Chrystel Deulvot | Université de Bourgogne (original) (raw)

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Papers by Chrystel Deulvot

Research paper thumbnail of DNA Analysis of Herbarium Specimens of the Grass Weed Alopecurus myosuroides Reveals Herbicide Resistance Pre-Dated Herbicides

PLoS ONE, 2013

Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to he... more Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to herbicides have been identified in arable grass weed populations where resistance has evolved under the selective pressure of herbicides. In an effort to determine whether herbicide resistance evolves from newly arisen mutations or from standing genetic variation in weed populations, we used herbarium specimens of the grass weed Alopecurus myosuroides to seek mutant ACCase alleles carrying an isoleucine-to-leucine substitution at codon 1781 that endows herbicide resistance. These specimens had been collected between 1788 and 1975, i.e., prior to the commercial release of herbicides inhibiting ACCase. Among the 734 specimens investigated, 685 yielded DNA suitable for PCR. Genotyping the ACCase locus using the derived Cleaved Amplified Polymorphic Sequence (dCAPS) technique identified one heterozygous mutant specimen that had been collected in 1888. Occurrence of a mutant codon encoding a leucine residue at codon 1781 at the heterozygous state was confirmed in this specimen by sequencing, clearly demonstrating that resistance to herbicides can pre-date herbicides in weeds. We conclude that point mutations endowing resistance to herbicides without having associated deleterious pleiotropic effects can be present in weed populations as part of their standing genetic variation, in frequencies higher than the mutation frequency, thereby facilitating their subsequent selection by herbicide applications. Citation: Délye C, Deulvot C, Chauvel B (2013) DNA Analysis of Herbarium Specimens of the Grass Weed Alopecurus myosuroides Reveals Herbicide Resistance Pre-Dated Herbicides. PLoS ONE 8(10): e75117.

Research paper thumbnail of Effect of 2,4-Diacetylphloroglucinol on Pythium : Cellular Responses and Variation in Sensitivity Among Propagules and Species

Phytopathology, 2003

de Souza, J. T., Arnould, C., Deulvot, C., Lemanceau, P., Gianinazzi-Pearson, V., and Raaijmakers... more de Souza, J. T., Arnould, C., Deulvot, C., Lemanceau, P., Gianinazzi-Pearson, V., and Raaijmakers, J. M. 2003. Effect of 2,4-diacetylphloroglucinol on Pythium: Cellular responses and variation in sensitivity among propagules and species. Phytopathology 93:966-975.

Research paper thumbnail of Effect of 2,4diacetylphloroglucinol of Pythium: cellular responses and variation in sensitivity among propagules and species

Phytopathology, 2003

de Souza, J. T., Arnould, C., Deulvot, C., Lemanceau, P., Gianinazzi-Pearson, V., and Raaijmakers... more de Souza, J. T., Arnould, C., Deulvot, C., Lemanceau, P., Gianinazzi-Pearson, V., and Raaijmakers, J. M. 2003. Effect of 2,4-diacetylphloroglucinol on Pythium: Cellular responses and variation in sensitivity among propagules and species. Phytopathology 93:966-975.

Research paper thumbnail of Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea

BMC Genomics, 2010

Background Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications... more Background Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction. In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set. Results We obtained clear allelic data for more than 92% of the SNPs (356 out of 384). Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers. Conclusion Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics.

Research paper thumbnail of Comparative Genetic Diversity of the narG, nosZ, and 16S rRNA Genes in Fluorescent Pseudomonads

Applied and Environmental Microbiology, 2003

The diversity of the membrane-bound nitrate reductase (narG) and nitrous oxide reductase (nosZ) g... more The diversity of the membrane-bound nitrate reductase (narG) and nitrous oxide reductase (nosZ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overall, there was a good correspondence between the reductase activities and the presence of the corresponding genes. Distribution in the different ribotypes of strains harboring both the narG and nosZ genes and of strains missing both genes suggests that these two groups of strains had different evolutionary histories. Both dissimilatory genes showed high polymorphism, with similarity indexes (Jaccard) of between 0.04 and 0.8, whereas those of the 16S rRNA gene only varied from 0.77 to 0.99. No correlation between the similarity indexes of 16S rRNA and dissimilatory genes was seen, suggesting that the evolution rates of ribosomal and functional genes differ. Pairwise comparison of similarity indexes of the narG and nosZ genes led to the delineation of two types of strains. Within the first type, the similarity indexes of both genes varied in the same range, suggesting that these two genes have followed a similar evolution. Within the second type of strain, the range of variations was higher for the nosZ than for the narG gene, suggesting that these genes have had a different evolutionary rate.

