Gentec provides valuable contribution to Europe-led BovReg project

As of September 2019, Germany’s Leibniz-Institut für Nutztierbiologie (FBN) is home to BovReg—a $9 million, EU-funded project dedicated to generating a comprehensive functional annotation map of the bovine genome and applying that knowledge to validate novel models for biology-driven genomic prediction. The knowledge will allow breeders and producers to improve traits, such as robustness, health (especially udder health) and biological efficiency. A parallel focus on animal welfare will consider the physical limits of cattle, ensure that efficiency in one trait does not harm others, and provide options for reducing antibiotic use safely.

“Functional genomics in the livestock sector is very much a ‘black box’,” says Dr. Christa Kühn, Director of the FBN. “It’s like driving a car without a map. You want to go to Munich but all you can do is go in that general direction. You might reach the city… you might not.”

Furthermore, phenotypic data collected from the big breeds cannot be applied directly to the smaller breeds. Former Gentec CEO Steve Moore remembers being aghast to find out that gEBVs do a great job on Holsteins but not on Jerseys.

“We have a causal variant and some markers ‘in the neighbourhood’ but, for the small breeds, we’re not reaching Munich,” says Kühn, staying with the metaphor. “Data that BovReg collects from, for example, Brown Swiss, Braunvieh, Montbeillarde, Normande and Nordic red cattle will be important for those regional breeds and for others, too. They will help maintain biological diversity in the national herds.”

To achieve its goals, BovReg brings together experts in bioinformatics, molecular genetics, quantitative genetics, animal breeding, reproductive physiology, ethics, social science and dissemination/ commercialization from 13 countries (11 European, plus Australia and Canada). Canada, in particular, plays a special role.

At the core of the project Gentec will provide 24 tissue samples from Kinsella crossbred animals characterized for feed efficiency and methane production. These samples are one of three sets that will undergo detailed next-generation genomic analysis in the European labs collaborating in BovReg. In addition, Gentec will provide data from 7,000 samples of composite, Angus and Charolais phenotypes for feed efficiency, methane production, carcass and quality traits and 500 samples of commercial crosses  for health traits. The samples have been comprehensively analyzed for genomic structures, and have produced genotypic, phenotypic and transcriptomic data, which are an important component of genetic analysis. BovReg reviewers rated this contribution so highly that they recommended funding for it.

“It is quite exceptional that the EU funded Canada’s contribution—even as a symbolic gesture,” says Kühn. “It happens in less than 5% of cases. The reviewers insisted, due to the substantial impact of the samples. The Kinsella animals bring diversity, which is an issue in livestock breeding, and an advantage of the Kinsella vs purebred beef cattle populations.”

BovReg will be a first official collaboration between Gentec and this European team, even though Gentec CEO Graham Plastow (seen hiding behind his sunglasses at the BovReg kick-off meeting here) and Christa Kühn have known each other for a number of years.

“This is a really exciting opportunity for the Gentec team, which includes Ellen Goddard, Carolyn Fitzsimmons, Leluo Guan, ChangXi Li, John Basarab and Paul Stothard,” says Plastow. “It allows us to build on our investments over the last 10 years in characterizing the populations at the Roy Berg Kinsella Research Ranch, the Lacombe Research and Development Centre and beyond, placing our animals at the centre of a major international initiative with many of the world’s leading bovine research teams. That work was funded by Alberta Agriculture and Forestry, Agriculture and Agri-Food Canada, Alberta Innovates, Genome Alberta, Genome Canada and the Beef Cattle Research Council, industry partners and other organizations.”

Within BovReg, team members and partners will have access to an internal database. Externally—and part of the data-sharing plan—eight partners are active in the global FAANG (Functional Annotation of ANimal Genomes) consortium, whose data are publicly available, free of charge, opening the possibility of citizen scientists becoming involved in the spirit of Open Science. Key partner, European Molecular Biology Laboratory, hosts the FAANG Data Coordination Centre (the official repository of all FAANG-related data produced globally) and will ensure that data deposited are convenient for input and retrieval, giving them extra value. In addition, four partners are Steering Committee members of the 1000 Bull Genomes Consortium. Integration into these global initiatives will facilitate dissemination to a wider academic community. Although BovReg is dedicated to basic research, it will reach out to the public and policy makers to ensure support for its objectives.

