SPIRAL 2 injector diagnostics

International audienceThe future SPIRAL2 facility will be composed of a multi-beam driver accelerator (5 mA/40 MeV deuterons, 5 mA /14.5 MeV/u heavy ions) and a dedicated building for the production of radioactive ion beams (RIBs). RIBs will be accelerated by the existing cyclotron CIME for the post acceleration and sent to GANIL's experimental areas. The injector constituted by an ion source a deuteron/proton source a L.E.B.T. and a M.E.B.T. lines and a room temperature R.F.Q. will produces, transports and accelerates beams up to an energy of 0.75 MeV/u. An Intermediate Test Bench (B.T.I.) is being built to commission the SPIRAL2 injector through the first rebuncher of the M.E.B.T. line in a first step and the last rebuncher in a second step. The B.T.I. is designed to perform a wide variety of measurements and functions and to go more deeply in the understanding of the behaviour of diagnostics under high average intensity beam operations. A superconducting LINAC equipped with two types of cavity will allow reaching 20 MeV/u for deuterons beam. This paper describes injector diagnostic developments and gives information about the current status

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

<p>Abstract</p> <p>Background</p> <p>Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (<it>Pinus pinaster </it>Ait.), the main conifer used for commercial plantation in southwestern Europe.</p> <p>Results</p> <p>We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 <it>in vitro </it>SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 <it>in silico </it>SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for <it>in silico </it>and <it>in vitro </it>SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a <it>Pinus taeda </it>linkage map, made it possible to align the 12 linkage groups of both species.</p> <p>Conclusions</p> <p>Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation sequencing technologies and will include SNPs from comparative orthologous sequences that were identified in the present study, providing a wider collection of anchor points for comparative genomics among the conifers.</p

High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

<p>Abstract</p> <p>Background</p> <p>High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera.</p> <p>Results</p> <p>We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of <it>Eucalyptus </it>from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for <it>E. grandis</it>. A systematic assessment of <it>in silico </it>SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous <it>in silico </it>constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species.</p> <p>SNP reliability was high across nine <it>Eucalyptus </it>species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased.</p> <p>Conclusions</p> <p>This study indicates that the GGGT performs well both within and across species of <it>Eucalyptus </it>notwithstanding its nucleotide diversity ≥2%. The development of a much larger array of informative SNPs across multiple <it>Eucalyptus </it>species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in <it>Eucalyptus</it>.</p

Mesures du courant faisceau sur l'accélérateur SPIRAL2

Le projet Spiral2 se compose d'un accélérateur et d'une section faisceaux radioactifs. L'accélérateur, composé principalement d'une source d'ions, d'une source deuton, d'un RFQ et d'un linac supraconducteur, pourra accélérer des faisceaux de 5 mA de deutons jusqu'à 40MeV et 1mA d'ions q/A= 1/3 jusqu'à 14,5MeV/u. Une nouvelle électronique a été développée au Ganil pour mesurer des courant provenant de diagnostiques interceptifs (Coupelles de Faraday) et non-interceptifs (Transformateur d'Intensité). Le but étant d'assurer des mesures de rendement, de suivi et de surveillance d'intensité Le principe employé consiste à effectuer une conversion linéaire (courant tension) permettant de faire des mesures de courant avec une grande précision sur une large gamme d'intensité.. Les diagnostiques et l'électronique sont présentés