Robert Mukiibi is finishing up his PhD in bovine quantitative and functional genomics related to feed efficiency. He’s been with Gentec for nearly four years. During that time, he has focused on improving feed efficiency in beef cattle through the genetic selection of more efficient animals using high throughput genomic tools. His research aims to identify genes and gene variants associated with feed efficiency through sequence transcriptomic data analyses of coding and non-coding species of RNA. The information obtained is then used to improve genomic merit estimation for breeding animals. Robert is also involved in imputation of genotypes from low density panels to high density and full sequence genotypes, and genomic prediction for feed efficiency traits in beef cattle.

This is where the Irish angle comes in. Canada and Ireland have common research interests in beef cattle genomics. In 2014, Robert’s supervisor Dr. Changxi Li at Gentec, UAlberta and Dr. Sinead Waters at Teagasc (the Agriculture and Food Development Authority, Ireland) were awarded a Teagasc-UAlberta Walsh Fellowship to work on the project: “DNA-based biomarkers for feed efficiency in beef cattle,” which helped support Robert’s own project: “Quantitative and molecular genetics of feed efficiency traits in Irish and Canadian beef cattle.”

“For my project, we are using the functional information of the bovine genome to improve accuracy,” says Robert. “I perform the gene expression, gene functional characterization analyses and genomic analyses in Canada. In Ireland, I perform the lab work to validate the gene expression results.”

Caption: Robert, Dr. Sinead Waters and Dr. Changxi Li at National University of Ireland, Galway

Robert has visited Ireland twice for his project, first in 2016 and again in 2018 with Dr. Li to enhance the joint research activities. During the 2018 visit, the pair presented at the National University of Ireland, Galway, and at Grange(see below). Robert’s Irish co-supervisor, Dr. Waters, is expected to visit Canada as part of the exchange.In 2017, Gentec hosted Teagasc’s Tara Carthy, who was working with Gentec’s Dr. Paul Stothard to identify structural variants in the bovine genome associated with important economic traits.

In Ireland, Robert worked at theAnimal Bioscience Research Centre Grange, one of the world’s leading beef production research facilities, outside a small heritage town called Trim in County Meath.

“Ireland really is as green as they say,” he winces. “It rains several times every day. It’s vital to carry an umbrella but it’s not always useful because of the strong winds.”

Similar to Gentec, the lab experience was all Robert could hope for. Cooperative and collaborative colleagues, unlimited access to lab tools and everything he might need to obtain reliable and reproducible results for the scientific community and industry. While there, Robert expanded on his social experience with visits to the pubs to see live bands, and watching Gaelic football. Such was the warm and welcoming working environment, that fellow students picked Robert up from his lodgings and brought him back—for which he was extremely grateful.

“The bus rarely runs on time and the frequency is very low,” he remembers. “So when it breaks down, I had to wait an hour for the next one.”

In terms of key points that might help other students decide where to study, Robert believes that Canada is a bit more student-friendly than Europe in terms of easily accessible healthcare, availability of student partner employment permits, availability of extra merit-based scholarships and affordable and efficient transportation through student passes. A major difference he highlights is the high cost of student accommodation in Canada compared to Europe.

Robert thanks Dr. Li and Dr. Waters, Teagasc, Alberta Innovates and the Department of Agricultural, Food & Nutritional Science at UAlberta for the wonderful opportunity of the Walsh Fellowship. He is already looking for a postdoc position for the fall.

“I’ve now lived out of my home country, Uganda, for more than 10 years in countries including Egypt for my undergrad, Sweden and the Netherlands for my MSc and now Canada for my PhD. So the next stop can be anywhere in the world. I’m open to suggestions.”

Hands-on practice helps student learning stick

The Ruminant Digestion, Metabolism and Nutrition course at UAlberta benefits from hands-on industry participation

ANSC461/AFNS561 is a “must-have” course for any student wanting to improve their knowledge and understand the principles of ruminant nutrition, digestive physiology and metabolism—and apply this knowledge in commercial dairy and beef operations.

