SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population

International audienceBackground - Progress in genetics and breeding in pea still suffers from the limited availability of molecular resources. SNP markers that can be identified through affordable sequencing processes, without the need for prior genome reduction or a reference genome to assemble sequencing data would allow the discovery and genetic mapping of thousands of molecular markers. Such an approach could significantly speed up genetic studies and marker assisted breeding for non-model species. Results - A total of 419,024 SNPs were discovered using HiSeq whole genome sequencing of four pea lines, followed by direct identification of SNP markers without assembly using the discoSnp tool. Subsequent filtering led to the identification of 131,850 highly designable SNPs, polymorphic between at least two of the four pea lines. A subset of 64,754 SNPs was called and genotyped by short read sequencing on a subpopulation of 48 RILs from the cross 'Baccara' x 'PI180693'. This data was used to construct a WGGBS-derived pea genetic map comprising 64,263 markers. This map is collinear with previous pea consensus maps and therefore with the Medicago truncatula genome. Sequencing of four additional pea lines showed that 33 % to 64 % of the mapped SNPs, depending on the pairs of lines considered, are polymorphic and can therefore be useful in other crosses. The subsequent genotyping of a subset of 1000 SNPs, chosen for their mapping positions using a KASP™ assay, showed that almost all generated SNPs are highly designable and that most (95 %) deliver highly qualitative genotyping results. Using rather low sequencing coverages in SNP discovery and in SNP inferring did not hinder the identification of hundreds of thousands of high quality SNPs. Conclusions - The development and optimization of appropriate tools in SNP discovery and genetic mapping have allowed us to make available a massive new genomic resource in pea. It will be useful for both fine mapping within chosen QTL confidence intervals and marker assisted breeding for important traits in pea improvement

Advanced backcross QTL analysis and comparative mapping with RIL QTL studies and GWAS provide an overview of QTL and marker haplotype diversity for resistance to Aphanomyces root rot in pea (Pisum sativum)

Aphanomyces euteiches is the most damaging soilborne pea pathogen in France. Breeding of pea resistant varieties combining a diversity of quantitative trait loci (QTL) is a promising strategy considering previous research achievements in dissecting polygenic resistance to A. euteiches. The objective of this study was to provide an overview of the diversity of QTL and marker haplotypes for resistance to A. euteiches, by integrating a novel QTL mapping study in advanced backcross (AB) populations with previous QTL analyses and genome-wide association study (GWAS) using common markers. QTL analysis was performed in two AB populations derived from the cross between the susceptible spring pea variety “Eden” and the two new sources of partial resistance “E11” and “LISA”. The two AB populations were genotyped using 993 and 478 single nucleotide polymorphism (SNP) markers, respectively, and phenotyped for resistance to A. euteiches in controlled conditions and in infested fields at two locations. GWAS and QTL mapping previously reported in the pea-Aphanomyces collection and from four recombinant inbred line (RIL) populations, respectively, were updated using a total of 1,850 additional markers, including the markers used in the Eden x E11 and Eden x LISA populations analysis. A total of 29 resistance-associated SNPs and 171 resistance QTL were identified by GWAS and RIL or AB QTL analyses, respectively, which highlighted 10 consistent genetic regions confirming the previously reported QTL. No new consistent resistance QTL was detected from both Eden x E11 and Eden x LISA AB populations. However, a high diversity of resistance haplotypes was identified at 11 linkage disequilibrium (LD) blocks underlying consistent genetic regions, especially in 14 new sources of resistance from the pea-Aphanomyces collection. An accumulation of favorable haplotypes at these 11 blocks was confirmed in the most resistant pea lines of the collection. This study provides new SNP markers and rare haplotypes associated with the diversity of Aphanomyces root rot resistance QTL investigated, which will be useful for QTL pyramiding strategies to increase resistance levels in future pea varieties

Idées suicidaires de l'adolescent en médecine générale (conception et validation d'une méthode de dépistage réalisée et appliquée en consultation de médecine générale)

POITIERS-BU Médecine pharmacie (861942103) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Developing for other cultures. A Cultural Model for Learning Tools Design in the Nasa (Paez) Amerindian Context

ISBN : 142006945

An experience about developing educational tools for revitalizing language and culture of a Colombian native community

International audienceRevitalizing mother tongue and culture is a priority for the Nasa Colombian native people [9, 2]. Since 1970 they are running processes to revert the consequences of the persecution and punishment that the use of Nasa Yuwe, the Nasa language, suffered during earlier periods of their history. This text briefly describes a project that aims to support such revitalization efforts through Human-Computer Interaction. The intent of the authors is to take into account cultural particularities of the target population in the design of educational tools

A worldwide bread wheat core collection arrayed in a 384-well plate

Bread wheat (Triticum aestivum), one of the world's major crops, is genetically very diverse. In order to select a representative sample of the worldwide wheat diversity, 3,942 accessions originating from 73 countries were analysed with a set of 38 genomic simple sequence repeat (SSR) markers. The number of alleles at each locus ranged from 7 to 45 with an average of 23.9 alleles per locus. The 908 alleles detected were used together with passport data to select increasingly large sub-samples that maximised both the number of observed alleles at SSR loci and the number of geographical origins. A final core of 372 accessions (372CC) was selected with this M strategy. All the different geographical areas and more than 98% of the allelic diversity at the 38 polymorphic loci were represented in this core. The method used to build the core was validated, by using a second set of independent markers [44 expressed sequence tag (EST)-SSR markers] on a larger sample of 744 accessions: 96.74% of the alleles observed at these loci had already been captured in the 372CC. So maximizing the diversity with a first set of markers also maximised the diversity at a second independent set of locus. To relate the genetic structure of wheat germplasm to its geographical origins, the two sets of markers were used to compute a dissimilarity matrix between geographical groups. Current worldwide wheat diversity is clearly divided according to wheat's European and Asian origins, whereas the diversity within each geographical group might be the result of the combined effects of adaptation of an initial germplasm to different environmental conditions and specific breeding practices. Seeds from each accession of the 372CC were multiplied and are now available to the scientific community. The genomic DNA of the 372CC, which can be entirely contained in a 384-deep-well storage plate, will be a useful tool for future studies of wheat genetic diversity

