Plant Genome Facility
Our work is supported by CNAP’s Plant Genome Facility, where dedicated teams focused on key activities use cutting edge technologies including metabolite profiling, bioinformatics and molecular breeding to deliver high throughput data collection, data mining, and screening for improved plant varieties. 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:
The Molecular Breeding Unit 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 Unit is currently being used to undertake fast-track breeding on a number of non-food crop species including industrial hemp, Artemisia annua and opium poppy (Papaver somniferum) as well as two species of filamentous fungi. The molecular breeding work is supported by a range of charitable, industrial and governmental funding, and is facilitated by access to the Feedstock Development Unit of the Biorenewables Development Centre.
The Molecular Breeding team is led by Dr Thilo Winzer
An example of genotyping F1 progeny using SNP molecular markers with multiplexing technology on the ABI 3730
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 expertise in the analysis of fatty acids, triacylglycerols, acyl CoAs, oxylipins, plant hormones, terpenes and alkaloids. Analysis can be target compound or data-led, using a suite of in-house developed bioinformatics tools.
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 data-processing, database, and intranet servers. 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 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. For more information on this project click here
The Bioinformatics Unit is led by Dr Yi Li.
CNAP scientists led by Ian Graham have found that a regulator gene called SPATULA can control the expression of five other genes known to affect when a seed germinates. A report on the work has just been published in the PNAS journal early online edition.
Researchers in CNAP together with colleagues at the University of Portsmouth and the National Renewable Energy Laboratory in the USA have determined the structure and function of a key enzyme used by gribble to digest wood. An article by the team has just been published in the journal PNAS.
New Scientist journal article features work by Rob Edwards and his team to address the problems posed by the presence of herbicide resistant weeds such as black-grass and annual ryegrass in cereal crops. An in-depth report by the team has just been published in the journal PNAS.
CNAP, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK