Probe : newsletter for the USDA Plant Genome Research Program

30 Pages·1996·2.2 MB·English

by  USDA Plant Genome Research Program

Historic, Archive Document
Do not assume content reflects current
scientific knowledge, policies, or practices.

Newsletter for the USDA Plant Genome Research Program
Volume6, Final July 1996
Comparative Mapping Sows Seeds
of Progress
Andrew H. Paterson
Department ofSoil and Crop Sciences
College ofAgriculture and Life Sciences
A&M
Texas University
College Station, Texas
n important component of the USDA Plant Comparative mapping of quantitative trait loci
Genome Research Program has been com- Recent results suggest that comparative mapping may
parative mapping, the alignment ofthe have even greater utility than previously envisioned,
chromosomes of related crop species based reaching directly into the molecular dissection of com-
on genetic mapping of common DNA markers. Com- plex traits that are the basis of agricultural productiv-
parative mapping affords many benefits to crop ity. (6) A collaborative research project involving
genome analysis, including greater utility of Andrew Paterson, James Stansel, and James Irvine at
existing DNA probes, effectively Texas A&M University, together with USDA-ARS
increasing the density of genetic researchers Keith Schertz (College Station, Texas),
markers in many species Shannon Pinson (Beaumont, Texas), and John
simultaneously. In addi- Doebley at the University of Minnesota was
tion, comparative formed. The results of this collaborative effort
mapping offers new revealed that quantitative trait loci (QTL) associated
opportunities for with domestication of sorghum, rice, and maize
investigating plant • ' frequently fall at corresponding genetic map loca-
evolution. tions.
,
Detailed compara- Specifically, close correspondence appears to
tive maps are being occur among QTL affecting
assembled for several plant traits such as seed size;
families, such as the (1) shattering of the inflores-
Solanaceae, (2) Poaceae, cence; and short-day flower-
Fabaceae (N. D. Young, ing of sorghum, sugarcane,
pers. comm.), (3) maize, and rice. This corre-
Biassicaceae, and (4) Malvaceae, which include many of spondence is mirrored by (7) a companion study in
the crops that feed and clothe humankind. (5) In one which 185 genes and QTL reported by many indepen-
particularly well-studied plant family, the Poaceae, dent investigators to affect height and flowering of
extensive conservation of gene repertoire and gene maize and other species were collated with each other
order along the chromosomes has led to the suggestion and with a new map of the genes associated with height
that the cultivated cereals might be treated as essentially and flowering in sorghum. (8) An independent study of
a single genetic system. a smaller set of QTL in maize and sorghum reinforces
Probe
2 July 1996
this theme of correspondence. systems, and minimizing redun- ute to productivity of many forage
While correspondence of QTL in dancy. and turf grasses, essential to the
different species of the plant For example, recent results U.S. agroecosystem both for animal
genera (9) Lycopersicon and (10) describe a set of QTL largely fodder and in erosion control.
Vigna had previously been re- responsible for rhizomatousness of Research in progress seeks to
ported, such correspondence spans johnsongrass, one of the world's determine whether growth enhance-
relatively short periods of genetic most important agricultural weeds ment of several forage and turf
divergence, and in fact the relative (11). Such research is difficult to species may derive from use of
promiscuity of plant species makes conduct, as rhizomes grow under- DNA markers closely linked to
it difficult to preclude the possibil- ground, and are very laborious to rhizomatousness in sorghum.
ity of recent gene flow. measure accurately. Rhizomatous Correspondence of QTL across
Correspondence between forms ofboth sugarcane and rice diverse taxa also provides a strong
QTL has been suggested, not only harbor genes of potential value to empirical foundation in support of
between different taxa, but also agriculture but cannot be grown in model systems research on complex
between duplicated chromosome the United States for fear of phenotypes. For example, the ease
segments within a particular introducing new weed species to ofgenetic analysis possible in
species, indicating that chromo- these crops. rodents and agricultural mammals
some duplication may contribute Comparative mapping may has permitted mapping of genes
to polygenic inheritance. Specifi- afford the means to breed associated with diabetes, hyperten-
cally, (6) pairs of loci affecting rhizomatousness out of these sion, obesity, alcohol/drug addic-
shattering of the maize inflores- weedy relatives, affording safe tion, and other medically important
cence, (7) maize height and flower- access to valuable genes held in phenotypes. The inherent difficulties
ing, and sorghum height, fall on these exotic gene pools. On the flip associated with mapping complex
chromosome segments that appear side, aggressive rhizomes contrib- traits in humans are partly amelio-
to correspond, based on genetic
mapping of duplicated DNA
markers. While only a subset of Table of Contents
QTL appear to be associated with
chromosome duplication, it is Comparative Mapping Sows Seeds ofProgress 1
offered as one of many mecha- Report on the 1995 Plant GenomeAwards 4
nisms by which quantitative traits —
USDA National Research Initiative Competitive Grants Program Plant Genome Grants
might evolve.
