Award details

Integrating the genome sequence and genetic linkage map of Physcomitrella patens: a platform for map based gene cloning

Reference	BB/F001797/1
Principal Investigator / Supervisor	Dr Andrew Cuming
Co-Investigators / Co-Supervisors
Institution	University of Leeds
Department	Ctr for Plant Sciences
Funding type	Research
Value (£)	366,185
Status	Completed
Type	Research Grant
Start date	01/10/2007
End date	30/09/2010
Duration	36 months

Abstract

The first-draft annotated genome sequence of the moss Physcomitrella patens is released in January 2007. This will be the first sequenced genome of a non-flowering land plant, and reinforces the demonstrated utility of Physcomitrella for the 'reverse genetic' analysis of gene function using gene targeting by homologous recombination. The basal position of Physcomitrella within the land plant phylogeny has established it alongside Arabidopsis as the pre-eminent model for comparative functional genomic studies of plants: a priority area of the Plants and Microbial Sciences Committee. Although powerful, reverse genetics is not by itself a sufficiently powerful tool to reveal the functions of all Physcomitrella genes. Forward genetic strategies: moving from mutant phenotypes to the underlying genes are equally (if not more) powerful approaches to the discovery of gene function and interaction. This proposal will establish a platform for the routine cloning of genes identified using a forward-genetic approach. - We have constructed a 1300-marker AFLP-based genetic linkage map of Physcomitrella. - We shall integrate this map with SSR and SNP markers to link it directly to the genome sequence. - We shall establish a collection of mutagenised plants and develop a pipeline for the map-based cloning of genes identified through their mutant phenotype. - We shall demonstrate the power of this approach as a 'proof of principle' by identifying and cloning a selected Physcomitrella gene. We shall focus on a gene responsible for a characteristic feature of early land plants, but with additional strategic potential: candidates might include the regulation of polarized cell growth, the homologous-recombination mediated DNA repair pathway or ABA-mediated environmental stress tolerance. This work will enhance the utility of Physcomitrella for comparative plant genomics, providing a new resource for the UK and international plant science communities.

Summary

Our research: BBSRC support of Leeds University over a period of 30 years has led us to pioneer the establishment of the moss Physcomitrella patens as an internationally adopted 'model organism' for the study of plant cell and developmental biology. This support enabled us to (i) develop techniques for the isolation of mutants aberrant in basic plant processes - the first step to identify the genetic basis of biological processes (ii) optimise a technique for genetic engineering by 'gene targeting' - a precision tool not possible in any other plant (iii) initiate a programme of gene discovery that has culminated in the complete sequencing of the Physcomitrella genome by an international consortium. Now we shall establish the final tool to enable the rapid and routine identification of genes that underlie abnormal mutants: the integration of the Physcomitrella genome sequence with its genetic linkage map. This will enable the international and UK plant science community to extract maximum value from the newly released Physcomitrella genome through the application of 'comparative functional genomics' - a BBSRC research priority. The value of comparative studies: Our understanding of complex biological processes has been revolutionised by genetic experiments conducted using a small number of well characterised model organisms. In the Animal Kingdom, the study of the nematode worm, the fruit fly, the zebra fish and the mouse allows analysis of animal development across a wide evolutionary spectrum encompassing increasing levels of complexity. Such wide comparative analysis enables us to discern the evolutionary processes that have generated these disparate creatures, and the ways in which essentially similar genes have been differently utilised in the course of evolution. Within the Plant Kingdom, the comparable model organisms that allow a similarly wide evolutionary perspective to be achieved are the flowering plant, Arabidopsis thaliana, and the moss, Physcomitrella patens. Model organisms are chosen for their experimental tractability. All these organisms have had their whole genome sequences determined. All can be manipulated by the introduction of foreign DNA: in the case of the mouse and the moss, foreign DNA can be introduced to specific sites within their genomes with exquisite precision. In all these organisms, random mutations can be induced that cause radical defects in their normal developmental processes. By identifying the genes in which such mutations have occurred, we identify the genes that normally regulate these processes. This identification is possible only where the sequenced genome is supported by a 'genetic linkage map': a representation of the genome based on the inheritance of large numbers of mutations in a large population. Mutations that lie in adjacent sections of the genome are typically inherited together, and are said to be 'genetically linked'. A gene that is responsible for a mutant trait can be isolated if that trait is co-inherited (genetically linked) with neighbouring, known 'genetic markers' - typically lengths of DNA whose sequence is known. This potent experimental approach allows the functional identification of genes without prior knowledge of their sequence. Such an approach is routine in Arabidopsis. This proposal will make it routine in Physcomitrella and accessible to all plant scientists. Physcomitrella is not a flowering plant. It is a member of the earliest group of land plants - the bryophytes - an ancient and biodiverse group which emerged ca. 300 million years before the flowering plants. It therefore represents an ancestral reference by which divergence in plant gene structure and function has occurred. It also provides insights into 'primitive' plant traits such as enhanced dehydration tolerance (essential for a successful colonisation of the land) and the origins of plant multicellularity, that retain their value for future plant improvement.

Committee	Closed Committee - Plant & Microbial Sciences (PMS)
Research Topics	Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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