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.
A detailed comparative map of Brassica oleracea and Arabidopsis thaliana has been established based largely on mapping of Arabidopsis ESTs in two Arabidopsis and four Brassica populations. Based on conservative criteria for inferring synteny, "one to one correspondence" between Brassica and Arabidopsis chromosomes accounted for 57% of comparative loci. Based on 186 corresponding loci detected in B. oleracea and A. thaliana, at least 19 chromosome structural rearrangements differentiate B. oleracea and A. thaliana orthologs. Chromosomal duplication in the B. oleracea genome was strongly suggested by parallel arrangements of duplicated loci on different chromosomes, which accounted for 41% of loci mapped in Brassica. Based on 367 loci mapped, at least 22 chromosomal rearrangements differentiate B. oleracea homologs from one another. Triplication of some Brassica chromatin and duplication of some Arabidopsis chromatin were suggested by data that could not be accounted for by the one-to-one and duplication models, respectively. Twenty-seven probes detected three or more loci in Brassica, which represent 25.3% of the 367 loci mapped in Brassica. Thirty-one probes detected two or more loci in Arabidopsis, which represent 23.7% of the 262 loci mapped in Arabidopsis. Application of an EST-based, cross-species genomic framework to isolation of alleles conferring phenotypes unique to Brassica, as well as the challenges and opportunities in extrapolating genetic information from Arabidopsis to Brassica and to more distantly related crops, are discussed.Arabidopsis thaliana, a weed-like member of the Cruciferae family (tribe Sisymbrieae), offers many advantages for basic and applied plant research. These features include small stature, short life cycle, small genome size (2n=10, estimated physical genome size of 100-120 Mb), low frequency of repetitive sequences (∼10% of the nuclear genome; Leutwiler et al. 1984), and prolific seed production. These features, combined with research of the past several decades yielding many mutants, efficient transformation systems, detailed genetic and physical maps, the availability of several P1, YAC, and BAC libraries, and 36,569 public ESTs (http:// www.cbc.umn.edu/ResearchProjects/Arabidopsis), make A. thaliana an ideal model for further molecular and genetic study (Meyerowitz and Somerville 1994). A multinational genome research initiative aiming to completely sequence the Arabidopsis genome by year 2004 (The Multinational Science Steering Committee 1997) is ahead of schedule. Such an accomplishment will undoubtedly create new scientific challenges and opportunities. One of the core issues will be how to apply the information obtained from the Arabidopsis genome project to the improvement of the world's leading crops.The genus Brassica (tribe Brassiceae), including many important crops, is in the same taxonomic family as Arabidopsis thaliana. Such a close relationship suggests that crop plants of the genus Brassica will be among the earliest beneficiaries of a complete sequence of Ara...
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