Source: WASHINGTON STATE UNIVERSITY submitted to NRP
TREE FRUIT GDR: TRANSLATING GENOMICS INTO ADVANCES IN HORTICULTURE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
0220157
Grant No.
2009-51181-06036
Cumulative Award Amt.
$1,999,148.00
Proposal No.
2010-03255
Multistate No.
(N/A)
Project Start Date
Sep 1, 2009
Project End Date
Aug 31, 2014
Grant Year
2011
Program Code
[SCRI]- Specialty Crop Research Initiative
Recipient Organization
WASHINGTON STATE UNIVERSITY
240 FRENCH ADMINISTRATION BLDG
PULLMAN,WA 99164-0001
Performing Department
Horticulture & Landscape Architecture
Non Technical Summary
Edible products from Citrus (orange, grapefruit, tangerine, mandarin, lemon, lime, and pummelo) and Rosaceae (almond, apple, apricot, blackberry, cherry, nectarine, peach, pear, plum, raspberry and strawberry) have major economic and nutritional value in the U.S. Constituting much of the economic backbone for many rural communities, the production value for Rosaceae and Citrus crops in 2007 amounted to $12.7 billion, representing 67% of U.S. fruit and nut crop production and 8.9% of all U.S. crop production. The economic viability of the U.S. tree fruit industries is now under serious threat. Rising labor, energy, water and land costs, rapid spread of pests and disease, and consumer demand for high quality and environmentally safe products pose real challenges to our global competitiveness. Overcoming these challenges requires the development of improved cultivars which contain desirable traits such as resistance to pathogens, superior fruit quality, and machine harvestability. To do this, we need to identify the genes associated with the traits of interest and assess their heritability; identify DNA markers so we can screen the genes/traits in existing varieties; create new crosses; identify the crosses that have successfully inherited the traits of interest; and then evaluate their performance under different environmental conditions. The research in genomics, genetics and breeding is generating large-scale datasets that require access to bioinformatics capabilities for analysis, archiving, integration, and interpretation. Translating this data into knowledge that can be used by experts in genomics, genetics, breeding, and production requires the development of a robust and high-throughput computational and database platform. Tree Fruit Genome Database Resources (tfGDR, www.tfgdr.org) will build on the existing capabilities of the Genome Database for Rosaceae (GDR, www.rosaceae.org) and will provide a standardized, integrated, user-friendly specialty crop database platform for tree fruit to facilitate efficient collection, analysis, and translation of genomics, post-genomics, genetics, and cultivar performance data into solutions for tree fruit industry production and processing problems.
Animal Health Component
75%
Research Effort Categories
Basic
25%
Applied
75%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2010999208010%
2011110208010%
2011112208010%
2011114208010%
2011119108010%
2011119303010%
2011122208010%
2011123208010%
2011212208010%
2012499108010%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1114 - Peach; 1119 - Deciduous tree fruits, general/other; 1110 - Apple; 1112 - Cherry; 1212 - Almond; 0999 - Citrus, general/other; 1122 - Strawberry; 1123 - Raspberry; 2499 - Plant research, general;

Field Of Science
2080 - Mathematics and computer sciences; 1080 - Genetics; 3030 - Information and communication;
Goals / Objectives
The objectives of this project are to: collect, analyze, integrate genomics, genetics and breeding data to facilitate gene discovery and marker-trait associations; provide data-mining resources of genomic, genetic, breeding and cultivar performance data for breeders and growers to expedite development and adoption of new and existing cultivars, and extend community outreach in genomics, genomics-assisted breeding and crop management. The outputs of this project will be: EST unigene data and associated sequence polymorphisms; genome views and tools facilitating community data annotation; in silico developed eMarkers, such as SSR and SNPS; comparative maps; allelic diversity data in breeding populations and germplasm collections; phenotypic data with the environmental/locality data; integrated phenotypic and genotypic; development of the RosaCyc and RutaCyc pathway databases with visual representations of pathways and characterization of numerous pathways prevalent in the Rosaceae and Rutaceae that have not been characterized in Arabidopsis and rice; collaboration among biochemists, molecular biologists, breeders, and bioinformaticists; the first database schema that can integrate genomics, genetics, and phenotyping/genotyping data from various breeding programs will be implemented using the open-source database schema Chado and Drupal; a collection of open source software tools for creating and managing biological databases using Chado and Drupal; a comprehensive yet expandable database schema, facilitate collaboration between researchers in Rosaceae, Solananceae and Citrus; Intuitive and comprehensive interface for breeders to utilize genomics and genetics data in breeding programs; secure sites where breeders can upload and analyze their private data in comparison with other tfGDR data; web resources to boost interaction between breeders, industry sectors, and supporting researchers; a comprehensive interface for growers and other industry members to view and search cultivar performance data; a platform for industry to evaluate performance of new cultivars for objective decision-making on adoption; feedback solicited from tfGDR training workshops used to target future community needs; ncreased awareness of tfGDR within the research and extension professional community through yearly tfGDR training workshops; establishment of an effective conduit of information between researchers, extension professionals and stakeholders; evaluation of extension and outreach efforts to assess effectiveness of communication between research, extension professionals, and stakeholder groups; examples of tfGDR utilization in improving specialty crop breeding efforts and ultimately food quality will build support amongst stakeholders and the general public.
Project Methods
We will collect, curate, analyze, and integrate genomics and genetics data including full genome sequences, predicted and verified genes, ESTs, proteins, genetic and physical maps, and the molecular and phenotypic diversity data of Rosaceae and Citrus. The data collection will involve computational download, literature curation and direct submission from researchers. Synteny and orthology analysis will be conducted using the Sybil program and visualized in SynBrowse or SynView. Unigene builds will be developed using in-house algorithms and eMarkers mined from the assembled sequences and genome sequences. Loci data (genes, traits, qtls) and associated phentoypic data will be integrated and ontologies assigned using gene ontology, trait ontology, plant ontology and environment ontology. Genetic and physical map data will be uploaded into CMap and WebFPC. Genome sequence and annotations will be viewable in GBrowse. The Metacyc framework will be used to create the pathways database. Chado will be expanded to house all the features of a comprehensive plant genomics, genetics, breeding and producer database and web access provided via Drupal modules incorporating existing and new data mining tools. We will provide data-mining resources of genomic, genetic, breeding and cultivar performance data for breeders and growers via inter- connected breeder and grower gateway interface pages. Community outreach in genomics, genomics-assisted breeding and crop management will be offered through tfGDR training workshops at national and international conferences, and through onsite and online workshops aimed at specific target audiences including growers, traditional plant breeders, geneticists, genomicists, bioinformaticists and molecular biologists. These workshops will enable all the interested parties to work collectively on crop improvement issues. Video presentations will be developed on each aspect and made available over the tfGDR website via a section titled "Grower's Corner". We will utilize various avenues to assess the impact of the proposed project. Our website will include a form for users' to submit feedback at anytime. We will also have surveys to test the usability and solicit any new ideas. The survey will be performed quarterly and the results will be discussed in Advisory Panel meetings. Dr. Brown and his team will be responsible for the development of the survey and the analyses of the results. They will also develop tools to assess the impact of workshops and the overall project. We will also have forums for users to discuss various subjects such as genome annotation, comparative mapping, fruit quality traits/QTLs, breeding and fruit tree growing, etc. We will also have email lists for rapid communication and also have quarterly newsletters to notify users of any new developments in tfGDR and the Rosaceae and Citrus communities. We will provide quarterly updates of our progress to the Advisory Panel and have an annual Advisory Panel meeting where will discuss progress and challenges with the project. Finally, we will use Google Analytics to generate monthly reports on database use.

Progress 09/01/09 to 08/31/14

Outputs
Target Audience: Primary: Basic, translational and applied Rosaceae researchers worldwide Secondary: plant and computational biology researchers worldwide Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Participating scientists have attended and presented at conferences, research meetings and provided training at computer demonstrations and GMOD workshops. How have the results been disseminated to communities of interest? Through conference presentations, peer-reviewed publications, webinars and individual research group training. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Major Goals: The objectives of this project are to: collect, analyze, integrate genomics, genetics and breeding data to facilitate gene discovery and marker-trait associations; provide data-mining resources of genomic, genetic, breeding and cultivar performance data for breeders and growers to expedite development and adoption of new and existing cultivars, and extend community outreach in genomics, genomics-assisted breeding and crop management. The outputs of this project will be: EST unigene data and associated sequence polymorphisms; genome views and tools facilitating community data annotation; in silico developed eMarkers, such as SSR and SNPS; comparative maps; allelic diversity data in breeding populations and germplasm collections; phenotypic data with the environmental/locality data; integrated phenotypic and genotypic; development of the RosaCyc and RutaCyc pathway databases with visual representations of pathways and characterization of numerous pathways prevalent in the Rosaceae and Rutaceae that have not been characterized in Arabidopsis and rice; collaboration among biochemists, molecular biologists, breeders, and bioinformaticists; the first database schema that can integrate genomics, genetics, and phenotyping/genotyping data from various breeding programs will be implemented using the open-source database schema Chado and Drupal; a collection of open source software tools for creating and managing biological databases using Chado and Drupal; a comprehensive yet expandable database schema, facilitate collaboration between researchers in Rosaceae, Solananceae and Citrus; Intuitive and comprehensive interface for breeders to utilize genomics and genetics data in breeding programs; secure sites where breeders can upload and analyze their private data in comparison with other tfGDR data; web resources to boost interaction between breeders, industry sectors, and supporting researchers; a comprehensive interface for growers and other industry members to view and search cultivar performance data; a platform for industry to evaluate performance of new cultivars for objective decision-making on adoption; feedback solicited from tfGDR training workshops used to target future community needs; increased awareness of tfGDR within the research and extension professional community through yearly tfGDR training workshops; establishment of an effective conduit of information between researchers, extension professionals and stakeholders; evaluation of extension and outreach efforts to assess effectiveness of communication between research, extension professionals, and stakeholder groups; examples of tfGDR utilization in improving specialty crop breeding efforts and ultimately food quality will build support among stakeholders and the general public Overall: Provision of a single source for integrated genomic, genetic and breeding resources for publicly-available Rosaceae and Citrus annotated genomics and genetic data, facilitating gene functional characterization, trait identification and genomics-assisted breeding in tree fruit. From September 1, 2013 to August 31, 2014, GDR was visited 39,908 times, by 15,465 unique visitors from 147 countries, with 185,685 pages viewed. The top ten countries accessing GDR are China, US, Italy, France, Japan, Spain, Chile, India. Germany and the United Kingdom. From September 1, 2013 to August 31, 2014, the Citrus Genome Database was visited 6,039 times, by 4,021 unique visitors from 122 countries, with 21,248 pages viewed. From its re launch in May 2014, the tfGDR tree fruit extension site has received 825 visits, from 623 unique users with 2,279 pages viewed. The Genome Database for Rosaceae was significantly enhanced with data and functionality. Web Interface development included: (a) new species summary page and species detail pages with images (b) Improvement of phenotypic search page in Breeders toolbox to include better filtering options (c) Development of a parser for NCBI nr data to parse out detailed data such as gene, mRNA, CDS, gene symbol, function, source variety and comments and improved search page added (d) Improved search interface for molecular diversity data and (e) RGC7 conference site built within GDR including registration and abstract submission and moderation functionality; Data newly integrated in GDR in 2014 includes the Pyrus communis genome v1.0; RNA-seq data from apple and strawberry; phenotypic and genotypic data from the RosBreed project; genetic data (marker, map, QTL, genotypic data) from publications; Rosaceae gene/mRNA data parsed from the NCBI nr database; detailed information on various species of Malus and updated Rosaceae publications. The increase of data points for each data type are as follows: Genomes ( 1), genotypes ( 5,486), Phenotypes ( 155,775), germplasm ( 4,887), Genetic maps ( 39), QTL/MTL ( 1,008), Species ( 49), publications ( 1,137). The Citrus Genome Database (CGD) was also significantly enhanced with data and functionality. Web Interface development include the addition of new search and data detail pages for marker, QTL/MTL, and molecular diversity data as well as a new browse page for genetic map data. Data newly integrated to CGD in 2014 includes new gene, marker, map, trait, species, germplasm, genotypic data and publications. The increase of data points for each data type are as follows: genes ( 48,882), marker ( 3,427), Genetic maps ( 51), genotypes ( 23), germplasm ( 4,887), QTL/MTL ( 79), Species ( 168), publications ( 217). A growers and scientists gateway was developed through the revamped tree fruit genome Database Resources portal (www.tfgdr.org), which now contains lots of useful information on varietal development and cultivar performance information, useful audio visual resources for growers, the public and scientists on the use of genomics and genetic data to help more efficient breeding and information on successes and challenges being face. During this period, we further expanded the generic database infrastructure Tripal that we are directly developing through this project to provide a freely available, organism independent, user-friendly, open-source, off-the shelf solution for construction of whole genome websites supporting community collaboration. In the past year, Tripal databases are becoming accepted as the community standard for genome databases and many of the large commodity database are converting to this platform (GrainGenes, TreeGenes, all the legume databases and the Arabidopsis Information Portal). We furthered collaboration between the horticultural and forestry genomics, genetics and breeding communities and held a joint meeting to strategize further on building even closer ties.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Jung S, Ficklin SP, Lee T, Cheng C-H, Blenda A, Zheng P, Yu J, Bombarely A, Cho I, Ru S, Evans K, Peace C, Abbott AG, Mueller LA, Olmstead MA, Main D (2014) The Genome Database for Rosaceae (GDR): year 10 update. Nucleic Acids Research 41(D1) 1237-1244, DOI: 10.1093/nar/gkt1012
