Saint-Denis – RSMA-R, Nouvelle route du littoral (tranche 2)

Sur la commune de Saint-Denis, le diagnostic de la Nouvelle route du littoral a traité une emprise susceptible d’être impactée par la reprise de la RN6, dans l’enceinte du Régiment du service militaire adapté de La Réunion (RSMA-R). Le site est localisé à 200 m de l’océan et culmine à 14 m d’altitude sur un petit plateau basaltique préservé en rive gauche de la Rivière Saint-Denis, au pied de La Montagne. L’opération a été réalisée en janvier et février 2012 par l’Inrap sous la responsabilité..

La Possession – Batterie côtière, Nouvelle route du littoral (tranche 2)

Sur la commune de La Possession, le diagnostic de la Nouvelle route du littoral a traité l’emprise de l’aire de repos, affectée par l’extrémité de l’ouvrage en digue. L’emprise diagnostiquée, d’une superficie de 1,6 ha, est une zone triangulaire allongée comprise entre le haut du cordon littoral, fortement impacté par la pose dans les années 2000 d’une canalisation d’eaux usées (disposée parallèlement au rivage et en fonctionnement), les infrastructures de l’aire de repos, et la route nationa..

Saint-Denis, La Possession – Nouvelle route du littoral (tranche 1)

La Nouvelle route du littoral est l’ouvrage routier construit sur l’océan par la Région Réunion entre Saint-Denis et La Possession, afin de remplacer la route actuelle dite en corniche ouverte en 1976 (fig. 1). Fig. 1 – Vue aérienne de l’actuelle route du littoral Cliché : É. Jacquot (Dac-OI). Ce grand projet d’infrastructure est le premier dans l’île de La Réunion à être accompagné d’une opération d’archéologie préventive, et entraîna avec lui la continuité de ce service public dans l’océan..

Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce

<p>Abstract</p> <p>Background</p> <p>To explore the potential value of high-throughput genotyping assays in the analysis of large and complex genomes, we designed two highly multiplexed Illumina bead arrays using the GoldenGate SNP assay for gene mapping in white spruce (<it>Picea glauca </it>[Moench] Voss) and black spruce (<it>Picea mariana </it>[Mill.] B.S.P.).</p> <p>Results</p> <p>Each array included 768 SNPs, identified by resequencing genomic DNA from parents of each mapping population. For white spruce and black spruce, respectively, 69.2% and 77.1% of genotyped SNPs had valid GoldenGate assay scores and segregated in the mapping populations. For each of these successful SNPs, on average, valid genotyping scores were obtained for over 99% of progeny. SNP data were integrated to pre-existing ALFP, ESTP, and SSR markers to construct two individual linkage maps and a composite map for white spruce and black spruce genomes. The white spruce composite map contained 821 markers including 348 gene loci. Also, 835 markers including 328 gene loci were positioned on the black spruce composite map. In total, 215 anchor markers (mostly gene markers) were shared between the two species. Considering lineage divergence at least 10 Myr ago between the two spruces, interspecific comparison of homoeologous linkage groups revealed remarkable synteny and marker colinearity.</p> <p>Conclusion</p> <p>The design of customized highly multiplexed Illumina SNP arrays appears as an efficient procedure to enhance the mapping of expressed genes and make linkage maps more informative and powerful in such species with poorly known genomes. This genotyping approach will open new avenues for co-localizing candidate genes and QTLs, partial genome sequencing, and comparative mapping across conifers.</p

