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Newsletter 1 Volume 2 Issue 3 GRAMENE News May/June 2007 A New Era for Barley Genetics Recent developments in opments in barley genomics and diversity analysis platform sequencing and genotyping was the generation of a BAC based on more than 3,000 gene Gramene News technologies are changing the library from the American cul- sequence based markers and will landscape of scientific opportu- tivar, Morex. This was followed lay the foundation for a series FAQ . p3 nities for large genome cereal by the creation of significant of major new projects such as species such as wheat and barley. EST sequence resource (cur- the UK, SEERAD and BBSRC LINK Upcoming Outreach The existing sequence of rice, to- rently standing at >450,000; see funded, AGOUEB (http://www. p3 gether with the rapidly accumu- http://harvest.ucr.edu) which led agoueb.org) and the US, USDA lating sequence information from in turn to a series 5520-925 funded, Barley- 2.00 the maize, sorghum and Brachy- of sequence based 1.80 CAP (http://www. podium genomes, are providing genomics resourc- 1.60 barleyCAP.org) Community News 1.40 a valuable set of comparative es, including the 1.20 projects inte- R 1 A New Era for Barley rm cereal sequence and functional Barley1 Affymetrix o grated through a Genetics . p1 N0.80 genomics resources that can GeneChip (one 0.60 common infor- be exploited in large genome of the first major 0.40 matics infrastruc- High School Outreach 0.20 . p 2 species. Despite the inherent arrays for a crop 0 ture (Figure 3 34 0 62 difficulties that come from work- plant [see http:// -0.20 and http://germi- 0 0.20 0.40 0.60 0.80 1 Opportunities . .p 3 ing with a large genome, barley www.plexdb. Norm Theta nate.org.uk/). Figure 2. Single locus SNP genotypes (Hordeum vulgare), with with 5.3 org/]) and a series These de- Recommended Reading from a set of barley lines visualized us- . p4 billion letters of genetic code, has of Barley TILLING ing the Illumina Bead Studio software. velopments are many advantages - an extensive populations (e.g. bringing a new collection http://germinate. dimension to barley breeding of mutants scri.sari.ac.uk/barley/ and genetics which will lay the (http://ace. mutants/). foundation for our understand- untamo. The International ing of the barley genome and net/) and a Barley Sequencing increase the value of barley as continuum Consortium (IBSC) the temperate cereal crop of of interfertile (http://barleygen- choice to exploit major scientific germplasm ome.org/), formed developments in “model” plants that spans from a nucleus of such as Arabidopsis and rice. the range leading barley from wild H. Figure 1. A stand of wild barley (H. sponta- research groups, neum) in the foreground growing in a mixed spontaneum sward of other wild barley and wheat species is now working (Figure1 ) in a reserve in Northern Israel. to develop a material in physical map the Fertile Crescent to landraces based on BAC on High Infor- and advanced modern cultivated mation Content Fingerprint- DNA extracted from germplasm. It is also a simple ing and BAC end sequencing rice plants in High diploid with 7 chromosome pairs, from a recently extended School Labs - see page which are essentially equivalent series of Morex BAC libraries. 2. to those in each of the 3 ge- A recent major advance Figure 3. Barley chromosome 7H Illumina SNP graphical genotypes for a series of European (Photo by Claire Hebbard, nomes of hexaploid wheat. in barley genetics has come barley lines clustered by their similarity at 7H Gramene) One of the first major devel- from the development of a high telomeric markers, using the GVT Java applica- throughput SNP platform for tion (http://germinate.org.uk/) International Barley Sequencing Consortium (IBSC) (http://barleygenome. barley based on the Illumina org/) members: Golden Gate Assay (Proc Australian Centre for Plant Functional Genomics (ACPFG), AUS; USDA-Agri- Natl Acad Sci USA (Figure 2) Article and images contribut- cultural Research Service (USDA-ARS) at Iowa State University, USA; Leibniz 103:18656–18661). This high ed by Dr David Marshall, Genetics Institute of Plant Genetics and Crop Plant Research (IPK), DEU; National throughput SNP platform Programme, SCRI. Invergowrie, Institute of Agrobiological Sciences (NIAS), JPN; Okayama University (OU), will provide barley research- Dundee, DD6 5DA Scotland. JPN; Scottish Crop Research Institute (SCRI), GBR; MTT Agrifood Research ers around the world with a [email protected] unique integrated mapping (MTT) & University of Helsinki (UH), FIN Check out these educational resources: High School Outreach WheatCap http://maswheat.ucdavis.edu/education/ RiceCap http://www.ricecap.uark.edu/outreach.htm Encouraging the next generation Dolan DNA Learning Center http://www.dnalc.org/home.html An exciting part of working at a