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Background  The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major  Pisum  germplasm collection to gain a broad understanding of the diversity and evolution of  Pisum  and provide a new rational framework for designing germplasm core collections of the genus.    Results  3020  Pisum  germplasm samples from the John Innes  Pisum  germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP) markers by the Tagged Array Marker (TAM) method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus  Pisum . Structure revealed three Groups (1-3) corresponding approximately to landrace, cultivar and wild  Pisum  respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of  Pisum , domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of  Pisum .    Conclusions  These data provide a clear picture of the major distinct gene pools into which the genus  Pisum  is partitioned and their geographical distribution. The data strongly support the model of independent domestications for  P. sativum ssp abyssinicum  and  P. sativum . The relationships between these two cultivated germplasms and the various sub-divisions of wild  Pisum  have been clarified and the most likely ancestral wild gene pools for domesticated  P. sativum  identified. Lastly, this study provides a framework for defining global  Pisum  germplasm which will be useful for designing core collections.

bmc evolutionary biology

The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis