TITLE: Probe Newsletter(complete), January-June 1993, Vol. 3, No. 1/2
PUBLICATION DATE: June, 1993
ENTRY DATE: November, 1994
EXPIRATION DATE: None
UPDATE FREQUENCY: As needed
CONTACT: Plant Genome Data and Information Center
pgenome@nalusda.gov
DOCUMENT TYPE: Text
DOCUMENT SIZE: 57K
Table of Contents
USDA's High Priority Commitment to the Plant Genome Research Program.....1
Progress Reported at the Forest Tree Genome Mapping Workshop.............4
China's Rice Genome Research Program.....................................7
In Memoriam, Dr. Robert Warmbrodt........................................5
SuperGene(tm) Software Assists DNA Marker Analysis Via Graphical Display.9
New Service From National Center for Biotechnology Information...........12
Calendar of Upcoming Genome Events.......................................13
Introducing Dr. Ed Coe...................................................17
A Celebration of the Life of Dr. Barbara McClintock......................18
Genome Conservation Highlighted at Plant Genome I Conference.............21
USDA's High-Priority Commitment to the Plant Genome Research Program
Dr. Duane Acker
Former Assistant Secretary for Science and Education
U.S. Department of Agriculture
Washington, DC
The U.S. Department of Agriculture (USDA) is committed to the Plant Genome Research Program. The efficiency and effectiveness of the program during its first 2 years of existence have demonstrated the worthiness of the Department's scientific and financial investments.
The Plant Genome Research Program ranks as one of the most important research program areas in USDA. Achievement of the program's goals will have significant, long-term impacts on improving the quality, productivity, and other characteristics of plants and their products.
The program will provide essential information that will help us keep moving forward with improvements in crops. In some crops, such as corn, soybeans, and wheat, we may be approaching the limits of improvement we can make based on traditional breeding and our current knowledge of the crop.
We must make more rapid progress in adapting major crops and their products to the needs and desires of both U.S. and foreign processors and consumers. In addition, by the year 2050 the world's population will double, and agriculture will be faced with providing an adequate food supply for an additional 5 billion people, while the land available for agriculture will be decreasing.
Genome map data will allow plant breeders, both traditional and those in molecular biology, to combine their efforts and make more rapid and more predictable progress in their important work. This efficiency can only come as the result of developing a precise description of the gene structure and the traits controlled--information that will reduce the long and difficult task of selective breeding.
We believe that indepth, coordinated research on the genomes of the agronomically important crops is vital to insuring the future food supply of the United States and the world.
It is especially important that work on plant genomes be a cooperative effort among Federal, university, and industry scientists, fostering an exchange of information and results. Communication and cooperation are essential. AResources are too tight now to allow for duplicative research--for the wheel to be re-invented again and again.
HIGH PRIORITY DESIGNATION
Research priorities for USDA are the result of a consultative process involving 33 public and private organizations and agencies. AProblems and opportunities that should be considered for priority designation are identified by producers, consumers, scientists, educators, and professional societies.
These items are then evaluated and ranked by the Joint Council, in collaboration with the Research and Extension Users Advisory Board, and suggestions for high priority designation are sent to the Secretary of Agriculture.
In May 1992, 21 areas were assigned a high priority designation for fiscal year 1993. This list included plant genome mapping and genetic enhancement. "New knowledge about the molecular and cellular processes of animal and plant inheritance is the key to developing new products and to enhancing the safety and nutrition of food," according to the Joint Council report on research priorities.
In addition, results from the Plant Genome Research Program identify genes that control tolerance to an insect pest, then crops with more insect resistance can be developed. AWith such resistant crops, the need for pesticide application will be reduced, and the possibility of pesticide runoff into groundwater will be lessened. Water quality will be easier to maintain or enhance.
Results from the program will also have a ripple effect, helping to improve rural economies as higher value crops with more potential for processing are developed.
USDA COMMITMENT
To date, USDA has allocated a budget of $14.7 million in fiscal year 1991 and $15 million in fiscal year 1992; we are anticipating a funding level of $18 million for fiscal year 1993.
As an additional sign of USDA's commitment to the Plant Genome Research Program, Dr. Jerome Miksche's appointment as Director of the Plant Genome Research Initiative has been changed from a part-time to a full-time program officer position for the National Research Initiative Competitive Grants Program.
And the National Agricultural Library, with $2.38 million in interim funding from the Agricultural Research Service, has taken the lead in making the vast amount of information being developed available through computer database systems.
The Plant Genome Research Program has received authorization for 5 years of support. In 1996, at the close of those 5 years, the program will be evaluated and a report made to the Secretary of Agriculture and the Congress of the progress made to that point.
Re-authorization will depend on the program having achieved tangible results. The Plant Genome Research Program is mission oriented. While basic research is important and technique development is essential, the program must remain focused on economically important traits of crops. Currently, research in this program is addressing agronomic traits in more than 40 crop and tree species.
The impetus for the continuation of the program will come from the successful isolation and transfer of genes that control such traits and their regulatory systems; the development of new gene mapping, sequencing, and automation systems; and the implementation of a national and international database on genetic information.
The clear exchange of information and the prevention of research duplication will also help ensure the re-authorization of the program. The cooperation of the four USDA agencies directly involved in this program-- Agricultural Research Service, Cooperative State Research Service, National Agricultural Library, and Forest Service--has been excellent. Such cooperation must continue and increase.
Cooperation and coordination between this program and the Human Genome Project at the National Institutes of Health and the Department of Energy have also enhanced the productivity and efficiency of both projects. There has been a practical interchange of information on new technologies and basic genomic research data.
In the short time--just 2 years--that the NRI Plant Genome Competitive Grants Program has been under way, the identification and mapping of some insect and plant disease resistance gene systems are already nearing the point where they can be tested by breeders.
This bodes well for the effectiveness of a targeted competitive grants approach to solving difficult, critical agricultural problems.
