eprintid: 198
rev_number: 4
eprint_status: archive
userid: 6
dir: disk0/00/00/01/98
datestamp: 2009-01-08
lastmod: 2015-05-29 19:49:13
status_changed: 2009-04-08 16:55:49
type: report
metadata_visibility: show
item_issues_count: 0
creators_name: Iannetta, Pietro
contributors_name: Wishart, Jane
contributors_name: Evans, Kim
contributors_name: Kypraios, Theodore
contributors_name: White, Simom
contributors_name: Preston, Simon
contributors_name: Begg, Graham
contributors_name: Dryden, Ian
title: Measuring Plant Genetic Diversity Using Inter-Simple Sequence Repeats (ISSRS)
ispublished: pub
subjects: other
studygroups: mpssg1
companyname: Scottish Crop Research Institute
full_text_status: public
abstract: Simple sequence repeats (SSRs) have great utility as they are conserved and present in all eukaryotic genomes. Here we report the use of a simple PCR with fluorescently-labelled primers to amplify inter-SSR markers (ISSRs) for diversity assessments. The use of ISSR markers does not rely upon specific genetic sequence information, or prolonged method development and may be measured rapidly using the automated equipment. The major restriction of the ISSR method is at the analysis stage, as the markers are dominant it is not possible to distinguish heterozygotes as loci. We obtained ISSR data from ca. 60 phenotypically characterised Capsella bursa pastoris L. Medic (shepherds purse)accessions that had been isolated from a diverse mix of arable field sites throughout the UK. We developed mathematical scripts for use with the free statistical software tool R (http://www.rproject.org/), that processed the molecular data in a binary format to estimate genetic diversity (using the Jaccard co-efficient), and that related genotype to the plant phenotypic and environmental (site specific) traits. The methodology established has the power to predict the relationship between environmental and plant morphological characteristics.
problem_statement: The relationship between biodiversity and the functioning of essential ecosystem process should be quantified at the intraspecific level, and in terms of the relative abundances of ecologically important significant plant life-history traits. Maximum uptake of this approach for environmental monitoring purposes demands that genetic data must be acquired using an easy and universal method. To this end, Inter Simple Sequence Repeat (ISSR) genotyping has been used to acquire data for ca. 150 individual accessions of the common annual weed Capsella bursa pastoris L. Medic (shepherds purse): that is being developed as a (global) biomonitor species. The data provides specific markers (peaks), the presence of which can ascribe accessions into particular trait-groups. As the accessions were collected from different environments across the UK (that were also characterised), and with several accessions per site, we ask the key question: 'can the success and utility of the data be extended even further to provide information on the biodiversity within communities too?'. This provision of this information is critical: the tools that allow this evaluation would relate diversity estimates directly to heritable phenotypic traits and the environment. Consequently, and most significantly: could this information generate a predictive model that assesses the future resilience of species within changing environments?'.

   1. What statistic from the ISSR data would provide a measure of genetic diversity?
   2. How would the statistic be estimated?
   3. How would the statistic be compared between populations?
   4. Can the statistic relate phenotypic variation within and between populations?
   5. Could this be modelled in a way which includes predictions based on knowledge of the selective effects of environmental changes?
   6. How many loci would have to be considered?
   7. How many individuals from each population would have to be tested?
date: 2007-12
date_type: published
pages: 12
citation:   Iannetta, Pietro  (2007) Measuring Plant Genetic Diversity Using Inter-Simple Sequence Repeats (ISSRS).  [Study Group Report]     
document_url: http://miis.maths.ox.ac.uk/miis/198/1/report2.pdf