Search

RNA silencing serves key roles in a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity. Dicer, Argonaute (AGO), double-stranded RNA binding (DRB), RNA-dependent RNA polymerase (RDR) and DNA-dependent RNA polymerases known as Pol IV and Pol V form core components to trigger RNA silencing. Common bean (Phaseolus vulgaris) is an important staple crop worldwide. In this study, we aimed to unravel the components of the RNA-guided silencing pathway in this non-model plant taking advantage of the availability of two genome assemblies of Andean and Meso-American origin. We identified six PvDCLs, thirteen PvAGOs, 10 PvDRB, 5 PvRDR, in both genotypes, suggesting no recent gene amplification or deletion after the gene pool separation. In addition, we identified one PvNRPD1 and one PvNRPE1 encoding the largest subunits of Pol IV and Pol V, respectively. These genes were categorized into subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different organs using online data and quantitative RT-PCR after pathogen infection. Several of the candidate genes were up-regulated after infection with the fungus Colletotrichum lindemuthianum.

International audience; The common bean (Phaseolus vulgaris L.) is the main representative of its genus and one of most important sources of proteins in African and Latin American countries. Although it is a species with a small genome, its pericentromeric and subtelomeric heterochromatin fractions are interspersed with single-copy sequences and active genes, suggesting a less compartmentalized genome organization. The present study characterized its chromatin fractions, associating the distribution of repetitive sequences and resistance genes with histone and DNA epigenetic modifications with and without biotic stress. Immunostaining with H3K4me3 and H4K5ac were generally associated with euchromatic regions, whereas H3K9me2, H3K27me1, and 5mC preferentially labeled the pericentromeric heterochromatin. The 45S rDNA and centromeric DNA sequences were hypomethylated as were most of the terminal heterochromatic blocks. The largest of them, which is associated with resistance genes, was also hypomethylated after the plants were infected with virulent and avirulent strains of the fungus Colletotrichum lindemuthianum, suggesting no correlation with control of resistance gene expression. The results highlighted the differences between subtelomeric and pericentromeric heterochromatin as well as variation within the pericentromeric heterochromatin. (C) 2014 S. Karger AG, Basel

*In plants, the evolution of specific resistance is poorly understood. Pseudomonas syringae effectors AvrB and AvrRpm1 are recognized by phylogenetically distinct resistance (R) proteins in Arabidopsis thaliana (Brassicaceae) and soybean (Glycine max, Fabaceae). In soybean, these resistances are encoded by two tightly linked R genes, Rpg1-b and Rpg1-r. To study the evolution of these specific resistances, we investigated AvrB- and AvrRpm1-induced responses in common bean (Phaseolus vulgaris, Fabaceae). *Common bean genotypes of various geographical origins were inoculated with P. syringae strains expressing AvrB or AvrRpm1. A common bean recombinant inbred line (RIL) population was used to map R genes to AvrRpm1. *No common bean genotypes recognized AvrB. By contrast, multiple genotypes responded to AvrRpm1, and two independent R genes conferring AvrRpm1-specific resistance were mapped to the ends of linkage group B11 (Rpsar-1, for resistance to Pseudomonas syringae effector AvrRpm1 number 1) and B8 (Rpsar-2). Rpsar-1 is located in a region syntenic with the soybean Rpg1 cluster. However, mapping of specific Rpg1 homologous genes suggests that AvrRpm1 recognition evolved independently in common bean and soybean. *The conservation of the genomic position of AvrRpm1-specific genes between soybean and common bean suggests a model whereby specific clusters of R genes are predisposed to evolve recognition of the same effector molecules.

Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.

The imperfect fungus Colletotrichum lindemuthianum is the causal agent of the anthracnose disease of the common bean, Phaseolus vulgaris L. Studies on the inheritance of resistance to this pathogen led to the definition of several major genes for resistance in the plant. Recombinant inbred lines (RILs), issued from a cross between extremely polymorphic parents representating the two major gene pools, BAT93 (Mesoamerican) and Jalo EEP558 (Andean), were used to map anthracnose resistance genes. A complex locus containing several clustered resistance genes, from either Andean or Mesoamerican origin, was identified on the B14 linkage group. Degenerate oligonucleotide primers, deduced from conserved domains of the Nucleotide Binding Site (NBS) regions of the two Arabidopsis RPM1, RPS2 and the tobacco N disease resistance genes were used to amplify related sequences in common bean. The sequencing of the PCR products obtained from BAT93 and Jalo EEP558 genotypes indicated that at least 3 subfamilies of sequences, containing the different NBS domains conserved among RPS2, RPM1 and N resistance genes, coexist in these genotypes. They correspond to low- or moderately low-copy number sequences, as expected for resistance genes. One of these subfamilies of NBS-containing sequences was located within the clustered resistance genes previously identified in the linkage group B14. The NBS-containing sequences are, now, used to screen both genomic and cDNA libraries. The candidate resistance genes will be sequenced and used in transformation experiments in order to confirm their function and to identify their specificity. (Texte intégral)

La majorité des gènes de résistance clonés appartiennent à une grande famille de gènes codant pour des protéines présentant des motifs répétés riches en leucine. Les mêmes familles de gènes ont été identifiées chez des angiospermes très éloignées phylogenètiquement. Elles déterminent des spécificités de résistance contre des virus, des bactéries, des champignons voire des nématodes. Des mécanismes de duplication, mutation et recombinaison génétique semblent être les éléments majeurs de l'évolution du répertoire des gènes de résistance. Des expériences réalisées in vitro ont permis de démontrer que le produit d'un gène de résistance pouvait interagir directement avec le produit du gène d'avirulence de l'agent pathogène et que cette interaction constituait le facteur déclenchant de l'expression des gènes de défense de la plante conduisant à la résistance. De nombreuses applications à la sélection variétale apparaissent d'ores et déjà.