ASCB Newsletter --A Special Education Issue
The July 1993 issue of the ASCB Newsletter will be devoted to educational activities of the American Society for Cell Biology. This issue will included special features on:
A new ASCB Cell Biology teaching video that will be featured at the 1993 Annual Meeting.
Examples of local educational programs throughout the country.
The Coffee Break Forums during the ASCB Annual Meeting.
CELS and AAAS Symposiums.
The ASCB Summer Teacher Fellowship Program.
Details about the new Education and Minority Affairs Committees exhibit booth at the ASCB 1993 Annual Meeting in New Orleans, December 11-15, 1993.
For more information on how to obtain this ASCB Newsletter, write to the American Society for Cell Biology, 9650 Rockville Pike, Bethesda, Maryland. 20814-3992
Progress Reported at Forest Tree Genome Mapping Workshop
Dr. David B. Neale
Molecular Geneticist
Institute of Forest Genetics
USDA, Forest Service
Albany, CA
Forest trees present many unique and interesting challenges for researchers constructing genetic maps. For example, in forest trees, inbreeding is generally not possible, multigeneration pedigrees are rare, generation times are long, genome sizes are large, and resources are limited.
Recently forest tree genome researchers met to discuss approaches to mapping in trees and to report on the progress of various mapping projects. The meeting was the first Forest Tree Genome Mapping Workshop, one segment of the Plant Genome I Conference held in San Diego, CA. Approximately 80 persons attended the workshop, organized by David Neale (Institute of Forest Genetics, Albany, CA). Fourteen invited speakers participated.
Progress Reports
The workshop opened with a progress report by Toby Bradshaw (University of Washington) on the mapping of Populus (P. trichocarpa x P. deltoides). The map will be used to identify quantitative trait loci (QTL) infuencing growth and form characteristics. Bradshaw noted that severe segregation distortion was observed at one locus, which was attributed to a recessive lethal allele in the P. trichocarpa female parent.
Dario Grattapaglia (North Carolina State University, presented by Ron Sederoff) reported on a 548 RAPD marker map in hybrid Eucalyptus (E. grandis x E. urophylla) based on a pseudo-testcross mapping strategy. This approach avoids the loss of information associated with dominant markers in diploid mapping populations. Andrew Groover (Institute of Forest Genetics) presented preliminary results on the mapping of QTL's influencing wood specific gravity in a 3-generation loblolly pine (Pinus taeda) pedigree.
In another presentation, John Carlson (University of British Columbia) reported on RAPD mapping in white spruce (Picea glauca) and localization of rDNA loci using fluorescence in situ hybridization (FISH). Michael Devey (Institute of Forest Genetics and CSIRO) reported on a novel method to map a dominant gene for resistance to white pine blister rust (Cronartium ribicola) in sugar pine (Pinus lambertiana). His strategy employed bulked segregation analysis of haploid megagametophytes from a mother tree heterozygous for the dominant resistance gene. Ten RAPD markers were very closely linked to the resistance gene.
In addition, Keith Hutchison (University of Maine) described the method of single-stranded conformational polymorphism of RAPD fragments to reveal codominant markers in larch and a method to detect variation by PCR from single pollen grains. Warren Nance (Forest Service) reported on the construction of RAPD maps in slash pine (Pinus eliottii) and automation technology for large-scale mapping projects. David O'Malley (North Carolina State University) presented a RAPD map for loblolly pine based on haploid segregations from a single mother tree. A method to map QTL's in open-pollinated families was also presented. Dave Harry (Institute of Forest Genetics) described approaches to developing codominant PCR-based markers for trees to avoid the limitations imposed by RFLP's and RAPD's. Gavin Moran (CSIRO) reported on mapping in Monterey pine (Pinus radiata) and Eucalyptus nitens in Australia.
Statistical Problems
The second part of the workshop addressed statistical problems specifically related to linkage mapping, QTL mapping, and marker breeding in forest trees.
Steve Knapp (Oregon State University) discussed linkage mapping in outbreeding populations; Tom Mitchell-Olds (University of Montana) addressed similar issues related to QTL mapping. Claire Williams (Weyerhaeuser Company) described how molecular marker information might be incorporated into a loblolly pine breeding program.
Database Development
The last part of the workshop focused on the development of a genome database for forest trees. Brad Sherman (Institute of Forest Genetics) presented an on-line demonstration of APtDB, A Pinus taeda database. He showed how forest tree genome researchers could contribute data to the database and how it could be accessed by users through the Internet.
1994 Workshop
Plans are underway to hold a second workshop at the Plant Genome II meeting in early 1994. Low-density maps have just been completed for a few of the major species. It is expected that by the next meeting many more maps will have been completed, QTL's for important traits will have been identified, and numerous other applications of molecular markers and maps will be commonplace in forest genetics research.
In Memoriam, Dr. Robert Warmbrodt
On December 15, 1992, the National Agricultural Library (NAL) regretfully learned of the death of Dr. Robert Warmbrodt, who had been coordinator of the NAL's Biotechnology Information Center since December 17, 1990. Dr. Warmbrodt, 45, died of AIDS-related complications. Memorial services and interment were held by his family in Missouri.
Dr. Warmbrodt had been a plant physiologist with 20 years of professional experience prior to joining the staff of NAL. He had conducted laboratory research in the Climate Stress and the Plant Physiology Laboratories at the Agriculture Research Service, Beltsville Agricultural Research Center from 1978-90. His primary interests concerned the cellular and molecular aspects of photosynthate partitioning.
A native of Boonville, Missouri, Dr. Warmbrodt had an AB degree in botany and chemistry from the University of Missouri-Columbia, and a master's degree in botany and a Ph.D in botany and horticulture, both from the University of Wisconsin-Madison. He also was an Alexander von Humboldt Fellow at the University of Go”ttingen in G”ttingen, Germany.
Dr. Warmbrodt's other work experience included research in horticulture at the University of Maryland-College Park and in botany at the University of Wisconsin-Madison; teaching assignments in botany at Ohio State UniversityColumbus and the University of Wisconsin-Madison; and a year collecting plants in Panama and Costa Rica for the Missouri Botanical Gardens.
