15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Abstract

The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.

Figure 1.

Synteny Viewer in GDR. (A) Home page of Synteny Viewer allows users to choose a reference genome and a chromosome and multiple genomes for comparison. Users can also choose a synteny block ID. (B) A circular diagram and a table shows the synteny blocks between a chromosome of a reference genome and all chromosomes of another genome being compared. (C) A bar diagram and a table that shows all the genes in a syntenic block. The table displays E-value between the matching genes and the gene names have hyperlinks to the gene detail page. (D) A gene detail page with resource side bar and the hyperlink to JBrowse. (E) JBrowse around the mRNA of interest with tracks such as gene, mRNA, SNP and genes parsed from NCBI nucleotide database.

Figure 2.

SNP Genotype Search Page in GDR. (A) Users can search SNP genotype data by dataset name, species, germplasm name, SNP name, genome location and/or gene name. Users can also upload a file with a list of germplasm names. (B) Search result table that shows SNP name, genome location, allele and the genotype data of all the germplasm chosen in the order of SNP location in the genome. The red square highlights the options to download the genotype for all the marker displayed in the result page or the genotype data that are polymorphic in the germplasm set chosen.

Figure 3.

BIMS in GDR. (A) ‘Template List’ subsection in ‘Data Import’ section provide downloadable templates for users to enter various breeding data. (B) Search’ section allows users to search and save the list of accessions using any combination of properties and trait cut of values: name, trial, location, cross, parent and trait values. The middle section shows the statistical information on the filtered dataset for the trait chosen and the right section shows the number of accessions filtered so far. (C) A page with the search result table. Users can add more columns in the table using ‘Column options’ and save/download the result table. (D) ‘Data Analysis’ section that allows users to choose two datasets, using the categories or saved accession lists and compare the trait statistics between the two datasets.