L’application de la géophysique marine au diagnostic subaquatique

Les surfaces des diagnostics subaquatiques prescrits peuvent très vite frôler le gigantisme, ce qui rend inadéquate la méthode traditionnelle de prospection de la totalité des fonds avec des plongeurs. La recherche d’artefacts, tant en milieu maritime que fluvial, nécessite le recours aux outils acoustiques et magnétométriques. A la création du service des activités subaquatiques de l’Inrap en 2011, une réflexion a été menée afin de transposer les protocoles d’acquisition de données géophysiques issues de l’industrie et de la Marine aux opérations de diagnostics préventifs. Trois catégories de systèmes sont identifiables : ceux qui permettent d’« observer » le fond (sonar latéral ou sidescan sonar) voire de le topographier (sondeurs multifaisceaux ou SMF), ceux qui mesurent le champ magnétique et ceux qui pénètrent le sédiment en profondeur (sondeur de sédiments ou subbotom profiler).The size of the areas that need to be surveyed underwater can quickly get out of hand, which means that traditional survey methods of total survey of the seabed by divers are not up appropriate. Acoustic and magnetometric tools are necessary to detect features in both marine and river environments. When an underwater section was set up by Inrap in 2011, we assessed how the geophysical data-capture protocols that industry and the Navy use could be adapted for archaeological evaluations. Three systems are relevant here: those that allow us to “observe” the seabed (lateral sonar or sidescan sonar) or map it (multi-probe array), those that measure the magnetic field, and those that penetrate the sediments in depth (sediment corers or sub-bottom profilers).Las superficies de los diagnósticos subacuáticos prescritos pueden alcanzar rápidamente tamaños insospechados, por lo que recurrir al método tradicional de prospección de los fondos con buzos resulta totalmente inadecuado. Además, la búsqueda de artefactos en los medios marino o fluvial requiere el uso de herramientas acústicas y magnetométricas. En 2011, tras la creación del servicio de actividades subacuáticas del Inrap, se inició una reflexión destinada a transponer los protocolos de adquisición de datos geofísicos obtenidos a partir de la industria y de la Marina a las operaciones de diagnósticos preventivas. Así, es posible distinguir tres categorías de sistemas: los que permiten «observar» el fondo (sonar lateral o side scan sonar), e incluso de topografiarlo (sonda multihaz o SMF); aquellos que miden el campo magnético; y los que penetran el sedimento en profundidad (sonda de sedimentos o sub-botom profiler)

QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data

Sitka spruce (Picea sitchensis (Bong.) Carr) is the most common commercial plantation species in Britain and a breeding programme based on traditional lines has been in operation since the early 1960s. Rotation lengths of 40-years have led breeders to adopt a process of indirect selection at younger ages based on traits well correlated with final selection, but still the generation interval is unlikely to reduce much below twenty years. Recent successful developments with genomic selection in animal breeding have led tree breeders to consider the application of this technology. In this study a RAD sequence assay was developed as a means of investigating the potential of molecular breeding in a non-model species. DNA was extracted from nearly 500 clonally replicated trees growing in a single full-sibling family at one site in Britain. The technique proved successful in identifying 132 QTLs for 5-year bud-burst and 2 QTLs for 6-year height. In addition, the accuracy of predicting phenotypes by genomic selection was strikingly high at 0.62 and 0.59 respectively. Sensitivity analysis with 200 offspring found only a slight fall in correlation values (0.54 and 0.38) although when the training population reduced to 50 offspring predictive values fell further (0.33 and 0.25). This proved an encouraging first investigation into the potential use of genomic selection in the breeding of Sitka spruce. The authors investigate how problems associated with effective population size and linkage disequilibrium can be avoided and suggest a practical way of incorporating genomic selection into a dynamic breeding programme

Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce

Conifers are characterized by a large genome size and a rapid decay of linkage disequilibrium, most often within gene limits. Genome scans based on noncoding markers are less likely to detect molecular adaptation linked to genes in these species. In this study, we assessed the effectiveness of a genome-wide single nucleotide polymorphism (SNP) scan focused on expressed genes in detecting local adaptation in a conifer species. Samples were collected from six natural populations of white spruce (Picea glauca) moderately differentiated for several quantitative characters. A total of 534 SNPs representing 345 expressed genes were analysed. Genes potentially under natural selection were identified by estimating the differentiation in SNP frequencies among populations (FST) and identifying outliers, and by estimating local differentiation using a Bayesian approach. Both average expected heterozygosity and population differentiation estimates (HE = 0.270 and FST = 0.006) were comparable to those obtained with other genetic markers. Of all genes, 5.5% were identified as outliers with FST at the 95% confidence level, while 14% were identified as candidates for local adaptation with the Bayesian method. There was some overlap between the two gene sets. More than half of the candidate genes for local adaptation were specific to the warmest population, about 20% to the most arid population, and 15% to the coldest and most humid higher altitude population. These adaptive trends were consistent with the genes’ putative functions and the divergence in quantitative traits noted among the populations. The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels