Descriptive Data in the EDIT Platform for Cybertaxonomy

This paper describes the integration of structured descriptive data in the EDIT platform for Cybertaxonomy. The platform is composed of several software modules supporting the taxonomic workflow from data capture and storage to publication. Descriptive data play an important role within the taxonomic work process. The integration of these data via import/export modules to and from the platform and the publication as natural language output or as keys are explained

Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding

<p>Abstract</p> <p>Background</p> <p>Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for several traits involved in peanut productivity and adaptation as well as domestication.</p> <p>Results</p> <p>A total of 95 QTLs were mapped in the two water treatments. About half of the QTL positive effects were associated with alleles of the wild parent and several QTLs involved in yield components were specific to the water-limited treatment. QTLs detected for the same trait mapped to non-homeologous genomic regions, suggesting differential control in subgenomes as a consequence of polyploidization. The noteworthy clustering of QTLs for traits involved in seed and pod size and in plant and pod morphology suggests, as in many crops, that a small number of loci have contributed to peanut domestication.</p> <p>Conclusion</p> <p>In our study, we have identified QTLs that differentiated cultivated peanut from its wild relatives as well as wild alleles that contributed positive variation to several traits involved in peanut productivity and adaptation. These findings offer novel opportunities for peanut improvement using wild relatives.</p

Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology

Chromosome segment substitution lines (CSSLs) are powerful QTL mapping populations that have been used to elucidate the molecular basis of interesting traits of wild species. Cultivated peanut is an allotetraploid with limited genetic diversity. Capturing the genetic diversity from peanut wild relatives is an important objective in many peanut breeding programs. In this study, we used a marker-assisted backcrossing strategy to produce a population of 122 CSSLs from the cross between the wild synthetic allotetraploid (A. ipae¨nsis6A. duranensis)4x and the cultivated Fleur11 variety. The 122 CSSLs offered a broad coverage of the peanut genome, with target wild chromosome segments averaging 39.2 cM in length. As a demonstration of the utility of these lines, four traits were evaluated in a subset of 80 CSSLs. A total of 28 lines showed significant differences from Fleur11. The line6trait significant associations were assigned to 42 QTLs: 14 for plant growth habit, 15 for height of the main stem, 12 for plant spread and one for flower color. Among the 42 QTLs, 37 were assigned to genomic regions and three QTL positions were considered putative. One important finding arising from this QTL analysis is that peanut growth habit is a complex trait that is governed by several QTLs with different effects. The CSSL population developed in this study has proved efficient for deciphering the molecular basis of trait variations and will be useful to the peanut scientific community for future QTL mapping studies. (Résumé d'auteur

Target enrichment sequencing coupled with GWAS identifies MdPRX10 as a candidate gene in the control of budbreak in apple

The timing of floral budbreak in apple has a significant effect on fruit production and quality. Budbreak occurs as a result of a complex molecular mechanism that relies on accurate integration of external environmental cues, principally temperature. In the pursuit of understanding this mechanism, especially with respect to aiding adaptation to climate change, a QTL at the top of linkage group (LG) 9 has been identified by many studies on budbreak, but the genes underlying it remain elusive. Here, together with a dessert apple core collection of 239 cultivars, we used a targeted capture sequencing approach to increase SNP resolution in apple orthologues of known or suspected A. thaliana flowering time-related genes, as well as approximately 200 genes within the LG9 QTL interval. This increased the 275 223 SNP Axiom® Apple 480 K array dataset by an additional 40 857 markers. Robust GWAS analyses identified MdPRX10, a peroxidase superfamily gene, as a strong candidate that demonstrated a dormancy-related expression pattern and down-regulation in response to chilling. In-silico analyses also predicted the residue change resulting from the SNP allele associated with late budbreak could alter protein conformation and likely function. Late budbreak cultivars homozygous for this SNP allele also showed significantly up-regulated expression of C-REPEAT BINDING FACTOR (CBF) genes, which are involved in cold tolerance and perception, compared to reference cultivars, such as Gala. Taken together, these results indicate a role for MdPRX10 in budbreak, potentially via redox-mediated signaling and CBF gene regulation. Moving forward, this provides a focus for developing our understanding of the effects of temperature on flowering time and how redox processes may influence integration of external cues in dormancy pathways

Testing the 'zero-sum game' hypothesis: An examination of school health policy and practice and inequalities in educational outcomes