University is to do out- reach to local schools and to get kids excited about science. crops, all with larger genomes than rice. Teachers commented For the past 5 years about feedback from the students on the the McCouch Rice presentation. “They are always amazed Lab group from by her (McCouch’s) presentation, because Cornell (http:// they have not previously been forced to ricelab.plbr.cornell. see food and water as a privilege.” edu/) has worked The students learned about techniques with three upstate that molecular biologists and geneticists NY schools to bring use in their labs everyday to try to solve equipment, re- some of the problems that the world is sources and experi- facing. This challenge was accepted Susan McCouch teaching rice genomics to high school students. enced researchers by grinning students, who froze and into the classroom to benefit their students taking the Living crushed plant leaves in liquid nitrogen and used finely cali- Environment course, usually students in 9th or 10th grade. Once brated pipettes to measure DNA into the agarose gel plates. again, early in May, Dr. Susan McCouch worked with students Their interest was obvious as they asked questions about how who participated in two laboratory exercises - DNA extraction genomics and biotechnology affect them. A student from one and gel electrophoresis – that helped them to understand the school stated, “That was cool, everything we did in lab I saw on biological concepts behind modern DNA testing procedures. CSI (a television drama) last week.” A ninth grader said “I’m go- The teachers participate because students get the oppor- ing to go home and tell my father about this, and he isn’t going tunity to do college level activities while gaining insight into to believe it!” Some students also had the option to grow a rice future roles that science plays in the world. Traditionally the plant and to view a rice flower under a microscope. concepts of genomic DNA are taught to high school students in One of the senior teachers said that guest presenters are abstract form – through discussion and reading. “This lab allows important in order to keep the students’ interest. His comment, the students to apply it in real life, to understand the process, “There are so many job opportunities in science . When you and to work with tools that are otherwise unavailable to them,“ tell kids about them they don’t ‘get it’, but when they see it they one teacher reported. “It also allows them to interact with pro- get excited,” proved true as many students remarked that grind- fessionals in the field - to ask them about their experiences and ing rice leaves and using pipettes was fun, and they were inter- get answers to questions they have about working in a lab.” ested in doing further laboratory work. Another teacher had his McCouch captivated students as she set the background for students participate in the event because “This class puts it all the lab work. She told of how rice and rice genomics together – taking are crucial to addressing the challenges facing the the different con- world today. Although agricultural grain production cepts and units has more than tripled since 1945, the world popula- that we teach tion growth has outgrown grain production. And and putting them many of the world’s poorest people consume the into one lab.” less nutritional white rice because it uses less fuel for McCouch and cooking and has better storage characteristics in hot her laboratory moist climates. With over 250,000 germplasm acces- staff - includ- sions of rice available to researchers, the genomic ing graduate diversity from these varieties can be used to breed students - plan rice cultivars adaptable to a wide range of environ- A student pipettes DNA into an agarose gel as Prof. McCouch, Mr Knight (principal) and Mrs Krichbaum-Stenger (teacher) observe. on continuing ments and with better nutritional quality and higher to offer this lab yield production. For example, in Africa flooded rice fields would experience to the local schools, and are looking forward to new harbor diseases such as malaria – which is the number -one students and new experiences next year. killer of children under the age of five, so current work is on de- veloping better varieties for the production needs of Africa. Im- Share your lab experiences here. Send them to provements in rice can also direct improvements in other cereal the GrameneNews editor at [email protected] Upcoming Outreach: Gramene FAQ Gramene will be at these upcoming meetings. Contact Gramene through the “Feedback” link at the top of any page to ask ques- You may attend these workshops and post- tions. Here are some recent questions that have been answered. ers to learn about Gramene or get answers to questions. See the Calendar below for dates and locations.
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