Research paper thumbnail of DNA Analysis of Herbarium Specimens of the Grass Weed Alopecurus myosuroides Reveals Herbicide Resistance Pre-Dated Herbicides

PLoS ONE, 2013

Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to he... more Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to herbicides have been identified in arable grass weed populations where resistance has evolved under the selective pressure of herbicides. In an effort to determine whether herbicide resistance evolves from newly arisen mutations or from standing genetic variation in weed populations, we used herbarium specimens of the grass weed Alopecurus myosuroides to seek mutant ACCase alleles carrying an isoleucine-to-leucine substitution at codon 1781 that endows herbicide resistance. These specimens had been collected between 1788 and 1975, i.e., prior to the commercial release of herbicides inhibiting ACCase. Among the 734 specimens investigated, 685 yielded DNA suitable for PCR. Genotyping the ACCase locus using the derived Cleaved Amplified Polymorphic Sequence (dCAPS) technique identified one heterozygous mutant specimen that had been collected in 1888. Occurrence of a mutant codon encoding a leucine residue at codon 1781 at the heterozygous state was confirmed in this specimen by sequencing, clearly demonstrating that resistance to herbicides can pre-date herbicides in weeds. We conclude that point mutations endowing resistance to herbicides without having associated deleterious pleiotropic effects can be present in weed populations as part of their standing genetic variation, in frequencies higher than the mutation frequency, thereby facilitating their subsequent selection by herbicide applications. Citation: Délye C, Deulvot C, Chauvel B (2013) DNA Analysis of Herbarium Specimens of the Grass Weed Alopecurus myosuroides Reveals Herbicide Resistance Pre-Dated Herbicides. PLoS ONE 8(10): e75117.

Research paper thumbnail of Effect of 2,4-Diacetylphloroglucinol on Pythium : Cellular Responses and Variation in Sensitivity Among Propagules and Species

Phytopathology, 2003

de Souza, J. T., Arnould, C., Deulvot, C., Lemanceau, P., Gianinazzi-Pearson, V., and Raaijmakers... more de Souza, J. T., Arnould, C., Deulvot, C., Lemanceau, P., Gianinazzi-Pearson, V., and Raaijmakers, J. M. 2003. Effect of 2,4-diacetylphloroglucinol on Pythium: Cellular responses and variation in sensitivity among propagules and species. Phytopathology 93:966-975.

Research paper thumbnail of Effect of 2,4diacetylphloroglucinol of Pythium: cellular responses and variation in sensitivity among propagules and species

Phytopathology, 2003

de Souza, J. T., Arnould, C., Deulvot, C., Lemanceau, P., Gianinazzi-Pearson, V., and Raaijmakers... more de Souza, J. T., Arnould, C., Deulvot, C., Lemanceau, P., Gianinazzi-Pearson, V., and Raaijmakers, J. M. 2003. Effect of 2,4-diacetylphloroglucinol on Pythium: Cellular responses and variation in sensitivity among propagules and species. Phytopathology 93:966-975.

Research paper thumbnail of Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea

BMC Genomics, 2010

Background Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications... more Background Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction. In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set. Results We obtained clear allelic data for more than 92% of the SNPs (356 out of 384). Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers. Conclusion Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics.

Research paper thumbnail of Comparative Genetic Diversity of the narG, nosZ, and 16S rRNA Genes in Fluorescent Pseudomonads

Applied and Environmental Microbiology, 2003

The diversity of the membrane-bound nitrate reductase (narG) and nitrous oxide reductase (nosZ) g... more The diversity of the membrane-bound nitrate reductase (narG) and nitrous oxide reductase (nosZ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overall, there was a good correspondence between the reductase activities and the presence of the corresponding genes. Distribution in the different ribotypes of strains harboring both the narG and nosZ genes and of strains missing both genes suggests that these two groups of strains had different evolutionary histories. Both dissimilatory genes showed high polymorphism, with similarity indexes (Jaccard) of between 0.04 and 0.8, whereas those of the 16S rRNA gene only varied from 0.77 to 0.99. No correlation between the similarity indexes of 16S rRNA and dissimilatory genes was seen, suggesting that the evolution rates of ribosomal and functional genes differ. Pairwise comparison of similarity indexes of the narG and nosZ genes led to the delineation of two types of strains. Within the first type, the similarity indexes of both genes varied in the same range, suggesting that these two genes have followed a similar evolution. Within the second type of strain, the range of variations was higher for the nosZ than for the narG gene, suggesting that these genes have had a different evolutionary rate.