“Industry contribution provides great opportunities for students to better understand the industry and put their skills in practice,” said course co-teacher and Gentec researcher, Dr Ghader Manafiazar.

One beef farm Blindman Beef and Bison Farm (check out the incredible photography) and one dairy farm Tuxedo Farm Ltd kindly volunteered to host the students and provide the required information for them to complete their project.

Blindman Beef and Bison Farm sits beside the Blindman River in the south-central region of Alberta, with about 300 Angus and Beefbooster cow-calf pairs. The farm backgrounds its own calves as a better marketing practice. Assar Grinde, the owner, is highly concerned about and focused on the animals’ welfare, practising antimicrobial stewardship and environmentally sustainability, and having third-party verification for the farm’s practices. Assar shared his pasture management, bale grazing, weaning, and grain processing practices in addition to feed and water analysis with the students.

Tuxedo farms Ltd. is a family owned and operated farm located northeast of Westlock, in North-Central Alberta. Diversification is a major goal. The farm feeds high-quality, home-grown corn, barley and hay to its dairy (337 cows, of which 285 milking cows) and beef herds. Management added 120 free-stalls in 2018, and will add more in coming years. The farm is equipped with advanced technologies, such as Herd Navigator and a body-condition scoring camera. Herd Navigator detects sick animals for treatment and those producing less than 10 L/day to go dry. Nelson Jespersen, the manager, asked his nutritionist, Jamie McAlister, and herd manager, Francis Kavanagh, to participate in our two visits, allowing the students to discuss many aspects of the dairy farm business and management in smaller groups with them.

At the end of the semester, teams of students presented their recommendations to Ghader and the farmers, with an opportunity for discussion and feedback.

“It’s one thing to learn theory in class,” says Ghader. “Learning by doing sticks better. Overall, the students appreciated the opportunity to act as a consultant and put their knowledge into practice.”

Ghader also invited Barry Robinson (a private consultant), Kris Wierenga (regional manager with Shur-Gain feed mills), Myrddin Jespersen (farm owner) and John Stephen (Senior Sales Professional with Elanco) to present on the opportunities and challenges in different segments of the industry. Barry talked about his experience as a nutritionist; Myrddin discussed the opportunities and challenges of owning and managing a dairy, beef and grain farm; John shared his insight about the pharmaceutical industry; and Kris talked about the commercial feed industry. This session encouraged students to look for the opportunities in these sectors and expand their networks.

“It’s important for industry to be part of this course,” says Ghader. “Their contribution allows students to see where they can fit their skills and what other skills they need before entering the workforce.”

One woman’s search for a research home

From the Middle East to Europe and North America, Marzieh Heidaritabar talks to Gentec about the meaning behind international science.

Already, as a thirty-something, Marzieh Heidaritabar has lived in six countries as part of her studies and career. Such is the life of a scientist, these days.

“I always knew I wanted to go abroad for my advanced degrees,” she says. “The level of achievement at European and North American universities is higher than at home.”

Building on a Bachelor’s in her native country, Iran, Marzieh won a European Master of science in Animal Breeding and Genetics (EMABG) scholarship. She spent the first year at the renowned SLU (Swedish University of Agricultural Sciences in Uppsala) and the second at the Norwegian University of Life Science (NMBU) in Sá.

“Wageningen University & Research (WUR) (in the Netherlands, where Marzieh completed her PhD in 2016 on genomic selection in egg-laying chickens) is my second home,” she says. “It’s a small—but highly social and connected—society of students. I was never bored.” Then, over to Aarhus University Foulum for a post-doc, where she already knew several researchers from collaborations with Wageningen.

“I was right about the European universities,” she says. “All of these are in small towns where students are the majority of the population. The facilities, computer labs and digital libraries are excellent, so are the teaching and technical support.

As a testament to the connectivity of the European science community, Marzieh didn’t have to learn any languages. With international reputations and a large international student body, almost all MSc courses are taught in English and the townsfolk are keen to practise their own language skills.”