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Jung S and D Main. 2014. Genomics and bioinformatics resources for translational science in Rosaceae. Plant Biotechnology Reports 8(2): 49-64. DOI 10.1007/s11816-013-0282-3
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Main D, Jung S, Lee T, Ficklin S, Cheng CH, Blenda A, Yu J, Zheng P, Piaskowski J, Ru S, Peace C, Evans K, Oraguzie N, Olmstead M, Abbott A (2014) GDR: Current functionality and future direction. 7th International Rosaceae Genomics Conference; June 24-26, 2014; Seattle
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Zhu Y, Zheng P, Shin S, Fazio G, Mazzola M, Main D (2014) Transcriptome profiling on apple root defense responses to infection by Pythium Ultimum. 7th International Rosaceae Genomics Conference; June 24-26, 2014; Seattle
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Jung S, Bassett C, Bielenberg D, Cheng CH, Dardick C, Main D, Meisel L, Slovin J, Troggio M, Schaffer R (2014) A proposed naming convention for genes in Rosaceae species . 7th International Rosaceae Genomics Conference; June 24-26, 2014; Seattle
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Bassil N, Davis T, Amaya I, Bellon L, Bianco L, Brew F, Denoyes B, van Dijk T, Ficklin S, Iezzoni A, Jung S, Mahoney L, Main D, Mittman M, Monfort A, Peace C, Pirani A, Rosyara U, Sargent D, Verma S, Webster T, Wood D, Yang Y, Zhang H, Whitaker V, Van De Weg E (2014) First Evaluation of the IStraw90Axiom Array in the Cultivated Strawberry (Fragaria x ananassa). 7th International Rosaceae Genomics Conference; June 24-26, 2014; Seattle
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Johnson F, Zheng P, Main D, Rudell D, Evans K, Zhu Y (2014) Profiling the transcriptomic and metabolomic changes associated with the apple fruit controlled-atmosphere storage related peel disorder. 7th International Rosaceae Genomics Conference; June 24-26, 2014; Seattle
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Peace C, Jung S, Lee T, Ru S, Fazio G, Main D (2014) Cross Assist: Online software to identify efficient cross combinations, integrating rosaceous crop genomics, genetics, and breeding. 7th International Rosaceae Genomics Conference; June 24-26, 2014; Seattle
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ru S, Edge-Garza D, Harshman J, Evans K, Jung S, Main D, Peace C (2014) Seedling Select: A web-based software tool to facilitate cost modeling of marker-assisted seedling selection (MASS) in Rosaceae tree fruit. 7th International Rosaceae Genomics Conference; June 24-26, 2014; Seattle
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Bassil N, Davis T, Amaya I, Bellon LR, Brew F, Denoyes B, Dijk TV, Ficklin S, Iezzoni A, Jung S, Mahoney LL, Main D, Mittmann M, Monfort A, Peace C, Pirani A, Rosyara U, Sargent DJ, Webster TA, Wood DJ, Yang Y, Zhang H, Van de Weg WE (2014) Development and Preliminary Evaluation of the IStraw90 Axiom Array in the Cultivated Strawberry (Fragaria xananassa). International Plant and Animal Genome Conference XXII; January 11-15, 2014; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Jung S, Ficklin SP, Lee T, Cheng CH, Blenda A, Zheng P, Yu J, Ru S, Evans KM, Peace C, Abbott AG, Mueller L, Olmstead M, Main D (2014) GDR, the Genome Database for Rosaceae, in Chado and Tripal. International Plant and Animal Genome Conference XXII; January 11-15, 2014; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Jung S, Lee T, Ficklin SP, Evans KM, Peace C, Main D (2014) Building a Breeding Database in GDR, Genome Database for Rosaceae. International Plant and Animal Genome Conference XXII; January 11-15, 2014; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Chen C, Jung S, Main D (2014) Expressed Haplotypes and Polymorphisms in Prunus Species. International Plant and Animal Genome Conference XXII; January 11-15, 2014; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Main D (2014) Tree Fruit Genome Database Resources for Basic to Applied Research. International Plant and Animal Genome Conference XXII; January 11-15, 2014; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ru S, Peace C, Evans K, Carter P, Jung S, Harshman J, Edge-Garza D, Main D (2014) Seedling Select: a web-based software tool to facilitate cost modeling of marker-assisted seedling selection (MASS) in Rosaceae tree fruit. Poster presentation at 2014 WSU Academic Showcase, March 25, Pullman, WA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ru S, Peace C, Evans K, Carter P, Jung S, Harshman J, Edge-Garza D, Main D (2014) Seedling Select: a web-based software tool to facilitate cost modeling of marker-assisted seedling selection (MASS) in Rosaceae tree fruit. Poster presentation at 2014 WSU Molecular Plant Sciences Retreat, March 1, Pullman, WA
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Main D (2014) Database Resources for Crop Genomics, Genetics and Breeding Research. SAAESD Spring Meeting; March 10, 2014; Savannah, GA.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Main D (2014) Database Resources for Crop Genomics, Genetics and Breeding Research. WAAESD Spring Meeting; April 10, 2014; San Diego.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Main D (2014) Database Resources for Crop Genomics, Genetics and Breeding Research. National Plant Germplasm Committee Meeting; June 10, 2014; Beltsville, MD.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Main D (2014) Database Resources for Crop Genomics, Genetics and Breeding Research. AES Directors from the North Central and the North East region Summer Meeting; July 14, 2014; Online
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Main D, Jung S, Lee T, Ficklin S, Cheng CH, Blenda A, Yu J, Zheng P, Piaskowski J, Ru S, Peace C, Evans K, Oraguzie N, Olmstead M, Abbott A (2014) GDR: Progress and Workplan. AppleGGB Review, Pasco, Washington, Jan 28, 2014.