As Coordinator of the Biotechnology Information Center, Dr. Warmbrodt managed the acquisition, compilation, and dissemination of information on the impact of the science of biotechnology on agriculture in the United States and the world. He was concerned with all aspects of agricultural biotechnology as well as the theory and techniques of genetic engineering, plant and animal tissue culture, risk assessment of the release of genetically-engineered organisms, and regulation of the field of biotechnology. He authored or coauthored numerous NAL publications, particularly in the two series Quick Bibliographies and Bibliographies and Literature of Agriculture.
China's Rice Genome Research Program
Guo-Fan Hong
Head, Rice Genome Research Program
Shanghai Institute of Biochemistry
Academia Sinica
Shanghai, China
The Chinese Rice Genome Research Program (RGP) is one effort initiated to help modernize China's agriculture. China possesses the largest rice-producing land area in the world--rice output accounts for about half of the country's total grain yield.
China has a long history in rice cultivation and accumulated experiences in breeding. The results obtained from RGP will be applied to plant breeding. New concepts derived from the research should prove useful in improving one's understanding of the plant life phenomena as a whole.
RESEARCH AREAS
The mapping and sequencing of the entire rice genome is expected to be completed in about 15 years, so that the complex genetic machinery of the entire genome would be elucidated at the DNA level.
The extent to which the DNA sequences will be determined will depend on the degree of development in related fields of technology. Currently research is focused on the following:
(1) Isolating, characterizing, and sequencing genes of biological importance;
2) Characterizing and mapping agronomically important genes, and applying the results to breeding when possible;
(3) Constructing an ordered set of genomic DNA clones, used toconstruct physical and genetic maps of the chromosomes;
(4) Elucidating the mechanisms for coordinated and programmed gene expression; and
(5) Establishing an internationally connected computer center.
GENE RESEARCH MOSAIC
Under the State Commission of Science and Technology (SCST) the scientific board that directs RGP was established. Consigned by SCST, the Chinese Academy of Sciences will establish a National Center for Gene Research (NCGR) in Shanghai. NCGR's primary responsibilities will be as follows:
(1) Carrying out the RGP in full scale, and
coordinating research activities nationwide;
(2) Collecting materials and analyzing data;
(3) Providing quality control; and
(4) Organizing scientific meetings and promoting
international academic exchange.
SATELLITE LABORATORIES
In addition to NCGR, five satellite laboratories will be assigned research tasks based on their respective expertise. These laboratories are located in the Institute of Genetics, the Chinese Academy of Sciences; Beijing University; Hua-Zhong Agricultural University; Fudan University; and the National Rice Institute.
FUNDING
Approximately $4 million (23 million yuan) has been allocated by the Chinese government to support the program for the first 5 years. During this period, some adjustments may be made to meet new development requirements.
COLLABORATIVE EFFORT
Participants in RGP anticipate international collaboration and hope to share their research results with interested scientists worldwide.
For more information, contact the Shanghai Institute of Biochemistry, Academia Sinica, 320 Yue-Yang Road, Shanghai, 200031 China. Phone: +86-21-4374430; FAX +86-21-4338357.
SupergeneTM Software Assists DNA Marker Analysis Via Graphical Display
Drs. Sam Boutin and Nevin Young,
Department of Plant Pathology,
University of Minnesota, Minneapolis; and
Dr. Randy Shoemaker, USDA, Agricultural Research Service,
Department of Agronomy, and Dr. Lisa Lorenzen,
Department of Zoology and Genetics; Iowa State University, Ames
Genomic analysis based on DNA genetic markers leads to vast amounts of information. This information can be stored in various ways, including spreadsheets and databases, and presented in a multitude of different text or graphical displays.
Graphical display allows for rapid visualization of data and can potentially simplify interpretation. One example is the display of linkage maps and pedigrees derived from DNA marker studies in a color graphic format. Such graphical images give a powerful visual overview of the genetic relationships between individuals in a single population or between varieties in a species.
SUPERGENETM
A recently developed computer software package, SupergeneTM was developed to assist in DNA marker analysis using graphical display. SupergeneTM converts DNA marker data into a color graphic format and gives the user the ability to (1) draw a graphical genotype for a selected individual, (2) draw a single linkage group for many selected individuals, and (3) draw a DNA-based pedigree to or from a genotype.
SupergeneTM enables genetic comparisons on a macro level by comparing whole genomes, as well as more focused comparisons, such as linkage groups. In a graphical genotype, each portion of the genome is drawn to scale based on genetic distance between markers. The region around each marker is colorized according to the DNA genotype. Finally, for DNA marker-based pedigrees, a graphical image for each linkage group (or genome) is simultaneously displayed for a selected individual, its parents, and grandparents.
Interesting genomic regions, such as those that may carry desirable genes, can be highlighted in the graphical genome representations. This should be helpful in breeding programs for selecting individuals based on genotype and in monitoring the DNA genotypes of progeny individuals.
USING SUPERGENETM
SupergeneTM can be used in the analysis and comparison of any type of genome. For studies in plants, it has been used to detect differences and similarities in the genomes of various cultivars, plant introductions, and their progeny. SupergeneTM allows the user to list various genotypes, their parents, their loci, map location, and their DNA marker scores in a table. The user can then view a graphical representation of an individual's genome, a side-by-side linkage group comparison between individuals or varieties, and graphical displays of the pedigree for a single linkage group or entire genome.
WHAT YOU SEE: DATA TABLE
When SupergeneTM is first started, a data table containing individual names, DNA marker names, DNA marker loci, parent names, and numerical genotype scores is displayed on the screen. This information can be entered manually, but would be imported from a spreadsheet program. Figure 1 illustrates a typical data table.
The first column of the table contains the genotypes, the second and third columns contain the names of parent lines, and the remaining columns contain the scores for the genetic markers. The name for each marker and its map location are located at the top of these columns. Presently, the table handles up to 200 markers and 335 individuals.
