Measuring Plant Genetic Diversity Using Inter-Simple Sequence Repeats (ISSRS)

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.