Progress 09/01/12 to 08/31/13

Outputs
Target Audience: Primary: Basic, translational and applied Rosaceae researchers worldwide Secondary: plant and computational biology researchers worldwide Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Participating scientists presented at conferences and provided training at computer demonstrations and GMOD workshops How have the results been disseminated to communities of interest? Through conference presentations, peer-reviewed publications, webinars and individual research group training. What do you plan to do during the next reporting period to accomplish the goals? Continue as we are doing to complete/exceed our stated project goals.

Impacts
What was accomplished under these goals? Overall: Provision of a single source for integrated genomic, genetic and breeding resources for publicly-available Rosaceae and Citrus annotated genomics and genetic data, facilitating gene functional characterization, trait identification and genomics-assisted breeding in tree fruit. From September 1, 2012 to August 31, 2013, GDR was visited 40,244 times, by 14,504 unique visitors from 132 countries, with 173,229 pages viewed. Of these 66% were returning users and 34% were new users. Compared to the period of the previous year, visits had increased 9.62%, unique visitors increased by 5.6% and pages viewed had increased by 15%. The top ten countries accessing GDR are the US, China, France, Japan, Italy, Spain, Germany, Canada, Portugal and Chile. From September 1, 2012 to August 31, 2013, the Citrus Genome Database was visited 30,567 times, by 4,837 unique visitors from 81 countries, with 30,567 pages viewed. The top ten countries accessing Citrus Genome Database are the US, China, Japan, Brazil, Italy, India, Spain, UK, South Korea and France. The Genome Database for Rosaceae was significantly enhanced with data and functionality. This included: (1) All data moved to the Chado schema. (2) Web Interface development included: (a) New search/browse web interfaces developed in Tripal for gene, sequence trait loci (QTL, MTL), diversity data, marker, map and publication; (b) New data pages in Tripal for gene, QTL, MTL, map, germplasm, marker, polymorphism,allele and publication; (c) New tutorial added; (d) Navigation on website reorganized to be more standardized with other Tripal databases; (e) New/updated tools included (i) new sequence retrieval tool, tools for breeders updated (cross-assist, marker converter and technology portfolio), and FragariaCyc pathway tool added. (3) Data Analysis/Annotation/Integration included: (a) pear genome sequence (in-house functional annotation done); (b) NCBI Rosaceae genes (in-house functional annotation and anchoring to reference genomes); (c) Large scale phenotypic and genotypic data for apple, peach, cherry and strawberry added from the RosBREED project; (d) Genetic data curation (from literature and authors) and integration (map, genetic marker, Mendelian loci and QTL) included 2,183,699 markers, 969 QTLs and 47 maps. The Citrus Genome Database also significantly enhanced with data and functionality. This included: 1) Web Interface development included: (a) New search/browse web interfaces developed in Tripal for trait loci (QTL, MTL), marker, map and publication; (b) New data pages in Tripal for QTL, MTL, map, germplasm, marker, and publication; (c) Navigation on website reorganized to be more standardized with other Tripal databases. (2) Data Analysis/Annotation/Integration included: (a) New assembly of Citrus Clementine genome v1.0 (in-house functional annotation done); (b) Genetic data curation (from literature and authors) and integration (map, genetic marker, mendelian loci and QTL) included 2,855 markers, 6 QTLs and 13 maps. Work is on-going to develop a growers gateway, with a survey for Apple and Cherry tree fruit growers conducted at the Annual Meeting of the Washington State Horticulture Association. During this period, we further expanded the generic database infrastructure Tripal that we are directly developing through this project to provide a freely available, organism-independent, user-friendly, open-source, off-the shelf solution for construction of whole genome websites supporting community collaboration. Several additional databases are now implementing Tripal for their crops including Cotton, Legumes (LIS in process of converting to Tripal), Wheat, Oyster among others. We furthered collaboration between horticultural and forestry genomics, genetics and breeding communities.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Jung S., T. Lee, S. Ficklin, C. Cheng, A. Blenda, S. Ru, P. Zheng, K. Evans, C. Ross, N. Oraguzie, A. Abbott, D. Layne, M. Olmstead, F. Gmitter, C. Chen, L. Mueller, D. Main. Building database resources for translational research in Rosaceae. 2013. ASHS; July 22-25 2013; Palm Desert, CA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Jung S., T. Lee, S. Ficklin, C. Cheng, P. Zheng, A. Blenda, S. Ru, K. Evans, C. Peace, N. Oraguzie, A. Abbott, M. Olmstead, F. Gmitter, C. Chen, L. Mueller, D. Main. New data and functionality of GDR, the Genome Database for Rosaceae. 2013. International Plant and Animal Genome Conference XXI; January 12-16, 2013; San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Main D., S. Jung, S. Ficklin, P. Zheng, C. Cheng, M. Olmstead, A. Abbott, A. Blenda, C. Chen, L. Mueller, F. Gmitter. Citrus Genome Database: Updates and New Functionality. 2013. International Plant and Animal Genome Conference XXI; January 13-16, 2013; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Main D., T. Lee, P. Zheng, S. Jung, S. Ficklin, J. Humann, J. Wegrzyn, D. Neale. GenSAS: Genome Sequence Annotation Server, a Tool for Online Annotation and Curation. 