The scientific sessions at the 2022 World Congress on Genetics Applied to Livestock Production  (WCGALP ) in Rotterdam, the Netherlands, covered many aspects of livestock genetics including genomic predictions (with subtopics of methodologies and tools, challenges, use of complete DNA sequence for genomic predictions), statistical genetics, animal health and welfare, animal breeding in developing countries, novel phenotyping tools, and utilizing genetic diversity. Gentec Research Associates Marzieh Heidaritabar, Liuhong Chen and Dan Hailemariam provide some insights here.

A topic Marzieh is interested in is how to improve the accuracy of predicting genomic breeding values to improve animal selection to enhance genetic progress in commercial livestock breeding programs. She notes that University of California Davis scientists have developed a novel method called “NN-LMM”, which incorporates intermediate omics features (such as gene expression, metabolomics and DNA methylation) by adding middle layers between genotypes and phenotypes. NN-LMM has significantly better prediction accuracy than the commonly-used (standard) single-step genomic prediction approach. This shows the added value of omics data in genetic evaluations and, in Marzieh’s view, this novel approach could be a more useful way than the conventional method of estimating the genomic breeding values in companies’ routine genetic evaluations . Gentec is investigating these areas as part of the international BovReg project.

Liuhong is particularly interested in new methods for genomic selection since it has revolutionized livestock breeding. The methods have evolved from classic approaches to two-step approaches and to single-step approaches which have become the standard. As a result, single-step genomic selection was one of the hot topics at the conference. What will next-generation genomic selection look like? Listening to the talks from top researchers around the world, one could imagine next-gen genomic selection would integrate multiple innovative technologies, such as precision phenotyping, alternative genotyping, machine learning, functional genomics, and multi-omics approaches (as above) as well as gene editing. Gentec researchers have been working on many of these fascinating areas. See some of our 2022 articles on gene editing here and here.

Liuhong presented a new approach that enables the parallel implementation of Bayesian methods (a statistical workhorse for large datasets) for genomic prediction. He is continuing to improve the approach so that it can run efficiently with whole-genome sequence data. He is also working with Gentec CEO Graham Plastow, Gentec Director of Beef Operations John Basarab, and AAFC/Gentec researcher ChangXi Li to develop approaches that use breed-specific haplotypes to improve the estimation of genomic breed composition, retained heterosis and multi-breed genomic predictions in beef cattle. He comments “Attending conferences like this provided opportunities to learn from others and stay at the forefront of genetics and genomics research in livestock.”

Marzieh also attended presentations related to animal health and well-being. Novel welfare-related traits are increasingly receiving more attention in breeding programs in relation to maintaining social license and being included in breeding objectives (using multi-trait selection indices), particularly for group-housed species like chickens and pigs. These animals interact socially and can affect each other’s phenotype, meaning that, besides the direct genetic effects of the animal itself, the indirect genetic effects of its housemates can impact the phenotype of the animal. This seems to be particularly important for aggressive interactions/behaviours. For instance, in pigs, social interaction traits related to aggression were moderately heritable, and there were positive genetic correlations between the aggression traits and pig skin lesions. New findings showed that social interactions are also relevant for beef and dairy cattle for welfare and disease transmission. Researchers at Wageningen University developed a novel method, an extension of the classic social genetic model, for the breeding value estimation for social traits in large groups. This method, along with proper recordings of social interactions, could be very applicable in animal breeding  (see here).

Another interesting presentation from Wageningen was on the development and validation of an approach for pig breeders to better predict the purebred-crossbred genetic correlation from phenotype and genotype data of parental lines (based on approximated genetic variance components of parental lines). This approach could also be applied for other livestock animals in which crossbreeding is the main breeding scheme. (This is another area where Gentec and partners are active in pigs and beef cattle, where the majority of the commercial herd is crossbred. A recent publication on our pig work is here. ) On the cattle side, Ben Hayes (University of Queensland), leader of the 1000 Bull Genomes  project and an adjunct professor at UAlberta presented new work on improving genomic prediction in crossbred cattle in Northern Australia. He acknowledged some older Gentec work as one of two approaches that enabled their innovation (see here ).

