that pack their meat. These bones can't be easily removed during processing, so "you can't just get a nice, clean steak," says Benjamin Reading, a reproductive physiologist at North Carolina State University.
Researchers are studying the biology of these fillet bones to see if they could one day be removed through breeding or genetic engineering. A few years ago, Hilsdorf heard that a Brazilian hatchery had discovered a mutant breeding population of a giant Amazon fish, the widely farmed tambaqui, that lacked these fillets. After trying and failing to breed a boneless strain, he is studying tissue samples from the mutants for clues to their genetics.
Geneticist Ze-Xia Gao from Huazhong Agricultural University focuses on sea bream, a carp grown in China. Guided by five genetic markers, she and her colleagues are raising the sea bream to have few fillet bones. It could take 8 to 10 years for her to get there, she says. They have also had some success with gene editing - they have identified and removed two genes that control the presence of fillet bones - and plan to test the method in other carp species. "I think it will be doable," says Gao.
New menu items
Aquaculture projects around the world are striving to domesticate new species, a kind of gold rush rare in terrestrial agriculture. In New Zealand, researchers are domesticating native species because they are already adapted to local conditions. The New Zealand Food and Plant Research Institute started breeding the Australasian snapper in 2004. Early work focused simply on getting the fish to survive and reproduce in a tank. A decade later, researchers began breeding for growth enhancement, and since then juvenile growth rates have increased by between 20% and 40%.
Genomic techniques have been critical. Snappers are massive breeders, so it was difficult for breeders to identify parents of promising offspring, which is crucial to optimize selection and avoid inbreeding. DNA analysis solved that problem, because the markers reveal ancestry. The institute is also breeding another local fish, silver horse mackerel, with the goal of a strain that will breed in captivity without hormonal implants. "It's a long-term effort to breed a wild species to be suitable for aquaculture," says Maren Wellenreuther, evolutionary geneticist at the New Zealand Institute and the University of Auckland.
THESE BREEDING EFFORTS require money. Despite the growth of aquaculture, funding for field research lags behind amounts invested in livestock, although some governments are pushing investments.
Looking globally, geneticist Dennis Hedgecock of Pacific Hybreed, a small US company developing hybrid oysters, sees a "huge disparity" between investment in farming in developed countries, which produce a fraction of total crops but have the largest budgets. research, and the rest. of the world. Simply applying classical breeding techniques could quickly improve production, especially in the developing world, he says. However, the hundreds of species now in cultivation could overwhelm breeding programs, especially those aimed at improving resistance to disease, Hedgecock adds. "Growth and production are outpacing scientific capacity to deal with disease," he says, adding that it would be beneficial to focus on fewer species.
For genomics to help, experts say costs must continue to fall. One promising development in SNP arrays, they note, is a technique called imputation, in which cheaper arrays that look for fewer genetic changes are combined with a handful of higher-cost chips that scan the genome in more detail. Such developments suggest that genomic technology is "at a pivot point where you will see it being widely used in aquaculture," says John Buchanan, president of the Center for Aquaculture Technologies, a contract research organization.
Many companies are already planning larger harvests. SalMar will decide next year whether to commission a companion for Ocean Farm 1. He has already drawn up plans for a successor that can operate offshore and is more than twice the size, large enough to house 3-5 million. salmon at a time.
Source: Science Magazine