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.”

Sustainability starts in the microbiome

Part 1: Cows and climate change
When Canada’s beef industry says its priority objective is to be sustainable, what does that mean, specifically?

The answer isn’t a simple as you might think. A comprehensive definition should include animal health, eating quality, the impact of production on the environment and the ecosystem services returned to Canadians, stewardship of the land, and the circular economy that includes the ability of cattle to use byproducts as feed and the production of energy from manure.

“The short answer,” says Tim McAllister, Principal Research Scientist for Agriculture and Agri-Food Canada in Lethbridge, Alberta, “is that we have to take a systems approach to sustainability.”

McAllister’s research focuses on cow microbiology, nutrition and biology, and how their influence on sustainability depends on their interaction with the rest of the cow. This isn’t simple, either. Interaction could refer to the microbiome of the respiratory tract and the cow’s likelihood of developing pneumonia that needs treatment with antibiotics. Or it could be the microbiome of the digestive tract and the cow’s resulting feed efficiency and methane production, the likelihood of digestive disturbances, or the influence the microbiome has on establishing human pathogens within the cow’s digestive tract, which can even influence the amount of methane produced from biodigested manure.

McAllister is collaborating with Gentec researcher Leluo Guan on the two-way communication between these microbiomes and the cow.

“The microbiome is heavily controlled by the immune system and the metabolic end products that the microbes produce. Since proteins and vitamins play a key role in immune response, we’re looking at the nutritional elements of the cow’s diet, especially since, in feedlots, cows are fed byproduct feed, such as distillers’ grains, that would be a liability to the ethanol industry without a market for them as feed.”

The microbiome allows cattle to ferment forages, which results in methane as a byproduct. McAllister points out that the origin of this methane is different than that of methane that is used to heat our homes. Carbon in cow methane comes from the forages it has just eaten, and it has just been captured by the plant through photosynthesis. In most cases, this carbon was carbon dioxide in the atmosphere less than a year before capture.

“So carbon in methane from cattle originates from short-term carbon in the atmosphere as CO2, the season before the animal grazed the plant” he says. “That’s very different from the carbon from fossil fuels. That methane was deposited and stored millions of years ago. Most of it is ancient carbon.”

McAllister points out that cattle and other ruminants were producing methane long before the Industrial Revolution without any significant consequence for climate change. There were 30-60 million buffalo roaming North America’s Great Plains—all far less efficient as they consumed only forages, unlike the forage/grain system used to produce cattle today. Therefore, climate change is really a consequence of the release of ancient—not short term—carbon into the atmosphere. While the methane molecules from these two sources are the same, their origin is vastly different.

Another component is the native and tame grasslands that are managed by Canada’s cow-calf producers. These lands store vast amounts of carbon that would be released into the atmosphere if they were to be cultivated. Using these lands as pasture preserves the land and its biodiversity, with the added benefit of carbon storage.

“Consumers need to understand the nuances associated with beef production in Canada and the roll beef cows play in nutrient recycling,” says McAllister.

Indeed, one of the major issues of the day is food waste. The world actually produces more than enough food for its population but loses over half through poor storage and distribution before it even reaches consumers. In Canada, 30-50% of some foods can end up in composting facilities or landfills—this is after the fuel, fertilizer and transportation energy has been spent to produce it. Once it enters a landfill, there is a good chance it will produce methane during decomposition.

“If we could line up supply channels, food waste doesn’t have to be a net liability,” says McAllister. “Unlike poultry and pigs, which have defined nutritional requirements and a narrow profile for adjusting it, cows live in an outdoor environment and have to deal with a range of forages and feed types. The rumen microbiome is capable of breaking down many different types of toxins, making cattle the logical end user of food waste streams.”

On that note, we’re going to leave you with that cliff-hanger. Next month’s article will continue the story on McAllister’s vision for cutting food waste.