During her PhD, she also spent several months at Iowa State University (ISU) in Ames, USA. “The ISU group is one of the best in quantitative genetics,” she says. “I learned a lot from my supervisors (Jack Dekkers is a long-time Gentec collaborator). People are hard workers and the group is so dynamic. I also met some faculty members and geneticists from other USA universities and companies.”

Then on to Canada. During Marzieh’s PhD, the Dutch company (Hendrix Genetics) that supplied her data also worked with Gentec CEO, Graham Plastow. Throw in some reminders about Gentec over the years through workshops, colleagues, some reading and fellow Iranians, and Marzieh decided to reach out.

Marzieh has been in Canada since late summer 2018. These days, she is working on swine data for the first time (data provided by Hendrix). She is exploring the potential benefits of whole-genome sequence (WGS) data to improve meat and carcass quality traits in genomic selection programs of purebred and crossbred pigs. Incorporating the biological information from WGS into genomic prediction models will lead to a better understanding of the genomic architecture underlying carcass and meat quality in swine.

Of course, there are pros and cons to moving around so much. Marzieh has learned about different research styles, communication styles, PhD content (North Americans expect PhD students to teach and take subject matter courses: not so in Europe), new cultures and lifestyles—an openness that hasn’t been available to her friends who chose to stay home.

“The disadvantage is that I always feel I’m not settled yet,” she says. “There’s a cost to physically moving your life from place to place. And there’s definitely an anxiety at the beginning about not being familiar with new towns, colleagues, culture and research. Special thanks to Dr. Plastow and other people from Gentec who welcomed me warmly so that I felt at home. I am very glad to be a member of Gentec.”

For someone who was raised to be quiet, it’s been a positive learning experience.

“I was shy,” she says. “Too shy to ask my supervisor for help. The student culture in Wageningen helped change that. You either get help or you don’t, but you have to ask! If I hadn’t left Iran, I wouldn’t be the person I am now.”

“Canada is ahead of the game when it comes to beef sustainability,” affirms Graeme Finn, a member of the Canadian delegation at the Global Conference on Sustainable Beef held in Ireland on October 9-12, 2018.

“What we’re doing here is right on track to keep the public informed. It’s good to see progress from the McDonalds’ pilot program to getting a cheque from BIX/Cargill for sustainable beef—and most of all, that other countries are looking to us for guidance. I’m pretty proud of where we are right now in the world.”

The Global Roundtable for Sustainable Beef (the conference host) is a global initiative that aims to improve the sustainability of the global beef value chain through leadership, science and stakeholder engagement/collaboration. It is the umbrella organization and governing body for initiatives in member countries, which includes Canada (hence our interest in this).

Caption: Canadian representatives at the conference

Of the 245 attendees, Canada had the biggest delegation: 15 people representing organizations as diverse as the Canadian Cattlemen’s Association, McDonald’s, A&W, BIX, Ducks Unlimited, World Wildlife Fund Canada, and three producers (including Graeme, who also represented the Canadian Roundtable).

On Day 1, Graeme took the Dawn Meats tour. Dawn Meats is one of the largest suppliers of beef into the McDonald’s system in Europe at the company’s fossil-fuel free (!!!) plant in Waterford. In 2017, the site became the first Irish food manufacturing company to be awarded BITC Ireland’s prestigious BWR (Business Working Responsibly) mark.

“Dawn buys all its meat from Verified Sustainable operations,” says Graeme. “No common market cattle. McDonalds does the same thing in Canada, so we’re aligned with Ireland on that. Cargill and McDonalds are the prime buyers of sustainable beef here. All our own beef goes into that chain, and we get the quarterly cheque.”

The tour also stopped at John and Catherine Powers’ farm in Waterford where calves are reared and finished as beef cattle for the McDonald’s Flagship Farm Program.

“It’s all bull meat,” says Graeme. “They don’t castrate any animals so, obviously, no synthetic hormones. It must be quite boisterous on that farm when the animals are young!”

