Adaptive evolution of the symbiotic gene NORK is not correlated with shifts of rhizobial specificity in the genus Medicago

<p>Abstract</p> <p>Background</p> <p>The <it>NODULATION RECEPTOR KINASE </it>(<it>NORK</it>) gene encodes a Leucine-Rich Repeat (LRR)-containing receptor-like protein and controls the infection by symbiotic rhizobia and endomycorrhizal fungi in Legumes. The occurrence of numerous amino acid changes driven by directional selection has been reported in this gene, using a limited number of messenger RNA sequences, but the functional reason of these changes remains obscure. The <it>Medicago </it>genus, where changes in rhizobial associations have been previously examined, is a good model to test whether the evolution of <it>NORK </it>is influenced by rhizobial interactions.</p> <p>Results</p> <p>We sequenced a region of 3610 nucleotides (encoding a 392 amino acid-long region of the NORK protein) in 32 <it>Medicago </it>species. We confirm that positive selection in <it>NORK </it>has occurred within the <it>Medicago </it>genus and find that the amino acid positions targeted by selection occur in sites outside of solvent-exposed regions in LRRs, and other sites in the N-terminal region of the protein. We tested if branches of the <it>Medicago </it>phylogeny where changes of rhizobial symbionts occurred displayed accelerated rates of amino acid substitutions. Only one branch out of five tested, leading to <it>M. noeana</it>, displays such a pattern. Among other branches, the most likely for having undergone positive selection is not associated with documented shift of rhizobial specificity.</p> <p>Conclusion</p> <p>Adaptive changes in the sequence of the NORK receptor have involved the LRRs, but targeted different sites than in most previous studies of LRR proteins evolution. The fact that positive selection in <it>NORK </it>tends not to be associated to changes in rhizobial specificity indicates that this gene was probably not involved in evolving rhizobial preferences. Other explanations (<it>e.g</it>. coevolutionary arms race) must be tested to explain the adaptive evolution of <it>NORK</it>.</p

Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula

BACKGROUND: Exploiting genetic diversity requires previous knowledge of the extent and structure of the variation occurring in a species. Such knowledge can in turn be used to build a core-collection, i.e. a subset of accessions that aim at representing the genetic diversity of this species with a minimum of repetitiveness. We investigate the patterns of genetic diversity and population structure in a collection of 346 inbred lines representing the breadth of naturally occurring diversity in the Legume plant model Medicago truncatula using 13 microsatellite loci distributed throughout the genome. RESULTS: We confirm the uniqueness of all these genotypes and reveal a large amount of genetic diversity and allelic variation within this autogamous species. Spatial genetic correlation was found only for individuals originating from the same population and between neighbouring populations. Using a model-based clustering algorithm, we identified four main genetic clusters in the set of individuals analyzed. This stratification matches broad geographic regions. We also identified a set of "admixed" individuals that do not fit with this population structure scheme. CONCLUSION: The stratification inferred is discussed considering potential historical events like expansion, refuge history and admixture between neighbouring groups. Information on the allelic richness and the inferred population structure are used to build a nested core-collection. The set of inbred lines and the core collections are publicly available and will help coordinating efforts for the study of naturally occurring variation in the growing Medicago truncatula community

How and When Does Outcrossing Occur in the Predominantly Selfing Species Medicago truncatula?

International audienceEmpirical studies on natural populations of Medicago truncatula revealed selfing rates higher than 80%, but never up to 100%. Similarly, several studies of predominantly selfing species show variability in the level of residual outcrossing between populations and also between temporal samples of the same population. However, these studies measure global selfing rates at the scale of the population and we do not know whether there is intra-population variation and how outcrossing events are distributed, between genotypes, plants, flowers, or seeds. Theoretical studies predict the maintenance of residual outcrossing in highly selfing species due to environmental (e.g., pollen biology) and/or genetic determinants and decompositions of the variation in outcrossing rate using experimental data can be very informative to test these hypotheses. Here, we focus on one natural population of M. truncatula in order to describe precisely its mating system. In particular, we investigated the determinants of the selfing rate by testing for seasonal variations (environmental determinism) and variations between genotypes (genetic determinism). We measured selfing rates in maternal progenies from plants collected widely across a natural population. For each plant, we collected pods from flowers produced at the beginning and at the end of the flowering season to test for a seasonal variation in the outcrossing rate. For each collected offspring, we also estimated the likelihood that it was issued from a self-fertilization event and assessed the genetic component of variation of this mating system measure. We found a significant, albeit small, increase in outcrossing rate in progenies collected at the end [t(m) = 0.137 (SD = 0.025)] compared to those collected at the beginning [t(m) = 0.083 (0.016)] of the flowering season. A significant between genotypes variation in selfing rate was also detected, resulting in a heritability of 9% for the rate of residual outcrossing. Altogether, our work shows that despite a predominantly selfing reproductive mode, M. truncatula displays variation in residual outcrossing rate, and that this trait is likely under a complex determinism combining environmental and genetic factors. We discuss the evolutionary implications of our results for the population

Fitness consequences of hybridization in a predominantly selfing species: insights into the role of dominance and epistatic incompatibilities