“The use of the Democs card game and the availability of free resources will improve the public’s motivation to engage in the discussion on the promises, values and consequences of science in livestock genomics in general—and of BovReg deliverables in particular,” says Kuhn. “I truly hope this will advance our efforts in sustainable agriculture and food security.”

The First Outbreak of Porcine Epidemic Diarrhea (PED) in Alberta

Julia Keenliside DVM MSc
Veterinary Epidemiologist
Alberta Agriculture and Forestry

The porcine epidemic diarrhea (PED) virus first made the jump from Asia to the USA in 2013. Since then, it has spread rapidly across the USA and parts of Canada. Until 2019, the Alberta pork industry had succeeded in keeping the virus out of the province. That changed on January 7th when the first case was confirmed near Drumheller. Three more cases followed in February and March in the Lethbridge area. As of July 2019, the outbreak is still limited to four farms.
PED is a viral disease that affects only swine and their relatives (including wild boar). Symptoms are often unmistakable, with large numbers of pigs affected by severe diarrhea, vomiting and refusal to eat. It is generally fatal in young piglets, but older pigs will recover completely within a week or so. An outbreak typically spreads rapidly, and 3-5 weeks of piglet production may be lost, taking an emotional toll on pig caretakers. Despite its spectacular appearance, people cannot become infected, and pork from affected animals is safe to eat.
The virus survives well in pig feces and on surfaces contaminated with feces from infected animals, especially when frozen. Transport trailers, equipment, boots and loading docks can all become contaminated and serve as sources of infection, allowing outbreaks to spread between farms. Biosecurity measures are the best prevention. However, it only takes a very small amount of virus to cause disease in nursing piglets, so it can occasionally sneak into even the most biosecure farms. Often, the source of the spread is never found.
PED likely entered Ontario in 2014 through feed containing contaminated porcine plasma from the USA. In contrast, evidence in Manitoba suggests the virus was brought in by contaminated American trucks loading pigs at Canadian assembly yards. Manitoba has reported 160 cases since then and Ontario 125 cases. Manitoba has confirmed 60 cases as of July 2019.
Despite a detailed investigation, we still can’t be sure how the virus spread into Alberta. Swine traceability program data showed no transport links with PED-positive premises or contaminated vehicles coming from outside Alberta. Environmental surveillance samples did not show any contamination of assembly yards, abattoirs and truck washes in Alberta throughout 2019.
However, we did find some risk factors. For example, feed ingredient trucks from Manitoba and the USA did deliver ingredients directly to the first Alberta case. A piece of used clean manure equipment from Manitoba was also brought onto the farm. Feed ingredients found on the affected farms originated from nine countries, four US states and five provinces, most of which are infected with PED.
Unlike Manitoba, Alberta farms are generally far apart, which slowed the spread of the virus. There were no direct transport links between any of the affected farms, and the industry did a good job in keeping biosecurity tight. The exact method of spread between the Alberta cases was not clear, as the usual risk factors of contaminated transport vehicles, assembly yards and abattoirs were ruled out. The three southern cases are within 20 km of each other. We know that the virus spreads more easily through transport, people traffic or even the air when farms are closer together.
Risk factors that were identified during the investigation that producers should address include:
a) Changing boots and clothing every time before entering and leaving the barn, even when just going to the feed mill;
b) Washing, drying and disinfecting trailers every time they are used, even if going to abattoirs or assembly yards that have had negative environmental test results;
c) Working with suppliers to understand and reduce the risk from feed trucks and feed ingredients coming from PED-positive regions
d) Being extra careful when equipment and visitors come from PED-positive regions.
All four affected producers are working closely with their veterinarian, Alberta Pork and Alberta Agriculture and Forestry (AF) to eliminate the virus. One farm has depopulated, and is testing in preparation to refill. The other three are farrowing again, and moving hogs to market without any clinical signs. All four farms are working towards achieving presumptive negative status by the fall 2019.
PED is a reportable disease in Alberta. If you suspect PED, call a veterinarian and notify (mandatory) the office of the Chief Provincial Veterinarian.

Happy Birthday, gEBVs!

