While many cutting-edge techniques are now routinely applied in the medical field, the use of such genomic and metabolomic tools in agriculture is lagging behind. The Applied Genomics Centre is focused on using these tools to solve various challenges faced by industry partners in the agriculture and health sectors.
Animal & Plant Agriculture
Advances in agricultural science allow for increased food yields, improved animal health and the development of more sustainable farming practices.
Here are a couple of examples of how our lab is using genetics and metabolomics to support current agriculture partners as they improve farming practice and product development:
Varietal Development and Consistency
Different varieties of a plant species can have very similar appearance (phenotype) throughout different stages of growth and development, even when their genetic information (genotype) is different. By looking at the genetics of a plant, a grower can be much more confident of the variety at any stage of development from seed to adult.
The Applied Genomics Centre has a range of tools - including DNA microsatellites, single nucleotide polymorphism, next-generation genotype by sequencing and real-time quantitative polymerase chain reaction (PCR) - that can be used to determine the genetic 'fingerprint' (genotype) of any individual plant for accurate identification of species, subspecies, strain or variety.
These are being used in the lab to ensure varietal consistency for our industry partners during product development of numerous crops, including ornamental plants, fungi, and hops. Genetic fingerprinting is also used to aid in product registration and in securing patents.
Current Projects
- Ornamental Plant Genotyping
- Industry Partner: Van Belle Nurseries
- Hops Genotyping
- Industry Partner: Greenflora Greenhouses
- Biocontrol Agent Development
- Academic Partner: KPU Institute for Sustainable Horticulture
Microbe Detection
Microorganisms, including bacteria and fungi, are known to be critical in soil health and fertility, as well as the health and disease of livestock. It is now accepted that in many cases the number of beneficial (symbiotic) microorganisms and their combined genetic information far exceed that of their hosts.
On the other hand, some of the microorganisms can cause moderate to serious disease (pathogens). The relationship between symbiotic and pathogenic microorganisms and their eukaryotic (a cell with a clearly defined nucleus) hosts are complex.
However, recent advances in DNA technologies, such as quantitative PCR and DNA sequencing, have revolutionized the ability to detect and understand microorganisms in animal hosts.
The Applied Genomics Centre uses custom real-time quantitative PCR assays designed in the lab to detect the presence and abundance of pathogens in a variety of sample types, including bodily fluids and soil samples. Detection of these pathogens is more accurate and faster than traditional culture methods and can have important implications for soil and livestock health. Currently assays are in development for bacteria, fungi, and nematodes (roundworms).
Current Projects
- Bacteria Detection in Dairy Cows
- Industry Partners: WestGen, Semex, Boviteq
- Nematode Detection and Quantification in Soil
- Abbotsford Agriculture Centre, Ministry of Agriculture
Metagenomics
The Applied Genomics Centre is currently using next-generation sequencing to characterize complete bacterial communities by targeting a region of the 16S rRNA gene unique to bacteria. Among other purposes, this metagenomic analysis can be used to to investigate gut health in animals by studying fecal bacterial content, or to create a profile of the bacterial population present in a soil sample, leading to a better understanding of the impact of the microbiome (a collection of microbes) on plant production and health. Future research will expand our metagenomic analysis to allow for further insight into microbial and microorganism communities.
Current Projects
- 16S Metagenomic Analysis in Equines
- Industry Partner: AgWest Veterinary Group
Hops Metabolomics
Hops, the crop that gives beer its bitter taste and aroma, are of major interest to farmers and brewers in BC. DNA fingerprinting and chemical analysis lead to a greater understanding of the flavour profile of different hop varieties and aid in the development of new hop varieties.
The Applied Genomics Centre uses high performance liquid chromatography , gas chromatography and mass spectrometry technology for in-depth analysis of hop metabolites (the products of chemical reactions that sustain an organism). Chemical analysis is combined with DNA analysis to support the breeding and development of different hop varieties to support precision brewing in BC.
Accurate evaluation of alpha and beta acids and other compounds can help identify new hop varieties and ensure consistent flavour profiles, which is beneficial to the craft brewing industry.
Current Projects
- Hops Breeding, Genotyping, and Chemical Analysis
- Industry Partner: Greenflora Greenhouses
Human Health
Although the Applied Genomics Centre has a major focus on applied research and development in agriculture, it is also involved in several human health projects.
The lab uses Sanger and next generation DNA sequencing and molecular techniques to understand the genetic foundations of several human neurological diseases. Recent projects include identification of the genetic cause ataxia, a degenerative disease of the nervous system, and of migraines that run in families.
Current Projects
- Mutation Detection in Ataxia
- Industry Partner: BC Ataxia Society