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

by 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 7 when the first case was confirmed in central Alberta. Three more cases followed in February and March in the Lethbridge area. As of August 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 producers may lose three to five weeks of piglet production, which takes an emotional toll. Despite its spectacular symptoms, 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. Manitoba experienced a large outbreak this spring with 60 cases since January.

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 and cleaned 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 whom have PED cases.

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 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:

  • Changing boots and clothing every time before entering and leaving the barn, even when just going to the feed mill;
  • 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;
  • Working with suppliers to understand and reduce the risk from feed trucks and feed ingredients coming from PED-positive regions;
  • Being diligent in enforcing biosecurity 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 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  at 1-800-524-0051 (780-427-3448 after hours).

2019 ASAS-CSAS Annual Meeting Highlights

by Xuechun Bai

Austin, Texas, is a fantastic place for passionate ASAS and CASA members to feel the heat of summer and devote themselves to research and industry work of animal science. I feel so lucky to have been able to attend such a great conference, meet a great roster of speakers, take part in their research communication, and question a panel of experts. A big Thank You to Livestock Gentec and Dr. Graham Plastow for sending me and granting me a CSAS Graduate Student Travel Award.

There were too many amazing moments and symposia discussing hot topics and advanced research in animal science to share them all here, so be sure to check out all the event materials through the Meeting App.

Dr. Ignacy Misztal (University of Georgia) opened the Breeding and Genetics symposium with a keynote on the current status of genomic selection that has been dramatically simplified by the development of new methodologies, such as ssGBLUP—single-step genomic best linear unbiased prediction. Dr. Tom Lawlor (US Holstein Association), Dr. Egbert Knol (Topigs Norsvin Research Center) and Dr. Dan Moser (Angus Genetics Inc.) gave great talks about the tremendous impact of genomic selection on dairy, swine, and beef industries, respectively, including current achievements, challenges and future directions. Sessions about animal breeding and genetics broached the central question of how genomic selection has changed livestock breeding. Dr. Makram Geha (Corteva Agriscience) shared his research experience on genomic selection and gene editing in plant breeding, which allow us to broaden our horizons and learn advanced methodologies developed in plant science. Dr. Jack Dekkers (Iowa State University) provided an excellent summary of the meeting with an outlook of the future of increasing genetic gain and precision livestock breeding through machine learning, deep learning, and the development of breeding technologies.

The primary topic of the WAAP-CSAS symposium was improving the efficiency of livestock production. Dr. Graham Plastow gave a very inspiring talk about the role of genomics in enhancing efficiency in swine by addressing social and environmental aspects (such as disease and stress), to improve the sustainability of swine production.

Genome editing via CRISPR-Cas was another popular topic that sparked heated discussion. Dr. Kristin Whitworth (University of Missouri) presented exciting results of creating pigs that are fully resistant to PRRSV (porcine reproductive and respiratory syndrome virus) and TEGV (transmissible gastroenteritis virus) through genome editing. (However, they did not succeed with PEDV.**) Accordingly, talks focused on the global regulatory landscape for evaluation of products derived from gene editing and earning public trust in gene editing, which could help researchers, regulators, governments, and consumers to build better communications strategies on the development and application of this technique.

Other breeding and genetics sessions covered many different and exciting topics, such as the use of APY (Algorithm for Proven and Young) in many studies of genomic selection at the University of Georgia; the integration of microbiome information into the studies of meat quality, carcass composition traits, and host responses to PRRSV in swine.

As well, many sessions on animal nutrition, animal behaviour and welfare, animal health and companion animals were available. Taken together, they gave us new insights into animal science, current science and the next steps.

Last but not least, attending was an excellent opportunity to communicate with people from academia and industry, and to receive feedback and constructive criticism on my research during my poster presentation. It was also a great chance to network, share thoughts, and expand my knowledge with other academics and experts.

** See also the accompanying article (link above) by Julie Keenliside on PEDV in Alberta in 2019. Gentec also drew something of a blank in our initial work on genomics and PEDV suscpetibility.

