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Recommendations for Prunus QTL nomenclature

by Jim Olmstead

Dear Rosaceae Community Members, During the Prunus workshop at the RGC3 Conference in New Zealand, Cameron Peace, Eben Oqundiwin and I were asked to work on developing a draft of QTL nomenclature suggestions that could be used to standardize QTL reporting within Prunus. I've attached a working document for the community as a whole to comment on. Although we have concentrated on Prunus, please note that the opportunity exists to expand these suggestions to the entire Rosaceae family. If you find this topic interesting and would like to be included in future mailings, please follow this link to the Genome Database for Rosaceae website http://www.mainlab.clemson.edu/cgi-bin/gdr/signup_ROSACEAE-QTL-LIST.cgi and sign up for the QTL topics mailing list. Once you have signed up for the mailing list, you can use the email address rosaceae-qtl-list(a)genome.clemson.edu to send mail to the subscribed group. Communications from this mailing list can then be viewed at: http://www.mainlab.clemson.edu/pipermail/rosaceae-qtl-list/ You may also address any comments and suggestions concerning this topic directly to me - you'll find the contact information below. I look forward to hearing from you! Sincerely, Jim Olmstead Cherry Breeding - Washington State University -- James Olmstead WSU-Prosser 24106 N. Bunn Rd. Prosser, WA 99350 Office: 509-786-9249 Fax: 509-786-9370 Email: jwolmstead(a)wsu.edu