It all started with an idea…. Former Gentec CEO, Steve Moore’s PhD student, Stephanie McKay, thought about developing a SNP chip for applications in cattle, a project that eventually became part of her thesis. With input from Gentec bioinformatician Paul Stothard, plus Tim Smith and Curt van Tassel at the USDA and Jerry Taylor at University of Missouri, that first commercial SNP for cattle on a 50K chip ushered in a new era.

It wasn’t long before 50K SNPs grew to 700K thanks to the advancement of technology. The objective was to develop a tool to predict genetic merit in an animal. The 50K and 700K became the first tools used for large-scale genotyping of cattle and then other livestock species.

Until then, it took 5-7 years to get an accurate reading on a dairy bull’s merit. (Until somebody figures out how to milk a bull, any measure of milk production has to come from daughters, hence the delay.)

To illustrate the old system,” remembers Moore, “I was telling researchers in Australia that we’d sequenced the top bull in Canada, called Braedale Goldwyn. They said they’d sequenced the top bull in Australia… also called Braedale Goldwyn. He’d been dead for four years but was still the top bull in both countries because of the amount of semen stored and how long producers had to wait for new data.”

The dairy industry’s widespread use of artificial insemination (AI) turned out to be a good thing. All those stored straws turned into an amazing reference population that other livestock didn’t have.

“We could go back to the Fifties!” says Filippo Miglior, former Gentec-associated researcher, now Chief Scientific Officer and Vice President, Sector Innovation and Programs at Ontario Genomics. “Having this reference population provides the biggest difference in terms of accuracy.”

For the first time, producers pushed instead of needed pushing. Dairy producers export a lot of high-end animals and embryos. They wanted quality assurance of their genetics, not just third-party evaluation. With genomic testing at $45/animal (now down to $33) they could test their heifer calves, which helps improve herd management decisions such as which ones to keep or sell, which ones to breed with sexed semen, which ones carry a genetic recessive characteristic, etc.

“The rate of increase in usage in Canada was fantastic,” remembers Miglior. “One of the fastest across all dairy countries—5%/year.”

Now, bulls could be assessed at one year old or even at the embryo stage. The accuracy of genetic information for newborn males and females doubled and a major shift happened towards the use of much younger animals as parents and a significant gain in the intensity of selection, especially for young bulls bought by AI companies. As a result, those genomic-tested young bulls now occupy 70% of the market share and the progeny proven sires only 30-35%, a 180-degree switch. Rates of genetic progress have now more than doubled—even tripled for some traits.

A sea change happened in the AI sector,” says Brian Van Doormaal, Chief Services Officer at Lactanet Canada. “Any AI company can easily have their bulls receive a Canadian genomic evaluation simply with a DNA genotype so the industry has become extremely competitive. Most multi-nationals now own females, with internal programs to produce the most elite young bulls possible. Before buying bulls, which is now based on a new step of pre-genomic selection, they assess each bull’s genomic evaluations and a long list of characteristics, including undesirable recessive traits and haplotypes that negatively affect fertility.”

Since data was only required from a subset of bulls, other traits, such as fat content, A1 vs A2 milk, protein, volume, conformation, hornless or polled, embryonic death, mastitis, lameness, metabolic diseases could be included as well.

Beef cattle were a different story. First, the data simply weren’t there. Second, bulls are come and gone by the time they’re three years old. Third, AI isn’t the norm. But the real holdup is phenotyping animals that you don’t see close up very often. All of which led to a lag compared to dairy. That gap is closing as the larger operations realize they don’t need to wrassle down every last bull to pull a tail hair. While all the Canadian breed associations offer testing, the clear leader is the American Angus Association, which tests a massive 300,000 head/year.

“We always assumed that progeny is 25% related to each grandparent,” says Doug Blair (former CEO, Alta Genetics Inc.). “Genomics found that it’s more variable than that. The contribution from any grandparent may vary from extremes of 15% to 35% rather than 25%. Thus two fullsibs may have very different contributions from the 4 grandparental genomes. My analogy is that we used to forecast weather with ships in the ocean. Now we have satellites. Genomics has done the same for estimated progeny differences.”

So what might the future bring? As genotyping becomes cheaper, it will become a mainstream tool for every producer. It may even be possible to genotype every animal in Canada. This will be useful for traceability, genetic defects, parentage—and for solving issues such as fertility.

“We obtained huge benefits from genomic selection, very fast” concludes Miglior. “It’s a huge success story for Canada that we’ve achieved that in such a short time.”