Days 2 and 3 were in a more traditional conference format. Justin Sherrard, Global Strategist Animal Protein, Rabobank RaboResearch, Food & Agribusiness delivered the keynote address, focusing on leadership and the concept that the customer is always right.

“I didn’t totally agree with that,” points out Graeme. “How can customers be right if they don’t have the correct or the full information—or if they’ve watched Cowspiracy on Netflix? It makes sense that veggie burgers are trendy in a first-world urban setting but in developing countries, the cheaper option will always be meat. As their standard of living improves, they are moving towards more animal protein.”

Graeme presented on the impact of technology on producers and their operations. He believes the BSE crisis of 2003 drove producers to know their costs and to improve their winter management and grazing management—which turned out to be the best thing for the industry as it relates to sustainability.

“We already have traceability,” he says. “South Africa doesn’t even have RFID tags. The UK and Ireland have passports that follow every animal through the system throughout its life. It’s intense! They need to get with the Canadian model.”

Other presentations focused on the environmental side of sustainability, reducing emissions through innovative feeding strategies, sustainable beef production on the Canadian prairies and genetic improvement for animals on pasture.

Michael Lee, Chair of Sustainable Livestock Systems at Rothamsted Research, delivered the capstone address focusing on how livestock fit into the environment, not just as meat but also as wool fibre, cosmetics, leather, milk, fertilizer and beasts of burden. All biodegradable. Styrofoam… not so much.

“Attending a conference like this makes us more aware of where the trends are going,” says Graeme. “It’s important to know what’s going on in the world.”

…where the jobs come looking for you, not the other way round.

In his lab in the Faculty of Agriculture, Life and Environmental Sciences at UAlberta, Paul Stothard and his students pore over their computers and monitors. Stothard is a bioinformatician; that is, he uses computers and software to analyze DNA and protein sequences and to connect them to traits of interest or mutations that could have beneficial effects.

Typically, bioinformatics “starts” after somebody has generated enormous amounts of ACGT letters (the sequence), recorded them in a giant text file, and handed the file over. Stothard then has to manage these huge datasets so that the data are stored safely yet accessible to others in an organized way.

To do this, Stothard relies on powerful computing resources. The innocuous-looking screens and computers in the lab are just the interface that connects to a remote hive of computer clusters that have tens of thousands of processors and thousands of terabytes of storage. Then there’s the software…. Stothard and his team do a lot of computer programming.

“A lab might get a new device for measuring gene expression that produces different data,” he explains. “We simply can’t rely on—or wait for—commercial software packages to follow so we create our own. We publish the code, and it becomes open source for others to build on.”

And that, as they say, is where it all began. Stothard’s background is in molecular genetics. It’s as he was working in the lab, studying how an embryo nematode decides to develop into a male or female, that he realized the tools were inadequate.

“I started writing my own software. I enjoyed it, and people started asking if they could use it, too. I decided to do a post-doc in David Wishart’s lab in Computing Science, where I could really focus on that.”

Bioinformatics is one of the fastest-evolving fields around. One exciting direction it is taking relates to how DNA is sequenced. Currently, when the sequences arrive from the lab, the data are in billions of small pieces of about 300 nucleotides (the letters) long. Stothard and his team have to stitch them back together into whole chromosomes. It’s not that much fun.

“Thank goodness ultra-long read technologies are on the horizon,” he says. “We may one day get entire chromosomes as single reads. We’ll be able to catch differences between individuals that we can’t see now because of the breaks.”

As well, the cost of sequencing will continue to fall so that, in a few years, hundreds of thousands of individual people, cattle, pigs, plants can be sequenced. That will provide more enormous datasets to work from.

In practical terms, any trait that can be improved through breeding can be addressed using bioinformatics. Essentially it leads to faster genetic improvement and can lead to new diagnostics. Stothard and his team are working on a variety of projects. One is a mutation in Dalmatians and Bedlington terriers that causes copper toxicosis. Finding the mutation could lead to a DNA test, and breeders would know which dogs to avoid breeding. A similar test would have been extremely useful in the last 20 years when hip dysplasia was accidentally bred into German shepherd dogs. Everybody is familiar with those consequences.

