Genetics, Vol. 177, 2123-2133, December 2007, Copyright © 2007
doi:10.1534/genetics.107.076943

Investigation of the Demographic and Selective Forces Shaping the Nucleotide Diversity of Genes Involved in Nod Factor Signaling in Medicago truncatula

Stéphane De Mita^*,1, Joëlle Ronfort^*, Heather I. McKhann, Charles Poncet^*, Redouane El Malki and Thomas Bataillon^*,

^* Diversité et Adaptation des Plantes Cultivées (UMR1097), INRA, 34394 Montpellier, France, Etude du Polymorphisme des Génomes Végétaux (UR1279), INRA-Centre National de Génotypage, 91057 Evry, France and Bioinformatics Research Center-Institute of Biology, Section of Genetics and Ecology, University of Aarhus, 8000 Aarhus C, Denmark

¹ Corresponding author: Laboratory of Molecular Biology, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, The Netherlands.
E-mail: demita{at}gmail.com

Symbiotic nitrogen-fixing rhizobia are able to trigger root deformation in their Fabaceae host plants, allowing their intracellular accommodation. They do so by delivering molecules called Nod factors. We analyzed the patterns of nucleotide polymorphism of five genes controlling early Nod factor perception and signaling in the Fabaceae Medicago truncatula to understand the selective forces shaping the evolution of these genes. We used 30 M. truncatula genotypes sampled in a genetically homogeneous region of the species distribution range. We first sequenced 24 independent loci and detected a genomewide departure from the hypothesis of neutrality and demographic equilibrium that suggests a population expansion. These data were used to estimate parameters of a simple demographic model incorporating population expansion. The selective neutrality of genes controlling Nod factor perception was then examined using a combination of two complementary neutrality tests, Tajima's D and Fay and Wu's standardized H. The joint distribution of D and H expected under neutrality was obtained under the fitted population expansion model. Only the gene DMI1, which is expected to regulate the downstream signal, shows a pattern consistent with a putative selective event. In contrast, the receptor-encoding genes NFP and NORK show no significant signatures of selection. Among the genes that we analyzed, only DMI1 should be viewed as a candidate for adaptation in the recent history of M. truncatula.

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