 

 

 

Rumen microbiome affects feed efficiency and is associated with host genetics in beef cattle

With our global human population continuing to grow, there is increased competition for resources (e.g., land, water, and cereal grains) between people and livestock, especially beef cattle operations. Improving the feed efficiency of cattle would reduce the amount of feed consumed (especially cereals that could feed humans instead) with equal or higher production performance. Improving feed efficiency can also reduce the negative environmental effects (methane emissions and manure) caused by beef cattle operations.

By applying cutting-edge DNA and RNA sequencing technologies, we explored the rumen microbiome of beef cattle from three breeds on the same diet but divergent in feed efficiency [1]. We aimed to evaluate the breed effect on the rumen microbiome and generate a more conclusive understanding of the role of the rumen microbiome in feed efficiency. We observed differences between the rumen microbiomes of different breeds, as well as microbial features that differed between efficient and inefficient steers. These aspects were also specific to each breed, suggesting that interactions between the host breed and the rumen microbiome influence feed efficiency. We conducted a follow-up study [2], surveying a large cohort of beef cattle (n=709) raised under the same farm environment. Multiple factors, including breed, sex, and diet were identified to determine rumen microbiome profiles. We found that ~34% of rumen microorganisms are heritable elements affected by host genetics and genotypes, that are also associated with host feed efficiency traits and rumen metabolic measures. Therefore, cattle may control their rumen microbiome genetically and consequently influence their rumen fermentation and feed efficiency.

The cattle sampled for these papers were part of the Gentec “Kinsella Cattle Project” (Improvement of cow feed efficiency and the production of consistent quality beef using molecular breeding values for RFI and carcass traits). The Kinsella Project enabled the measurement of feed-efficiency and provided the genotypes and pedigree information for the genome-wide association analysis with rumen microbes.

Overall, our findings highlight a potential to manipulate and obtain a desirable and efficient rumen microbiome using genetic selection and breeding. It could be a useful strategy to further improve feed efficiency and optimize rumen fermentation through targeting both cattle and their rumen microbiome.

The work, funded by Alberta Livestock and Meat Agency, Alberta Agriculture and Forestry, NSERC, and an Alberta Innovates-Technology Futures Graduate Student Scholarship, brought together researchers in beef production, rumen microbiology, functional genomics, quantitative and statistical genomics. Notably, Agriculture and Agri-Food Canada scientists Changxi Li and Carolyn Fitzsimmons, both co-located at UAlberta, were essential in providing these elements for Fuyong’s analysis.

“Rumen microbe composition and abundance are novel quantitative traits in beef cattle. Characterizing variations of rumen microbes among animals and estimating their genetic parameters will also allow us to incorporate rumen microbe measurements into a multiple trait selection index to improve beef production efficiency” says Changxi Li.

The EC project on Ruminomics led by Prof. John Wallace in the UK subsequently reported similar results in dairy cattle.

The Gentec team is now investigating the genetic links of rumen microbes with other beef performance traits.

Fuyong’s papers are:

  1. Li, F., Hitch TCA, Chen Y, Creevey CJ, Guan LL. 2019. Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattleMicrobiome7:6.
  2. Li, F., Li, C., Chen, Y., Liu, J., Zhang, C., Irving, B., Fitzsimmons, C., Plastow, G., Guan, L.L. (2019) Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle. Microbiome, 7:92.

A career well-remembered

Cambridge, UK 1988. Young post-doc Steve Moore stares out of the window at another rainy English day. In front of him, in the journal Nature, is an advert for a job at CSIRO, Australia’s national science agency, in Queensland. The accompanying image shows palm trees….

Steve got the job. Foregoing cancer research and the UK, Steve would remain with cattle for the rest of his career. He spent the next three years at the Rendle Research Laboratory and Belmont Research Station, the premierresearch stationfor the north Australianbeef industry and nicely situated on the aptly-named Tropic of Capricorn. He spent the following nine years in Brisbane, also for CSIRO, researching tropically-adapted animals.

