系统的介绍了水稻一生。非常实用。

实验室全体同仁：
和谐社会，节约为先。节约当从小事做起，从身边事做起。生物信息小组通过认真观察并对本室电脑进行随机抽样，结果显示很多电脑的电源管理设置不尽合理，一定程度上造成了电力的浪费。经过研讨，本着“节约能源，不浪费资源”的原则，我们提出如下倡议：电脑电源使用“最少电源管理”方案，并设置显示器自动关闭时间为5分钟，系统待机时间为15分钟。
具体操作如下（限于Microsoft Windows系列操作系统）：
http://www.ncpgr.cn/proposal.pdf

此外，生物信息小组开发了可以使显示器立即进入节能模式的小程序“CloseMonitor”，欢迎大家下载使用：http://www.ncpgr.cn/closemonitor.exe 。

生物信息小组
2006年2月28日

Nature 436, 793-800 (11 August 2005) | doi: 10.1038/nature03895

The map-based sequence of the rice genome

International Rice Genome Sequencing Project *

Top of pageAbstractRice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

Affiliations for participants: National Institute of Agrobiological Sciences/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), 500 Caobao Road, Shanghai 200233, China
Centre National de Séquençage, INRA-URGV, and CNRS UMR-8030, 2, rue Gaston Crémieux, CP 5706, 91057 EVRY Cedex, France
UMR PIA, Cirad-Amis, TA40-03 avenue Agropolis, 34398 Montpellier Cedex 05, France
Department of Plant Sciences, BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, USA
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11723, USA
Institute of Botany, Academia Sinica, 128, Sec. 2, Yen-Chiu-Yuan Rd, Nankang, Taipei 11529, Taiwan
National Cheng Kung University, No. 1, Ta-Hsueh Road, Tainan 701, Taiwan
National Yang-Ming University, 155, Sec. 2, Li-Nong St, Peitou, Taipei 112, Taiwan
Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India
Waksman Institute, Rutgers University, Piscataway, New Jersey 08854, USA
National Institute of Agricultural Science and Technology, RDA, Suwon, 441-707 Republic of Korea
Rice Gene Discovery Unit, Kasetsart University, Nakron Pathom 73140, Thailand
Centro de Genomica e Fitomelhoramento, UFPel, Pelotas, RS, l 96001-970, Brazil
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
Washington University Genome Sequencing Center, 3333 Forest Park Boulevard, St. Louis, Missouri 63108, USA
University of Wisconsin, Department of Horticulture, Madison, Wisconsin 53706, USA
University of Wisconsin, Department of Plant Pathology, Madison, Wisconsin 53706, USA
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan
Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
Plant Breeding Dept, Cornell University, Ithaca, New York 14850-1901, USA
Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montreal, Quebec H3A 1B1, Canada
Department of Biology, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
Biometrics and Bioinformatics Unit, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
List of participants and affiliations appear at the end of the paper*
Correspondence to: Correspondence and requests for materials should be addressed to Takuji Sasaki (Email: ). The genomic sequence is available under accession numbers AP008207−AP008218 in international databases (DDBJ, GenBank and EMBL).

Received 29 December 2004; Accepted 25 May 2005


Supplementary information can also be downloaded.

2004年SCI期刊影响因子列表，给大家作为投稿时的参考。

Article
Nature 434, 980-986 (21 April 2005) | 10.1038/nature03449

The genome sequence of the rice blast fungus Magnaporthe grisea

Ralph A. Dean1, Nicholas J. Talbot2, Daniel J. Ebbole3, Mark L. Farman4, Thomas K. Mitchell1, Marc J. Orbach5, Michael Thon3, Resham Kulkarni1,12, Jin-Rong Xu6, Huaqin Pan1, Nick D. Read7, Yong-Hwan Lee8, Ignazio Carbone1, Doug Brown1, Yeon Yee Oh1, Nicole Donofrio1, Jun Seop Jeong1, Darren M. Soanes2, Slavica Djonovic3, Elena Kolomiets3, Cathryn Rehmeyer4, Weixi Li4, Michael Harding5, Soonok Kim8, Marc-Henri Lebrun9, Heidi Bohnert9, Sean Coughlan10, Jonathan Butler11, Sarah Calvo11, Li-Jun Ma11, Robert Nicol11, Seth Purcell11, Chad Nusbaum11, James E. Galagan11 and Bruce W. Birren11

Abstract
Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.

1. Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA
2. School of Biological and Chemical Sciences, University of Exeter, Washington Singer Laboratories, Exeter EX4 4QG, UK
3. Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
4. Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546, USA
5. Department of Plant Pathology, University of Arizona, Tucson, Arizona 85721, USA
6. Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
7. Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JH, UK
8. School of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea
9. FRE2579 CNRS-Bayer, Bayer Cropscience, 69263 Lyon Cedex 09, France
10. Agilent Technologies, Wilmington, Delaware 19808, USA
11. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
12. *Present address: RTI International, Research Triangle Park, North Carolina 27709, USA
Correspondence to: Ralph A. Dean1 Correspondence and requests for materials should be addressed to R.A.D. ( Email: ). The whole-genome shotgun data has been deposited at GenBank/EMBL/DDBJ under the project accession number AACU00000000.

Received 4 November 2004; Accepted 7 February 2005

Letters to Nature
Nature 435, 95-98 (5 May 2005) | 10.1038/nature03480

Epistasis and balanced polymorphism influencing complex trait variation
Juergen Kroymann1 and Thomas Mitchell-Olds1

Complex traits such as human disease, growth rate, or crop yield are polygenic, or determined by the contributions from numerous genes in a quantitative manner. Although progress has been made in identifying major quantitative trait loci (QTL), experimental constraints have limited our knowledge of small-effect QTL, which may be responsible for a large proportion of trait variation1, 2, 3. Here, we identified and dissected a one-centimorgan chromosome interval in Arabidopsis thaliana without regard to its effect on growth rate, and examined the signature of historical sequence polymorphism among Arabidopsis accessions. We found that the interval contained two growth rate QTL within 210 kilobases. Both QTL showed epistasis; that is, their phenotypic effects depended on the genetic background. This amount of complexity in such a small area suggests a highly polygenic architecture of quantitative variation, much more than previously documented4. One QTL was limited to a single gene. The gene in question displayed a nucleotide signature indicative of balancing selection, and its phenotypic effects are reversed depending on genetic background. If this region typifies many complex trait loci, then non-neutral epistatic polymorphism may be an important contributor to genetic variation in complex traits.

Max Planck Institute for Chemical Ecology, Department of Genetics & Evolution, Hans-Knoell-Str. 8, D-07745 Jena, Germany
Correspondence to: Juergen Kroymann1 Correspondence and requests for materials should be addressed to J.K. ( Email: ). Sequence data are deposited at EMBL under accession numbers AJ864968−AJ864998.

Received 22 November 2004; Accepted 17 February 2005

Structure of linkage disequilibrium and phenotypic associations in the maize genome
David L. Remington*, Jeffry M. Thornsberry*, Yoshihiro Matsuoka, Larissa M. Wilson*, Sherry R. Whitt*, John Doebley, Stephen Kresovich, Major M. Goodman? and Edward S. Buckler IV*,?
Departments of * Genetics and ?Crop Science, North Carolina State University, Raleigh, NC 27695-7614; Department of Genetics, University of Wisconsin, Madison, WI 53706; and Department of Plant Breeding, Cornell University, Ithaca, NY 14853

Contributed by Major M. Goodman, July 27, 2001

Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance (r2 < 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial selection on flowering time may have played a role in generating population structure. Provided the effects of population structure are effectively controlled, this research suggests that association studies show great promise for identifying the genetic basis of important traits in maize with very high resolution.


--------------------------------------------------------------------------------
?To whom reprint requests should be addressed. E-mail:

www.pnas.org/cgi/doi/10.1073/pnas.201394398

Linkage Disequilibrium Mapping of Arabidopsis CRY2 Flowering Time Alleles
Kenneth M. Olsen*, Solveig S. Halldorsdottir*, John R. Stinchcombe, Cynthia Weinig, Johanna Schmitt and Michael D. Purugganan*,1
* Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108

1 Corresponding author: Department of Genetics, Box 7614, 3513 Gardner Hall, North Carolina State University, Raleigh, NC 27695.
E-mail:

The selfing plant Arabidopsis thaliana has been proposed to be well suited for linkage disequilibrium (LD) mapping as a means of identifying genes underlying natural trait variation. Here we apply LD mapping to examine haplotype variation in the genomic region of the photoperiod receptor CRYPTOCHROME2 and associated flowering time variation. CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene; in addition, a haplotype possessing a radical glutamine-to-serine replacement (AS) occurs within the more common haplogroup. Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering. Data from six genes flanking CRY2 indicate that these haplogroups are limited to an 65-kb genomic region around CRY2. Whereas the B haplogroup cannot be delimited to <16 kb around CRY2, the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype. This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.

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