2013. International Plant and Animal Genome Confeence XXI; January 13-16, 2013; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Jung S., T. Lee, S. Ru, D. Main, A. Iezzoni, C. Peace, G. Fazio. The RosBREED Pedigree-Based Breeding Information Management System. 2013. International Plant and Animal Genome Conference XXI; January 12-16, 2013; San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Bassil N., I. Amaya, F. Bellon, T. Davis, B. Denoyes-Rothan, T. Van Dijk, S. Ficklin, A. Iezzoni, S. Jung, L. Mahoney, D. Main, M. Mittman, A. Monfort, C. Peace, A. Pirani, D. Sargent, T. Webster, D. Wood, Y. Yang, H. Zhang, E. van de Weg. Development and preliminary evaluation of the IStraw90 Axiom� array in cultivated strawberry (Fragaria xananassa). 2013. ASHS; January 12-16, 2013; Palm Desert, CA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Peace C., N. Bassil, M. Coe, G. Fazio, R. Gallardo, K. Gasic, J. Luby, D. Main, J. McFerson, C. Weebadde, E. van de Weg, C. Yue, A. Iezzoni. Marker-assisted breeding in apple, peach, and cherry targets valuable functional alleles. 2013 Jan 12. International Plant and Animal Genome Conference XXI; January 12-16, 2013; San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: van de Weg E., N. Bassil, T. Davis, H. Zhang, L. Mahoney, S. Ficklin, D. Main, S. Jung, C. Peace, A. Monfort, I. Amaya, F. Bellon, B. Denoyes-Rothan, A. Iezzoni, M. Mittman, A. Pirani, T. Webster, F. Brew, M. Troggio, R. Velasco, F. Laurens, R. Crowhurst. Evaluation and design of the strawberry and apple chips. 2013 Jan 12. International Plant and Animal Genome Conference XXI; January 12-16, 2013; San Diego, CA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Ru S., D. Edge-Garza, C. Peace, K. Evans, P. Carter, S. Jung, D. Main. Blueprint for RosMASS: A Web-based Rosaceae marker-assisted seedling selection decision support tool. 2013. International Plant and Animal Genome Conference XXI; January 13-16, 2013; San Diego, CA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Ru S., D. Edge-Garza, D. Main, C. Peace. Blueprint for Seedling Select: A web-based Rosaceae marker-assisted seedling selection decision support tool. 2013. WSU Academic Showcase; March 29, 2013; Pullman, WA
  • Type: Websites Status: Published Year Published: 2013 Citation: www.rosaceae.org
  • Type: Websites Status: Published Year Published: 2013 Citation: www.tfgdr.org
  • Type: Websites Status: Published Year Published: 2013 Citation: www.citrusgenomedb.org
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Piaskowski, JL, Olmstead MA, Main D. "Creation of the Growers Toolbox: a Decision-Making Toolkit for New Plantings of Apple, Cherry and Peach." Annual Meeting of the Washington State Horticulture Association. Dec 2-4, 2013. Wenatchee
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Jung S, Ficklin SP, Lee T, Cheng C-H, Blenda A, Zheng P, Yu J, Bombarely A, Cho I, Ru S, Evans K, Peace C, Abbott AG, Mueller LA, Olmstead MA, Main D (2013) The Genome Database for Rosaceae (GDR): year 10 update. Nucleic Acids Research DOI: 10.1093/nar/gkt1012
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Sanderson LA, Ficklin SP, Cheng C-H, Jung S, Feltus FA, Bett KE, Main D (2013) Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. Database (Oxford). DOI: 10.1093/database/bat075
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Evans K, Jung S, Lee T, Brutcher L, Cho I, Peace C, Main D (2013) Addition of a breeding database in the Genome Database for Rosaceae. Database (Oxford). DOI:10.1093/database/bat078
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Jung S and D Main. 2013. Genomics and bioinformatics resources for translational science in Rosaceae. Plant Biotechnology Reports May 2013. DOI 10.1007/s11816-013-0282-3
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Salazar JA, Ruiz D, Campoy JA, S�nchez-P�rez R, Crisosto CH, Mart�nez-Garc�a PJ, Blenda A, Jung S, Main D, Mart�nez-G�mez P, Rubio M. 2013. Quantitative Trait Loci (QTL) and Mendelian Trait Loci (MTL) analysis in Prunus: A breeding perspective and beyond. Plant Molecular Biology Reporter DOI 10.1007/s11105-013-0643-7
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: The International Peach Genome Initiative, I Verde, AG Abbott, S Scalabrin, S Jung, S Shu, F Marroni, T Zhebentyayeva, MT Dettori, J Grimwood, F Cattonaro, A Zuccolo, L Rossini, J Jenkins, E Vendramin, LA Meisel, B Sosinki, S Prochnik, T Mitros, A Policriti, G Cipriani, L Dondini, S Ficklin, DM Goodstein, P Xuan, C Del Fabbro, V Aramini, D Copetti, S Gonzalez, DS Horner, R Falchi, S Lucas, E Mica, J Maldonado, B Lazzari, D Bielenberg, R Pirona, M Miculan, A Barakat, R Testolin, A Stella, S Tartarini, P Tonutti, P Arus, A Orellana, C Wells, D Main, G Vizzotto, H Silva, F Salamini, J Schmutz, M Morgante and DS Rokhsar. 2013. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics 45:487-494. DOI 10.1038/ng.2586
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Genome wide identification of chilling responsive microRNAs in Prunus persica. BMC Genomics 13:481. DOI 10.1186/1471-2164-13-481
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Zhu, Y, P Zheng, V Varanasi, S Shin, D Main, E Curry and J Mattheis. 2012. Multiple plant hormones and cell wall metabolism regulate apple fruit maturation patterns and texture attributes. Tree Genetics & Genomes 8:1389-1406. DOI 10.1007/s11295-012-0526-3
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy R, Main D (2013) CottonGen: A Genomics, Genetics and Breeding Database for Cotton Research. Nucleic Acids Research DOI: 10.1093/nar/gkt1064
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Main D., S. Jung, T. Lee, S. Ficklin, P. Zheng, C. Cheng, S. Ru, A. Blenda, L. Mueller, D. Layne, M. Olmstead, C. Peace, K. Evans, N. Oraguzie, F. Gmitter, A. Abbott. Genome Database for Rosaceae. 2013. International Plant and Animal Genome Conference XXI; January 12-16, 2013; San Diego, CA