Genetic marker data identifies the genetic constitution of the genomes at a particular locus. If the genomes of the two different individuals are the same at a locus, the score is the same. When the genomes differ at the same locus, the scores differ. With the types of DNA markers currently in use (RFLP and RAPD's), only two alternate alleles are often observed at each locus for inbred crop species. Improved and more polymorphic DNA markers are likely to show several alleles available at a single locus. SupergeneTM can handle several alleles at the same locus through the use of different colors.
The user can then display the desired graphic via the Graphics menu. These displays include the entire genome, single linkage group comparison (Fig. 2), linkage group pedigree (Fig. 3), and genome pedigree.
GENOME DISPLAY
The Create Map command illustrates all the linkage groups of an individual genome with their loci colorized according to their numerical genotype score. After the individual's name is entered, the software draws each linkage group, labels the loci, and colorizes the loci according to the score.
SINGLE LINKAGE GROUP DISPLAY
Often a side-by-side comparison of the same linkage group from different individuals is desired (Fig. 2). When the Single Linkage Group command in the Graphics menu is selected, the user is prompted for the linkage group number to be drawn. The software draws the same linkage group for all individuals listed in the table. The same locus on the same linkage group among different individuals can be compared by color.
LINKAGE PEDIGREE DISPLAY
A comparison of the same linkage group among ancestors of a particular individual is often desired (Fig. 3). The Linkage Pedigree command under the Graphics menu prompts the user for an individual name. The software draws the pedigree for the individual, the parents, and grandparents that reside in the table. The same locus on the same linkage group from different ancestors can be compared, since each allele is a different color. The inheritance of that locus through the pedigree can be followed.
Genome Pedigree Display
If a macroscopic comparison of all the genomes in a pedigree is desired, the Genome Pedigree command can be used. The user is again prompted for the individual; the software then draws out the genome for that desired individual, its parents, and grandparents in a pedigree format. All the linkage groups for each individual in the pedigree can then be compared.
Macro and Micro Views
Since both macro and micro views of the genome and linkage groups are of interest, SupergeneTM allows for scaling the various graphics. The user has the option of selecting a scaling factor. This allows for squeezing as much into the display as possible or expanding the view so that markers only a few centimorgans apart can be resolved.
What SupergeneTM Isn't
The purpose of SupergeneTM is to transform data into useful graphical images rendering genetic information. The software does not have sophisticated graphics or spreadsheet capability. However, many packages are available on the market for users who desire additional manipulation of the graphics or data.
The data should be manipulated in a spreadsheet prior to importing it into SupergeneTM; additional detail should be added to the graphics by copying the drawings and pasting them into a graphics application. Significantly, the graphics output are "draw" objects (as opposed to "paint" or bit-mapped graphic), so each component of a graphical image can be manipulated individually by a suitable computer software application.
Computer Environment
SupergeneTM is a stand-alone application written in Supertalk,TM a scripting language of Aldus Supercard. SupergeneTM runs on all Macintosh II family computers. However, converting numerical data into graphical images requires considerable processing, so the higher end of the line is strongly recommended. A color display is obviously preferred, but the software draws different patterns for black and white models.
Support
SupergeneTM was supported by a specific cooperative agreement for the USDA, Agricultural Research Service Plant Genome Database Program. This paper is a contribution of the Minnesota Agricultural Experiment Station series on research conducted under Project 015, supported by GAR funds.
Contact
Readers who desire additional information should contact Sam
Boutin via Internet at boutin@molbio.cbs.umn.edu or via FAX (612) 625-9728.
E-Mail Searching of Sequence Databases--
New Service From National Center for Biotechnology Information
Dennis Benson
National Center for Biotechnology Information
National Library of Medicine
Bethesda, MD
The National Center for Biotechnology Information (NCBI), National Library of Medicine, now provides e-mail server access for sequence similarity searching (BLAST) and for record retrieval from sequence databases.
The BLAST e-mail server accepts either a DNA or amino acid query sequence in FASTA format; runs the search against a combined (non-redundant) or a single database; and returns the results in a mail message.
The RETRIEVE e-mail server accepts single or multiple text strings (locus names, accession numbers, keywords, author names, etc.) as queries; runs an IRX search against a specified database; and returns the matching full record(s) as a mail message.
To receive documentation on how to use the servers, send a mail message with the word "help" in the body of the message to:
BLAST server: blast@ncbi.nlm.nih.gov
RETRIEVE server: retrieve@ncbi.nlm.nih.gov
The following BLAST Databases are available:
Peptide Sequence Databases
Name Description
nr Non-redundant protein database
(selected automatically by
blastp; includes SWISS-PROT, PIR,
GenPept, and GenPept updates)
swissprot SWISS-PROT protein database
pir PIR protein database
genpept GenPept (translated GenBank)
gpupdate GenPept update (cumulative daily
updates)
tfd Transcription Factors Database
Nucleotide Sequence Databases Name
Description
nr Non-redundant DNA database
(selected automatically by
blastn; includes GenBank,
GenBank updates, EMBL, and EMBL
updates)
genbank GenBank DNA sequence database
(does not include updates)
gbupdate GenBank update (cumulative
daily updates)
embl EMBL DNA sequence database (does
not include updates)
emblu EMBL update (cumulative weekly
updates)
vector Vector subset of GenBank (LANL)
dbest Database of Expressed Sequence
Tags (EST's)
ADDITIONAL ASSISTANCE
For additional general information, send e-mail to: info@ncbi.nih.gov. For specific information on the operation of the servers, not covered in the documentation, send e-mail to: blast- help@ncbi.nlm.nih.gov or retrieve-help@ncbi.nlm.nih.gov.
Readers may also write to Dennis Benson at The National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894 or contact him by phone on (301) 496-2475 or by e-mail: benson@ncbi.nlm.nih.gov.