Fiscal Year 1995 6
Implications of Interagency Program: Arabidopsis thaliana Genome Sequencing Project 9
corresponding QTL for life New Release ofthe RiceGenes Database 10
sciences research BeanGenes 11
The suggestion that mutations in Organelle Genomics 12
corresponding genes may account
Introducing: Dr. David Grant 15
for phenotypic variation in species
such as sorghum, maize, and rice, A Guide to Scientific Names ofVascular Plants 16
reesptriomdautcetdi6v5elmyililsioolnatyeedarfso,r ahnas Biosafety Proceedings Available From PGDIC; Japan Selectedfor Fourth Symposium . ... 18
widespread implications. Perhaps Germplasm Resources on the Internet 19
first and foremost, QTL analysis in NAL Catalog on Internet 19
one taxon may be predictive of
Calendar of Upcoming Events 20
results in other taxa. Such predic-
tive value would afford broader Stock Center Profile: The C.M. Rick Tomato Genetic Resources Center 23
utility of QTL mapping results Using Fuzzy Searching to Retrieve Plant Genome Information at the USDA, National
than was previously envisioned, Agricultural Library 25
enabling research on easy systems —
SGML Enhances Access to Digital Information 27
to be extrapolated to more difficult
Transitions 28
Probe
Volume6, Final 3
rated by the possibility of cloning References
QTL in mouse (for example) that Probe
account for phenotypic variation in 1) Bonierbale, M.D., R.L. Plaisted,
S.D. Tanksley. 1988. Genetics
humans. In a like manner, crop
plants that grow particular plant 120:1095; S.D. Tanksley et al.
1993. Genetics 1132:1141.
organs of extraordinary size, such as
the enlarged root of turnip, inflores- 2) Hulbert, S.H., T.E. Richter, J.D.
ISSN: 1057-2600
cence (curd) of cauliflower, or fruit Axtell, and others. 1990. Proceed-
of tomato, might be used to identify ings of the National Academy of The official publication of the
developmentally important genes in Sciences, United States 87:4251; USDA Plant Genome Research
which genetic variants impair Ahn, S., S.D. Tanksley. 1993. Program. This newsletter is aimed
survival or reproduction in other PArcoacdeeedmiyngosfoSfcitehneceNsa,tiUonniatled atthefapclialnittatgiengnoimnteermaactpipoinntghrcooumghmouu-t
species. nity and beyond.
States 90:7980; Ahn, S., J.A.
Anderson, M.E. Sorrells, and Probe is a publication ofthe Plant
Maximizing the value of Genome Data and Information
others. 1993. Molecular and.
future genome mapping Center, National Agricultural
General Genetics. 241:483; N.
Library, ARS, USDA.
results Kurata, and others. 1994. Bio/
Many investigators are enhancing Technology 12:276. Managing Editor
Susan McCarthy, Ph.D.
the value of their results to the 3) Kowalski, S.D., T. Lan, K.A.
scientific community by making an Feldmann, and others. 1994. Editor
Joanne Meil
extra effort to facilitate comparative Genetics 138:499.
Assistant Editor
analysis. There is growing aware- 4) Brubaker, C.L., A.H. Paterson, Marti Asner
ness that once a gene hasbeen J.F. Wendel, in preparation. Production Manager
DmNaAp-pbeadsbeydatneychonfiaquweisdneorwanagveaiolf- 5) Bennetzen, J.L., M.A. Freeling. Terrance Henrichs
1993. Trends in Genetics 9:259- Layout andDesign
able, it is important that the diag- 261 (1993); Helentjaris, T. 1993. Terrance Henrichs
nostic marker(s) be linked to a Proceedings of the National Special Thanks to:
comprehensive genetic map (or Academy of Sciences, United Barbara Buchanan
previously mapped DNA clones) States 90:8308-8309; Shields, R. Marti Asner
that affords integration with related 1993. Nature 365:297-298. Correspondence Address
taxa. Genetic maps based on con- 6) A.H. Paterson et al. Science, in Susan McCarthy, Ph.D.
served DNA sequences are becom- press. USDA, ARS, NAL, 4th Floor
ing increasingly prevalent, mapped 10301 Baltimore Ave.