Progress 09/01/11 to 08/31/12

Outputs
OUTPUTS: Predicted genes from the genome sequences of apple, peach, strawberry, sweet orange and mandarin were annotated through the Tripal analysis pipeline and made browsable/searchable and downloadable through a new gene search page that was developed. Functional data available includes pathway information from Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene ontology mapping, and domains though InterPro analysis. Browsable, searchable, and downloadable, PlantCyc databases were also added for the predicted genes from apple (AppleCyc), strawberry (FragariaCyc), and peach (CitrusCyc) genome sequences. Relevant Rosaceae publications were added to the publications database on a monthly basis. Synteny analysis was updated with the latest version (1.1) of the strawberry genome and made available through GBrowse-Syn. The Breeders toolbox on Genome Database for Rosaceae (GDR) has been expanded to include RosBREED phenotype and genotype data for sweet and tart cherry, strawberry, apple and peach and genotype interface search pages have been developed. More marker, map and quantitative trait loci (QTL) data has been added and the peach growers website continues to be updated on the Clemson site with several new peach educational videos targeted at growers and consumers. Components of the tfGDR project were presented at 6 meetings (local, national and international). PARTICIPANTS: Doreen Main (PD): Project leader who organized meetings, supervised overall project work, presented the project at meetings.
Sook Jung (CoPD): Addition of breeding and molecular diversity data, development of breeders toolbox, presented project at meetings.
Cameron Peace, Kate Evans and Nnadozie Oraguzie (CoPDs): provided data and design of breeders toolbox interface.
Stephen Ficklin (database administrator, programmer and data analyst): data conversion, data upload, interface design and implementation, database administration and systems updates.
Chunxian Chen (postdoctoral researcher): collection and analysis of citrus genomics and genetics data.
Anna Blenda (postdoctoral researcher): Collection and curation of QTL and mapping data.
Taein Lee (developer): breeders toolbox developer and other interface development, development of online genome curation tools.
Naama Menda (postdoctoral researcher): Chado schema development and pathway database development).
Lukas Mueller (CoPD): oversaw Chado development and pathaway database development.
Chun-Huai Cheng (developer): Drupal module developer and data analysis.
Sushan Ru (graduate student): Breeders toolbox coordination and development.
Desmond Layne and Mercy Olmstead (CoPDs): Development of online resources for growers and consumers.
The Rosaceae Genomics, Genetics and Breeding Exective Committee (RosEXEC) provided feedback on all aspects of GDR functionality. TARGET AUDIENCES: The target audience is scientists, growers and the public. Scientists have been engaged through presentations, emails about the website, and RosEXEC committee meetings. Growers are being engaged through online educational videos (so far about peaches) and presentations at commodity group meetings. PROJECT MODIFICATIONS: Moved the final two workshops to years 4 and 5 (one year no-cost project extension)

Impacts
We are providing a single source for integrated genomic, genetic and breeding resources for publicly-available Rosaceae and Citrus annotated genomic and genetic data, facilitating gene functional characterization, trait identification and genomics-assisted breeding in tree fruit. From September 1, 2011 to August, 2012, GDR has been visited 39,884 times, by 13,726 unique visitors from 122 countries, with 170,332 pages viewed. Of these 67% were returning users and 33% were new users. Compared to the same period of the previous year, visits had increased 9.62%, unique visitors increased by 20% and pages viewed increased by 15%. The top ten countries accessing GDR are the US, China, Japan, Italy, Spain, Germany, Chile, India and the Netherlands. Access to The Citrus Genome Database increased hugely during the past year; visits increased by 285% from 1,891 to 7,291 and unique visitors increase by 261% from 1,171 to 4,228, with 30,652 pages viewed. Of these, 57% were new users discovering the database and 43% were returning users. Researchers from 125 countries used the Citrus database, with the top ten user countries being the US, Japan, China, Italy, India, Brazil, Spain, France, Canada, and the United Kingdom. We believe the increased use of the component databases of GDR and the Citrus Genome Database reflect the valuable new data added during this period and the increased presentation of both of these databases at international, national and local conferences and via the community mailing lists and publications. During this period, we further expanded the generic database infrastructure Tripal that we are directly developing through this project to provide a freely available, species-independent, user-friendly, open-source, off-the shelf solution for construction of whole genome websites supporting community collaboration. Several additional databases are now implementing Tripal for their crops including Cotton, Legumes, Wheat, and Oyster amongst others. We furthered collaboration amongst horticultural and forestry genomics, genetics and breeding communities.

Publications

  • Wegrzyn JL, Main D, Figuero B, Choi I, Yu J, Neale, DB, Jung S, Staton M, Zheng P, lee T, Ficklin S, Cho I, peace C, Evans K, Volk G, Oraguzie N, Chen C, Gmitter FG, and Abbot AG. 2012. Uniform Standards for Genome Databases in Forest and Fruit Trees. Tree Genetics and Genomes 8(3) 549-557.
  • Jung S, Cestaro A, Troggio M, Main D, Zheng P, Cho I, Folta K, Sosinski B, Abbott A, Celton JM, Arus P, Shulaev V, Verde I, Morgante M, Rokhsar DS, Velasco R and Sargent D. 2012 Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. BMC Genomics 2012, 13:129.
  • Rowland L, Alkharouf N, Darwish O, Ogden E, Polashock J, Bassil N and Main D. 2012. Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. BMC Plant Biology 12:46
  • Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arus P, Iezzoni A, Morgante M, and C. Peace (2012) Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm (2012) PLoS ONE 10.1371/journal.pone.0035668
  • Chagne D, Crowhurst R, Troggio M, Davey M, Gilmore B, Lawley C, Vanderzante S, Hellens R, Kumar S, Cestaro A, Velasco R, Main D, Rees J, Iezzoni A, Mockler T, Wilhelm L, van de Weg E, Gardiner S, Bassil N, and C Peace (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 10.1371/journal.pone.0031745
  • Jung S and Main D. 2012. Bioinformatics as a tool for stone fruit research. Chapter 10 in C. Kole and AG Abbott (Eds.), Genetics, Genomics and Breeding in Stone Fruits, Eds. C Kole and AG Abbott. CRS Press, Boca Raton, USA, p. 270-291.
  • Sargent D, Jung S and Main D. 2012.Compartive Genetics and Genomics Initiatives. Chapter 13 in C. Kole and AG Abbott (Eds.), Genetics, Genomics and Breeding in Stone Fruits, Eds. C Kole and AG Abbott. CRS Press, Boca Raton, USA, p. 355-377.
  • Wang A, Aldwinckle A, Forsline P, Main D, Fazio G, Brown S and Xu K. 2011 EST contig-based SSR linkage maps for MalusXdomestica cv Royal Gala and an apple scab resistant accession of M. sieversii, the progenitor species of domestic apple. Molecular Breeding 29(2) 379-397.
  • Jung S, Menda N, Redmond S, Buels RM, Friesen M, Y Bendana Y, Sanderson LA, Lapp H, Lee T, MacCallum B, Bett KE, Cain S, Clements D, Mueller LA and D Main (2011) Natural Diversity module: A new generic schema for large-scale phenotyping and genotyping data. Database DOI: 10.1093/database/bar051.
  • Ficklin SP, Sanderson LA, Cheng CH, Staton ME, Lee, T, Cho IH, Jung S, Bett KE and D Main (2011) Tripal: a construction toolkit for online genome databases. Database. DOI: 10.1093/database/bar044.


Progress 09/01/10 to 08/31/11

Outputs
OUTPUTS: Annotated whole genome sequences added for apple, strawberry, mandarin and sweet orange, with the two Citrus species made available ahead of publication. the genome and annotation data is available to browse, search and download using a variety of tools. Movement of Rosaceae data from old GDR schema to Chado schema completed. Expanded rose resources by adding 4 genetic maps and providing analysis support to rose genome sequencing as part of the International Rose Genome Sequencing Consortium. Synteny analysis completed for a peach-apple-strawberry publication, peach-strawberry synteny publicly available in GBrowse-Syn. Further developed and released Tripal, the generic model organism database off-the shelf solution for genome database construction, publication submitted. Publication submitted on the new Chado natural diversity module which was developed in collaboration with other database communities. The module allows breeding data, large scale phenotype and genotype data, germplasm data with pedigree,to be stored, as well as the details of marker and trait data. A standard data submission format for breeders to facilitate breeding data submission to tfGDR has been completed and is available. QTL data for apple, cherry, peach and strawberry have been collected from publications, uploaded to GDR and available through a new QTL search site. As part of this effort we developed a standardized nomenclature for naming traits. These are mapped to the names given by authors and are searchable by QTL label, symbol, trait name, trait category and taxon. Collection, curation and upload of 15 years of apple genotype and phenotype data from the Washington Apple Breeding Program has been completed and is available to query and download on a secure site within tfGDR for the WA apple breeder. An online breeders toolbox created for private and public breeding data from the RosBREED project is available containing the apple crop reference and breeding pedigree data sets. Cultivars can be browsed; searched by name, traits, parentage; and the data downloaded as an input file for a breeding software Pedimap or as an excel file in wide or long format. Transferable Rosaceae COS markers are mapped in the peach, apple and strawberry genomes and viewable in GBrowse. Candidate and selected markers identified by the international SNP consortiums are mapped to the genome sequences and available to download in excel and fasta files. The peach growers website is continuing to be updated at the Clemson site. Three new peach educational videos targeting growers and consumers have been developed. Components of the tfGDR project were presented at six meeting (local, national and international). PARTICIPANTS: Doreen Main (PD): Project leader, organized meetings, supervised overall project work, presented project at meetings. Sook Jung (coPD): Addition of molecular diversity data to Chado, collection of Rosaceae data, development of breeders toolbox, presented project at meetings, attended project meetings; Stephen Ficklin(database administrator and developer): data conversion, data upload. Drupal module development, database administration); Isaac Westmoreland (undergraduate programmer): Drupal module developer); Chunxian Chen (postdoctoral bioinformaticist): collection and analysis of Citrus genomics data; Naama Menda (postdoctoral bioinformaticist): Chado schema development and pathway database development; Taein Lee (developer): breeders toolbox data conversion and interface development, development of online genome sequence annotation server; Chun-Huai Cheng (bioinformaticist): Drupal module developer and data analysis; Ping Zheng (postdoctoral bioinformaticist): collection and curation of Rosaceae QTL data; Sushan Ru (graduate student): collection and curation of Rosaceae QTL data. TARGET AUDIENCES: The target audience is scientists, growers and the public. Scientists have been engaged through presentations, emails about the website and press releases about the peach genome. Growers are being engaged through online educational videos (so far about peaches) and presentations at commodity group meetings. PROJECT MODIFICATIONS: Moved two outreach workshops from year 2 to year 3.