18 years, 8 months

GDR Newsletter May 2006

by Sook Jung

GDR Newsletter May 2006 Welcome to the fifh issue of the GDR newsletter. This newsletter is to inform users about new or updated data and features in GDR and community related news. Please feel free to provide feedback and news either directly by email or via our online form. The online version can be found at http://www.mainlab.clemson.edu/gdr/newsletter/newsletter0506.shtml Attached is the pdf version of this newsletter. Community News White Paper The US National Rosaceae Genomic, Genetics and Breeding Executive Committee have completed the US white paper on Rosaceae Genomics. It can be downloaded from GDR and any comments can be addressed to the executive committee chair, Dr Amy Iezonni. Funding 1. A US based proposal, supported by strong international collaboration, is being submitted to the NSF Plant Genome Comparative Sequencing program in June. We are proposing to sequence the peach genome as a reference for Rosaceae, with skim sequencing of strawberry and apple, and targeted deep coverage of selected loci across multiple species. For more information contact Bryon Sosinski of NC State. 2. A US based proposal is being submitted to the NSF Networking program in June to fund a Rosaceae Informatics Network where international bioinformatics researchers will meet regularly and develop a collaborative bioinformatics infrastructure for the community database. For more information contact Dorrie Main or Bert Abbott. Conferences The 3rd International Rosaceae Genomics Conference was held March 19-22, 2006, in Napier, New Zealand. Download the conference outcomes and the abstracts from this meeting. The 4th International Rosaceae Genomics Conference is scheduled to be held in Pućon, Chile in March 2008. More details will be posted in the GDR conferences page as they become available. Employment A faculty position in plant breeding is available at the Pontificia Universidas Catolica de Chile. What's new at GDR? 1. SNPs (Single Nucleotide Polymorphisms) 2. Updates to the peach physical map 3. Updates to the Comparative Mapping Viewer CMap 4. Marker/Map data template available 5. Rosaceae Genomics White papers 6. Species page/Project page 7. New header bar 8. Community pages and mailing lists 9. New publication from GDR 10. Additions to the publication database 1. SNPs (Single Nucleotide Polymorphisms) The new Fragaria, Malus, Prunus, Pyrus, and Rosa unigenes have been searched for SNPs using the software package AutoSNP. A total of 14,801 SNPs are available to be viewed and searched, including 10426 SNPs from Malus, 3776 from Prunus, 316 from Rosa, and 283 from Fragaria. 2. Updates to the peach physical map The latest peach physical map contains 18387 BACs and 1367 contigs. Physical length of the contigs is appoximately 210-230Mb and that of the anchored contigs is 33Mb. WebFPC / WebChrom displays the peach physical map. Anchored peach BAC contigs can be accessed directly from the prunus reference TxE map from the GDR map viewer. 3. Updates to the Comparative Mapping Viewer CMap Four new maps (Apricot GxV F1 2002, Apricot LxL F2 2003, Peach AxJ 2005 and 815x903BC diploid Fragaria 2006) have been added to the genetic maps available through CMap. This now makes a total of 24 Rosaceae CMaps are available through CMap at GDR. These include: Prunus: Prunus bin map 2005, TxE almond x peach F2 2004, Myrobalan Plum x Almond- Peach hybrid 2004, GxN almond x peach F2 2001 Peach: Peach AxJ 2005, Peach PMP2 2005, Peach peach x P. ferganensis BC1 PxF 2001, Peach JxF 2004, Peach Sc x B 1998 Apricot: Apricot GxV F1 2002, Apricot LxL F2 2003 Almond: Almond FxT 2000, Almond FxB F1 1998 Sour Cherry: PcerasusEB, PcerasusRS Strawberry: FVxFN diploid Fragaria reference map, 815x903BC diploid Fragaria 2006 Apple: MNY75441-58, MNY75441-67, MWijcik_McIntosh, MRomeBeauty, MRomeBeauty_2, MWhiteAngel, MWhiteAngel_2 If you have mapping data that we can add, please contact us and we will work with you to make your data available via GDR. 4. Marker/Map data template available Efforts are underway to curate more extensive genetics data to GDR, and data templates for map/marker/trait/polymorphism/gene/QTL/Diversity are available. 5. Rosaceae Genomics White papers The US National Rosaceae Genomic, Genetics and Breeding Executive Committee have completed the US white paper on Rosaceae Genomics. They can be downloaded from GDR and any comments can be submitted to the executive committee chair, Dr Amy Iezonni. 6. Species page/Project page GDR has been reorganized to enhance navigation in the website. We have created specific species pages, under each genus where you can access all the information related to that species in GDR. Go to apple, prunus, almond, apricot, cherry, peach, rose, strawberry pages for all GDR structural genomics, functional genomics and funded project information. 7. New header bar Dropdown and left side navigation bars remodeled to enhance ease of access to GDR data. 8. Community pages and mailing lists The community page at GDR has been modified to make it easier to access the community pages of interest. In addition new International and US communication pages have been added, with new mailing lists to join (via a web form). We encourage you to join the appropriate mailing lists and use them to communicate to the community using these tools. 9. New publication from GDR Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes. Sook Jung, Dorrie Main, Margaret Staton, Ilhyung Cho, Tatyana Zhebentyayeva, Pere Arus and Albert Abbott. BMC Genomics 2006, 7:81 10. Additions to the publication database The publication database on GDR now contains publication data from Agricola, the catalog of articles maintained by the National Agricultural Library. 564 relevant publications are online and can be searched by title, authors, keywords, and date published. Subscription Visit our mailing lists be added/removed to the available GDR mailing lists. Once you have registered you may use the mailing lists to send out relevant information the community and it will be stored in searchable web archives. More information is available on each page on how to use them. If you have any difficulties please contact us. The GDR mailing list. The International Rosaceae Genomics Community mailing list. The USA Rosaceae Genomics Community mailing list. Work in progress 1. Efforts to integrate more extensive map/marker data We are updating our map/marker database structure to integrate the details of molecular marker data such as primer sequences, source BAC/ESTs, produce size and much more. 2. Creation of other databases within GDR We are also creating new database modules such as gene, trait loci, QTL, polymorphism/allele, germplasm, and diversity data.

18 years, 11 months

(no subject)

by Yanmin Zhu

19 years, 2 months

Team Members Needed for Planning

by Sook Jung

Dear Rosaceae colleagues, I am forwarding a note from Dr. Susan Brown at Cornell about forming four sub-committees that was discussed in Rosaceae community meeting held at IFTA conference in Hershey, PA. > Team Members Needed for Planning: > There are four general theme areas of research in the Rosaceae white paper (indicated in bold text below) and we are forming four sub committees for planning purposes. Anyone with an interest in one or more of these topics, and a willingness to participate in some pre-organization work for strategic planning are encouraged to contact the scientific coordinator for each group at the Email addresses below. Please do not reply to the list serve. We would appreciate a response by March 10th. Identifying those in each core area interested in participating in the discussion will facilitate future strategic planning. The Committee is charged with figuring out how such strategic planning will happen and how it will be structured. The entire Rosaceae community will participate in the strategic planning, but this committee sets the framework. > Reducing the dependence on chemical pesticides by improving biological resistance: Herb Aldwinckle at hsa1(a)cornell.edu. > Reducing labor costs (Plant architecture): Susan Brown at skb3(a)cornell.edu. > Improving fresh and processed fruit quality, storage and safety: Abhaya Dandekar at amdandekar(a)ucdavis.edu. Improving profitability of the Rosaceae fruit industry (abiotic stress tolerance): Michael Wisniewski at mwisniew(a)afrs.ars.usda.gov.

