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.”

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.”