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

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.

Nitrogen fertilization rates in a subtropical peach orchard: effects on tree vigor and fruit quality.

BACKGROUND: Nitrogen is a key component of crop production and is commonly related to increases in yield and fruit size. The N fertilization rates used for low-chill peach cultivars were adapted from other peach production regions, where environmental and soil conditions are different. The growth and production as well as the effect on fruit physical and compositional attributes of two low-chill peach cultivars - 'TropicBeauty' (TB) and 'UFSharp' (UFS) - with five different N fertilization rates (0 (N0), 45 (N1), 90 (N2), 179 (N3) and 269 (N4) kg ha-1 applied each year from 2011 to 2017) were examined. RESULTS: Peach trees under higher N rates had higher pruning weights compared to the lower N0 or N1 rates. Yield was only affected in 2017 for the two cultivars tested. Physical attributes were inconsistently affected by N. Fruit from the higher N rates had lower a* value (more green) than fruit from the trees under low or zero N. While fruit firmness was not affected by N, fruit from trees under zero/low N had higher total soluble solids in some years. CONCLUSION: Considering that N is recycled in the trees, being retained and reused each season to resume growth, it is important to address peach orchard fertilization based on peach tree N status. The results of this experiment show that an increase in N beyond what is required for tree maintenance does not increase yield. In addition, reducing N does not strongly affect fruit quality, although the color and soluble solids results suggest that lower N rates may advance fruit maturation. © 2019 Society of Chemical Industry.

The Genome Database for Rosaceae (GDR): year 10 update.

The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse or download with a range of annotations, including gene model predictions, aligned transcripts, repetitive elements, polymorphisms, mapped genetic markers, mapped NCBI Rosaceae genes, gene homologs and association of InterPro protein domains, GO terms and Kyoto Encyclopedia of Genes and Genomes pathway terms. Annotated sequences can be queried using search interfaces and visualized using GBrowse. New expressed sequence tag unigene sets are available for major genera, and Pathway data are available through FragariaCyc, AppleCyc and PeachCyc databases. Synteny among the three sequenced genomes can be viewed using GBrowse_Syn. New markers, genetic maps and extensively curated qualitative/Mendelian and quantitative trait loci are available. Phenotype and genotype data from breeding projects and genetic diversity projects are also included. Improved search pages are available for marker, trait locus, genetic diversity and publication data. New search tools for breeders enable selection comparison and assistance with breeding decision making.