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

GnpAnnot community annotation system: features, qualifiers, values

International audienceIn January 2009, 991 complete genomes have been already published and 3376 genome sequencing projects are ongoing, leading to an explosion of data that needs to be stored, curated and analyzed. GnpAnnot is a project on green genomics which intends to develop a system of structural and functional annotation supported by comparative genomics and dedicated to plant and bio-aggressor genomes allowing both automatic predictions and manual curations of genomic objects. The core of GnpAnnot is a community annotation system (CAS) based on GMOD components: Chado / GBrowse / Apollo / Artemis. The system should also enable to browse comparative genomics results, to build queries and to export sets of gene lists and gene reports in various formats. The system should allow the annotation reconciliation, history, integrity, consistency and update and the management of public and private projects. To facilitate the work of the curators, four steps are crucial: 1. To provide homogeneous features, qualifiers and values for genomic objects; 2. To share a strong CAS: run high quality combiners / pipelines to predict automatically genomic objects which are stored in a relational database management system and then available from graphical and textual fast browsers and powerful editors; 3. To define annotation rules, train the annotators and organize annotation jamborees; 4. To submit the results in public sequence knowledge bases in an easy way. In this work we focus on the first and third steps. A mapping between different known sources: sequence ontology, DDBJ / EMBL / GenBank feature definition, GFF3, Chado, gene nomenclatures, transposable element classification and annotation guidelines from various genome project consortia is described. Homogeneous feature keys, qualifiers and value format with a maximum of controlled vocabularies for genes and transposable elements are proposed. Rules to annotate, in a coherent way, the structure and the function of genes and the structure and the classification of transposable elements are proposed. These rules could be useful both for automatic predictions and manual curation. Examples of annotations on a BAC sequence of a monocot are presented

URGI genome annotation system:an integrated system for structural and functional genome annotation

The URGI platform (http://urgi.versailles.inra.fr) develops a genome annotation system dedicated to plants and their pathogens. This Integrated System relies on: (i) pipelines for Transposable Elements annotation (REPET) and gene structural and functional predictions (ii) databases and user-friendly interfaces to browse and query the data (URGI Information System GnpIS, Genome Report System GRS), (iii) A distributed annotation system for curation of gene structure