Calendar of Upcoming Genome Events
MEETINGS
July 17-24: 5th International Symposium on Genetics and Molecular Biology of Plant Nutrition, Davis, CA. Contact: D.W. Rains, Dept. of Agronomy and Range Science, University of California, Davis, CA 95616-8515. Telephone: (916) 752-1711, FAX: (916) 752-4361
July 18-23: Plant and Fungal Cytoskeleton, Andover, NH. Contact: Dr. Alexander M. Cruickshank, Director, Gordon Research Conferences, ColbySawyer College, New London, NH 03257. Telephone: (603) 526-2870, FAX: (603) 526-4717.
July 24-29: 90th Annual Meeting of the American Society for Horticultural Science, Nashville, TN. Contact: American Society for Horticultural Science, 113 South West St., Suite 400, Alexandria, VA 22314- 2824. Telephone: (703) 836-4606, FAX: (703) 836-2024.
July 25-30: 3rd International Symposium on the Molecular Biology of the Potato, Santa Cruz, CA. Contact: Dr. William Belknap, USDA-ARS, 800 Buchanan St., Albany, CA 94710. Telephone: (510) 559-6072, FAX: (510) 559- 5775, EMAIL: wrb@pw.usda.gov.
July 31-August 4: DNA Damage - Effects on DNA Structure and Protein Recognition, Burlington, VT. Contact: New York Academy of Sciences, Conference Dept., 2 East St., New York, NY 10021. Telephone: (212) 838-0230, FAX: (212) 838-5640.
July 31-August 4: 1993 Joint Meeting of The American and Canadian Societies of Plant Physiologists, Minneapolis, MN. Contact: Dorothy Croft, American Society of Plant Physiologists, 15501 Monona Dr., Rockville, MD 20855-2768. Telephone: (301) 251-0560, FAX: (301) 279-2996.
August 1-6: Photosynthesis: Biochemical Aspects of, New Hampton, NH. Contact: Dr. Alexander M. Cruickshank, Director, Gordon Research Conferences, Colby-Sawyer College, New London, NH 03257. Telephone: (603) 526-2870, FAX: (603) 526-4717.
August 2-4: 44th American Institute of Biological Sciences Annual Meeting, Ames, IA. Contact: AIBS, 730 11th Street NW, Washington, DC 20001- 4521. Telephone: (202) 628-1500, FAX: (202) 628-1509.
August 2-7: 4th Gordon Research Conference on Quantitive Genetics and Biotechnology, Ventura, CA. Contact: University of Minnesota, Dr. F. Enfield, Dept. of Genetics and Cell Biology, St. Paul, MN 55108.
August 4-6: 1st International Symposium on Plant Dormancy, Corvallis, OR. Contact: Dr. G. Lang, Symposium Convenor, 137 Julian C. Miller Hall, Louisiana State Univerrsity, Baton Rouge, LA 70803-2120. Telephone: (504) 388-1043, FAX: (504) 388-1068.
August 6-10: Science Innovation '93: New Techniques in Bimolecular Research, Boston, MA. Contact: AAAS Meetings Office, 1333 H St., NW, Washington, DC 20005. Telephone: (202) 326-6450, FAX: (202) 289-4021.
August 6-9: Plant Growth Regulator Society of America 20th Annual Meeting, St. Louis, MO. Contact: Dr. L. Ferguson, Program Chair, University of California, Kearny Agricultural Research Center, 9240 S. Riverbend Ave., Parlier, CA 93648. Telephone: (209) 891-2500.
August 15-21: 17th International Congress of Genetics, Genetics and the Understanding of Life, Birmingham, UK. Contact: Congressional Secretariat Derek Smith, Research Support and Industrial Liaison, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK. Telephone: (021) 414-5888, FAX (021) 414-3850.
August 19-22: ARABIFLORA: The 5th International Conference on Arabidopsis Research, Ohio State University, Columbus, OH. Contact: Arabidopsis Conference, Conference Unit, The Ohio State University, 225 Mount Hall, 1050 Carmack Rd., Columbus, OH 43210-1002. Telephone: (614) 292-8571, FAX: (614) 292-0492.
September 6-10: Sixth International Conference on Applied Algology, Trebon, Slovak Republic. Contact: Institute of Microbiology, Jiri Doucha, Dept. of Autotrophic Microorganisms, 37981 Trebon, Slovak Republic. Telephone: 42-333-2421, FAX: 42-333-2268.
September 9-10: Down Regulation of Gene Expression by Antisense and Other Technologies Symposium, Ames, IA. Contact: Dr. Cecil Stewart, Dept. of Botany, Iowa State University, Ames, IA 50011. Telephone (515) 294-1063, FAX: (515) 294-1337, EMAIL: sl.sto@isumvs.iastate.edu.
September 12-16: Symposium on Improvement of Cereal Quality by Genetic Engineering: 43rd Australian Cereal Chemistry Conference, Coogee Beach, Sydney, Australia. Contact: Dr. R. Henry, Vice-Chairman Cereal Chemistry Division RACI, Queensland Agricultural Biotechnology Centre, Gehrmann Laboratories, University of Queensland 4067. Telephone: (07) 3654962; FAX: (07) 3654980.
September 13-17: 24th Annual Meeting of the European Society for New Methods in Agricultural Research, Leipzig, Germany. Contact: Wye College, Prof. D.A. Baker, Dept. of Biochemistry, Ashford, Kent TN25 5AH, UK.
September 19-22: 2nd National Symposium on PLANAR CHROMATOGRAPHY: Modern Thin-Layer Chromatography, Research Triangle Park, NC. Contact: Planar Chromatography Symposium Manager, Mrs. Janet Cunningham, Barr Enterprises, P.O. Box 279, Walkersville, MD 21793. Telephone: (301) 898-3772, FAX: (301) 898-5596.
September 27-October 1: DNA Repair and DNA Replication Strategies, St. Johns College, Cambridge, UK. Contact: Dr. R.T. Johnson, Dept. of Zoology, Downing St., Cambridge CB2 3EJ, UK.
October 10-15: Photosynthetic CO2 Fixation and Metabolism in Plants, Irsee, Germany. Contact: Dr. Alexander M. Cruickshank, Director, Gordon Research Conferences, Colby-Sawyer College, New London, NH 03257. Telephone: (603) 526-2870, FAX: (603) 526-4717.
