The tribe Fabeae (formerly Vicieae) contains some of humanity?s most important grain legume crops, namely Lathyrus (grass pea/sweet pea/chickling vetches; about 160 species); Lens (lentils; 4 species); Pisum (peas; 3 species); Vicia (vetches; about 140 species); and the monotypic genus Vavilovia. Reconstructing the phylogenetic relationships within this group is essential for understanding the origin and diversification of these crops. Our study, based on molecular data, has positioned Pisum genetically between Vicia and Lathyrus and shows it to be closely allied to Vavilovia. A study of phylogeography, using a combination of plastid and nuclear markers, suggested that wild pea spread from its centre of origin, the Middle East, eastwards to the Caucasus, Iran and Afghanistan, and westwards to the Mediterranean. To allow for direct data comparison, we utilized model-based Bayesian Analysis of Population structure (BAPS) software on 4429 Pisum accessions from three large world germplasm collections that include both wild and domesticated pea analyzed by retrotransposon-based markers. An analysis of genetic diversity identified separate clusters containing wild material, distinguishing Pisum fulvum, P. elatius and P. abyssinicum, supporting the view of separate species or subspecies. Moreover, accessions of domesticated peas of Afghan, Ethiopian and Chinese origin were distinguished. In addition to revealing the genetic relationships, these results also provided insight into geographical and phylogenetic partitioning of genetic diversity. This study provides the framework for defining global Pisum germplasm diversity as well as suggesting a model for the domestication of the cultivated species. These findings, together with gene-based sequence analysis, show that although introgression from wild species has been common throughout pea domestication, much of the diversity still resides in wild material and could be used further in breeding. Moreover, although existing collections contain over 10,000 pea accessions, effort should be directed towards collecting more wild material in order to preserve the genetic diversity of the species.Peer reviewe

Eighty-nine accessions of wild and cultivated peas (12 Pisum fulvum Sibth. et Smith., 7 P. abyssinicum A. Br., 31 wild and 42 cultivated forms of P. sativum L.) were analysed for presence of the variants of three functionally unrelated polymorphic markers referring to different cellular genomes. The plastid gene rbcL either contains or not the recognition site for restriction endonuclease AspLEI (rbcL+ vs. rbcL-); the mitochondrial gene cox1 either contains or not the recognition site for restriction endonuclease PsiI (cox1+ vs. cox1-); the nuclear encoded seed albumin SCA is represented by slow (SCA S ) or fast (SCA F ) variant. Most of the accessions possessed either of two marker combinations: 24 had SCA F cox1+ rbcL+ (combination A) and 49 accessions had SCA S cox1-rbcL-(combination B), 16 accessions represented 5 of the rest 6 possible combinations. All accessions of P. fulvum and P. abyssinicum had combination A, the overwhelming majority of cultivated forms of P. sativum had combination B while wild representatives of P. sativum had both combinations A and B, as well as rare combinations. This pattern indicates that combination A is the ancestral state in the genus Pisum L., inherited by P. fulvum and P. abyssinicum, while combination B seems to have arisen in some lineage of wild P. sativum which rapidly fixed mutational transitions of the three markers studied, most probably via a bottleneck effect during the Pleistocene. Then this 'lineage B' spread over Mediterranean and also gave rise to cultivated forms of P. sativum. Rare combinations may have resulted from occasional crosses between 'lineage A' and 'lineage B' in nature or during cultivation, or represent intermediate evolutionary lineages. The latter explanation seems relevant for an Egyptian cultivated form 'Pisum jomardii Schrank' (SCA F cox1-rbcL-) which is here given a subspecies rank. Wild representatives of P. sativum could be subdivided in two subspecies corresponding to 'lineage A' and 'lineage B' but all available subspecies names seem to belong to lineage B only. Presently all wild forms would better be considered within a fuzzy paraphyletic subspecies P. sativum subsp. elatius (Bieb.) Schmalh. s. l.

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Twelve accessions classified as Pisum sativum subsp. elatius, mostly from West and Central Mediterranean, were analysed for three markers from different cellular genomes: rbcL (plastid genome), coxI (mitochondrial genome) and SCA (nuclear genome). Based on geographical distribution of their allele combinations analysed in this and the earlier study, we suggest a putative history of wild representatives of P. sativum. The ancestor of this species belonged to lineage A (coxI?, rbcL?, SCA f ); it appeared in East Mediterranean, then spread westward most probably during one of the Pleistocene coolings when the sea was smaller, so that representatives of lineage A remained in the Eastern Mediterranean and on the islands of Sicily and Menorca. Mutation leading to the loss of the restriction site for PsiI in coxI-, gave rise to lineage C (coxI-, rbcL?, SCA f ) which spread widely in the Mediterranean and is now found in France, Greece and Ethiopia. Mutation leading to rbcL-gave rise to lineage D (coxI-, rbcL-, SCA f ), now found in Egypt (P. sativum subsp. jomardii) and Spain. Mutational transition of SCA f to SCA s most probably took place in North-Eastern Mediterranean since the resulting lineage B (coxI-, rbcL-, SCA s ) now occupies the Tauro-Caucasian area. In Asia Minor and North Israel, line B met the ancestral line A so that both lines coexist there presently. The lineage B gave rise to the cultivated P. sativum subsp. sativum.