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Plant Ontology Release #21 Now Available

We are pleased to announce that the latest release of the Plant Ontology, version #21, is now available on our browser at http://www.plantontology.org

One major change you may see is that on August 1, 2015, all the ontology files and issue tracker were moved to a shiny new GitHub Site: (https://github.com/Planteome/plant-ontology) as part of the Planteome Project. Please update your local browser bookmarks, and come check out the new functionalities.

* This full release of the PO features the addition of 37 new PO terms, for both the ''Plant Anatomical Entity (PAE)'' (31) and ''Plant Structure Development Stage (PSDS)'' (6) branches of the ontology.

* Names have been revised for 23 PAE terms and 21 PSDS terms, and definitions of many more terms have also been revised and updated.

* This Release also includes new and updated annotation data for five species: Maize (307), Arabidopsis (3339), soybean (34), Medicago (81), and tomato (147), generated as part of the Plant Phenotype Pilot Project (http://www.phenotypercn.org/?p=1099 ) and compiled by the POC. The rice annotations (279) were added in Version #20. All these annotations refer to genes associated with characterized mutant phenotypes.

* Additional annotation data was contributed by our collaborators for Soybean QTLs (SoyBase) and and Arabidopsis thaliana genes (TAIR).

For complete information about the changes in Release #21, please see: http://wiki.plantontology.org/index.php/Release_21 and refer to the Release Notes on PO home page: (http://plantontology.org/docs/release_notes/index.html).

High School Students Genotype Einkorn Wheat Varieties in DNA Biology Summer Camp at Oregon State University. Our 2nd STEM camp

Twelve students (9th-12th grade) from local schools attended DNA Biology Summer Camp organized by Jaiswal laboratory at Oregon State University in July 2014. The activities in the camp included short introductory lectures and follow up exercises using models and laboratory experiments. The learning in a collaborative environment was encouraged to further enrich their camp experience. Dr. Laurel Cooper, a research associate in the Jaiswal laboratory, introduced the students to the basics of the plant cell, and genetic material. Using a plant cell model, students identified the parts of the plant cell, including the subcellular structures such as organelles. In the following hands-on exercise using DNA model kits, they constructed a DNA sequence and its complementary strand, and then worked together as a group to form a double helix molecule. These exercises demonstrated how DNA, RNA, and proteins are all related and how they are responsible for the various functions of living cells.

Matthew Geniza, a graduate student in the Jaiswal lab, explained various types of mutations, the concept of genetic markers (SNPs and SSRs), and how the polymerase chain reaction (PCR) can be used to detect differences in the DNA sequences of two closely related individuals or plant varieties. To illustrate these principles and gain practical experience, students genotyped two varieties (G3116 and DV92) of Einkorn wheat (Triticum monococcum). OSU STEM camp students at building the DNA chain

Einkorn wheat has a diploid genome, and is a close relative of hexaploid common wheat. Thus, it is often used as a model to study wheat genetics. Einkorn wheat, Triticum monococcum, originated around the Karacadağ Mountains in Turkey, and is one of the few crops that were domesticated by early agriculturists prior to 7000 B.C. during the Neolithic period. Triticum monococcum G3116 is a wild winter wheat, while, DV92 is the domesticated spring wheat. The wild accessions normally have brittle rachis that allows plant to disperse seed over a span of a few months, which helps it to survive in nature. But in order to maximize the crop yields, humans selected for tough rachis to avoid seed loss. Other traits that were selected for were plumper seeds, and for break of dormancy.

Under the supervision of Matthew Geniza and Dr. Sam Fox (former postdoc of Jaiswal and now a Faculty at Linfield College), students isolated genomic DNA from the G3116 and DV92 seedlings and genotyped the two varieties by PCR amplifying a known SSR marker and analyzed the DNA fragments using agarose-gel electrophoresis. This marker was identified in the Jaiswal laboratory by sequencing and assembly of transcriptomes of G3116 and DV92 varieties published recently (Fox et al 2014).

DNA Biology summer camp was a collaborative effort of the Gramene project, and Plant Ontology project, with Oregon State University STEM Academy. The 9th-12th graders were from various local high schools including Crescent Valley High School, Corvallis High School, Philomath High School, and Lebanon High School. Other participants included one home-school student from halsey, OR and one international student visitor. Dr. Pankaj Jaiswal, Associate Professor at Oregon State University, led the instruction, planning and coordination of this course. Dr. Cathy Law, Director of the STEM Academy at OSU, coordinated student enrollment and logistics. Funds for this course were provided by the National Science Foundation (NSF) funded projects; The Plant Ontology (IOS:0822201) and Gramene: A Comparative Genomics Database (IOS: 1127112).

News source: Source: Gramene News (http://www.gramene.org/node/311)

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