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Newsletter 1 Volume 2 Issue 5 GRAMENE News September/October 2007 Gramene Receives NSF PGRP Award Gramene Gramene, the only platform dormancy, drought tolerance, tionary biologists and breed- News for plant research that enables and resistance to diseases. In ers by providing compelling, Gramene Recieves NSF both forward and reverse addition, the tools developed intuitive, user interfaces. Lastly, PGRP Award . p 1 genetics, has been awarded will allow for the estima- the project will reach out to Gramene funding resources through tion of the breeding value of students, the public, and to Release 26 . p 2 the NSF Plant Genome Re- individual genetic variants, underrepresented minorities FAQ . p 3 search Resource award, Award thereby providing breeders via a series of online tutorials #0703908 . This abstract is with the ability to select the and on-site workshops that Upcoming shown here: ideal combinations of seed involves a novel, and cost-ef- Outreach . p 3 stocks to create varieties that fective, public/private partner- Community The Gramene database have desirable traits such as ship. News (http://www.gramene.org) robustness, the ability to grow Opportunities . .p 3 is an online resource, jointly in marginal environments, or All the information resourc- supported by NSF and the US have high potential as a source es generated by Gramene Recommended Department of Agriculture’s for biofuels and other materi- will be available to scientists, Reading . p 4 Agricultural Research Service. als of high economic value. breeders, and members of the It integrates the genomic, general public free of charge For an example of how a researcher genetic and phenotypic Information resources and without intellectual prop- has used the information in rice, maize and developed, and being de- erty restrictions. Gramene Da- tabase in their other cereals, thereby giving veloped, through genomics research, see scientists and other end-users efforts are key elements to PI: Lincoln Stein (Cold Spring Joshua C. John- easy access to this integrated advance our fundamental Harbor Laboratory) son, Rudi Appels, CoPIs: Doreen Ware (Cold Spring Mrinal Bhave. information. This project will knowledge base for a future (2006). The PDI provide for the enhancement bio-based economy and to Harbor Laboratory), Susan Mc- genes of wheat of Gramene by incorporat- address the expected need Couch, Edward Buckler, and and their syntenic Pankaj Jaiswal (Cornell University; relationship to ing biological pathway and for feeding an expanding subawardee) the esp2 locus of genetic diversity informa- world population. Many of the rice. Functional & Integrative tion from maize, rice, wheat, information resources are still Genomics, 6(2), sorghum, and other cereals underutilized because of the 104-21. into the resource. Compara- fragmentation of the datasets tive genomics tools will be and the absence of tools to developed, thereby allowing make meaningful connections researchers to use knowledge among them. To fully unlock gained in one plant species the potential of plant genome to identify and characterize data, the diverse datasets must functionally significant genes be integrated so that informa- and other elements in the tion is shared both within and genomes of other species. Sci- between species. It is one of entists can use the resource to the goals of Gramene to pro- make advances in our funda- vide that integration. Another For information on mental understanding of the goal of the project is to deliver the “Rice: Research to plant processes of economic the integrated dataset into Production” course last May, see: importance such as hybrid the hands of plant geneticists, www.ricehapmap. org/courses.aspx vigor, grain development, seed molecular biologists, evolu- Gramene Release 26 Have you visited Gramene’s web-accessible database and then mapped to theOryza sativa TIGR v5 assembly recently? If not, you may be in for a few surprises! using BLAT. The succesfully mapped sequences can be The Gramene website layout was reformatted back in viewed as DNA aligned features in the contigview. January, and now the majority of the Gramene datasets New markers of note are 2,243 maize eSSRs from the (modules) have a consistent interface to aid in the inte- Maize Genome Sequencing Project. gration of all the data sets. Rather than having module Data in the Maps Module is built out of the mappings sub-menus, the Genes, Markers, QTL, Proteins, Ontolo- in the Markers Module. Updates in the latter module are gies, Diversity and Publications present a new layout encorporated here. Of note is the new sequence map with collapsible and expandable sections (see Figure 1). for indica, and, as noted in the “Genomes” section above, When opening the information page for an item in any the OMAP sets have all been updated. of these categories, Most of the rice genes with the first char- the