Progrès génétique et maintien de la variabilité génétique : sont-ils incompatibles ? Le cas du ray-grass anglais au travers de 40 ans d'amélioration de variétés fourragères et à gazon

National audienceLe ray-grass anglais est l'espèce de graminées la plus communément cultivée en Europe avec cette particularité d'une double utilisation, en tant que fourrage à destination des ruminants et comme gazon pour la couverture du sol et à des fins esthétiques. L'amélioration de cette espèce n'a débuté significativement que très progressivement dans les années 1950 avec le développement d'objectifs de sélection spécifiques pour une utilisation en gazon encore plus tardivement vers la fin des années 1960. Une évaluation sous les deux modes d'utilisation a été entreprise de 2006 à 2008 au travers de 14 essais conduits dans le réseau de l'Association des Créateurs de Variétés Fourragères (ACVF) et de 61 populations spontanées ou variétés inscrites entre 1974 et 2004 dont 32 au catalogue français des variétés à gazon et 14 à celui des variétés fourragères. L'évaluation phénotypique a été également complétée par deux essais de production de semences. Parallèlement, l'ensemble de la collection a été génotypé à l'aide de 16 marqueurs moléculaires PCR1-spécifiques après un tri de polymorphisme et de portabilité sur séquenceur parmi 197 marqueurs publics de différentes natures et disponibles en 2005. Les résultats montrent l'émergence d'une différenciation phénotypique marquée désormais entre les deux types sur les caractères de morphologie foliaire, de productivité et de valeur alimentaire tandis que les deux directions de sélection convergent vers une meilleure tolérance aux maladies et l'élimination de caractères de la reproduction sexuée défavorables comme l'alternativité et la remontaison en été. Cependant, aucun impact du processus de sélection variétale n'a été mis en évidence sur la productivité grainière, toujours caractérisée par une extrême variabilité entre variétés quelles qu'elles soient. Au plan moléculaire, la différenciation génétique entre fourrage et gazon ne se développe que très lentement devant la différenciation entre variétés au sein de chaque type, désormais significativement supérieure à celle entre populations naturelles. L'amélioration du ray-grass anglais au travers de sélections récurrentes, de variétés synthétiques et du fonctionnement des catalogues illustre ainsi un système collectif particulièrement efficace pour réaliser un progrès génétique régulier tout en limitant l'érosion de la diversité génétique de l'espèce

Reference-free high-throughput SNP detection in pea: an example of discoSnp usage for a non-model complex genome

International audienceBackground / Purpose:Detecting Single Nucleotide Polymorphisms (SNPs) between genomes is a routine task with Next Generation Sequencers (NGS) data. SNP detection methods generally need a reference genome. As non-model organisms are increasingly investigated, reference-free methods are needed. The discoSnp method detects SNPs directly from raw NGS data set(s) without using any third-party information. The pea non-model organism has a 4.5 GB complex genome without reference. We compared, on the same set of low depth pea sequences, the SNPs generated by discoSnp with those published with a previous SNP discovery pipeline, and those generated using classical mapping approach with the association of Bowtie2 and GATK tools.Main conclusion:The quality of discoSnp results in association with its very low memory needs and low time footprints led us to choose this software for a SNP discovery and direct Genotypin. By Sequencing project on a set of 48 pea genomic DNA libraries from a recombinant inbred lines subpopulation sequenced with Illumina HiSeq2000 technology. The analysis enabled to identify 88,851 SNP polymorphs on this population, from which around 60k SNPs will be genetically mapped

Construction and evaluation of Near-Isogenic Lines for resistance to Aphanomyces euteiches in pea

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Five Regions of the Pea Genome Co-Control Partial Resistance to D. pinodes, Tolerance to Frost, and Some Architectural or Phenological Traits

International audienceEvidence for reciprocal links between plant responses to biotic or abiotic stresses and architectural and developmental traits has been raised using approaches based on epidemiology, physiology, or genetics. Winter pea has been selected for years for many agronomic traits contributing to yield, taking into account architectural or phenological traits such as height or flowering date. It remains nevertheless particularly susceptible to biotic and abiotic stresses, among which Didymella pinodes and frost are leading examples. The purpose of this study was to identify and resize QTL localizations that control partial resistance to D. pinodes, tolerance to frost, and architectural or phenological traits on pea dense genetic maps, considering how QTL colocalizations may impact future winter pea breeding. QTL analysis revealed five metaQTLs distributed over three linkage groups contributing to both D. pinodes disease severity and frost tolerance. At these loci, the haplotypes of alleles increasing both partial resistance to D. pinodes and frost tolerance also delayed the flowering date, increased the number of branches, and/or decreased the stipule length. These results question both the underlying mechanisms of the joint control of biotic stress resistance, abiotic stress tolerance, and plant architecture and phenology and the methods of marker-assisted selection optimizing stress control and productivity in winter pea breeding