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Addition of a breeding database in the Genome Database for Rosaceae

Kate Evans, Sook Jung, Taein Lee, Lisa Brutcher, Ilhyung Cho, Cameron Peace, Dorrie Main
2013 Database: The Journal of Biological Databases and Curation  
Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington  ...  With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation.  ...  part of the web search pages and implemented Organic Group to use for data access control and group home page development.  ... 
doi:10.1093/database/bat078 pmid:24247530 pmcid:PMC3831303 fatcat:uifw43ssczgyxpuyovqmf42vjy

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

Sook Jung, Stephen P. Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Ping Zheng, Jing Yu, Aureliano Bombarely, Ilhyung Cho, Sushan Ru, Kate Evans, Cameron Peace (+4 others)
2013 Nucleic Acids Research  
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  ...  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  ...  ACKNOWLEDGEMENTS The authors thank their funding sources, the Rosaceae research community for providing data and feedback and the Tripal community of developers for developing and sharing Tripal modules  ... 
doi:10.1093/nar/gkt1012 pmid:24225320 pmcid:PMC3965003 fatcat:rkn52cq5avdjxlafga3l5o57aq

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

Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi Humann, Stephen P Ficklin, Ksenija Gasic, Kristin Scott, Morgan Frank, Sushan Ru (+11 others)
2018 Nucleic Acids Research  
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  ...  The volume of data in GDR has increased greatly over the last 5 years.  ...  ACKNOWLEDGEMENTS The authors acknowledge with thanks their funding sources, the Rosaceae research community for providing data, support and feedback, the Tripal and GMOD community of developers for developing  ... 
doi:10.1093/nar/gky1000 pmid:30357347 pmcid:PMC6324069 fatcat:mwwos4ljmnekvl4u6penvw2joa

Genomics and bioinformatics resources for translational science in Rosaceae

Sook Jung, Dorrie Main
2013 Plant Biotechnology Reports  
Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data.  ...  This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.  ...  In addition to the annotated whole genome sequences, a wealth of other genomic and genetic data is available for Rosaceae (Shulaev et al. 2008) .  ... 
doi:10.1007/s11816-013-0282-3 pmid:24634697 pmcid:PMC3951882 fatcat:4jygw6x3enas7bhe4yic7m76ou

An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals

Muzi Li, Yuwei Xiao, Steve Mount, Zhongchi Liu
2021 Frontiers in Plant Science  
This review summarizes major genomic resources and genome research progress in Rosaceae, highlights important databases, and suggests areas for further improvement.  ...  Additionally, due to the diversity of fruit types in Rosaceae, this plant family offers excellent opportunities for investigations into fleshy fruit diversity, evolution, and development.  ...  In addition, we present databases useful for the study of Rosaceae species.  ... 
doi:10.3389/fpls.2021.644881 pmid:33868343 pmcid:PMC8047320 fatcat:hd2zdeh565cc3iq3czl6zywt4a

CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)

William R Rolling, Douglas Senalik, Massimo Iorizzo, Shelby Ellison, Allen Van Deynze, Philipp W Simon
2022 Database: The Journal of Biological Databases and Curation  
CarrotOmics (https://carrotomics.org/) is a comprehensive database for carrot (Daucus carota L.) breeding and research.  ...  Data from CarrotOmics can be applied in genomic-assisted selection and genetic research to improve basic research and carrot breeding efficiency. Database URL https://carrotomics.org/  ...  Acknowledgements The authors would like to specifically thank Dorrie Main, Heidi Hough, Taein Lee, Katheryn Buble and Chun-Huai Cheng for assistance in setting up the database and the entire Tripal development  ... 
doi:10.1093/database/baac079 pmid:36069936 pmcid:PMC9450951 fatcat:sfdspfq7yzb4xjbucwe3aqqnqu

Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species

Ksenija Gasic, Yuepeng Han, Sunee Kertbundit, Vladimir Shulaev, Amy F. Iezzoni, Ed W. Stover, Richard L. Bell, Michael E. Wisniewski, Schuyler S. Korban
2008 Molecular breeding  
The large apple (Malus 9 domestica) EST database (over 300,000 sequences) provides a valuable resource for developing wellcharacterized DNA molecular markers.  ...  Transferability of apple EST-SSRs across the Rosaceae ranged from 25% in apricot to 59% in the closely related pear.  ...  Conclusions The apple EST database represents a valuable resource for developing PCR-based genetic markers not only for Malus, but also for other members of the Rosaceae.  ... 
doi:10.1007/s11032-008-9243-x fatcat:syd6enqg6vcqndds23yv6xujrm

GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data

S. Jung, M. Staton, T. Lee, A. Blenda, R. Svancara, A. Abbott, D. Main
2007 Nucleic Acids Research  
The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear  ...  GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkm803 pmid:17932055 pmcid:PMC2238863 fatcat:lgyvgqraijebnf64rkirqe73pq

RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit

Daniel Garcia-Seco, Yang Zhang, Francisco J Gutierrez-Mañero, Cathie Martin, Beatriz Ramos-Solano
2015 BMC Genomics  
A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limiting gene discovery and the breeding of improved varieties.  ...  The Fragaria reference genome belongs to a species in the same family as blackberry (Rosaceae) but to a different genus.  ...  Many genomic resources for these Rosaceae species are available on the Genome Database for Rosaceae website [8] .  ... 
doi:10.1186/s12864-014-1198-1 pmid:25608670 pmcid:PMC4311454 fatcat:dtgdbkm7xjabdjj7tp4sta5lcq

Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado

Sook Jung, Taein Lee, Stephen Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main
2016 Database: The Journal of Biological Databases and Curation  
The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis  ...  tools for Rosaceae crops and Gossypium (cotton).  ...  The Genome Database for Rosaceae (GDR) and CottonGen are (25) one of the first, if not the only, databases that adopted Chado/Tripal solely to store integrated genetic, genomic and breeding data comprised  ... 
doi:10.1093/database/baw010 pmid:26989146 pmcid:PMC4795932 fatcat:ulmoo7j3gvhync3j3lipxvbtgq

Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado

Sook Jung, Taein Lee, Stephen Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main
2016 Database: The Journal of Biological Databases and Curation  
The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis  ...  These online databases use Chado, an open-source, generic and ontology-driven database schema for biological data, as the primary data storage platform.  ...  The Genome Database for Rosaceae (GDR) and CottonGen are (25) one of the first, if not the only, databases that adopted Chado/Tripal solely to store integrated genetic, genomic and breeding data comprised  ... 
doi:10.1093/database/baw058 pmid:27141090 pmcid:PMC4852396 fatcat:ag5724tx6ndezh3qhs45l5eom4

Comparative transcriptomics identifies patterns of selection in roses

Shubin Li, Micai Zhong, Xue Dong, Xiaodong Jiang, Yuxing Xu, Yibo Sun, Fang Cheng, De-zhu Li, Kaixue Tang, Siqing Wang, Silan Dai, Jin-Yong Hu
2018 BMC Plant Biology  
The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding.  ...  Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues.  ...  Availability of data and materials The data sets supporting the results of the present study are included within this article (and its additional files).  ... 
doi:10.1186/s12870-018-1585-x fatcat:flbsvjqncnal7iywamoracf3tm

Multiple Models for Rosaceae Genomics

V. Shulaev, S. S. Korban, B. Sosinski, A. G. Abbott, H. S. Aldwinckle, K. M. Folta, A. Iezzoni, D. Main, P. Arus, A. M. Dandekar, K. Lewers, S. K. Brown (+4 others)
2008 Plant Physiology  
The development of additional markers for MAS is dependent on the ability to perform genome scans of a progeny from a population segregating for a trait of interest and then validating the trait-marker  ...  EST sequencing projects, and provide a reference genome for comparative genomics in Rosaceae.  ... 
doi:10.1104/pp.107.115618 pmid:18487361 pmcid:PMC2442536 fatcat:cbwyrpj35rc2vjmfl7ljl2zqza

Recent progress in whole genome sequencing, high-density linkage maps, and genomic databases of ornamental plants

Masafumi Yagi
2018 Breeding Science  
The databases that store this information for ornamentals are also described.  ...  Genome information is useful for functional analysis of genes, comparative genomic analysis, breeding of new varieties by marker-assisted selection, and map-based gene isolation.  ...  The Rosaceae family includes a large number of important crops such as pear, apple, peach, and cherry in addition to rose.  ... 
doi:10.1270/jsbbs.17080 pmid:29681748 pmcid:PMC5903975 fatcat:ek5nno5n7jfcfbm4nhllvpdslq

Genomics Approaches to Crop Improvement in the Rosaceae [chapter]

Cameron Peace, Jay Norelli
2009 Genetics and Genomics of Rosaceae  
The genetic systems of one or more species in the Rosaceae family can offer useful platforms for uncovering the genomic networks underlying these attributes, mechanisms, and processes.  ...  Genomic knowledge can be used for genetic improvement of cultivars through breeding or genetic engineering.  ...  A Centralized Web Portal and Database The Genome Database for Rosaceae (GDR) was created in 2003 in response to rapidly expanding volumes of genomic data in the public domain.  ... 
doi:10.1007/978-0-387-77491-6_2 fatcat:f5dstznamzbipa52rguh3qejyq
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