Gentec Research Highlights
Livestock Gentec Reference Database
Since Livestock Gentec’s founding in 2010, phenotypes (physical traits) and genotypes have been compiled from over 27,000 beef cattle, the majority of which are commercial crossbred animals located in Western Canada. In addition to growth, reproduction and carcass traits, the database also includes difficult to measure traits such as feed efficiency and methane emission. This specialized bovine data exists nowhere else and allows for the development of genomic tools and more accurate molecular breeding values specific to Canadian beef cattle.
Every year, researchers with Livestock Gentec add new phenotype and genotype data from both research (Lacombe and Kinsella Research Stations) and commercial beef cattle. This proprietary database allows Gentec to be a leader in genomics research in Canada as well as a valuable partner to industry, with the goal of bringing the benefits of commercial genomic tools to beef producers.
In the spring of 2021, the Livestock and Forage Centre of Excellence (LFCE) at the University of Saskatchewan was awarded $6.75 million by the Canada Foundation for Innovation for a new project, “Integrated Omics for Sustainable Animal Agriculture and Environmental Stewardship” also know as “IntegrOmes”. This project, with more than $15M in total funding, brings together experts in genomics, microbiomics and bioinformatics, as well as reproduction, nutrition and cattle health, to address challenges in the beef industry related to disease management, fertility improvement and environmental sustainability. The aim is to make is easier for cattle producers to identify and breed cows with desirable traits such as meat quality, disease resistance and production efficiency, and with better adaptation to their environment.
Graham Plastow (CEO of Livestock Genetc) is a partner on the IntegrOmes project and will provide expertise and data related to genomics. In addition to collecting phenotype and genotype information, the project will also establish a biobank at LFCE that will facilitate the collection of genetic material for the beef industry, as well as for bison conservation efforts using tools developed by Gentec’s Paul Stothard. Outcomes for the project include the development of genomic tools to improve selective breeding in the beef industry as well as rapid diagnostic tools for diseases and antimicrobial resistance.
In 2017, Delta Genomics and researchers led by Dr. John Basarab (Head of Beef Operations for Livestock Gentec) released the first made in Canada genomic tool for Canadian crossbred cattle producers, EnVigour HX™, which provides parentage, breed composition, and a Vigour Score that measures hybrid vigour. This genomic tool was developed from 1966 crossbred steers and heifers characterized for feed intake, feed efficiency and performance traits, with another 5053 slaughter heifers and steers characterized for carcass quality traits. All animals and potential herd bulls were genotyped, and the data was used to deploy sire assignment, genomic breed composition and genomic Hybrid Vigor Scores on progeny, sires and dams to 14 commercial beef farms through Dr. Troy Drake and the Herdtrax software program.
EnVigour HX enabled producers to design crossbreeding strategies that will optimize hybrid vigour in their cows, thus increasing fitness traits such as fertility, stayability, adaptability, general health, and lifetime productivity. Fertility is critical to environmental stewardship by maintaining a smaller cowherd that generates less carbon waste but still meets market demand, and to financial sustainability by reducing costs with fewer animals and increasing the pounds weaned per cow exposed. The economic benefits associated with maintaining high hybrid vigor in the cowherd are approximately $160/cow/year cumulative over five parities. In 2019, Delta Genomics granted a license to Neogen Canada for EnVigour HX™, which has been integrated into the Igenity® Beef suite of products and marketed in Canada, USA, Scotland, Australia, Brazil and China.
The global Dry Matter Initiative was started in 2011 with the goal of building an international database of phenotypes (individual dry matter intake) to enable the development of genomic evaluations for dairy cattle feed efficiency. The project included Canada (Livestock Gentec and its partners), Denmark, Germany, Netherlands, Ireland, the UK, Spain, the US, Australia and New Zealand. Gentec’s participation was supported via a series of Genome Canada projects beginning with the Canadian Cattle Genome Project (see above) and most recently the Resilient Dairy Genome Project led by Christine Baes at the University of Guelph. As a result, Lactanet Canada made history in April 2021 by publishing the first official Feed Efficiency genetic evaluations for the Holstein breed. Canada was one of the first countries around the world to deliver national genetic evaluations for feed efficiency. The project is continuing to build and mine the database including detailed analysis as part of the BovReg project (below).
BovReg was established in 2019 and is led by researchers in Germany and France with $9 million in funding from the European Commission. The goal of the project is to develop a comprehensive functional annotation map of the bovine genome, generating knowledge to improve genomic prediction of important traits with a focus on feed efficiency and animal health. 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).
Based on Livestock Gentec’s work with FAANG (below), samples from Kinsella cattle are being analyzed in the BovReg project with European funding. The samples from Gentec were considered high impact, due to the diversity of the composite breed and on-going selection for animals with extreme differences in feed efficiency and methane emission. Ninety-six samples were shipped to Europe for analysis and they are 1 of only 3 populations to be included in the project. Results from this project will bring detailed knowledge on cattle traits with respect to robustness, health and biological efficiency. The know-how from BovReg should also be particularly applicable in small cattle breeds of regional relevance and distribution and thus contribute to the conservation of biological diversity in farmed animals.
