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Contacts:
CNAP Director,
Professor Ian Graham
CNAP Manager, Dr Caroline Calvert
CNAP, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
CNAP - Centre for Novel Agricultural Products
Plant Genome Facility
CNAP has developed three areas of technology focussed around gene and molecular marker discovery and metabolic engineering using both GM and non-GM approaches.
The technology platforms are:
- molecular breeding led by Dr Thilo Winzer
- metabolite profiling led by Dr Tony Larson
- bioinformatics lead by Dr Yi Li
The Molecular breeding facility was established to undertake fast-track breeding of non-food crops. The facility uses both natural and induced genetic variation to screen and breed for improved traits in a number of different species. Accessing natural variation in non-domesticated, poorly understood species has been greatly facilitated by advances in DNA sequencing technology. This has allowed CNAP to rapidly develop suites of molecular markers (SNPs and SSRs) for a number of non-food crops. These markers are then used to generate molecular maps that allow key traits to be rapidly selected in fast-track breeding programmes.
High throughput reverse genetics screening methods (Heteroduplex Mapping also known as TILLING) are also employed to identify plants and fungi which possess mutations (natural or chemically induced) in specific genes. Individuals carrying such mutations can then be analysed to identify those that have desirable traits such as increased yield of specific metabolites or altered morphology.
The molecular breeding facility is currently being used to undertake fast-track breeding on a number of non-food crop species including industrial hemp, Artemisia annua and other medicinal plants as well as two species of filamentous fungi used as production systems by industry. The molecular breeding work is supported by a range of charitable, industrial and governmental funding.
An example of heteroduplex mapping of mutations in a target gene using LICOR apparatus
The Molecular breeding Team is led by Dr Thilo Winzer.
The facilities in the Metabolite Profiling Unit comprise of both high-throughput and high-resolution gas and liquid chromatography separation equipment coupled to sensitive and specific detectors, including mass spectrometers. The facilities are extensively used in collaborative projects, especially those where key metabolic differences are identified between plant samples. Metabolite profiling has proved to be a very useful technique in both forward and reverse genetic screening projects, where combinations of high-throughput assays and targeting specific compounds for quantitative phenotypic analysis are required. Metabolite Profiling Unit staff have particular expertise in the analysis of plant lipid derived molecules, such as fatty acids, triacylglycerols, acyl CoAs and oxylipins. Our expertise also includes high-throughput terpene profiling, developed for the analysis of the antimalarial compound artemisinin as part of the currently running CNAP Artemisia Research Project funded by the Bill & Melinda Gates Foundation.
An example of metabolite profiling of short chain acyl-CoA esters in wild type and mutant plants
The Metabolite Profiling Unit is led by Dr Tony Larson.
Dr Yi LI established bioinformatics as a technology platform within CNAP. CNAP’s bioinformatics facilities support data management and analysis using its own Unix-Silicon graphics server and workstations. Bioinformatics enables researchers to: undertake gene discovery using databases; investigate the molecular evolution of plant gene families and analyse gene expression profiles. Routine bioinformatics protocols have recently been established for the mining of large pyrosequencing datasets. In combination with in-house 454 sequencing technology CNAP can now efficiently perform gene discovery and development of SNP and SSR molecular markers from new species of plants and microbes. These molecular markers are being used for fast track molecular breeding of a number of non-food crop species.
An example of transcriptome classification of 454 pyrosequencing data from the gut of Limnoria quadripunctata, a marine animal that feeds on wood. more information on this project click here