19 years, 2 months

Rosace Roundtable Minutes from 1-15-06 (corrected)

by Angela M. Baldo

19 years, 3 months

3rd International Rosaceae Genomics Conference - March 2006

by Encore Events

Dear All This is to remind you that, registrations for the above conference close on 15 February 2006. Registrations can be done online by visiting www.rgc3.co.nz <http://www.rgc3.co.nz/> . Please complete both sections of the registration process. If you are requiring accommodation this also needs to be reserved through us by 15 February as after that date we need to release any unallocated rooms. Please ensure that when you register you include all activities that you may wish to partake in as numbers need to be confirmed prior to conference. If you have submitted an abstract and have not registered then we remind you that you need to do so. For those who have already registered, we look forward to meeting you at Conference. Regards Sue Page Encore Events PO Box 12097, Ahuriri, Napier B 06 833 7440 F 06 833 7447 M 027 669 1345 E sue(a)encore-events.net.nz

19 years, 3 months

GDR Newsletter January 2006 pdf attachment

by Sook Jung

19 years, 4 months

GDR Newsletter January 2006

by Sook Jung

GDR Newsletter January 2006 Welcome to the fourth issue of the GDR newsletter. This newsletter is to inform users about new or updated data and features in GDR and community related news. Please feel free to provide feedback and news either directly by email or via our online form. The online version can be found at http://www.mainlab.clemson.edu/gdr/newsletter/newsletter0106.shtml Attached is the pdf version of this newsletter. Community News 1. Fruit and Nut Workshop, Saturday January 14, 8 am-12 pm. Plant and Animal Genome Conference XIV, San Diego, January 14-18, 2006. Conference organizer: Dr Amy Iezzoni. A Rosaceae genomics roundtable meeting will be held on Sunday January 15th, 8-10 am and the Rosaceae executive committee will meet on Sunday January 15th, 10am-12pm. 2. 3rd International Rosaceae Genomics Conference will be held in Napier, New Zealand, March 19-23, 2006. 3. The International Fruit Tree Association Annual Conference will be held in Hershey, Pennsylvania, USA, February 26-March 1, 2006 What's new at GDR? 1. Proposal to renew funding for GDR submitted to the NSF Plant Genome Program. 2. New EST libraries are available. 3. Rosaceae Unigene v2 with enhanced annotation available. 4. Prunus bin map data is available in CMap and marker search engine. 5. Enhanced SSR server now available with primer generating option. 6. More databases are available for blast/fasta sequence similarity search. 7. Data available for the three peach BACs that are completely sequenced. 8. New Roseaceae Genomics Executive Committee web page. 9. The GDR publications database now contains 242 papers relevant to Rosaceae genetics/genomics. 1. GDR Renewal Proposal Submitted to NSF Plant Genome Program In November 2005, a multi-institution proposal was submitted to the National Science Foundation Plant Genome Program to renew funding support for GDR through August 2009. The proposal if funded will significantly enhance the functionality and usefulness of GDR for the rosaceae community. If you's like more information on this proposal please contact Dorrie Main. 2. New EST libraries are available. The diploid strawberry species, Fragaria vesca, a putative genome donor to the octoploid, cultivated species (Fragaria x ananassa) is being been developed as a model system for genetic and genomic research in strawberry.Tom Davis at the University of New Hampshire, USA, has provided 2717 ESTs from the unopened flower buds of diploid strawberries. A full analysis results of his library can be viewed/downloaded from the project page and the ESTs can be queried at the EST search site. Peach (Prunus persica) represents a model species for prunus and a reference species for Rosaceae. To develop an extensive Prunus EST database for identification and cloning of genes important to fruit and tree development, Bert Abbott at Clemson University, USA, generated 8832 high-quality expressed sequence tags (ESTs) from a peach cDNA library of shoot tissue. After assembly and annotation, a putative peach unigene set consisting of 5381 ESTs was defined. Full analysis results of his library can be viewed/downloaded from the project page and the ESTs can be queried at the EST search site. 3. Rosaceae Unigene v2 with enhanced annotation available. A second version of the Rosaceae family unigene is now available. A new assembly process is being utilized; the ESTs are assembled using CAP3 within each genera (Fragaria, Malus, Prunus, Pyrus, and Rosa), and these assemblies are compiled and re-assembled together to produce the family-wide unigene. The new Rosaceae Unigene contains 72114 unigenes. Putative function has been assigned using the arabidopsis protein database and will be further expanded using the swissprot and NCBI nr protein databases. The unigenes have been analyzed for microsatellites and the results including suggested primers can be downloaded. Please see each project page (Fragaria, Malus, Prunus, Rosa and Rosaceae) to view/download all the GDR unigene data. 4. Prunus bin map is available in CMap and marker search engine. A Prunus bin map (Howad et al., 2005), is now available in GDR. CMap displays the prunus bin map with bin names and the first/ last markers of each bin, and the bin-mappded markers are displayed in each bin page. For example, all the bin mapped markers of the first bin in G1 are shown in bin 1:14 page. All the markers in the prunus bin map can be queried through the GDR marker search page. 5. Enhanced SSR server now available with primer generating option. The online SSR server at GDR has been enhanced to include an option to have primers generated for the sequences that users wish to data mine for microsatellites. 