The phrase “in the age of genomics, phenotype is king” is one Mike Coffey (SRUC) introduced to us at different Gentec events. Not surprisingly the use of novel phenotyping tools received a lot of attention at WCGALP. The tools include video, GPS, sensors and milk spectra. Recording or tracking behavioural traits and dry matter intake with camera systems and using machine learning to analyze the mass of data generated shows great promise for hard-to-measure traits. Among the different machine learning algorithms, the use of artificial neural networks was emphasized, as it takes into account the non-linear relationships between variables. It is possible to automate computer vision for monitoring important behaviors (tail biting and lameness) in the pig industry (see here).  One example is the Virtual Tag (VTag) software that substitutes hand-annotated data to accelerate pig behavioural studies. A 3D camera technology has been developed by Danish researchers to measure feed intake and body weight on individual cows in commercial farms. A high squared correlation (R2 = 0.9) between feed intake measured with scales and cameras was reported.

Under the theme of Functional Annotation of Genomes, papers related to the discovery of causal genetic variants and recessive defects for different traits in different species were presented. One example was detecting recessive loci responsible for increased mortality in cattle. The researchers screened for homozygous haplotype enrichment/depletion in groups of females in different life trajectories and identified 34 deleterious haplotypes with frequencies ranging from 1.5 to 7.6%. A Gentec collaboration with this group identified a missense variant within the host Synaptogryin-2 gene significantly associated with PCV2b viral load. In this follow-on study, the Nebraska team generated a porcine kidney 15 (PK15) clone homozygous for the “favourable” SYNGR2 p.63Cys allele using in vitro CRISPR-Cas9 gene editing. Infection of this edited PK15 clone demonstrated a significant reduction in total PCV2b replication starting 48 hours after infection compared to wild-type PK15 cells.  A nice example of using gene editing to confirm the effect of causative mutations to help increase our knowledge of the underlying biology of complex traits such as disease resilience.

In summary, WCGALP 2022 was a successful event that brought together livestock genetics and breeding researchers around the globe to share their ideas and results on the challenges facing the sector. Improving resilience of livestock species to the changing environment including disease is another area where Gentec is very active and that was identified as an important approach for the future.

This month’s At The Grill feature by William Torres (former Research Manager at Cattleland Feedyards and popular presenter at Gentec conferences) tells us why cattle are NOT the villains of climate change, and how to argue that case.

Beef producers are under increasing attack by climate activists on the contribution to climate change cause by methane exhaled by cattle. Yet the world continues to lose common sense and deny the political weight this topic carries. Why is the obvious not so clear any more? If these politicians really cared about the environment like they say, they wouldn’t fly across the country for an impromptu photo op at the Calgary Stampede!

I’m not going to go into detail about how “bad” cattle are for the environment, instead let’s focus on the benefits of these ruminants.

First off, if ever you are defending the industry and/or are in an argument with an activist, NEVER—and I mean NEVER—just direct anyone to a scientific paper for proof of empirical evidence. When someone is arguing with emotion, they will never read a paper just for fun (Who does that, anyway?). Remember, this is like trying to convert someone to your religion, and telling them theirs is bad. If they’re not drinkers, why would you tell them to read John 2:1-11? That’s when Jesus converts water into wine. Just saying.

If you really want to present evidence, ask if they would watch a video? Let’s face it, most of us would rather watch something on YouTube than read a scientific paper. Here are some suggestions in my order of aggressiveness, lol

• Cows and climate. Cows and climate by Frank Mithloehner. Yes, I know he’s a doctor but if you push the science you’ll lose the emotional battle. Mention that he’s European and doing work in California, one of the most active states fighting environmental changes.
• How cattle impact climate change. How cattle impact climate change; a CBC report that summarizes all the great things Canadians are doing in under 3 minutes.
• Protestor Diets by Quick Dick McDick. As much as it may seem that this video attacks a vegan diet, it puts a visual demonstration of all the equipment and resources needed to provide such diet. We can all use that reminder!

From an environmental standpoint, cattle play a unique role in maintaining topsoil; they till and fertilize the land naturally. They promote biodiversity and protect wildlife habitat by grazing on land that would otherwise remain unproductive for humans. They reduce the spread of wildfires, providing natural fertilizer… and so much more. Additionally, we don’t just do this improperly, we actually take into account head numbers to land-water ratio. We CARE about what we do—and that is our emotional defence.  We are stewards of the land!

Beef is actually healthier and more sustainable than ever before. Thanks to innovation, education and improved efficiencies, we can produce the same amount of beef with one-third less cattle than in the mid-1970s. Industry initiatives have created policing guidelines and global organizations, such as round tables of sustainability, so that we don’t just say we’re going to do things better, we can prove that we are doing it. Such improvements are responsible for making sure that beef cattle production in North America is only responsible for ~3.3% of greenhouse gas emissions. Compare that to Canada’s road transportation sector (18% in 2018) and the oil and gas sector (20% in 2019)!

transportation and electricity, which made up ~56% of totals in 2016.

