Naturally occurring variations in the nod-independent model legume Aeschynomene evenia and relatives: a resource for nodulation genetics

Clémence Chaintreuil,Hervé Vandrot,Béatrice Thibaud,Mario Gomez-Pacheco,Eric Giraud,Jean-François Arrighi,Herizo Randriambanona,Laurent Brottier,Gwilym P Lewis,Xavier Perrier,Joël Fardoux,Heriniaina Ramanankierana,Pierre Mournet,Guillaume Martin,Mickaël Bourges,Léo Lamy,Ronan Rivallan

doi:10.1186/s12870-018-1260-2

Abstract

BackgroundAmong semi-aquatic species of the legume genus Aeschynomene, some have the unique property of being root and stem-nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the production of Nod factors. These species provide an excellent biological system with which to explore the evolution of nodulation in legumes. Among them, Aeschynomene evenia has emerged as a model legume to undertake the genetic dissection of the so-called Nod-independent symbiosis. In addition to the genetic analysis of nodulation on a reference line, natural variation in a germplasm collection could also be surveyed to uncover genetic determinants of nodulation. To this aim, we investigated the patterns of genetic diversity in a collection of 226 Nod-independent Aeschynomene accessions.ResultsA combination of phylogenetic analyses, comprising ITS and low-copy nuclear genes, along with cytogenetic experiments and artificial hybridizations revealed the richness of the Nod-independent Aeschynomene group with the identification of 13 diploid and 6 polyploid well-differentiated taxa. A set of 54 SSRs was used to further delineate taxon boundaries and to identify different genotypes. Patterns of microsatellite diversity also illuminated the genetic basis of the Aeschynomene taxa that were all found to be predominantly autogamous and with a predicted simple disomic inheritance, two attributes favorable for genetics. In addition, taxa displaying a pronounced genetic diversity, notably A. evenia, A. indica and A. sensitiva, were characterized by a clear geographically-based genetic structure and variations in root and stem nodulation.ConclusionA well-characterized germplasm collection now exists as a major genetic resource to thoroughly explore the natural variation of nodulation in response to different bradyrhizobial strains. Symbiotic polymorphisms are expected to be found notably in the induction of nodulation, in nitrogen fixation and also in stem nodulation. Subsequent genetic analysis and locus mapping will pave the way for the identification of the underlying genes through forward or reverse genetics. Such discoveries will significantly contribute to our understanding of the molecular mechanisms underpinning how some Aeschynomene species can be efficiently nodulated in a Nod-independent fashion.

Highlights

Among semi-aquatic species of the legume genus Aeschynomene, some have the unique property of being root and stem-nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the production of Nod factors
The nuclear ribosomal internal transcribed spacer region (ITS) region was used as a marker of the species identity and served to reconstruct a phylogeny of the whole group based on the Neighbor Joining (NJ) method (Additional files 2 and 3: Tables S2 and S3)
The ITS tree was composed of four lineages: one grouping A. filosa, A. rostrata and A. tambacoundensis, a monospecific one with A. deamii, a third one comprising A. evenia and its sister species, and a fourth one containing A. sensitiva and related species (Fig. 1a)

Summary

Introduction

Among semi-aquatic species of the legume genus Aeschynomene, some have the unique property of being root and stem-nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the production of Nod factors. Many legumes are pioneers plants improving soil fertility and moderating harsh environments Such economic and ecological success of the legume family is, in large part, due to the ability of the vast majority of its 20,000 species to develop symbiotic interactions with nitrogen-fixing bacteria collectively referred as rhizobia [1]. In this symbiosis, the rhizobia produce signal molecules, the Nod factors, whose specific recognition by the host plant is necessary to activate the formation of root nodules that correspond to symbiotic organs where the rhizobia are hosted. To broaden our understanding of the molecular mechanisms underlying the nitrogenfixing symbiosis, there has arisen a fast growing interest in uncovering the diversity of nodulation processes that are found in other legume species [5, 6]

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