DNA markers are widely available, 7) Lsionn,.YS.e,pKt.eFm.bSecrhe1r9t9z5,.AG.eHn.etPiactse,r-in BPehlotnsevi:l(l3e0,1M)D5042-06760153
and few, ifany, genetic mapping press. FAX: [phone]
l"apbustcoannermesoirstetmhaerokpeprorotnuntihteymtaop," 8) Pereira, M., M. Lee. Theoretical E-mail: [email protected]
and Applied Genetics, in press
especially one linked to an impor- USDA Program Office
tant phenotype. By using the 9) A.H. Paterson, and others. 1991. Dr. Henry Shands
Genetics 127:181. USDA/ARS/NPS/PNRS
fortuitous tools that nature offers us
for comparative analysis of plant 10) Fatokun, C.A., D.I. Menacio- Room 331C, Bldg 005
chromosomes, an ever larger and Hautea, D. Danesh, and others. BARC-WESMTD
1992. Genetics 132:841. Beltsville, 20705
more complex body of genetic data Phone:[phone]
on major crops can be integrated 11) A.H. Paterson et al. 1995. E-mail: [email protected]
into a more coherent and therefore Proceedings of the National
more useful information base, Academy of Sciences, United
States 92:6127.
valuable for improving the long-
term productivity and sustainability
of U.S. agriculture. NationalJlyriculturA]Library
Probe
$
CompetitiveEdge
Genome
Report on the 1995 Plant
Awards
n 1995, the National To be considered for the Award recipients represented
/
Research Initiative Com- awards, scientists from the research 37 research institutions (see next
petitive Grants Program community submitted mission- page) studying 30 species (see next
(NRICGP) made available oriented proposals that addressed page for number of awards per
$9,507,886 for plant genome re- the goal of improving agronomic species and dollar amounts).
search, out of which 68 grants were qualities of plants through genomic According to Ed Kaleikau, compara-
awarded. The Plants Division of the research. tive mapping and map-based
NRICGP in USDA's Cooperative Ed Kaleikau, acting division cloning were hot topics among
State Research, Education, and director of the Plants Division, and researchers across the board. He
Extension Service administered the Steve Tanksley, panel manager, of added that this trend underscores
grants. the Plant Breeding and Biometry the importance of the Plant Genome
The total grant amount is Department, Cornell University, Database, which centralizes such
lower than in previous years, as is selected peer panel members and ad information for researchers to use.
the number of awards given, largely hoc reviewers for the proposals in The data for the tables was
because of Federal budget reduc- concurrence with the NRI Chief supplied by the NRICGP staff, and
tions. Despite these developments, Scientist and USDA administration. compiled into tables by Dr. Garry
the average amount per award and The panel considered and discussed Smith, USDA-ARS, Fargo, North
average number of years per award all the reviews, then ranked the Dakota.
have increased from previous years, proposals based on scientific merit,
thus increasing the award's value to relevance to agriculture, and quality
recipients (see table 1). of research facilities and personnel.
Table 1
NRI PLANT GENOME REVIEWED AWARDS 1991-95
Year Awards $ Amount Avg Years Average $ Percent Success
Per Award Per Award Rate
1991 76 10,489,525 2.2 138,020 30
1992 95 12,191,822 2.1 128,335 34
1993 91 12,126,238 2.3 133,255 34
1994 104 11,730,074 2.0 112,876 33
1995 68 9,507,886 2.5 139,822 27
Totals/avg. 434 56,054,545 2.2 130,462 32
Probe
Volume6, Final
Institutions Receiving NRI Species Represented by Plant Genome Awards
Plant Genome Awards 1995 1995
No. of Pprrpnt
Species Amount
Auburn Awards ofTotal
Cal Berkeley
Cal Davis
Cal Riverside Agrobacterium 1 $100,000 1.1
Alfalfa 1 $50,000 0.6
Cal San Diego
Arabidopsis 7 $1,121,000 11.8
Case Western Barley 2 $440,000 4.6
Clemson Bean 3 $302,725 3.2
Cold Spring Harbor Brassica 3 $535,000 5.6
Colorado State Chokecherry 1 $50,000 0.5
Cornell Citrus 1 $185,000 1.9
Cotton 1 $49,947 0.5
Florida
£. coli 1 $100,000 1.1
Illinois Lettuce 1 $410,000 4.3
Indiana Loblolly pine 2 $325,143 3.4
Iowa State Maize 18 $2,182,000 22.9
Kansas State Millet 2 $245,000 2.6
Kentucky Pea 1 $120,000 1.3
Peach 1 $250,000 2.6
Louisiana State
Peanut 1 $100,000 1.1
Maine
Pearl millet 1 $105,000 1.1
Minnesota Petunia 1 $115,000 1.2
Missouri Pine 1 $210,000 2.2
Montana State Populus 1 $175,000 1.8
Nebraska Rice 4 $686,000 7.2
Sorghum 2 $286,000 3.0
North Carolina
Soybean 3 $393,000 4.1
North Carolina State
Spring wheat 1 $50,000 0.5
North Dakota
Sunflower 1 $320,000 3.4
North Dakota State Sweet potato 1 $49,476 0.5
Oregon State Tobacco 7 $975,000 10.3
Purdue Tomato 5 $920,000 9.7
Rhode Island Wheat 4 $350,000 3.7
Southern Mississippi Totals *68 *$9,507,886 *100.0
Texas A&M "Columntotalsdonotreflectsumofcolumnnumbersbecausesome
USDA/ARS, PGEC awardsinvolvemorethanonespecies.
USDA/ARS
USDA
Forest Service
Turn the page for listing of
V. Commonwealth
Washington 1995 Award Recipients >
Wisconsin
—
Probe
6 July 1996
USDA
National Research Initiative
Competitive Grants Program
Genome
Plant Grants Fiscal Year
1995
Henry V. Amerson, David M. O'Malley, Ronald R. Vicki L. Chandler
1995 Gordon Research Conference on Epigenetic Effects
Sederoff
on Gene Expression
Role of Major Genes for Resistance in the Loblolly Pine-
Fusiform Rust Forest Pathosystem University of Oregon
North Carolina State University
Christine D. Chase
Barbara Joan Baker Mitochondrial-Nuclear Interactions in S Male-Sterile
TMV Maize
Isolation of the Resistance Gene, AT
Plant Gene Expression Center, USDA/ARS University of Florida
Zong Ming Cheng
Patricia A. Bedinger
Analysis and Cloning of Male Sterility Genes Host/Pathogen Interactions and Inheritance of XMLO
Colorado State University Resistance in Chokecherry
North Dakota State University
Jeffrey L. Bennetzen
Multi-Institutional Research Coordination Group on Jeffrey L. Dangl
Integration of Grass Genome Studies Molecular Genetics ofDowny Mildew Resistance: The
Purdue University Arabidopsis Rpp8 Cluster
University of North Carolina
James A. Birchler
Molecular Analysis of Maize Centromeres William O. Dawson
University of Missouri Plant Resistance and Recognition of Tobamoviruses
University of Florida
Frederick A. Bliss
Molecular Tagging Genes for Nematode Resistance and Ismail Dweikat, Herbert W. Ohm
Tree Growth in Peach Detection of Hessian Fly Resistance Genes in Wheat
Purdue University
University of California, Davis
Harvey D. Bradshaw, William B. Eggleston
Jr.
Mapping Quantitative Trait Loci in Populus Origin and Interactions of a Naturally Occurring,
University of Washington < Tandem Duplication in Maize
Virginia Commonwealth University
Gordon C. Cannon
Nucleoid Protein Composition and Phosphorylation Elias M. Elias
During PlastidDevelopment in Soybean Molecular Mapping of High Grain Protein Content in
Durum Wheat
University of Southern Mississippi
North Dakota State University
Probe
Volume6, Final
Stephen K. Farrand Roger William Innes
CIS- and Trans-Acting Functions Mediating Ti Plasmid Use ofArabidopsis DNA Markers To Isolate a Disease
Transfer Resistance Gene From Soybean
University of Illinois at Urbana-Champaign Indiana University
Daniel R. Gallie
Richard A. Jorgensen
Isolation of RNA-Binding Proteins Involved in
Co-Suppression, Paramutation and Transgene-Elicited
Regulating Translation
Pigmentation Patterns
University of California, Riverside
University of California, Davis
Stanton B. Gelvin
Shawn Michael Kaeppler, K. Arumuganathan, Heidi
Early Events in T-DNA Transcription and Integration
Flewelling Kaeppler
Purdue University
Chromosome Specific Libraries for Maize Genome
Research
Giovannoni
J.J. University of Nebraska-Lincoln
High Density Mapping and Isolation of Genes
Regulating Tomato Fruit Ripening
A&M Harry John Klee
Texas University
Modulation of Ethylene Sensitivity in Tomato
University of Florida
Peter Goldsbrough, Gebisa Ejeta
Drought Tolerance in Sorghum: Mapping of QTLs and
Steven Knapp
Analysis of Near-Isogenic Lines A GenetJi.c Map and Mapping Resources for Sunflower
Purdue University
(Helianthus annuus. L.)