Gentec’s Chief Executive Dog (ie; belonging to CEO Graham Plastow) is a Bedlington.

In livestock, bioinformatics can help identify which animals are more feed-efficient than others, more disease-resistant or even the breed history. All lead to higher profit margins for producers. Disease-resistance also has implications for better animal welfare.

“If anybody is interested in a career in bioinformatics, now is the time,” says Stothard. “Research groups are drowning in data. They have a real need for people who can manage and analyze large DNA sequence datasets. And industry as well. My students have gone on to work in companies developing drugs, tools for animal breeding and even for software companies. There are openings from the Master’s to the post-doc level. As long as the candidate can demonstrate computer programming skills (not necessarily a degree).”

His own team is stretched to capacity. “I have way more projects than time to do them,” he says.

In the fairly near future Stothard will be looking to hire another bioinformatician for his team who can provide assistance to multiple researchers and isn’t tied to any given project. One of the first places he’ll look is: https://bioinformatics.ca/job-postings/. If this is a career that might interest you, it’s a good place to start.

…For some, you have to put your rubber boots and hat on.

This point was driven home in July as the Gentec team once again stepped into the pasture to organize two field days: this time, however, in collaboration with the Foothills Forage and Grazing Association, whose geographic area spans much of south-western Alberta.

The theme for the events was the ongoing interactions and efficiencies that can be achieved by managing the forages, the cow herd—and the interaction between the two. And as is always the case at these events, participants picked up many unanticipated practical nuggets as part of the official agenda or over coffee between sessions as well as the expected information on the application of new technologies and / or the novel application of existing technologies.

The first event began at the Waldron Ranch Grazing Cooperative near Longview where our host and Ranch Manager, Mike Roberts, provided a historical perspective of the ranch and its aim of maintaining the traditional grasses that hold much of their nutritional value throughout the winter. The most significant message was that preventing fire and grazing are not natural, economical or sustainable. On the contrary, they result in reduced soil health, less nutritious feed for the cattle, and reduced grassland efficiency for carbon sequestration. Ed Bork of the University of Alberta’s Rangeland Research Institute expands on that theme here.

Other practical nuggets included details on how introducing a sheep herd turned a $15,000/yr bill to control leafy spurge into a separate profit-centre for the ranch as well as the Waldron’s transition away from wood fenceposts and barbed wire to synthetic posts that don’t decompose (or burn) and two-strand electric fence. This option is less expensive, lasts longer, and is much easier for wildlife to figure out… which is also much easier on the fence!

For the second event, Gentec headed north to the Didsbury area to sessions hosted by Sean and Holly LaBrie (Difficulty Ranch) and Morrie and Debbie Goetjen (Whiskey Ridge Cattle). Both operations talked of the challenges involved in raising cattle in hot, dry summers and cold, snowy winters leading to heavy reliance on cell, swath and bale grazing.

Their practical experience with respect to the cow-herd mirrors the increasing empirical evidence that is part of the EnVigour HXTM project… that fertility is the most important factor influencing the viability of the cow herd by a wide margin, and that significant benefits can accrue by managing hybrid vigour with the herd. Alberta Agriculture and Forestry’s John Basarab and Gentec’s own Graham Plastow expanded on the benefits (and the $$ numbers) of hybrid vigour in greater detail on both days.

Barry Irving came out of retirement to challenge us to rethink some of the things we think we know for sure but evidence says otherwise. For example, producers commonly believe that cows won’t eat shrubs—or will eat shrubs under duress but won’t gain weight.

Using the results of a number of research projects, Barry showed that cattle will browse shrubs (aspen and others) by choice, that they can gain weight by doing so, and that knowing this gives the producer an additional option in managing how they feed their cattle (and the feed composition of their forage plots by limiting shrub propogation) by varying grazing intensity and stocking rates. Barry specifically declined to speculate on the degree of enjoyment experienced by the cattle in the shrub study!