Impacts
Provision of a single source for integrated genomic, genetic and breeding resources for publicly-available Rosaceae and Citrus annotated genomic and genetic data, facilitating gene functional characterization, trait identification and genomics-assisted breeding in tree fruit. From May 11, 2010 to June 29, 2011, GDR has been visited 27,035 times, by 8,516 unique visitors from 115 countries, with 111,396 pages viewed. The Citrus Genome Database has been visited 788 times by 479 unique visitors from 59 countries, with 2,863 pages viewed. 90% of the traffic to the citrus site occurred after the genome sequence became available in April 15, 2011. Expanded Tripal to provide a freely available, species-independent, user-friendly, open-source, off-the shelf solution for construction of whole genome websites supporting community collaboration. Five new databases currently in construction using the Tripal model (Cacao Genome Database, Vaccinium Genome Database, Cool Season Food Legume Database, Pulse crops Genomics and Breeding, and the Cotton Genome Database). Provision of annotated whole genome data of three species of Rosaceae and two species of Citrus to facilitate comparison and knowledge transfer among closely related species. Fostered greater interaction and collaboration among the horticultural and forestry communities, with particular emphasis on forest and orchard trees, and Solanaceae and Rosaceae crops.

Publications

  • Wegrzyn JL, Main D, Figuero B, Choi I, Yu J, Neale, DB, Jung S, Staton M, Zheng P, lee T, Ficklin S, Cho I, peace C, Evans K, Volk G, Oraguzie N, Chen C, Gmitter FG, and AG Abbot. 2011. Uniform Standards for Genome Databases in Forest and Fruit Trees. Tree Genetics and Genomes (submitted).
  • Ficklin SP, Sanderson AL, Cheng CH, Staton S, Lee T, Cho I, Jung S, Bett KE , and D Main. 2011. Tripal: a Construction Toolkit for Online Genome Databases. Databases (submitted).
  • Jung J, Menda N, Redmon S, Buels RM, Friesen M, Bendana Y, Sanderson LA, Lapp H, Lee T, MacCallum B, Cain S, Clements D, Mueller LA, and D Main. 2011. The Chado Natural Diversity module. A new generic schema for large-scale phenotyping and genotyping data. Databases (submitted).


Progress 09/01/09 to 08/31/10

Outputs
OUTPUTS: Drupal interface developed for tfGDR and GDR website interface converted to Drupal. Chado database schema expanded to include molecular diversity data, installed on development site. Citrus EST data assembled and annotated, uploaded to the new Chado schema and displayed in Drupal using searchable interfaces and downloadable data sets. Existing Rosaceae data is being transferred over to the new Chado schema. Peach genome sequence assembled and analyzed. The sequence and annotation made available online to community ahead of publication. Peach genome data integrated with the existing genetic marker and EST data in GDR. Apple genome sequence and annotation acquired, currently in the Rosaceae development site, ready for public release following journal publication. Strawberry genome sequence acquired and peach/strawberry/grape/poplar synteny analysis complete, apple in progress. GBrowse-Syn installed for display. Seven new genetic maps added to GDR-CMap. Publications database updated. Breeders modules are being developed that store breeders data and allow querying of data and upload of new data. Development of standard phenotype descriptor for Rosaceae (apple, strawberry, and peach) has been initiated. Five educational videos of peach targeting growers and consumers have been developed. The titles are; How to pick the best peach; How to determine peach ripeness; Different kinds of peaches; Clemson peach germplasm evaluation program, and the perfect peach. PARTICIPANTS: Doreen Main (PD): Project leader, organized meetings, supervised overall project work, presented project at meetings. Sook Jung (coPD): Addition of molecular diversity data to Chado, collection of Rosaceae data, development of breeders toolbox, presented project at meetings, attended project meetings; Margaret Staton (postdoctoral bioinformaticist); data conversion, sequence analysis and interface development; Randall Svancara (database administrator and developer): data conversion, data upload. Drupal module development, database administration); Isaac Westmoreland (undergraduate programmer): Drupla module developer); Chunxian Chen (postdoctoral bioinformaticist): collection of Citrus genomics data; Naama Menda (postdoctoral bioinformaticist): Chado schema development and pathway database development; Taein Lee (developer): breeders toolbox data conversion and interface development, development of online genome sequence annotation server. TARGET AUDIENCES: The target audience is scientists, growers and the public. Scientists have been engaged through presentations, emails about the website and press releases about the peach genome. Growers are being engaged through online educational videos (so far about peaches) and presentations at commodity group meetings. Resources are still being developed for the public, but non technical press releases about the peach genome reached the public and generated a lot of interest. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The release of the peach genome data on April 1, 2010 has had major impact for the Rosaceae and general plant community. Since that date, GDR has been accessed by 10,178 researchers from 102 countries, of which 4,281 were new visitors to the site (Google Analytics). The addition of molecular diversity data to the Chado schema, led by tfGDR, has been adopted by GMOD. Following the presentation of GDR in Drupal at the Plant and Animal Genome Conference in San Diego in January 2010, several bioinformatic groups have expressed interest in using Chado/Drupal combination for database development/redevelopment. A strategic alliance formed between the tfGDR and TreeGenes to develop standardized data types and standards for forest and orchard tree databases. To date we have met 90% of our goals and are on target to meet the other 10% by the end of year 1 on August 31, 2010.

Publications

  • Jung, S., Cho, I., Sosinski, B., Abbott, A., Main, D. 2010. Comparative genomic sequence analysis of strawberry and other rosids reveals significant microsynteny. BMC Research Notes (2010) 3:168.