October 11-12: International Conference on Strategic Business Information in Biotechnology, Research Triangle Park, NC. Contact: Institute for Biotechnology Information, North Carolina Biotechnology Center, P.O. Box 13547, Research Triangle Park, NC 27514-3547. Telephone: (919) 549-8880, FAX: (919) 990-952
October 13-16: DNA: The Double Helix - Forty Years: Perspective and Prospective, Chicago, IL. Contact: New York Academy of Sciences, Conference Dept., 2 East 63rd St., New York, NY 10021. Telephone: (212) 838- 0230, FAX: (212) 838-5640.
October 23-27: Genome Sequencing and Analysis Conference V, Hilton Head Island, SC. Contact: Susan Wallace, 932 Clopper Rd., Gaithersburg, MD 20878. Telephone: (301) 216-9567, FAX: (301) 977-7233, EMAIL: TIGR (swallace@bengal.tigr.org).
November 7-10: Electrophoresis '93, Charleston, SC. Contact: Janet Cunningham, Symposium Manager, c/o The Electrophoresis Society, P.O. Box 279, Walkersville, MD 21793. Telephone: (301) 898-3772, FAX: (301) 898-5596.
WORKSHOPS AND COURSES
July 12-16: Protein & Nucleic Acid Separation Techniques, Washington, DC. Contact: Director, Center for Advanced Training in Cell and Molecular Biology, 103 McCort-Ward Bldg., The Catholic University of America, Washington, DC 20064. Telephone: (202) 319-6161, FAX: (202) 319-4467 and (202) 319-5721.
July 29-31: ACEDB Developer's Workshop, Boston, MA. Contact: Mike Cherry, Dept. of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114. FAX: (617) 726-6893, Internet: curator@frodo.mgh.harvard.edu.
August 17-20: Plant Biotechnology Methods, University Park, PA. Contact: Patricia Phillips, Program Coordinator, Penn State Biotechnology Institute, Pennsylvania State University, 519 Wartik Laboratory, University Park, PA 16802-5807. Telephone: 1-800-833-5533, FAX: (814) 863-1357.
September 6-17: Techniques in Molecular Biology - Introductory Workshops in Proteins Nucleic Acids and Microbiology, Hatfield, UK. Contact: University of Hertfordshire, Science Training Centre, College Lane, Hatfield, AL10 9AB, UK. Telephone: (0707) 284 590; FAX: (0707) 284 514.
October 11-14: Recombinant DNA Methodology, Lake Tahoe, NV. Contact: Director, Center for Advanced Training in Cell and Molecular Biology, 103 McCort-Ward Bldg., The Catholic University of America, Washington, DC 20064. Telephone: (202) 319-6161, FAX: (202) 319-4467 and (202) 319-5721
October 11-14: DNA Sequencing, Lake Tahoe, NV. Contact: Director, Center for Advanced Training in Cell and Molecular Biology, 103 McCort-Ward Bldg., The Catholic University of America, Washington, DC 20064. Telephone: (202) 319-6161, FAX: (202) 319-4467 and (202) 319-5721.
October 11-14: PCR Techniques, Lake Tahoe, NV. Contact: Director, Center for Advanced Training in Cell and Molecular Biology, 103 McCort-Ward Bldg., The Catholic University of America, Washington, DC 20064. Telephone: (202) 319-6161, FAX: (202) 319-4467 and (202) 319-5721.
October 12-15: DNA Fingerprinting, Rockville, MD. Contact: American Type Culture Collection, 12301 Parklawn Dr., Rockville, MD 20852- 1776. Telephone: (301) 881-2600, FAX: (301) 231-5826.
November 2-5: Polymerase Chain Reaction/Cycle DNA Sequencing, Rockville, MD. Contact: American Type Culture Collection, 12301 Parklawn Dr., Rockville, MD 20852-1776. Telephone: (301) 881-2600, FAX: 231-5826.
FUTURE EVENTS
January 24-27, 1994: Plant Genome II, San Diego, CA. Contact: Scherago International, 11 Penn Plaza, Suite 1003, New York, NY 10001. Telephone: (212) 643-1750, FAX: (212) 643-1758.
February 7-11, 1994: Comparative Gene Mapping in Terrestrial and Aquatic Vertebrates, Oslo, Norway. Contact: Harris A. Lewin, Dept. of Animal Sciences, University of Illinois, 206 Plant & Animal Biotechnology Laboratory, 1201 W. Gregory Drive, Urbana, Il 61801. Telephone: (217) 333- 5998; FAX: (217) 244-5617; BITNET: BLOOD@UIUCVMD.
May 8-13, 1994: HPLC'94, 18th International Symposium on High Performance Liquid Chromatography, Minneapolis, MN. Contact: Barr Enterprises, P.O. Box 279, Walkersville, MD. Telephone: (301) 898-3772, FAX: (301) 898-5596.
June 19-24, 1994: 4th International Congress of Plant Molecular Biology, Amsterdam, The Netherlands. Contact: Congress Secretariat, c/o RAI Organisatie Bureau Amsterdam bv, Europaplein 12, 1078 GZ Amsterdam, The Netherlands. Telephone: +31 (0)20 549 1212, FAX: +31 (0)20 646 4469, Telex: 13499 raico nl.
July 17-24, 1994: 5th International Symposium on Genetics and Molecular Biology of Plant Nutrition, University of California, Davis, CA. Contact: D.W. Rains, Dept. of Agronomy and Range Science, University of California, Davis, CA 95616-8515. Telephone: (916) 752-1711, FAX: (916) 752- 4361.
August 4-6, 1994: 1st International Symposium on Plant Dormancy, Corvallis, OR. Contact: Dr. G. Lang, Symposium Convenor, 137 Julian C. Miller Hall, Louisiana State University, Baton Rouge, LA 70803-2120. Telephone: (504) 388-1043, FAX: (504) 388-1068.
