title: Transposable elements reveal the impact of introgression, rather than transposition, in Pisum diversity, evolution, and domestication.
abstract: The genetic structure and evolutionary history of the genus Pisum were studied exploiting our germplasm collection to compare the contribution of different mechanisms to the generation of diversity. We used sequence-specific amplification polymorphism (SSAP) markers to assess insertion site polymorphism generated by a representative of each of the two major groups of LTR-containing retrotransposons, PDR1 (Ty1/copia-like) and Cyclops (Ty3/gypsy-like), together with Pis1, a member of the En/Spm transposon superfamily. The analysis of extended sets of the four main Pisum species, P. fulvum, P. elatius, P. abyssinicum, and P. sativum, together with the reference set, revealed a distinct pattern of the NJ (Neighbor-Joining) tree for each basic lineage, which reflects the different evolutionary history of each species. The SSAP markers showed that Pisum is exceptionally polymorphic for an inbreeding species. The patterns of phylogenetic relationships deduced from different transposable elements were in general agreement. The retrotransposon-derived markers gave a clearer separation of the main lineages than the Pis1 markers and were able to distinguish the truly wild form of P. elatius from the antecedents of P. sativum. There were more species-specific and unique PDR1 markers than Pis1 markers in P. fulvum and P. elatius, pointing to PDR1 activity during speciation and diversification, but the proportion of these markers is low. The overall genetic diversity of Pisum and the extreme polymorphism in all species, except P. abyssinicum, indicate a high contribution of recombination between multiple ancestral lineages compared to transposition within lineages. The two independently domesticated pea species, P. abyssinicum and P. sativum, arose in contrasting ways from the common processes of hybridization, introgression, and selection without associated transpositional activity.
authors.affiliation: Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom. alexander.vershinin@bbsrc.ac.uk
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Vershinin
authors.forename: Theodore R
authors.initials: TR
authors.lastname: Allnutt
authors.forename: Maggie R
authors.initials: MR
authors.lastname: Knox
authors.forename: Mike J
authors.initials: MJ
authors.lastname: Ambrose
authors.forename: T H Noel
authors.initials: TH
authors.lastname: Ellis
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics; D019143:Evolution, Molecular; D005819:Genetic Markers; D014644:Genetic Variation; D008957:Models, Genetic; D018532:Pisum sativum / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D018626:Retroelements / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins; D013045:Species Specificity; D015534:Trans-Activators / Q000235:genetics; D014157:Transcription Factors; D016212:Transforming Growth Factor beta / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; D005819:Genetic Markers; C085480:PDR1 protein, S cerevisiae; D018626:Retroelements; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D016212:Transforming Growth Factor beta