Background: There is recognition that health and education are intrinsically linked, through for example the World Health Organizations' Health Promoting Schools' (HPS) framework. Nevertheless, promoting health via schools is seen by some as a 'zero-sum game'; that is, schools have nothing to gain, and in fact may experience detriments to the core business of academic attainment as a result of focussing resources on health. Crucially, there is a paucity of evidence around the impacts of health and well-being policy and practice on attainment, with recent Cochrane reviews highlighting this gap. This study explored the 'zero-sum game' hypothesis among schools with varying levels of deprivation; that is, the role of health and wellbeing interventions in schools in reducing, or widening, socioeconomic inequality in educational attainment. Methods: Wales-wide, school-level survey data on health policies and practices, reflective of the HPS framework, were captured in 2016 using the School Environment Questionnaire (SEQ). SEQ data were linked with routinely collected data on academic attainment. Primary outcomes included attendance and attainment at Key Stages 3 and 4. Interaction terms were fitted to test whether there was an interaction between FSM,overall HPS activity, and outcomes. Linear regression models were constructed separately for high (>15% of pupils) and low (<15%) Free School Meal (FSM) schools, adjusting for confounders. Findings: The final analyses included 48 low and 49 high FSM secondary schools. Significant interactions were observed between FSM and overall HPS for KS3 attainment (b=0.28; 95% CI: 0.09, 0.47) and attendance(b=0.05; 95% CI: 0.02, 0.09), reflecting an association between health improvement activities and education outcomes among high, but not low FSM schools. There was no significant interaction for KS4 attainment (b=0.18; 95% CI: -0.22, 0.57).Interpretation: Our findings did not support the 'zero-sum game' hypothesis; in fact, among more deprived schools, there was a tendency for better attendance and attainment at Key Stage 3. Schools must equip students with the skills required for good physical, mental health and well-being in addition to academic and cognitive skills. The study included a large, nationally representative sample of secondary schools;however, the cross-sectional nature has implications for causality

Mécanismes moléculaires et cellulaires impliqués dans le processus de morphogenèse du canal atrio-ventriculaire chez le poisson zèbre

Organ morphogenesis involves dynamic changes of tissue properties at the cellular scale. In addition, cells need to adapt to their mechanical environment through mechanosensitive pathways. How mechanical cues influence cell behaviors during morphogenesis, however, remains poorly understood. Here we studied the influence of mechanical forces during the formation of the atrioventricular canal (AVC) where cardiac valves develop. We show that in zebrafish the AVC forms within a zone of tissue convergence between the atrium and the ventricle which is associated with increased activation of the actomyosin meshwork and endocardial cell orientation changes. We demonstrate that tissue convergence occurs with a major reduction of endocardial cell volume triggered by mechanical forces and the mechanosensitive channels TRPP2/TRPV4. In addition, we show that the extracellular matrix component hyaluronic acid controls cell volume changes. Together, our data suggest that cell volume change is a key cellular feature activated by mechanical forces during cardiovascular morphogenesis. This work further unravels how mechanical forces and extracellular matrix can influence tissue remodeling in developing organs.La morphogenèse des organes implique des changements dynamiques des propriétés des tissus à l'échelle cellulaire. De plus, les cellules doivent s'adapter à leur environnement mécanique par des voies mécanosensibles. Cependant, la manière dont les signaux mécaniques influencent le comportement des cellules pendant la morphogenèse reste mal comprise. Nous avons étudié ici l'influence des forces mécaniques pendant la formation du canal atrio-ventriculaire (AVC) où se développent les valves cardiaques. Nous montrons que chez le poisson zèbre, le canal atrio-ventriculaire se forme dans une zone de convergence tissulaire entre l'atrium et le ventricule qui est associée à une activation accrue du réseau d'actomyosine et à des changements d'orientation des cellules endocardiques. Nous démontrons que la convergence tissulaire se produit avec une réduction majeure du volume des cellules endocardiques déclenchée par des forces mécaniques et les canaux mécanosensibles TRPP2/TRPV4. De plus, nous montrons qu’un composant de la matrice extracellulaire, l'acide hyaluronique, contrôle les changements de volume cellulaire. Ensemble, nos données suggèrent que le changement de volume cellulaire est une caractéristique cellulaire clé activée par les forces mécaniques pendant la morphogenèse cardiovasculaire. Ces travaux permettent de mieux comprendre comment les forces mécaniques et la matrice extracellulaire peuvent influencer le remodelage des tissus dans les organes en développement