Perhaps reflecting/reinforcing the age-old power of toys on boys, Thompson Rivers University’s John Church’s presentation on the ability of drones to manage, monitor, and track animals from kilometres away through dense bush, day and night—and read individual ear tags from a height of 70+ metres—had ranchers dreaming of flying above the trees. More on that in an upcoming newsletter.

Most importantly… Thank You to the members and Executive of the Foothills Forage & Grazing Association, The Waldron Ranch Grazing Cooperative, and the LaBrie and Goetjen families for inviting Gentec to see and hear the challenges and opportunities that keep our province’s producers awake at night. Knowing the right questions to ask/answer produces better science from the researchers and better application from those who deliver the food to our plates.

How to get past the destructive Mountain Pine Beetle using genomics

Most of the presentation was spent discussing policy implications of the impact of the Mountain Pine Beetle, containment challenges faced in limiting its expansion and the potential to mitigate economic impact on a limited budget. As is being done in livestock, genomics can be used to investigate tree resistance to disease and pests. The result in this case was discovering how drought impacts gene expression in various species of trees, reducing their ability to fend off Mountain Pine Beetle attacks.

Similarly, newly-developed genomic signatures for various populations of Mountain Pine Beetles enabled experts to determine the geographic areas from which they were invading new territories. In turn, this allowed an improved risk assessment process to feed into forestry policy due to a better understanding of range expansion and spread dynamics.

The research on gene expression showed that degree of drought has a significant impact on a tree’s resistance or ability to repel a Pine Beetle attack. Combined with the latter work on genomic signatures, this led to policy development directing resource use towards activites that defend vulnerable forest areas in times of drought and target the reduction of beetle populations from where they are most likely to invade.

From there, the discussion shifted to tree improvement, pointing out that, as is the case with breed improvement in livestock, the three main areas of investigation are end-product quality, health and efficiency. This was more accurately summarized as wood and pulp characteristics, growth and yield, drought tolerance, nutrient use or efficiency, and pest and pathogen resistance. Just like cows!

Up next was an overview of the importance of an accurate and efficient system of forestry traceability. Industry-wide, half a billion seedlings are grown each year as part of Canadian reforestation efforts. This involves massive efforts in cone collection and seed extraction (among others) as part of the transplantation back into sensitive natural environments where an unintended species can have a significant impact on the environment and equally significant financial consequences for the corporation responsible for introducing them. Genomic traceability initiatives have already played a major role as a fail-safe means of determining that the intended genetics are delivered into the intended stands

In closing, the discussion turned to the future and how in forestry, as in medicine and agriculture, the promise is in the emergence of genomics-led precision initiatives as conservation tools as well as a means to advance high-value areas of the Canadian forestry industry … or better said, as a means to better the Canadian environment, outdoor experience and economy.

From Brazil’s fierce milkers to Canada’s placid eaters

“These are Girolandos,” says Valente. “They’re a cross between Holsteins and Gyr, more adapted to hot climates and ectoparasites. The down side is that they produce less and are more… uhm… reactive during handling than the European breeds.”

Valente’s main interest is the genetic approach to behaviour in farm animals, focusing on temperament in cattle. In Brazil, one of the projects he is involved in relates to milking temperament in Girolando and associating the trait with production and health and welfare aspects. These pictures were taken at one of the farms involved in the project, the Fazenda Floresta in Sao Paolo State, which has a large herd of Gyr and Girolando. Valente’s visit had one key objective: training the heifers.

“First milking is a big problem. Sometimes they go absolutely crazy, break everything and hurt themselves,” he admits. “So we try to get the heifers used to the parlour facilities ahead of time.”

The idea is to reduce their reaction (their flight zone) and teach them about their new lives. Brave volunteers guide them into the parlour without restraints, walk around them, introduce them to new noises and new equipment. The pictures below show the “novel object test” to assess the Girolandos’ general fear of novelty.

“In this picture,” says Valente, “a group of us from Sao Paulo State University are at Girolando Bulls’ Performance Centre in Uberaba, State of Minas Gerais, measuring the bulls for temperament.”

Due to the cost of collecting semen from Girolando bulls (and, no doubt, the danger to life and limb!), a preselection test is done instead. Since 2014, bulls are measured once a month for four months for temperament, which comprises 10 percent of the selection index. The other factors are andrological parameters and body capacity measurements.

~ ~ ~ ~ ~ ~ ~ ~ ~

In Canada, nothing nearly so adrenalin-pumping. As a postdoc, Valente works with Gentec CEO Graham Plastow and Gentec-associated researchers John Basarab (Alberta Agriculture and Forestry), and John Crowley (Canadian Beef Breeds Council) on feed efficiency as it relates to feeding behaviour in beef cattle.

“We know some animals spend more time at the feed bunk but are not more efficient than those animals that spend less time” he says. “So we’re looking at two traits: one for time at the bunk (duration) and the other for ‘head down’. The second one means they are eating not just hanging around.”

Valente found Graham Plastow and Gentec through another Canadian. Karen Schwartzkopf-Genswein (Agriculture and Agri-Food Canada, Lethbridge R&D Centre) is a visiting professor at Sao Paolo State University, where Valente was doing his PhD under Mateus José R. Paranhos da Costa (Faculty of Agricultural and Veterinary Sciences). There, the two developed a close professional relationship and co-authored a publication. When he was searching for an internship for his PhD, he asked her where he might study genomic tools applied to beef cattle in Canada. She recommended Gentec.

“Graham is an excellent connection,” he says. “He helped improve the quality of my PhD thesis, invited me for the postdoc, and now I have an opportunity to build a bridge between two like-minded organizations.”

Indeed, Plastow is keen to collaborate with the Empresa Brasileira de Pesquisa Agropecuária (Embrapa), the Brazilian agricultural research corporation, which has precious datasets from breed associations and phenotypes that could be useful in the Canadian context.

“Travelling between Canada and Brazil, especially to work on different projects… it’s quite gratifying,” concludes Valente.

Combining genetics and enriched environments could improve pig welfare in commercial systems.

Yolande Seddon became fascinated in the alteration of behaviour through genes and that some behaviour is “hard-wired” while studying animal behaviour and welfare as an undergraduate student in the UK. For her Master’s, she began to focus on pigs, investigating the effects of long-distance transport.

“I was amazed by how many factors there are to consider—and this is just one aspect of one industry in a much larger sector,” she says. “I decided to specialize to help make real improvements.”

Today, Seddon’s mandate is to improve pig welfare in current production systems, with a particular interest in fully-slatted systems. She admits that a number of welfare improvements could be made by moving away from slatted systems but the reality of sustainable production and affordable meat ensure their survival. She was recently awarded nearly $2 million from NSERC, USask and industry for a 5-year program to explore, among other things, how enriched environments and positive welfare can influence health and resilience to disease (see media coverage here and here).

Good pig welfare concerns how the animal is feeling and copes with its environment. So, good physical and mental health, no fear, not in want of anything, and able to respond effectively to challenges. In Canada, we want good well-being and good production to be efficient. However, if pigs fail to cope with challenges, chronic stress can develop, which can influence susceptibility to disease

“Generally, producers are aware of the link between welfare and meat quality. The challenges come when we look at behavioural needs,” says Seddon. “Animals are driven to perform some behaviours even when domesticated. When a sow is about to farrow, for example, she still wants to build a nest. However, space is at a premium, and bedding isn’t often used for hygiene reasons, so the sow’s ability to express nest building behaviour fully can be reduced.”

Seddon’s Alberta Agriculture Funding consortium funding will piggy-back (no pun intended) onto Gentec-associated researcher Michael Dyck’s current Genome Canada project.

On entering the nursery, 50% of pens will serve as controls and 50% will receive an enrichment routine that will continue as they enter the disease challenge, recover and exit the finisher. Individuals and pens will be compared for susceptibility to disease, immune response and genetic expression.