6. More databases are available for blast/fasta sequence similarity search. The databases available for blast/fasta sequence similarity search includes the following: peach ESTs, unigenes and ESTs with SSR's, BAC anchored peach ESTs, mapped peach ESTs, almond ESTs and unigenes (Abbott, Clemson U); peach ESTs and unigenes, peach ESTs with SSR's (Vendramin, CRA ISF); octoploid strawberry ESTs, unigenes, and ESTs with SSRs (Folta, U of Florida); diploid strawberry ESTs and unigenes (Davis, U of New Hampshire); ESTs of Fragaria, Malus, Prunus, Pyrus, Rosa, and entire Rosaceae family from NCBI dbEST; NCBI Rosaceae genomic sequences; NCBI Rosaceae protein sequences; Arabidopsis protein sequences from TAIR. A detailed description of the databases is available in each search engine. The blast/fasta sequence servers return the output of the searches in both parsed excel file and as a raw output file with visual alignments. 7. Data available for the three peach BACs that are completely sequenced. Anchored ESTs/markers and the sequences for the three BACs (082I18, 028F08 and pPn31C7) can be accessed from BAC search site. An online annotation pipeline is currently under development by the GDR team. 8. New Rosaceae Executive Committee web page created to provide a communication portal for information and reports generated by the committee. 9. The GDR publications database now contains 242 papers relevant to Rosaceae genetics/genomics. New publications since our last newsletter are listed below: 1. Lazzari B et al. ESTree db: a tool for peach functional genomics. BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S16. 2. Patocchi A, Walser M, Tartarini S, Broggini GA, Gennari F, Sansavini S, Gessler C Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm. Genome 2005 Aug;48(4):630-6. 3. Oosumi T, Gruszewski HA, Blischak LA, Baxter AJ, Wadl PA, Shuman JL, Veilleux RE, Shulaev V High-efficiency transformation of the diploid strawberry (Fragaria vesca) for functional genomics. Planta. 2005 Dec 1;:1-12. 4. Gillen, A.M., Bliss, F.A. Identification and Mapping of Markers Linked to the Mi Gene for Root-knot Nematode Resistance in Peach J. Amer. Soc. Hort. Sci. 130(1):24-33. 5. Tzanetakis IE, Martin RR New features in the genus Ilarvirus revealed by the nucleotide sequence of Fragaria chiloensis latent virus. Virus Res 2005 Sep;112(1-2):32-7. 6. Verde I, Lauria M, Dettori MT, Vendramin E, Balconi C, Micali S, Wang Y, Marrazzo MT, Cipriani G, Hartings H, Testolin R, Abbott AG, Motto M, Quarta R Microsatellite and AFLP markers in the Prunus persica [L. (Batsch)]xP. ferganensis BC(1)linkage map: saturation and coverage improvement. Theor Appl Genet 2005 Aug 9;:1-9. 7. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arus P Mapping with a Few Plants: Using Selective Mapping for Microsatellite Saturation of the Prunus Reference Map. Genetics 2005 Aug 22;. 8. Holland D, Larkov O, Bar-Ya'akov I, Bar E, Zax A, Brandeis E, Ravid U, Lewinsohn E Developmental and varietal differences in volatile ester formation and acetyl-CoA: alcohol acetyl transferase activities in apple (Malus domestica Borkh.) fruit. J Agric Food Chem 2005 Sep 7;53(18):7198-203. 9. Gao ZS, Weg WE, Schaart JG, Arkel GV, Breiteneder H, Hoffmann-Sommergruber K, Gilissen LJ Genomic characterization and linkage mapping of the apple allergen genes Mal d 2 (thaumatin-like protein) and Mal d 4 (profilin). Theor Appl Genet 2005 Sep 6;:1-11. 10. Mohapatra A, Rout GR Identification and analysis of genetic variation among rose cultivars using random amplified polymorphic DNA. Z Naturforsch [C] 2005 Jul-Aug;60(7-8):611-7. 11. Lalli DA, Decroocq V, Blenda AV, Schurdi-Levraud V, Garay L, Le Gall O, Damsteegt V, Reighard GL, Abbott AG Identification and mapping of resistance gene analogs (RGAs) in Prunus: a resistance map for Prunus. Theor Appl Genet 2005 Sep 30;:1-10. 12. Mehli L, Kjellsen TD, Dewey FM, Hietala AM A case study from the interaction of strawberry and Botrytis cinerea highlights the benefits of comonitoring both partners at genomic and mRNA level. New Phytol 2005 Nov;168(2):465-74. 13. Lin C, Mueller LA, Carthy JM, Crouzillat D, Petiard V, Tanksley SD Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet 2005 Nov 5;:1-17. 14. Xie H, Sui Y, Chang FQ, Xu Y, Ma RC SSR allelic variation in almond (Prunus dulcis Mill.). Theor Appl Genet 2005 Nov 24;:1-7. Subscription Visit our mailing list site at GDR to be added/removed to the mailing list. http://www.mainlab.clemson.edu/gdr/MailingList.shtml Work in progress Online EST sequence processing pipeline Annotating peach, plum and apricot BACs. Annotating the rosaceae unigene. Developing a rosaceae BAC annotation pipeline Extending the gene and QTL data available in CMap Integrating data from the USDA CSREES NRI projects