Reorganizations started to feel like a fact of life at CSIRO. Steve no longer saw a future for himself there. Once again, he cracked open Nature, this time seeing an advert for a job in Alberta.

“Canada was spelled out in big letters down the side,” Steve remembers. “I thought I should jump before getting pushed.”

Steve got the job. In a 180-degree switch from the tropics, he found himself in Edmonton, where the temperature “soars” to -40C in winter. The job was Chair of Beef Genomics and the Alberta Bovine Genomics Program (ABGP), an organization he was to set up and run for 12 years at the University of Alberta.

“I remember going down to the Calgary-Airdrie area to look at yearling bulls with cross-breed producers,” says Steve. “We started to walk through the middle of them. I’m sure the guys were testing my mettle. They didn’t know that I’d been working with tropical bulls that are 6 ft at the hump. These bulls looked small in comparison. They parted like the Red Sea as we walked through.”

During that time, the ABGP enjoyed great support from the Government of Alberta, especially Cornelia Kreplin, and eventually morphed into Livestock Gentec, which broadened its mandate to other livestock industries in Alberta. Hence, Graham Plastow’s (a pig expert) appointment as incoming CEO after Steve. While the pig industry is completely integrated, with all sectors cooperating to achieve common goals, the beef industry is quite the opposite, making it very hard to work up and down the value chain. Canada has made significant efforts to change the information flow up and down the value chain, making all sectors better able to meet consumer preferences.

“Establishing Livestock Gentec remains one of the most satisfying parts of my career.,” says Steve. “Gentec is now a world-recognized centre for livestock genomics with links to other groups in Canada such as the University of Guelph, and beyond with groups in the USA and Europe. The best part was the students, who came from all over the world. They have since moved on and established their own careers in industry, government and academia in Canada, the USA, Europe, Asia and Africa.”

Initially, the position was for three years. Eventually, Steve and his family stayed for 12.By that time, he’d done what he set out to achieve, and he was happy to leave the ABGP/Gentec in Graham Plastow’s capable hands while he took on the role of Director, Centre for Animal Science for the Queensland Alliance for Agriculture & Food Innovation. This time, without the assistance of Nature.

Steve maintains his links to Alberta through research collaborations and as a Board member of Delta Genomics, a not-for-profit spin-off from Livestock Gentec serving the Canadian livestock industry. Steve and Fran’s children remain settled in Alberta, resulting in regular commutes across the Pacific.

Seven years later, Steve has once again achieved what he set out to do. This time, though, he decided to retire, although he will maintain his international engagements with the well-deserved new title of Professor Emeritus. And he has other plans.

“We just bought a property on the Gold Coast,” he says. “My next job is to tame it back to civilized state. That should keep me busy for a while.”

ISAG Meeting Highlights

by Elda Dervishi and Jiyuan Li

The 37th International Society for Animal Genetics (ISAG) conference was held in Lleida, Spain from July 7-12, 2019. Over 700 researchers from all over the world attended to present over 600 scientific contributions. Excellent oral presentations and posters demonstrated recent research advances in livestock and companion animal species. Canada was represented by 25 attendees. Among them, postdoctoral fellow Elda Dervishi and PhD student Jiyuan Li represented University of Alberta and Livestock Gentec with three posters.

ISAG had several plenary sessions, poster sessions and workshops. Dr. Yang Li (University of Chicago) proposed a formal model describing how genetic contributions to complex traits can be partitioned into direct effects from “core” genes and indirect effects from “peripheral” genes acting as trans-regulators. This model provides interesting new possibilities to help dissect complex traits in animal science.