August 4-6, 1994: Plant Growth Regulator Society of America 21st Annual Meeting, Portland, OR. Contact: Dr. L. Ferguson, Program Chair, University of California, Kearny Agricultural Research Center, 9240 S. Riverbend Ave., Parlier, CA 93648. Telephone: (209) 891-2500.
June 16-21, 1996: HPLC'96, 20th International Symposium on High Performance Liquid Chromatography, San Francisco, CA. Contact: Barr Enterprises, P.O. Box 279, Walkersville, MD. Telephone: (301) 898-3772, FAX: (301) 898-5596.
Introducing Dr. Ed Coe
Dr. Edward (Ed) Coe is a USDA Agricultural Research Service Research Geneticist and Professor of Agronomy at the University of Missouri in Columbia. He has served with USDA at the University for over 37 years.
Dr. Coe works in the Plant Genetics Research Unit where his responsibilities include conducting and supervising research on the genetic mechanisms of maize, the genetic control of plant development, and on homologous genetic systems in plant species. He also nurtures cooperative research efforts on higher plant genetics.
In addition, Dr. Coe is participating in USDA's Plant Genome Research Program efforts to develop and implement a plant genome database system. As chairman of the maize database project, he has been primarily responsible for directing and coordinating the maize database development.
In 1992, Dr. Coe was recipient of the prestigious Thomas Hunt Morgan Medal awarded by the Genetics Society of America. The award was presented to him in recognition of the importance of his basic research, his mentorship of students and postdocs, and his extensive and outstanding service to the maize genetics community. Dr. Coe was described as "the glue that holds the maize community together."
During his career, Dr. Coe has authored and co-authored numerous publications. Since 1975, he has served as editor of the Maize Genetics Cooperation News Letter. For several years, he served as a panel member for genetic mechanisms for USDA's Competitive Grants Program. He is a member of various professional organizations, including the Genetics Society of America, the American Genetic Association, and the Crop Science Society of America.
Prior to coming to Columbia, Dr. Coe was a research fellow in
biological sciences at the California Institute of Technology, Pasadena. He
earned a Ph.D. in botany at the University of Illinois, and received his M.S.
degree in plant genetics and a B.S. degree in agronomy and plant genetics
from the University of Minnesota.
Soybase Newsletter launched
The first issue of the Soybase newsletter was released this spring. The newsletter focuses on Soybase, the USDA Plant Genome Research Program soybean database. Regular features will include:
Update: listings of new data added to Soybase or the Soybean Gopher database.
Bug Report: sightings and fixes of software bugs.
Question and Answer: questions asked of electronic discussion groups and their answers.
Special Report: one topic, discussed in depth. The first issue of Soybase featured XWindow software.
Subscribe by writing to Lisa Lorenzen, G313 Agronomy, Iowa State University, Ames, Iowa 50011, USA, or send an Internet message to "curator@mendel.agron.iastate.edu"
Dr. Thomas Peterson
Senior Staff Investigator
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY
At a recent memorial service to celebrate the life of distinguished geneticist and Nobel laureate Dr. Barbara McClintock, friends and colleagues reminisced about her life and outstanding achievements.
Speakers at the service, held November 17 at Cold Spring Harbor Laboratory in New York, included Howard Green (Harvard Medical School), James Shapiro (University of Chicago), Evelyn Witkin (Rutgers University), V. Sundaresan (Cold Spring Harbor Laboratory), and Oliver Nelson (University of Wisconsin, Madison).
RECOGNITION
Howard Green noted that McClintock's early achievements in maize cytogenetics brought considerable recognition, including election to the National Academy of Sciences (1944) and election to President of the Genetics Society of America (1945). However, McClintock's reports of transposable genetic elements were not readily accepted by her scientific peers until her genetic insights were verified by molecular biologists in the 1970's.
McClintock was recipient of several major awards, including the National Medal of Science (1970), Lasker Prize (1981), MacArthur Foundation Award (1981), and an unshared Nobel Prize (1983). Green commented that McClintock bore these honors with a martyr's resignation, as she was well aware of the impact the attendant publicity would have on her solitary personal and scientific lifestyle.
Green said McClintock never considered science as a career-- instead, she was a prototypic non-careerist. McClintock was interested in a variety of vocations. While working in Missouri, she spent many hours at the local weather bureau. She later indicated that if she had not entered science, she would have pursued meteorology. Green noted that McClintock did not believe that graduate students should be coddled. "Let them sink or swim!" was her motto.
Contributions
James Shapiro (University of Chicago) summarized McClintock's contributions in several areas. In the area of genome structure, McClintock likened the genome to a sophisticated erector set (although she had an intense dislike for models), whose activities were regulated by controlling elements (her term for transposable elements). Although she did not agree with certain evolutionary tenets, she believed that "any organism can make any other." One suspects that this view was sparked by observations of certain maize mutations (eg. Corngrass), which radically alter the plant's appearance. McClintock's view has been confirmed by recent findings of protein domains whose structure and function have been conserved among widely diverged organisms (eg. "Myb"-type DNA binding domains of transcriptional regulatory proteins in plants, animals, and fungi).
Shapiro also stated that in the area of cellular information processing, McClintock wondered how plant cells sense the presence of broken chromosomes and activate the appropriate repair mechanisms, and she marveled at the "smart cells" that underwent specific migrations in animal embryogenesis. McClintock was known to ask seminar speakers, "How does it all fit together?" She considered reductionism as an approach, not an answer. Shapiro believed that the secret of McClintock's success, in the face of incomprehension and prejudice, was her fearless and complete intellectual freedom--to admit "I don't know," and then to wrestle the answer from the data.
HUMOR NOTED
Evelyn Witkin (Rutgers University) treated the audience to a fresh look at McClintock's humor. After receiving the Nobel Prize, McClintock received an invitation from Henry Kissinger to a dinner for Nobel laureates. While the invitation listed all the other guests as "Dr. so and so," Barbara was referred to as "Ms. B. McClintock." McClintock penned in the margin a line from comedian Rodney Dangerfield: "I don't get no respect!