general informa- acter of the gene symbol from “A” to “Z” in our tion will be displayed database now have ontology associations to and remain open at TO, GO and PO. Additionally, 3,385 new genes the top of the page. records were downloaded from GrainGenes. Below this general One recent improvement is that all QTL information will be have been described and annotated by sections for links to multiple ontologies. In addition to the Trait other datasets (with Ontology (TO) and Plant Ontology (PO) terms the number of links used in previous releases, Environment Ontol- identified for each ogy (EO) terms have been added this build section) and will vary to describe environmental conditions under depending upon the Figure 1 which a particular QTL has been identified. module you are in. These terms have been annotated by creating Each section can be expanded or collapsed by clicking a default mapping based on the expertly identified TO on the section title. Categories with no correspondences and EO associations. will be greyed out. On these pages, the “Map Positions” Another recent important improvement in this offers a “CMap Preview” option. Click on this option to release is the provision of QTL-associated molecular get a preview of the map in CMap, or click on “View marker info. We currently provide two types of associ- Comparative Map” to go to the actual map. ated markers for a particular QTL: Co-localized mark- The help documentation has also been put into this ers are the markers co-localized or overlapping with a consistent interface with expandable/collapsible sec- QTL region on the original QTL map; and neighboring tions. You may view it at http://www.gramene.org/db/ markers are those not overlapped but closely adjacent help (see Figure 2). to a QTL region. The associated marker info is crucial for The genome web server was upgraded to Ensembl QTL fine mapping, map-based positional cloning, and release 46 , and there is a new marker-assisted selection (MAS) for genome browser for Oryza plant breeding. sativa ssp. indica. New gene We are pleased to announce the tracks include a Gramene addition of five new species to the evidence-based gene track Gramene pathway tools (RiceCyc) (37,176 genes); a RAP (The Rice module. These are Capsicum anuum, Annotation Project, http:// Coffea canephora, Medicago truncat- rapdb.dna.affrc.go.jp) gene ula, Solanum lycopersicum and Sola- track (29,132 genes); and the num tuberosum. RiceCyc now allows Consensus gene track: (14,842 you to draw comparisons among genes). The OMAP sets have the data sets from eight species. Figure 2 been remapped, and, new Poa- Six pathways were added, two ceae EST/mRNA/GSS DNA sequences were downloaded pathways deleted, and five pathways modified during from NCBI GenBank to the Gramene Markers database, this round of curation. Upcoming Outreach: Gramene FAQ Contact Gramene through the “Feedback” link at the top of any page to ask ques- Gramene will offer a database presentation tions. Here are some recent questions that have been answered. at the 2008 PAG in January. This workshop is currently planned for Tuesday afternoon, Q: I want to search markers linked to a specific disease. Is this possible? January 15. In addition to the workshop, we will have a poster, and you can visit us, along A: Markers are associated with sequences or other mapped features, such as QTL with several other plant databases, in our - you cannot associate a marker with a trait. However, QTL are associated with traits, booth. and markers can be associated with QTL. Therefore, I suggest going to the QTL data- New: base and searching your trait (by name of disease) and finding a QTL on the chromo- Gramene now some you are researching. Follow the QTL information to its mappings, and using the uses Google comparative map viewer (CMAP) you can pull up maps that have correspondences, Calendars and look for the markers on your QTL or associated maps. to record Gramene Q: Why are the location and sequences in the Gramene database different outreach. The from the data provided by the McCouch Lab and available at http://www. calendar can be found on the web at gramene.org/microsat/50_ssr.html? http://www.gramene.org/outreach/cal- endar.html A: The positions of the SSRs in Gramene are based on the current rice pseudomol- ecules, as assemblies from TIGR. We re-run the pipeline that positions these SSRs on Community Calendar the rice genome (based on e-PCR with the primer pairs) with every build of Gramene. Thus, as the assemblies of the rice pseudomolecules are updated in Gramene, the bp 2007 positions of the SSRs change, reflecting their current positions on Oct. 9-14. 4th International Rice Blast Conference. Vaya the latest assembly of the pseudomolecules. In addition, you will Huatian International Hotel, Changsha, Hunan, China find that the positions of the SSRs published in 2005 were based on Oct.
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