Early AccessInternational audienceStudying the consequences of hybridization on plant performance is insightful to understand the adaptive potential of populations, notably at local scales. Due to reduced effective recombination, predominantly selfing species are organized in highly homozygous multi-locus-genotypes (or lines) that accumulate genetic differentiation both among- and within-populations. This high level of homozygosity facilitates the dissection of the genetic basis of hybrid performance in highly selfing species, which gives insights into the mechanisms of reproductive isolation between lines. Here, we explored the fitness consequences of hybridization events between natural inbred lines of the predominantly selfing species Medicago truncatula, at both within- and among-populations scales. We found that hybridization has opposite effects pending on studied fitness proxies, with dry mass showing heterosis, and seed production showing outbreeding depression. Although we found significant patterns of heterosis and outbreeding depression, they did not differ significantly for within- compared to among-population crosses. Family-based analyses allowed us to determine that hybrid differentiation was mostly due to dominance and epistasis. Dominance and/or dominant epistatic interactions increased dry mass, while decreasing seed production, and recessive epistatic interactions mostly had a positive effect on both fitness proxies. Our results illustrate how genetic incompatibilities can accumulate at a very local scale among multi-locus-genotypes, and how non-additive genetic effects contribute to heterosis and outbreeding depression

Hide and seek: hidden genetic variance contributing to the adaptive potential of selfing populations

Standing genetic variation is considered a major contributor to the adaptive potential of species. The low heritable genetic variation observed in self-fertilising populations has led to the hypothesis that species with this particular mating system would be less likely to adapt. However, a non-negligible amount of cryptic genetic variation for polygenic traits, accumulated through negative linkage disequilibrium, could prove to be an important source of standing variation in self-fertilising species. Using a classical quantitative genetics model, we demonstrate that selfing populations are better able to store cryptic genetic variance than outcrossing populations, notably due to their lower recombination rate. Following a shift in the environment, this hidden diversity can be partially released, increasing the additive variance and adaptive potential of selfing populations. In such conditions, even though the process of adaptation itself is mating system dependant, selfers reach levels of fitness that are equal to or higher than outcrossing populations within a few generations. Outcrossing populations respond better to selection for the new optimum, but they maintain more genetic diversity resulting in a higher genetic load. In selfing populations, genetic diversity is remobilised, and new close-to-optimum genotypes are generated and quickly increase in frequency, leading to more homogenous populations. Our results bring new insights into the role of standing genetic variation for adaptation in selfing populations

Mitochondrial DNA diversity and male sterility in natural populations of Daucus carota ssp carota

International audienceMitochondrial variability was investigated in natural populations of wild carrot (Daucus carota ssp carota) in different regions: South of France, Greece, and various sites in the Mediterranean Basin and Asia. Total DNA was digested with two restriction endonucleases (EcoRV and HindIII) and probed with three mitochon-drial DNA-specific genes (coxI, atp6, and coxlI). Twenty-five different mitochondrial types were found in 80 analyzed individuals. Thirteen mitotypes were found among the 7 French populations studied. On average, 4.4 different mitotypes were observed per population, and these mitotypes were well-distributed among the populations. All of the mitochondrial types were specific to a single region. However, the proportion of shared restriction fragments between 2 mitotypes from different regions was not particularly lower than that which occurred among mitotypes from a single region. On the basis of the sexual phenotype [male-sterile (MS) or hermaphrodite] of the plants studied in situ and that of their progeny, 2 mitotypes were found to be highly associated with male sterility. Eighty percent of the plants bearing these mitotypes were MS in situ, and all of these plants produced more than 30% MS plants in Communicated by R. Hagemann J. Ronfort ([]) D6partement de biologie des populations, Centre d'Ecologie Fon-ctionnelle et Evolutive (CEFE), CNRS, 1919, Route de Mende, B.P. 5051-34033 Montpellier Cedex France P. Saumitou-Laprade Laboratoire de G6netique et Evolution des populations v6g6tales, 237, Universitb Paris vi, 75252 Paris Cedex France their progeny. This association with male sterility was consistent in several populations, suggesting an association with a cytoplasmic male-sterility system. Moreover , these two mitotypes had very similar mitochon-drial DNA restriction patterns and were well-differentiated from the other mitotypes observed in wild plants and also from those observed in the two CMS types already known in the cultivated carrot. This suggests that they correspond to a third cytoplasmic sterility. Key words RFLP 9 Mitochondrial DNA diversity 9 Natural populations 9 Cytoplasmic male sterility 9 Daucus carota L

Predicting Endemism from Population Structure of a Widespread Species: Case Study in Centaurea maculosa Lam. (Asteraceae)

International audienceAmounts of genetic variability, genetic differentiation among taxa and populations, and population sizes were studied in five populations of Centaurea maculosa ssp. maculosa (a widespread taxon), all six populations of C. corymbosa (a narrowly endemic species), and the single population of C. maculosa ssp. albida. Seventeen isozyme loci were studied, of which nine were polymorphic. Results suggest that C. corymbosa and C. maculosa ssp. albida are likely derived from C. maculosa ssp. maculosa because the former represent a sample of the diversity of the latter. The percentage of polymorphic loci and Nei's genetic diversity were positively and significantly correlated with population size over all populations, but not within each taxon. Populations of both the widespread C. maculosa ssp. maculosa and the rare C. corymbosa were strongly differentiated: overall, FST values were 0.26 and 0.34, respectively. Differentiation among populations of different taxa was of the same order of magnitude as that observed among populations within taxa. Nevertheless, significant differentiation among the three taxa was found by a hierarchical analysis of variance on allele frequencies. We suggest that bottlenecks or founder effects associated with colonization events and ecological specialization in some populations of C. maculosa ssp. maculosa have led to new taxa such as C. corymbosa and C. maculosa ssp. albida. This may be a direct consequence of the particularly strong differentiation among populations of the widespread C. maculosa ssp. maculosa. Our study highlights the utility of considering closely related widespread taxa in order to understand the population biology and evolution of rare species, as well as to design proper management programs