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

Abstract

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.

Selection, genome‐wide fitness effects and evolutionary rates in the model legume Medicago truncatula

“…Absent from the list of selected nodulation‐related genes is DMI1 , a regulator of rhizobia–plant signalling that was previously identified as bearing a signature of adaptive evolution in M. truncatula (De Mita et al . ). The difference in the identification of DMI1 may reflect the dependency of selection scans on the composition of the intraspecific sample (De Mita et al .…”

Stabilizing Mechanisms in a Legume-Rhizobium Mutualism

“…In particular, an excess of nonsynonymous substitutions suggests that positive selection has driven the divergence of the NORK locus (a putative receptor of rhizobium signals, Endre et al 2002) among Medicago species (De Mita et al 2006). In addition, the DMI1 locus (likely a mediator of signal reception, Ané et al 2004) harbors an excess of rare polymorphisms in M. truncatula , suggestive of a recent selective sweep (De Mita et al 2007). As suggested by De Mita et al (2007), rhizobium signaling and plant perception of signals may coevolve in a scenario similar to host–parasite coevolution.…”

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

“…Medicago truncatula, a diploid, predominantly self-fertilizing close relative of alfalfa (M. sativa), serves as a model for investigating the genetics and evolution of legume-rhizobia symbiosis (3)(4)(5), legume genetics, and genome evolution (6) as well as the genetics and evolution of plant-mycorrhizal symbiosis (7), a symbiosis that is common among land plants but not found in the primary plant genetic model, Arabidopsis thaliana. The utility of M. truncatula as a model is built on a modest genome size of about 500 million bp (Mbp) (6), short seed to seed generation time (3-4 mo), excellent collections of tagged mutants (8), and large collections of diverse ecotypes (9).…”