Estimation of the average effects of specific alleles detected by the pseudo-testcross QTL mapping strategy

International audienc

An advanced transparent hydropolymer wound dressing for undisturbed post‐op management of surgical wounds following hip and knee replacement: A prospective observational series

Total hip arthroplasty (THA) and total knee arthroplasty (TKA) are standardised surgical procedures for patients with complex comorbidities. The enhanced recovery after surgery (ERAS) protocol has shown reduced lengths of hospital stay and reduced postoperative complications. Currently, there is a paucity of recommendations in regards to dressing selection for postoperative wound care within the ERAS protocol. The aim of this study was to investigate the usefulness of a transparent hydropolymer wound dressing in suit for 14 days in 20 orthopaedic patients following hip or knee arthroplasty under the ERAS protocol. The majority of participants (90%) had a wear time of 14 days without the need for dressing removal. Clinicians rated the dressing very easy to apply with very good visibility of the incision line (100%). All participants reported the dressing to be ‘very comfortable’ (95%, n = 19) or ‘comfortable’ (5%, n = 1). Overall, the transparent hydropolymer dressing provided sufficient incision site visibility, reducing the need for dressing changes. To the best of our knowledge, this is the first study to show that the use of a transparent hydropolymer dressing in situ for 14 days to allow undisturbed wound healing

O impacto do homem na estrutura de uma espécie: Portugal, um paradigma

A bacia do Mediterrâneo é caracterizada pelo tradicional desaparecimento da floresta devido à acção do Homem e o impacto humano tem tido influência na alteração da diversidade genética. O pinheiro bravo ocorre em populações fragmentadas na região oeste da bacia do Mediterrâneo e a sua área de distribuição tem sido alterada nos últimos séculos devido a intensa florestação, em particular no SW de França e no Noroeste da Península Ibérica e, também, devido ao comportamento invasivo desta espécie em áreas perturbadas do ponto de vista ecológico. Nesta apresentação pretendemos sintetizar e discutir o resultado de estudos que utilizaram técnicas moleculares para revelar a diversidade do pinheiro bravo e, também, o impacto humano na sua estrutura genética; que é demonstrado paradigmaticamente em Portugal. Os parâmetros genéticos estimados com base em microsatélites do cloroplasto (cpSSR) revelaram que a diversidade genética é muito elevada ao nível da distribuição da espécie. Observou-se uma clara e significativa diferenciação entre grupos de populações de diferente origem geográfica (Portugal, França, Itália, Espanha e Marrocos). Pelo contrário, o grau de divergência dentro dos países é geralmente muito baixo ou próximo de zero, o que indica uma variação homogénea dentro dos grupos. A presença de diferenciação entre grupos de populações de diferentes áreas reflecte a existência de diferentes refúgios durante o Quaternário. Em França, o padrão haplotípico sugere uma mistura de material proveniente de diferentes origens. Só foram encontrados 3 mitótipos, usando marcadores mitocondriais, marcador de herança maternal, o que proporciona uma imagem clara de áreas colonizadas a partir dos diferentes refúgios; nem uma só população possui uma composição mista. Uma análise filogenética feita com base em isoenzimas mostrou que a estrutura geográfica do pinheiro bravo na Península Ibérica (PI) é muito elevada. As populações de Noroeste formam um grupo e as de Sudeste outro. Observou-se níveis elevados de diversidade nas populações de Este e Sul e uma redução importante da variabilidade em populações da região Noroeste da PI. No entanto, pode ter existido em Portugal um refúgio, pois o pinheiro bravo pode ter sobrevivido durante a última glaciação em zonas abrigadas e de baixa altitude junto ao Oceano Atlântico, o que parece também ser evidente devido a descobertas de pólen e carvão fóssil. A distribuição da variação genética do pinheiro bravo em Portugal, observada através de cpSSR indica que a diferenciação entre populações é baixa e que a diversidade existe principalmente dentro das populações. Não se observa nenhum padrão geográfico, mas as evidências existentes de uma forte influência antrópica antropogénica associada a um fluxo genético extensivo poderiam explicar esse resultado

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference fullsib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance

Cellulose microfibril orientation of Picea abies and its variability at the micron-level determined by Raman imaging

The functional characteristics of plant cell walls depend on the composition of the cell wall polymers, as well as on their highly ordered architecture at scales from a few nanometres to several microns. Raman spectra of wood acquired with linear polarized laser light include information about polymer composition as well as the alignment of cellulose microfibrils with respect to the fibre axis (microfibril angle). By changing the laser polarization direction in 3° steps, the dependency between cellulose and laser orientation direction was investigated. Orientation-dependent changes of band height ratios and spectra were described by quadratic linear regression and partial least square regressions, respectively. Using the models and regressions with high coefficients of determination (R2 > 0.99) microfibril orientation was predicted in the S1 and S2 layers distinguished by the Raman imaging approach in cross-sections of spruce normal, opposite, and compression wood. The determined microfibril angle (MFA) in the different S2 layers ranged from 0° to 49.9° and was in coincidence with X-ray diffraction determination. With the prerequisite of geometric sample and laser alignment, exact MFA prediction can complete the picture of the chemical cell wall design gained by the Raman imaging approach at the micron level in all plant tissues

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

Plasticity of maritime pine (Pinus pinaster) wood-forming tissues during a growing season

Research• The seasonal effect is the most significant external source of variation affecting vascular cambial activity and the development of newly divided cells, and hence wood properties. Here, the effect of edapho-climatic conditions on the phenotypic and molecular plasticity of differentiating secondary xylem during a growing season was investigated. • Wood-forming tissues of maritime pine (Pinus pinaster) were collected from the beginning to the end of the growing season in 2003. Data from examination of fibre morphology, Fourier-transform infrared spectroscopy (FTIR), analytical pyrolysis, and gas chromatography/mass spectrometry (GC/MS) were combined to characterize the samples. Strong variation was observed in response to changes in edapho-climatic conditions. • A genomic approach was used to identify genes differentially expressed during this growing season. Out of 3512 studied genes, 19% showed a significant seasonal effect. These genes were clustered into five distinct groups, the largest two representing genes over-expressed in the early- or late-wood-forming tissues, respectively. The other three clusters were characterized by responses to specific edapho-climatic conditions. • This work provides new insights into the plasticity of the molecular machinery involved in wood formation, and reveals candidate genes potentially responsible for the phenotypic differences found between early- and late-wood