My final advice is to not argue but understand where someone is coming from. There’s a good chance that they might not understand what we do. After all, it’s not just a job, it’s a way of life.

The Rangeland Research Institute  and Gentec partnered up on July 20, 2022 to host a field day at the UAlberta’s Roy Berg Research Ranch  in Kinsella, Alberta. The event focused on innovations in land and animal technologies to build climate resilience and showcasing pioneering tools and approaches, such as precision ranching, virtual fencing, drone use, GrowSafe feed bunks and genomics tools.

“You can tell this is very valuable to producers as they are engaged and asking questions,” said Mark Redmond, CEO of Results Driven Agriculture Research (RDAR). This is the first time researchers and producers have been face-to-face since COVID-19 began.

One of the Field Day’s main goals was to demonstrate to producers the work being done by UAlberta, researching precision ranching technologies, their benefits, drawbacks, and development, all for the benefit of the beef industry.

With access to the ranch, Gentec can take advantage of the massive cattle resources and trait-measuring technologies like an integrated scale in squeeze chutes and GrowSafe Bunks that allow for measuring feed intake. The cattle at Kinsella (Angus, Charolais, Hays Converters and the Kinsella Composite herds), their DNA along with measuring technologies allow Gentec to produce genomics tools to improve sustainability and productivity.

The Field Day had an unofficial goal as well: to demonstrate the collaboration of institutions that share the commitment to improve the productivity of the beef industry. Although the event was hosted by the Rangeland Research Institute and Gentec, people from different organizations had the opportunity to talk and present. Carolyn Fitzsimmons from Agriculture and Agri-Food Canada and Research Lead at the ranch welcomed attendees and talked about GrowSafe. Susan Markus from Lakeland College spoke about replacement heifer selection, and John Church from Thompson Rivers University spoke about using drones to manage rangeland. Master’s students from UAlberta also spoke about their projects at the ranch, along with Diego Martinez Mayorga, a student working at Gentec this summer, who spoke on genomics tools for terminal sire selection.

The event’s overarching theme was precision ranching, which is all about “putting the right animal in the right place at the right time,” says Edward Bork, professor at UAlberta and Director and Mattheis Chair in Rangeland Ecology and Management.

Attendees were taken on pasture walks where presenters from UAlberta spoke about their research projects and the benefits to the Alberta cattle industry. Visitors were treated to demonstrations of John Church’s “flying border collie”, AKA drones, and saw a grazing line in the middle of a pasture where a virtual fence stood, investigated the GrowSafe feed bunk system, and heard from experts in precision ranching tools. Ed Bork stated that “[UAlberta] is the industry test run, globally”, referring to its status as a global leader for rangeland ecology and rangeland management research.

The day concluded with thanks from UAlberta to producers for coming out and learning about the work being done.

“I’ve been coming for a long time” says David Andrews, Gentec’s Board Chair. “There’s always lots to learn every time, always something new. You get to actually interact with researchers, and this is a spectacular facility for research”.

One cow/calf and backgrounding producer expressed his appreciation, declaring that this was a “very useful day”. He was excited about the new technologies in development, and saw the applications for his own operations today. As a multi-generational farmer, he expressed his eagerness for his children and grandchildren to put to use the tools seen at this Field Day to real life:

“I wish I had 20 more years to see it all happen,” he said.

Jacqui Gironella and Diego Martinez Mayorga

Livestock Gentec

Farm animals who interact socially can affect each other’s phenotype, meaning that the indirect genetic effects of their pen-mates can impact the phenotype of the individual animal. This seems to be particularly important for aggressive interactions/behaviours. For instance, in pigs, social interaction traits related to aggression were moderately heritable, and there was positive genetic correlation between the aggression traits and pigs’ skin lesions. Tail- and ear-biting are the most common behavioural vices in growing-finishing pigs. Besides being an important welfare problem, they also have economic repercussions due to reduced weight gain, on-farm veterinary treatment, reduced carcass weights and condemnations.

Social interactions are also relevant for beef and dairy cattle for welfare and disease transmission. For example, if welfare-related traits like the foot structure of Angus cattle are added to profit-driven selection indexes, recording levels increased and the accuracy of the evaluation for these traits improved. Researchers at Wageningen University developed a novel method, an extension of the classic social genetic model, for breeding value estimation for social traits in large groups. This method, along with proper recordings of social interactions, could be very applicable in animal breeding.

Using genetic selection by including indirect genetic effects greatly improves the interaction among pigs by reducing damaging behaviour. However, environmental factors, such as the number of pigs/pen and diet, are crucial in achieving the desired goal. Building on work done in collaboration with researchers at Wageningen and Topigs Norsvin, Gentec (Graham Plastow, Clover Bench and Elda Dervishi) and the Swine Research and Technology Center are leading a project to develop management strategies to monitor and manage tail- and ear-biting in pigs. Live observations focus on counting skin lesions and determining the severity of biting. However, live observation can miss behaviours of interest because it only takes place for a short time during the day. Video recordings are monitoring feeding, drinking, and tail-biting behavior every Monday for 8 hours. In combination with saliva and blood analysis collection, we hope to provide a more complete picture of these behaviours. Welfare-related traits, like the number of skin lesions, can be added to selection indexes to improve the accuracy of the evaluation for these traits. We can also monitor the frequency and time the pigs spend interacting with the enrichment objects (for example a KONG).

Overall the results may lead to new recommendations for the swine industry on how to avoid and manage tail- and ear-biting. In addition, it might inform welfare-related codes of practices in Canada.

BEEF

A machine learning approach for predicting the most and the least feed-effficient groups in beef cattle Shirzadifar, A.; Plastow, G.; Basarab, J.; Miar, Y.; Li, C.; Fitzsimmons, C.; Riazi, M.; Manafiazar, G.

From BovReg (and other projects eg GC Resilient Dairy etc)

Accuracy of genomic prediction of dry matter intake in Dutch Holsteins using sequence variants from meta-analyses Gredler-Grandl, B.; Raymond, B.; Chitneedi, P.K.; Cai, Z.; Panzanilla-Pech, C.I.V.; Fischer, D.; Bolormaa, S.; Chud, T.S.; Wang, Y.; Li, C.; Villanueva, B.; Fernandez, A.; Kuehn, C.; Lidauer, M.H.; Pryce, J.E.; Plastow, G.; Baes, C.F.; Charfeddine, N.; Veerkamp, R.F.; Bouwman, A.C.

Multi-dimensional functional annotation of bovine genome for the BovReg project Moreira, G.C.M.; Dupont, S.; Becker, D.; Salavati, M.; Clark, R.; Clark, E.L.; Plastow, G.; Kühn, C.; Charlier, C.

Comparative analysis of CAGE-Seq across tissues reveals transcription start sites unique to cattle Salavati, M.; Clark, R.; Becker, D.; Kühn, C.; Plastow, G.; Moreira, G.C.M.; Charlier, C.; Clark, E.L.

OTHER BOVINE

Functional SNPs and INDELs within regulatory elements associated with mastitis in Holstein cow using -OMICs technologies Asselstine, V.; Medrano, J.F.; Stothard, P.; Miglior, F.; Karrow, N.A.; Baes, C.F.; Schenkel, F.S.; Cánovas, A.

PIGS

Genome-wide association analyses and genomic prediction for pork meat quality traits using whole-genome sequence Heidaritabar, M.; Huisman, A.; Bink, M.C.A.M.; Charagu, P.; Plastow, G.

Prediction of breeding values for feed intake in pigs using individual versus group records along with correlated traits Zhang, C.; Kemp, R.A.; Dekkers, J.C.M.; Plastow, G.S.; Gao, H.

Multi-trait genomic estimation of genetic parameters for growth and carcass traits of Duroc pigs Akanno, E.C.; Thekkoot, D.M.; Zhang, C.; Bierman, C.; Plastow, G.; Kemp, R.A.

Large-scale cis-eQTL analysis of gene expression in blood of young healthy pigs using PigGTEx Kramer, L.M.; Teng, J.; Lim, K.S.; Gao, Y.; Yin, H.; Bai, L.; Liu, G.E.; Zhang, Z.; Fang, L.; Plastow, G.S.; Tuggle, C.K.; Dekkers, J.C.M.

Indicators of disease resilience from complete blood count and in vitro immunoassays data from young-healthy pigs Bai, X.; Cheng, J.; Fortin, F.; Harding, J.C.S.; Dyck, M.K.; Dekkers, J.C.M.; Field, C.J.; Rogel-Gailard, C.; Blanc, F.; Plastow, G.S.

GBP5 PRRSV resistance gene had no effect on pigs’ infectivity or susceptibility in a trial simulating natural infections Chase-Topping, M.E.; Plastow, G.; Dekkers, J.; Fang, Y.; Gerdts, V.; Van Kessel, J.; Harding, J.; Opriessnig, T.; Doeschl-Wilson, A.

Genetic relationships among immune response traits of young healthy pigs evaluated by immunoassays Bhatia, V.; Schmied, J.; Cheng, J.; Bai, X.; Mallard, B.; Fortin, F.; Harding, J.C.S.; Dyck, M.K.; Plastow, G.S.; Field, C.J.; Rogel-Gaillard, C.; Blanc, F.; Piggen Canada; Dekkers, J.C.M.

Methods and Tools: Software and Computing Strategies

Subsetted orthogonal data augmentation for fast parallel implementation of Bayesian models for whole-genome analyses Chen, L.; Plastow, G.

The stage was set on July 22, 2022, for over 100 kids from central Alberta to find out what their 6-month effort yielded. Members of 4H clubs had been feeding a steer through the winter, and were all keen to learn how their steer carcass placed in a regional and provincial competition. Oscar Lopez Campos from Agriculture and Agri-Food Canada graded the carcasses for both competitions. But before getting those all-exciting results, the 4Hers toured Olds College and attended a presentation on the beef market.

With this backdrop, enter Livestock Gentec. In the corner of the auditorium, on a foldable table sat reports with the name of each 4Her and the CCIA number of the steer they raised. Inside each report was an introduction to genomics, several individualized genomic values (genomically-enhanced gEPDs, a Feeder Profit Index value, genomic breed composition and genomic retained heterozygosity) and a description of each tool. This way, each 4Her could get a report on the expected performance of their steer/steer’s progeny, the steer’s breed makeup and the amount of hybrid vigour present in that animal—all from a small hair (DNA) sample. That might not seem significant to a 10-year-old 4Her but, in commercial operations, these data could be a deciding factor between a profit or loss when selling a given animal.

For Gentec, the benefits of attending 4H events and being involved with this organization are clear. We are reaching out to the future ranchers of Alberta and introducing them to a novel, easy and a relatively inexpensive way of gaining a large amount of information on their animals. Instead of having to backtrack through hundreds of records and pedigrees of sires and dams, they can get accurate gEPDs from a single hair strand.

While some of the 4Hers “get it”, plenty of them had no idea what we were here for. Parents, too. As one put it, “We thought you guys were here to make sure the carcasses weren’t swapped for the competition. We had no idea you could predict performance from DNA.”

Beef Industry Liaison Clinton Brons quickly changed that lack of knowledge with an introduction and appreciation for Gentec’s funders, as did Knowledge Translator Diego Martinez with a short presentation on the genomic reports. Soon after, parents and kids collected their reports and the Gentec’s team answered questions.

Questions ranged from what the Feeder Profit Index is, what the genomic breed composition of an animal tells them and how hybrid vigour impacts replacement heifers and cows.

Over 130 4Hers have been exposed to genomics through these reports since April 2022 so… does that mean that Gentec has 130 new producers willing to test their herds genomically? Not quite. Over the past few 4H events, we’ve seen that some parents are keener than others, ask for more information and even provide their contact for follow up. And some 4H leaders/executives have already introduced this tech to their farms, like Paul Franz who spoke to Gentec earlier this year. This showcases the importance for research organizations like Gentec to reach out to grassroots organizations like 4H to communicate and demonstrate the validity and importance of tools and resources that research yields for the industry.

The 4H experience in 2022 has been fantastic for Gentec as it has shown a new approach to share information. The approach is two-fold: 1. Educate young farmers about genomics so they might be willing to use these tools when they take the reins of an operation, and 2. Give young kids the information with the hope that Dad/Mom or Grandpa/Grandma read it, like it and use it on their farm (or at least reach out for more information).

It is Gentec’s mission to develop validated genomic solutions to improve the competitiveness of the beef industry. Collaborating with 4H has given us the opportunity to increase trust in our validated tools, which will overall increase the productivity and sustainability of the Canadian beef industry.

If you are a 4H member/parent/leader interested in collaborating with Gentec—or if you are a producer interested in talking to a Gentec representative about genomics or possible research projects you could be involved in, reach out to us at lsgentec@ualberta.ca.

By Diego Martinez Mayorga