A large number of the oral presentations reflected the wide interest in better understanding gene function in animal species and how this can improve different aspects of animal prediction and/or welfare. The Functional Annotation of Animal Genomes (FAANG) initiative investigates genomic functional analyses for cattle, sheep, fish and chicken, which were widely discussed. Dr. Christa Kuhn from the Leibniz Institute for Farm Animal Biology introduced the new EC Horizon 2020 project entitled “BovReg,” which is part of the FAANG initiative. Gentec is a member of BovReg; Elda and Jiyuan participated in the informal team get-together. The latter also participated in a post-conference FAANG workshop on metadata validation and data submission. The instructor emphasized the importance of standardizing and validating data to facilitate effective data sharing among the FAANG community.

Another topic was the potential role of the microbiome and epigenetics for gene editing. This is a “hot area” in animal genomics research. Dr. Luís Montoliu (Campus de Cantoblanco) gave a comprehensive talk on the current situation of genome editing including the tools used and their potential application in animal science.

Whole genome sequencing and RNA-seq are increasingly used in animal genomics research. New sequencing technologies such as ATAC-seq and single-cell RNA-seq have also become more popular together with ChIP-seq for chromatin analysis. These new technologies and analysis methods give us new insights into the function and network of genes and the genome. Again, they are an integral part of FAANG and BovReg.

An unforgettable gala dinner was served in the main building of the Old Cathedral built between 1300-1600, on top of the La Seu Vella mound. ISAG organizers really showed their hospitality. We tasted local cuisine and red wine produced by a local chateau. Everyone enjoyed the authentic Spanish food and the great view.

 

“Attending the conference was a great experience, giving us an opportunity to tell others about our work, to talk with so many excellent researchers from all over the world, to learn about new research going on in the world, to broaden our horizons and keep improving our academic ability,” reported Jiyuan and Elda. “We appreciate that our supervisor, Dr. Graham Plastow, supported our participation.”

21st Century Solutions for Canada’s Dairy Industry

Where once genetic and herd management services to the dairy industry came from separate sources, Lactanet Canada now integrates these services under one organization.

As of June 3, 2019, founding partners of the new Lactanet (Canadian Dairy Network, CanWest DHI and Valacta—the leading dairy herd improvement organizations responsible for genetic evaluations, milk recording and knowledge transfer) can offer access to modern herd management through improved technologies and software and more meaningful data. Not only will these integrated services make life easier for farmers, Lactanet will also offer new services, using the same current resources. These services will be offered before the end of 2020, and include remote electronic collection of on-farm data, a national dairy cattle traceability system and genomic evaluations for feed efficiency,

While the objective in creating the partnership was not to save money (although operational efficiencies are predicted), Lactanet’s Chief Services Officer, Brian Van Doormaal, points out that fees for current services to farmers and the staff delivering them, are not projected to change nor are genetic evaluation services to the industry.

What Lactanet will do is: better position the dairy sector to manage business risk, take advantage of operational synergies and efficiencies, integrate genetics with management services, stimulate innovation of new products and services, and build on the strengths of each partner.

“The sector as a whole will benefit,” says Brian. “We’ll be able to help farmers tackle the challenges of the Canadian dairy industry, which include lower milk prices, increased farm debt load and rising interest rates.”

Lactanet’s governance structure is designed to reflect the three founding organizations, and focus on services to Canadian producers: every member of the Board is a dairy farmer. Three additional important industry partners have a producer appointment to Lactanet: Dairy Farmers of Canada, Semex Alliance and Holstein Canada.

“Holstein represents over 90% of all dairy cows in Canada,” explains Brian. “And Semex is the largest Canadian farmer-owned A.I. company with national reach. Dairy Farmers of Canada is the national body that represents all licensed producers from coast to coast. In this way, the Lactanet Board covers the vast majority of services to farmers. As well, working with a Board of nine producers, with the ability to name two additional external directors, allows us to be more nimble in these early stages and ensure success. The Lactanet governance model is scalable, if needed, as the industry decides how to best meet the needs of dairy farmers and remain globally competitive.”