APPROACHABLE
V. Sundaresan (Cold Spring Harbor Laboratory) spoke from the perspective of younger scientists who were receiving their Ph.D.'s when McClintock won the Nobel. Sundaresan noted that visitors to Cold Spring Harbor Laboratory regarded McClintock with awe, and wondered whether it was safe to approach her. In fact, McClintock would talk with anyone as long as they were sincere and not just there to say they had met her.
Sundaresan noted that discussions with McClintock were likely to take some time--if you asked her a question, you had better be prepared to confer for a whole afternoon. According to Sundaresan, after several hours of intense dialogue, she would look closely at you and say, "We'd better stop now--you look tired!" Several days or even weeks following a session with her, one might suddenly realize the significance of something she had said that, at the time, seemed incomprehensible or irrelevant. Sundaresan emphasized that although McClintock had the reputation of a mystic, she always drew her conclusions from her observations--this is what she meant when she admonished us to "listen to the plant."
PREMIER CYTOGENETICIST
Oliver Nelson (University of Wisconsin, Madison) observed much of McClintock's progress during his own lengthy career in maize genetics. Nelson noted that she was the nation's premier cytogeneticist, using the best organism--maize!
Nelson recalled how McClintock's first reports of transposable elements were often met with skepticism. However, Nelson's colleague and mentor, Alexander Brink, quickly recognized that McClintock's transposable elements could explain his own observations on variegated pericarp in maize. With her help, Brink and his student demonstrated that McClintock's Ac transposable element was involved in the classic pericarp variegation, which had been first studied by R.A. Emerson--the grandfather of maize genetics and McClintock's own supervisor while she was a graduate student at Cornell.
Nelson concluded by noting that researchers are occasionally presented with bizarre results. McClintock possessed a special talent to recognize the underlying order and provide an explanation for the most perplexing observations. <body text>Following the scheduled speakers, Tom Brokaw, Jo Messing, and W. Szybalski added their own reminiscences. Far from a somber memorial service, this upbeat event brought McClintock's friends together to share their fond memories of an extraordinary colleague.
Susan McCarthy
Beltsville, MD
Genome organization is remarkably conserved between related species, reported participants at the recent Plant Genome I Conference, Nov. 9-11, 1992, in San Diego, CA. The meeting was co-sponsored by the USDA/ARS Plant Genome Research Program. Over 400 participants from around the world came together to share their research findings, with the belief that understanding genome conservation and organization should lead to faster and more efficient mapping across many species.
CONSERVATION
Conservation was observed primarily in the low copy DNA segments, while variability, including highly repetitive sequences, were found in flanking regions. These observations were made by a number of researchers, including Jeff Bennetzen (Purdue University, West Lafayette, IN), who found that low-copy sorghum sequences conserved in maize were also largely colinear. A similar finding was made by Steve Tanksley (Cornell University, Ithaca, NY) for maize and rice; 70% of single copy DNA was conserved and whole chromosome or chromosomal arms had maintained the same gene order.
Wheat and barley are largely syntenic, that is, the linear gene order is maintained along the chromosomes. Graham Moore (Cambridge Laboratory, Norwich, U.K.) observed 60% cross- hybridization of rice and wheat markers, and that copy numbers were also conserved in the low copy number segments. See Table 1 for a summary.
Data Management.
These exciting findings point to the need for data management. Tools for storing and analyzing data were discussed throughout the meeting. A mapping software workshop sponsored by Ed Coe (University of Missouri, Columbia, MO), Mary Berlyn (Yale University, New Haven, CT), and Stan Letovsky (Letovsky Associates, New Haven, CT) attracted a standing-room-only crowd of about 200 scientists. Software developments, capabilities, and needs were presented for MapMaker, GMendel, JoinMap, CProp, Hypergene, and others. Steve Knapp (GMendel: Oregon State University, Corvallis, OR)) and Steve Lincoln (MapMaker: Massachussets Institue of Technology, Cambridge, MA) have agreed to cooperate more fully in future software developments.
The Plant Genome Database, central database of the Plant Genome Research Program, was demonstrated, as were all of the species- specific sub-databases. Dave Kristofferson (Intelligenetics, Inc., Mountain View, CA) organized an informal workshop to look at electronic communications for Plant Biologists with the BioSci Newsgroups.
MAP-BASED BREEDING
The end product of genome mapping is map-based breeding and gene isolation. Steve Tanksley gave an elegant demonstration of map-based breeding in tomato. The process is as follows: wild-type tomatoes which did not exhibit desirable phenotypic traits were bred. A high-density molecular marker map was then used to eliminate such undesirable traits as small fruits or poor taste quality. The end result was a tomato that grew 15% faster and had a 15% greater yield than standard varieties.
Marker-assisted selections are especially important
for long-life-cycle species, including trees. Some markerassisted
selections are now being used, in apple tree breeding,
for example. A Forest Tree Genome Mapping Workshop, organized by
David Neale (U.S. Forest Service, Albany, CA), was held in
conjunction with the Plant Genome I conference (see the report on
page).
Plant Genome I in the news:
Dutton, G. (1992) Plant species gene maps yield surprises. Genetic
Engineering News 12(19):1,3,37.
Havukkala, I. (1992) Plant Genome I meeting highlights. Rice Genome 1(2):15.
Table 1 - Some Observations from Plant Genome I
Investigator Species Observations
J. Bennetzen sorghum maize Low copy sequences: cross
hybridize; same number
M. Gale wheat / rye Maps very similar: 7
translocations, 11
break-points found
J. Gustafson wheat/rye Considerable synteny for G. Moore barley/rice cereals in RFLP maps.
G. Moore wheat/rice Markers cross-hybridize;
significant micro-synteny
homologous exons
markers were also linked in maize.
but not as high as maize / rice
distinguish potato - tomato
wheat chromosomes 2 and maize 2S without major rearrangements
conserved in maize; synteny retained for whole and partial chromosomes