Showing papers by "Dominique Brunel published in 2006"

Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination “hot spots”

Abstract: Crossover (CO) is a key process for the accurate segregation of homologous chromosomes during the first meiotic division. In most eukaryotes, meiotic recombination is not homogeneous along the chromosomes, suggesting a tight control of the location of recombination events. We genotyped 71 single nucleotide polymorphisms (SNPs) covering the entire chromosome 4 of Arabidopsis thaliana on 702 F2 plants, representing 1404 meioses and allowing the detection of 1171 COs, to study CO localization in a higher plant. The genetic recombination rates varied along the chromosome from 0 cM/Mb near the centromere to 20 cM/Mb on the short arm next to the NOR region, with a chromosome average of 4.6 cM/Mb. Principal component analysis showed that CO rates negatively correlate with the G+C content (P = 3x10(-4)), in contrast to that reported in other eukaryotes. COs also significantly correlate with the density of single repeats and the CpG ratio, but not with genes, pseudogenes, transposable elements, or dispersed repeats. Chromosome 4 has, on average, 1.6 COs per meiosis, and these COs are subjected to interference. A detailed analysis of several regions having high CO rates revealed "hot spots" of meiotic recombination contained in small fragments of a few kilobases. Both the intensity and the density of these hot spots explain the variation of CO rates along the chromosome.

Evidence for a large‐scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium

Abstract: The existence of a large-scale population structure was investigated in Arabidopsis thaliana by studying patterns of polymorphism in a set of 71 European accessions. We used sequence polymorphism surveyed in 10 fragments of ∼ 600 nucleotides and a set of nine microsatellite markers. Population structure was investigated using a model-based inference framework. Among the accessions studied, the presence of four groups was inferred using genetic data, without using prior information on the geographical origin of the accessions. Significant genetic isolation by geographical distance was detected at the group level, together with a geographical gradient in allelic richness across groups. These results are discussed with respect to the previously proposed scenario of postglacial colonization of Europe from putative glacial refugia. Finally, the contribution of the inferred structure to linkage disequilibrium among 171 pairs of essentially unlinked markers was also investigated. Linkage disequilibrium analysis revealed that significant associations detected in the whole sample were mainly due to genetic differentiation among the inferred groups. We discuss the implication of this finding for future association studies in A . thaliana .

Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.)

Abstract: Information on single-nucleotide polymorphisms (SNPs) in hexaploid bread wheat is still scarce. The goal of this study was to detect SNPs in wheat and examine their frequency. Twenty-six bread whea...

Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploid plants.

Abstract: The application of high-throughput SNP genotyping is a great challenge for many research projects in the plant genetics domain. The GOOD assay for mass spectrometry, Amplifluor® and TaqMan® are three methods that rely on different principles for allele discrimination and detection, specifically, primer extension, allele-specific PCR and hybridization, respectively. First, with the goal of assessing allele frequencies by means of SNP genotyping, we compared these methods on a set of three SNPs present in the herbicide resistance genes CSR, AXR1 and IXR1 of Arabidopsis thaliana. In this comparison, we obtained the best results with TaqMan® based on PCR specificity, flexibility in primer design and success rate. We also used mass spectrometry for genotyping polyploid species. Finally, a combination of the three methods was used for medium- to high-throughput genotyping in a number of different plant species. Here, we show that all three genotyping technologies are successful in discriminating alleles in various plant species and discuss the factors that must be considered in assessing which method to use for a given application.

Weed response to herbicides: regional‐scale distribution of herbicide resistance alleles in the grass weed Alopecurus myosuroides

Abstract: Summary • Effective herbicide resistance management requires an assessment of the range of spatial dispersion of resistance genes among weed populations and identification of the vectors of this dispersion. • In the grass weed Alopecurus myosuroides (black-grass), seven alleles of the acetyl-CoA carboxylase (ACCase) gene are known to confer herbicide resistance. Here, we assessed their respective frequencies and spatial distribution on two nested geographical scales (the whole of France and the French administrative district of Cote d’Or) by genotyping 13 151 plants originating from 243 fields. • Genetic variation in ACCase was structured in local populations at both geographical scales. No spatial structure in the distribution of resistant ACCase alleles and no isolation by distance were detected at either geographical scale investigated. • These data, together with ACCase sequencing and data from the literature, suggest that evolution of A. myosuroides resistance to herbicides occurred at the level of the field or group of adjacent fields by multiple, independent appearances of mutant ACCase alleles that seem to have rather restricted spatial propagation. Seed transportation by farm machinery seems the most likely vector for resistance gene dispersal in A. myosuroides.

Identification of Glu-B1-1 as a candidate gene for the quantity of high-molecular-weight glutenin in bread wheat (Triticum aestivum L.) by means of an association study.

Abstract: A previous study in wheat (Triticum aestivum L.) identified two candidate genes controlling a quantitative trait locus (QTL) for high-molecular-weight glutenin subunit (HMW-GS) GluBx. These candidates were Glu-B1-1, the structural gene coding for Glu1Bx, and the B homoeologous gene coding for SPA (spa-B), a seed storage protein activator. The goal of this study was to identify the best candidate gene for this QTL. Single nucleotide polymorphisms (SNPs) are an abundant source of DNA polymorphisms that have been successfully used to identify loci associated with particular phenotypes. As no linkage disequilibrium was detected between Glu-B1-1 and spa-B, we performed an association study to identify the individual gene responsible for the QTL. Six SNPs, three located in Glu-B1-1 and three in spa-B, were genotyped by mass spectrometry in a collection of 113 bread wheat lines. These lines were also evaluated for protein content as well as the total quantity of HMW-GSs and of each HMW-GS in seed samples from two harvest years. Significant associations were detected only between Glu-B1-1 polymorphism and most of the traits evaluated. Spa-B was unambiguously discarded as a candidate. To our knowledge, this is the first report on an association study that was successfully used to discriminate between two candidate genes.