SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

<p>Abstract</p> <p>Background</p> <p>With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus <it>Citrus </it>of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated <it>Citrus </it>species.</p> <p>Results</p> <p>Fifty-four accessions covering the main <it>Citrus </it>species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within <it>C. maxima, C. medica, C. reticulata </it>and <it>C. micrantha</it>. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in <it>C. medica, C. maxima </it>and wild <it>Citrus </it>species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the <it>C. reticulata </it>diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping.</p> <p>Conclusions</p> <p>A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole <it>Citrus </it>gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around <it>C. maxima, C. medica </it>and <it>C. reticulata </it>as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in <it>Citrus </it>and genetic association in <it>C. reticulata</it>.</p

Genetically Based Location from Triploid Populations and Gene Ontology of a 3.3-Mb Genome Region Linked to Alternaria Brown Spot Resistance in Citrus Reveal Clusters of Resistance Genes

Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids

Environmental and socioeconomic correlates of extinction risk in endemic species

Aim Our current understanding of the causes of global extinction risk is mostly informed by the expert knowledge-based “threats classification scheme” of the IUCN Red List of Threatened Species. Studies based on this dataset came to different conclusions about the relative importance of threats to species, depending on which taxonomic groups and levels of extinction risk were considered, and which version of the database was used. A key reason may lie in data limitations as causes of threat are well known for charismatic and well-studied species, but not for the majority of species assessed. Here, we aim to fill current knowledge gaps about the importance of drivers of global extinction risks by focusing on endemic species. Location Global. Methods We examined country-level variation in the proportion of globally threatened and extinct endemic species (Index of Threat, IoT) with a range of spatially explicit information about anthropogenic pressures, mitigation measures and data limitations. Results IoT coincided with several anthropogenic pressures, with substantial differences among kingdoms, life-forms, levels of extinction risk and geographic locations. IoT of plants, particularly tropical woody plants of moderate extinction risk, was higher in countries with higher GDP and more invasive species. Furthermore, IoT of animals, particularly tropical mammals and invertebrates of moderate extinction risk, was higher in countries with higher GDP and smaller roadless areas. Main conclusions The extinction crisis for endemic species is associated with a complex network of potential drivers that need to be considered in concert in conservation policy and practice. Although our results require careful interpretation and remain sensitive to data limitations, we encourage similar studies at smaller scales to identify potential drivers of extinction risk at a higher resolution, particularly in regions where species assessments have been conducted consistently or on organisms with a uniform response time to pressures

Extensional faulting on Tinos island, Aegean sea, Greece: How many detachments?

Zircon and apatite fission track (ZFT and AFT) and (U-Th)/He, 40Ar/39Ar hornblende, and U-Pb zircon ages from the granites of Tinos Island in the Aegean Sea, Greece, suggest, together with published ZFT data, that there are three extensional detachments on Tinos. The Tinos granites crosscut the Tinos detachment. Cooling of the granites was controlled by the Livadi detachment, which occurs structurally above the Tinos detachment. Our U-Pb zircon age is 14.6 ± 0.2 Ma and two 40Ar/39Ar hornblende ages are 14.4 ± 0.4 and 13.7 ± 0.4 Ma. ZFT and AFT ages go from 14.4 ± 1.2 to 12.2 ± 1.0 Ma and 12.8 ± 2.4 to 11.9 ± 2.0 Ma. (U-Th)/He ages are from 10.4 ± 0.2 to 9.9 ± 0.2 Ma (zircon) and 11.9 ± 0.5 to 10.0 ± 0.3 Ma (apatite). All ages decrease northeastward in the direction of hanging wall transport on the Livadi detachment and age-distance relationships yield a slip rate of 2.6 (+3.3 / −1.0) km Ma−1. This rate is smaller than a published slip rate of 6.5 km Ma−1 for the Vari detachment, which is another detachment structurally above the Tinos detachment. Because of the different rates and because published ZFT ages from the footwall of the Vari detachment are ∼10 Ma, we propose that the Vari detachment has to be distinguished from the older Livadi detachment. We discuss various models of how the extensional detachments may have evolved and prefer a scenario in which the Vari detachment cut down into the footwall of the Livadi detachment successively exhuming deeper structural units. The thermochronologic ages demonstrate the importance of quantitative data for constraining localization processes during extensional deformation

GREAT — a randomized aneurysm trial. Design of a randomized controlled multicenter study comparing HydroSoft/HydroFrame and bare platinum coils for endovascular aneurysm treatment

International audienceThe effectiveness of a hybrid hydrogel platinum detachable coil (HydroCoil; MicroVention Inc., Tustin, CA) for endovascular aneurysm treatment has been proven in a recently published RCT. Due to technical restrictions (coil stiffness, time restriction for placement), the HydroSoft coil as well as a corresponding 3D framing coil, the HydroFrame coil (MicroVention Inc., Tustin, CA), a class of new softer coils containing less hydrogel and swelling more slowly than the HydroCoil, have been developed and brought to clinical practice. The present study aims to compare the effectiveness of endovascular aneurysm treatment with coil embolization between patients allocated HydroSoft/HydroFrame versus bare platinum coiling. GREAT is a randomized, controlled, multicentre trial in patients bearing cerebral aneurysms to be treated by coil embolization. Eligible patients were randomized to either coil embolization with HydroSoft/HydroFrame coils (>50 % of administered coil length), or bare platinum coils. Inclusion criteria were as follows: age 18-75, ruptured aneurysm (WFNS 1-3) and unruptured aneurysm with a diameter between 4 and 12 mm. Anatomy such that endovascular coil occlusion deemed possible and willingness of the neurointerventionalist to use either HydroSoft/HydroFrame or bare platinum coils. Exclusion criteria were as follows: aneurysms previously treated by coiling or clipping. Primary endpoint is a composite of major aneurysm recurrence on follow-up angiography and poor clinical outcome (modified Rankin scale 3 or higher), both assessed at 18 months post treatment. Risk differences for poor outcomes will be estimated in a modified intention-to-treat analysis stratified by rupture status (DRKS-ID: DRKS00003132)

Deciphering the genome structure and paleohistory of _Theobroma cacao_

We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome fusions. The _T. cacao_ genome can be considered as a simple living relic of higher plant evolution