Tracing the ancestry of modern bread wheats.

For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world's most important crops. We use exome sequencing of a worldwide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding has shaped the genetic makeup of modern bread wheats. We observe considerable genetic variation at the genic, chromosomal and subgenomic levels, and use this information to decipher the likely origins of modern day wheats, the consequences of range expansion and the allelic variants selected since its domestication. Our data support a reconciled model of wheat evolution and provide novel avenues for future breeding improvement.

RepetDB: a unified resource for transposable element references.

BACKGROUND: Thanks to their ability to move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors to genome plasticity and evolution. Their detection and annotation are considered essential in any genome sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements in high-throughput sequencing technologies. A fully automated de novo annotation process for TEs is therefore required to cope with the deluge of sequence data.However, all automated procedures are error-prone, and an automated procedure for TE identification and classification would be no exception. It is therefore crucial to provide not only the TE reference sequences, but also evidence justifying their classification, at the scale of the whole genome. A few TE databases already exist, but none provides evidence to justify TE classification. Moreover, biological information about the sequences remains globally poor. RESULTS: We present here the RepetDB database developed in the framework of GnpIS, a genetic and genomic information system. RepetDB is designed to store and retrieve detected, classified and annotated TEs in a standardized manner. RepetDB is an implementation with extensions of InterMine, an open-source data warehouse framework used here to store, search, browse, analyze and compare all the data recorded for each TE reference sequence. InterMine can display diverse information for each sequence and allows simple to very complex queries. Finally, TE data are displayed via a worldwide data discovery portal. RepetDB is accessible at urgi.versailles.inra.fr/repetdb. CONCLUSIONS: RepetDB is designed to be a TE knowledge base populated with full de novo TE annotations of complete (or near-complete) genome sequences. Indeed, the description and classification of TEs facilitates the exploration of specific TE families, superfamilies or orders across a large range of species. It also makes possible cross-species searches and comparisons of TE family content between genomes.

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data.

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.

Physical Map of the Short Arm of Bread Wheat Chromosome 3D.

Bread wheat ( L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning. It comprises 869 contigs with a cumulative length of 274.5 Mbp and represents 85.5% of the estimated chromosome arm size. Eighty-six Mbp of survey sequences from chromosome arm 3DS were assigned in silico to physical map contigs via next-generation sequencing of bacterial artificial chromosome pools, thus providing a high-density framework for physical map ordering along the chromosome arm. About 60% of the physical map was anchored in this single experiment. Finally, 1393 high-confidence genes were anchored to the physical map. Comparisons of gene space of the chromosome arm 3DS with genomes of closely related species [ (L.) P.Beauv., rice ( L.), and sorghum [ (L.) Moench] and homeologous wheat chromosomes provided information about gene movement on the chromosome arm.

transPLANT Resources for Triticeae Genomic Data.

The genome sequences of many important Triticeae species, including bread wheat ( L.) and barley ( L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT () is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.

A telephone questionnaire in order to assess functional outcome after post-traumatic limb salvage surgery: Development and preliminary validation.

BACKGROUND: Post-traumatic limb salvage surgery is challenging and evaluation of the results remains arduous. No questionnaire specifically assessing functional outcome after post-traumatic limb salvage surgery of the lower extremity exists. Due to regionalization of specialized care, the patients' travel time to the hospital increases. To overcome a higher patients' travel burden, patients' follow up by telephone is an option. We aimed to develop a telephone questionnaire in order to assess functional outcome after post-traumatic limb salvage surgery of the lower extremity. METHODS: From a review of scores of functional assessment of the lower limb surgery, we have developed a telephone questionnaire. A prospective study was performed to validate this telephone questionnaire. Twenty patients were included. The participants were called to complete the telephone questionnaire twice with an interval of a week. The Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) was completed during the second telephone call. The internal consistency was analyzed by the Cronbach's alpha (α). With the outcome scores of both completions, the test-retest reliability was analyzed by the interclass correlation coefficient (ICC) 2,k with a 95% confidence interval (95% CI). The outcome scores of the second telephone questionnaire and the WOMAC questionnaire were used for the construct validity analysis by the Spearman's rank correlation coefficient (r(s)) with a 95% CI. RESULTS: The internal consistency analysis revealed a α=0.62 which improved to α=0.92 after removing one question from the telephone questionnaire. The final version of the telephone questionnaire comprises 32 questions, divided in 3 subscales: function, daily life and psychology. The total score varies between 0 and 86 points. The test-retest reliability was ICC 2,k=0.93 (95% CI: 0.82-0.97) and the construct validity was r(s)=0.92 (95% CI: 0.81-0.97). CONCLUSIONS: We present a specific telephone questionnaire in order to assess functional outcomes after posttraumatic limb salvage surgery of the lower extremity. Further research on a large number of patients will be necessary to validate this newly developed questionnaire.

Balloon reduction and cement fixation in calcaneal articular fractures: a five-year experience.

PURPOSE: Balloon reduction and cement fixation of displaced articular fractures of the calcaneus have been described elsewhere but support for it lacks clinical evidence. We have been performing the technique since October 2006 and describe here our clinical experience including three to five-year follow up of our first ten cases with no patient lost to follow up. METHODS: From September 2006 to September 2009, ten patients were admitted with a calcaneus fracture, six were female and four male, one case was bilateral (11 fractures). Patients were operated upon in the prone position according to the technique we have described. Reduction was obtained in all cases. Patients were discharged after an average of four days postoperatively and were allowed weight bearing after two to three months. All patients were followed up regularly and were examined by an independent observer at the latest follow up. The clinical results were assessed using the AOFAS ankle score, the Babin score and the RAND-36 physical components score. A CT scan was obtained in all patients before, after the operation and at the latest follow up. RESULTS: After a minimal follow up of 36 months (three to five years), no patient was lost to follow up and none required further surgery. The AOFAS clinical results were rated good or excellent in 81.8 % of cases (nine fractures, eight patients), and the physical component of the RAND-36 was 74.6. One patient only (one fracture) had a bad clinical result and evidence of subtalar arthritis on the CT scan and was offered a subtalar fusion; she refused. All patients had returned to their former professional activities at the same level as before the fracture except one who had retired but had resumed leisure walking. CONCLUSION: Balloon reduction and cement fixation of fresh calcaneal fractures ("balloon calcaneoplasty") appears a safe and effective procedure in a variety of calcaneal fractures with lasting and excellent clinical results. More studies are needed to further refine the indications and the limits of the procedure.