Functional Annotation of Animal Genomes Project
The FAANG Consortium was established in 2014 with the goal to support and coordinate the international community in developing reference functional maps of domesticated animal genomes. Functional maps provide information as to which parts of the genome are functional, considering time, context and location, contributing to a greater understanding of predictive biology. The FAANG Consortium created a framework for organizing data standardization, collection and sharing from all collaborators.
Livestock Gentec is a collaborator in the FAANG Consortium, contributing genomic information for the bovine reference population. Livestock Gentec partnered with the University of Guelph and University of California, Davis to receive training in the bioinformatic analysis of FAANG assays. Tissue samples were collected from 17 crossbred animals and a subset of these samples are being analyzed in the European Commission BovReg project (above) and the data submitted to the FAANG database.
Gentec’s collaboration in this project aims to improve the characterization of the bovine genome to better predict complex phenotypes such as fertility, feed efficiency, disease resilience and carcass and meat quality. This will reduce the cost of production and reduce the environmental footprint of Canadian beef production. Gentec’s integration of research efforts with FAANG also served to build on its contribution to the international 1,000 Bull Genomes project (below).
1000 Bull Genomes Project
The 1000 Bull Genomes Project is an international effort to sequence the entire genome of beef and dairy bulls to improve the accuracy of genomic predictions and develop genomic tools to increase the efficiency and sustainability of beef and dairy production. The Canadian arm of this project was the Canadian Cattle Genome Project, which included cattle sampled from Alberta and across Canada by breed associations and researchers from Livestock Gentec. The Alberta populations included research animals from the AAFC Lacombe research station and the University of Alberta’s Kinsella research station. These research animals were crossbred or composite animals with purebred, crossbred or composite sires and were selected based on number of progeny and relationships to animals with feed efficiency and meat quality measurements.
This internationally collaborative project has contributed to a wealth of knowledge on the utility and use of sequence data that has benefited the cattle research community and beyond. The vast amount of data generated has also led to the discovery of deleterious mutations, facilitated genome-wide associations for complex traits, and improved the accuracy of genomic predictions. These benefits alone are worth millions of dollars to the beef industry and will lead to improvements in efficiency and sustainability of cattle farming.
Porcine reproductive and respiratory syndrome (PRRS) is one of the costliest diseases in the pork industry, impacting reproductive health, growth efficiency and mortality rates. The PRRS Host Genetic Consortium (PHGC) was established in 2007 with funding from the US and then Canadian groups led by Gentec in order to investigate how host genetics affect PRRS virus (PRRSV) infection, with the goal of using selective breeding to reduce the occurrence and/or severity of PRRS on the pork industry. The consortium brings together numerous stakeholders across North America, including producers, vets, industry, and researchers. Livestock Gentec has contributed genomic, immunological and trait data to the consortium.
To date, a major gene has been located on the porcine genome that is associated with the host response to PRRSV. Pigs can now be screened to determine susceptibility to PRRSV, with less susceptible animals showing quicker recovery times and increased growth rates. A genomic indicator for host antibody response to PRRS has also been identified, which could result in vaccine response being a selection trait for future breeding. Research is also continuing through Genome Canada with the industry group PigGen Canada to determine the effect of genomic selection for pigs less susceptible to PRRS on other diseases and important traits (i.e. meat quality and lifetime performance).
50K SNP Chip
In total, 99.9% of the DNA sequence is identical between cattle; the 0.1% that is different includes genes (which are the instructions for all traits of an individual animal) and single nucleotide polymorphisms or SNPs. SNPs are a single point in the DNA sequence that can be different between animals and there are around 4 million SNPs in the cattle genome. SNPs can be used as markers to identify genes that are different between cattle, and thus are associated with different traits, such as calving ease. To select for animals with desired traits, the SNPs associated with that trait must be identified and then animals can be tested for the presence of those SNPs.
SNP chips are used to identify SNPs present in an animal’s DNA. Researchers at Livestock Gentec helped to develop the first of these tools for any livestock species, the Illumina 50K Bovine SNP Chip. This enabled identification of 50,000 different SNPs spaced throughout the bovine genome representing a huge reduction in the cost per SNP datapoint (>1,000 fold). This was achieved in collaboration with the United States Department of Agriculture (USDA) Agricultureal Research Services (ARS), the University of Missouri and Illumina, the 50K Bovine SNP Chip revolutionized the field of genomics in cattle and subsequently all livestock species. With a vast array of SNPs measurable, the door was opened for more accurate and in-depth associations between genetic markers and desirable traits. The reduced cost of genomic testing, for both research and commercial purposes, paved the way for more dense Chips (700K) and cheaper, more targeted chips.
The 50K Bovine SNP Chip was used to drive genomic testing of bulls with increased accuracy, leading to more precise and effective genomic selection of superior animals.