19 years, 4 months

3rd International Rosaceae Genomics Conference - REMINDERS

by Neill & Sue Page

Goodday everyone Please note the following deadlines: REGISTRATION - early bird closes on 31 December 2005, New Zealand time. To take advantage of the early bird rate you can register online www.rgc3.co.nz and click on the registration tab where you will find all the options available. If you register online then please ensure you complete both sections. ABSTRACTS - for those who have submitted abstract titles and have not yet submitted their abstract these are due by 31 December 2005, New Zealand time. The instructions on the submission of abstracts and format requirements are also available on http://www.rgc3.co.nz Please do not forget to select the most appropriate topic area and include with the abstract. We have received a good number of very interesting titles and are looking forward to the meeting. Best wishes for a Very Merry Christmas and a Great 2006. Regards Sue Page Encore Events Management Ltd 13a Charles St, Westshore Napier, New Zealand Ph/Fax (06) 835 9549 Mobile (027) 669 1345 Email encore.events(a)clear.net.nz

19 years, 5 months

3rd International Rosaceae Genomics Conference - Abstract Titles

by Neill & Sue Page

Dear All Thank you to those who have already submitted Abstract Titles for the above conference. However, we wish to remind all those who haven't submitted anything yet that the FINAL DAY FOR SUBMISSION IS 31 OCTOBER 2005. If you have any queries please refer to www.rgc3.co.nz, or contact me direct. We look forward to receiving your Abstract Titles. Regards Sue Page Conference Manager Encore Events Management Ltd 13a Charles Street Napier, New Zealand Ph/Fax: (06)835 9549 Mobile: 027 669 1345 Email: encore.events(a)clear.net.nz

19 years, 7 months

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