If eating better and exercising seem like daunting challenges for the New Year, how about additional data transfer and structural variant detection? That’s just a small part of researcher focus this past year as three genome projects showed promising results and strong potential for 2017.
Genomics of Swine Health-2 Project
Formally titled “Application of Genomics to Improve Disease Resilience and Sustainability in Pork Production”, this project had a busy first year with the establishment of project accounts, animal models, new research collaborations and national and international partnerships. The project team published 15 papers, made 26 presentations at national/international conferences and prepared 18 public press articles.For Activity 1 – Animal Models to evaluate and select for disease resilience, in-barn High Immune Response (HIR) testing protocols were developed. Animal testing was initiated in year 1 and will be on-going throughout the remainder of the project. In addition, a novel and robust natural disease challenge model was successfully developed that has already garnered interest from other national and international researchers and stakeholders.
For Activity 2 – Modulating Host-Pathogen Interaction to improve disease resilience, pilot experiments were conducted to develop laboratory protocols to investigate host-pathogen interaction using in-vitro organ culture (IVOC) and intestinal epithelial cultures. This research will be on-going in year 2. The pig gut microbiome research will continue in years 2 and 3 to establish baselines for microbial variation in the GI tract of the pig and to characterize relationships between immune responses to vaccination and gut microbiome.
For Activity 3 – Next Generation ‘omics, the analysis of data originating from Activities 1 and 2 will continue in year 2 to estimate genetic parameters for disease resilience and performance phenotypes. Preliminary analysis will also be initiated to determine the relationship between genotypes and resilience phenotypes.
For Activity 4 – GE3LS (Genomics and its Ethical, Environmental, Economic Legal and Social Aspects), research is on-going in year 2 to understand how the public sees the importance of disease resilience in pig herds. It will also evaluate how consumers might make pork product consumption decisions and their willingness to pay for pork products if they are worried about human health, animal health or animal welfare.
Increasing Feed Efficiency and Reducing Methane Emissions Through Genomics
Among the 2016 accomplishments was securing a partnership with a commercial dairy farm to collect real on-farm data from a commercial herd. Over 200 GrowSafe bins will be installed at this commercial dairy farm to collect data on feed intake so researchers can identify links between the animals that are more feed efficient and their genomic information.
As well, analyses were performed to choose approximately 50 animals for sequencing. This data will be added to existing sequence data on dairy cattle. The data will be mined to look for variations in the genome that are linked with animals that are more feed efficient and that produce less methane.
For 2017, the project has some ambitious goals. Chief among them is creating a secure database for housing data collected by the project. This includes data that is being collected at the University of Alberta and the University of Guelph research dairy herds, as well as data collected at the commercial dairy farm. It also includes data that collaborating partners throughout the world (USDA, UK, Switzerland and Australia) will contribute from their research projects. Combining data from different countries makes the genomic predictions for feed efficiency and methane emissions more accurate.
In addition, whole genome sequencing on 50 animals will be completed in 2017 and the data will be mined to find structural variants that are associated with increased feed efficiency and reduced methane emissions.
The year ahead will also see work beginning on RNA-Seq, also known as whole transcriptome shotgun sequencing. This will provide information on gene expression levels in animals that are more feed efficient and help researchers better understand the underlying mechanisms that render certain animals more feed efficient.
Development and Deployment of MBVs/gEPDs for Feed Efficiency and Carcass Traits that Perform in Commercial Beef Cattle
Under Activity 1, bioinformatics pipelines are being developed and testing using real data is in progress; variant annotation method approaches are being tested. Additional sequence data have been received from a collaborating institution. 2017 will see more data transferred and continuation of structural variant detection and variant annotation.
Activity 2 saw 336 industry crossbred and 417 composite/research cattle completing feed intake testing in southern Alberta; carcass phenotyping is also complete. LD genotyping of approximately 2200 samples is completed and the data is being tested for quality control for use in a genome-wide association study (GWAS); results of parentage, genomic breed composition, and retained heterozygosity have been calculated and delivered in aggregate to the industry partner. In 2017, 1800 more samples will be collected from industry partners for genotyping.
Progress was also made with Activity 3 in developing a production system model to identify breeding objectives for maternal and terminal scenarios. Three selection indices are to be developed, including maternal, terminal, and “green” (i.e., “environmental”, developed by leveraging data from projects collecting methane phenotypes).
Finally, Project Management Committee and End-User Committee meetings have taken place in regard to Activity 4 and will continue in 2017.
All things considered, it was an impressive first year that offered high hopes for 2017. That’s not to say that eating right and exercising aren’t good resolutions; but if you can work in some structural variant detection and annotation along the way, so much the better.