Every two days, the pigs will be exposed to new objects that have properties known to be attractive and can be destroyed, manipulated and chewed—but not eaten (pigs like to eat their enrichment). Examples include cotton ropes for chewing, rubber mats and jute sacks for rooting, Porcichew hanging enrichment, a sheet of tarpaulin for group interaction, and rubber hoses. To help the novelty (don’t forget—pigs are pretty smart!), items are removed and rotated so they won’t see them again for another two weeks.

A study in the Netherlands showed that enrichment increases resistance to disease. In this study, pigs had more space, comingling, shavings, branches and peat moss. After a challenge with PRRS virus and Actinobacillus pleuropneumoniae (APP), the pigs with enrichment cleared the PRRS virus sooner and only 7% had APP lung lesions vs 57% of pigs in the barren environment.

However, because the pigs may have been eating their enrichment, the effect on the microbiome is unknown. Seddon’s project will help break that down by identifying whether non-edible enrichment that brings novelty to the pens and offers pigs an opportunity to investigate can influence disease resistance.

So what does enrichment cost?

“The cost/benefit needs to be identified,” says Seddon. “But, a specific enrichment routine could be targeted at a specific time of production to enhance immune response. Or, if you’re building a new barn, you might invest in an overhead rail to automate enrichment rotation. You can buy purpose-built systems for that. But if production quality is important, you just make it happen.”

The premier event for researchers and professionals involved in the genetic improvement of livestock

Over 10 Gentec members attended this important conference. Gentec CEO Dr Graham Plastow chaired the fantastic session on gene editing which is a hot topic in livestock genomics in recent years. Over five days, workshops updated the genomics progress in both research and application in livestock, which significantly renewed my knowledge in genomics. The one-day field trip (sheep/deer farm) gave me a better understanding about animal breeding and production in New Zealand. The excellent conference program and social activities did wonders for my professional networking with people from academia and industry.

For me, the most attractive session was the genomics methods and tools program which spread over all five days. Powerful statistical methodology and tools have been well developed and improved in recent years, driven by the rapid increase number of phenotypes and genotypes. Single step GBLUP (SSGBLUP) is considered the most popular one in practical breeding since it can handle large pedigree, genotypes and various types of phenotypes simultaneously. SSGBLUP + APY (algorithm-proven young for easier G inversion) is widely used in the US to evaluate beef cattle and by pig-breeding companies (e.g. Topigs Norsvin and Genesus Inc.). However, SSGBLUP still needs to improve minor issues, such as the weighting of SNPs.

Another valuable session was on how to improve genomic prediction accuracy especially with whole genome sequence data, which has been a main research topic in Gentec under several projects in cattle and pigs in collaboration with our industry partners. According to a discussion with Drs Mike Goddard and Ben Hayes, they both thought that, theoretically, by adding the TOP SNPs selected from whole sequence, the accuracy of GEBV should be better or at least remain the same.

As many reports in the conference demonstrated, results from practice data are not always consistent. We faced a similar situation as described in the paper we published recently (Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants). We all agreed that possible solutions include increasing the number of training animals especially including the target breed, increasing the number of SNPs especially the causal ones, using Bayesian methods (e.g. BayesRC) and multi-omic data (gene expression and annotations).

Another interesting area was genomic studies in pigs. Several presentations talked about GWAS and/or genomic prediction for economically important traits in pigs we have studied widely at Gentec. Their results were quite comparable with ours. For example, important QTL were reported for the number of stillborn (SSC9) and the number of born alive (SSC2, 5, 9, 14). Many putative lethal haplotypes associated with sow fertility were detected, and the region on SSC14 was also detected in our Duroc pigs. There were also a few talks in hot-topic areas such as novel predictors or selection criteria for pig growth, pork quality and reproduction, such as hemoglobin levels and gut microbiome. We have investigated these topics in recent projects to improve resilience to disease through genomics.