Rice Genetics IV - IRRI books - International Rice Research Institute

ice genome sequencing to organize an international collaborative project to decodethe sequence in an accelerated manner encompassing strict sequencing standards commonto all participating members (Sasaki and Burr 2000). At the beginning of IRGSP,five countries, Japan, the United States, the United Kingdom, China, and Korea, joinedtogether to discuss and agree upon guidelines on sequence standards, chromosomesharing, and so on. An in-depth description of the rules governing the collaboration isavailable on the Web at http://rgp.dna.affrc.go.jo/Seqcollab.html. The main points ofthese guidelines are summarized as follows: (1) japonica rice variety Nipponbare issequenced as a common DNA resource, (2) the sequencing strategy is clone-by-cloneusing a PAC/BAC library shared among IRGSP members, (3) accuracy of the sequencemust be 99.99%, (4) each member has a mandate to sequence at least 1 Mb peryear, and (5) sequence data will be released immediately to the public after the completionof sequencing. As of September 2000, a total of 102 PACs/BACs had been completelysequenced in the IRGSP, covering about 15 Mb of the rice genome. An additional100 PACs/BACs covering another 15 Mb have also been sequenced althoughseveral gap regions remain to be filled.Thus far, at most 10% of the rice genome has been sequenced. How can we acceleratecomplete sequencing under limited financial support? Sequencing can be enhancedwith funding support from sources other than IRGSP. In April 2000, a privatecompany, Pharmacia/Monsanto, announced the delivery of its rice genomic sequences,BAC clones, and other related data to IRGSP. The data have been generated for a projectto produce a rough draft sequence of the rice genome using rice variety Nipponbare.Two key points are expected to complement the IRGSP sequencing strategy: one is toconstruct a sequence-ready BAC/PAC physical map; the other is to supply shotgunsequence data for each target BAC. An agreement to combine both sets of data fromIRGSP and Pharmacia/Monsanto is under negotiation. Although key issues surroundingthe merging of data remain to be resolved, a blueprint of the rough draft sequenceof the rice genome should enhance early completion of the sequencing project.ReferencesBaba T, Katagiri S, Tanoue H, Tanaka R, Chiden Y, Saji S, Hamada M, Nakashima M, OkamotoM, Hayashi M, Yoshiki S, Karasawa W, Honda M, Ichikawa Y, Arita K, Ikeno M, Ohta T,Umehara Y, Matsumoto T, de Jong PJ, Sasaki T. 2000. Construction and characterization ofrice genomic libraries: PAC library of japonica variety Nipponbare and BAC library ofindica variety Kasalath. Bull. NIAR 14:24-36.Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY,Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, KhushGS, Sasaki T. 1998. A high-density rice genetic linkage map with 2275 markers using asingle F 2 population. Genetics 148:479-494.Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ,Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP. 1999.‘Green Revolution’ genes encode mutant gibberellin response modulators. Nature 400:256-261.The International Rice Genome Sequencing Project: . . . 195