Oregon State University
Carol M. Hamilton
Evaluation and Application of a New BAC Library
DNA Sondra G. Lazarowitz
VectorDesigned for Transfer of Large Inserts to
Molecular Genetics of Geminiviruses Pathogenesis
Cornell University
University of Illinois
Larkin Curtis Hannah
Peggy G. Lernaux
Intron-Enhanced Gene Expression in Maize
Targeted Gene Tagging by Generating Barley With
University of Florida Maize Ds at Defined Locations
University of California, Berkeley
Thomas K. Hodges, Leszek A. Lyznik
Homologous and Site-Specific DNA Recombination for
Yi Li
Genomic Modifications of Plants
High Performance Liquid Chromatography for Plant
Purdue University
Molecular Research
Kansas State University
Scot H. Hulbert
An Analysis of the Rpl and Rp3 Loci of Maize
George H. Liang, Daniel Z. Skinner
Kansas State University
Biolistic Gametophyte Transformation of Alfalfa
Kansas State University
Arthur Garfield Hunt
Characterization of a Plant Poly(A) Polymerase Din-Pow Ma
University of Kentucky
Characterization of Cotton Fiber Genes and Their
Regulatory Elements
Mississippi State University
Future updates posted at URL: John Munson Martin
Predicting Progeny Variation from ParentalDiversity in
http://www.nal.usda.gov/pgdic Spring Wheat
Montana State University
Probe
8 July 1996
Phillip E. McClean Thomas C. Osborn
Fine Structure Mapping ofDisease Resistance Related Defining Genes for Vernalization Requirement in
Genes in Common Bean Brassica
North Dakota State University University of Wisconsin
William Richard McCombie, Robert Martiensson Peggy Ozias-Akins, Wayne W. Hanna
Structural and Functional Analysis of a Region of the Development, Genomic Diversity, and Gene Expression
Arabidopsis Genome in Aposporous Genotypes
Cold Spring Harbor Faboratory University of Georgia
Michael D. McMullen, Patrick F. Byrne, Maurice E. Calvin O. Qualset
Snook, Neil W. Widstrom Research Collaboration Group on Molecular Mapping in
Genetic Control of Corn Earworm Resistance Factors Wheat and Its Relatives
in Maize University of California, Davis
University of Missouri
Sriyani Rajapakse, Janice R. Bohac
Richard W. Michelmore Molecular Analysis of Beta-amylase Gene in Sweet potato
Structure and Variation of Resistance Gene Complexes and Wild Ipomoea Species
in Lettuce Clemson University
University of California, Davis
Pamela C. Ronald
Gloria A. Moore, Frederick G. Gmitter Positional Cloning of a Major Gene From a Durably
Genetic Transformation of Mature Meristematic Tissue Resistant Rice Cultivar
in Perennial Plants University of California, Davis
University of Florida
Robert Schmidt, Martin F. Yanofsky
J.
Walter C. Mueller, Eric M. Roberts, Carl H. Beckman An Analysis of Floral Regulatory Genes in Maize
Mechanisms of Polygene Resistance in Tomato Plants University of California, San Diego
Infected With Fusarium
University of Rhode Island Mitchell M. Sewell, David E. Harry, David B. Neale
Comparative Mapping in the Genus Pinus
Norimoto Murai Institute of Forest Genetics/Pacific Southwest Research
Methionine Enhancement of the Bean Seed Storage Station
Protein Phaseolin = Plant Expression Assay
Louisiana State University William F. Sheridan, Inna N. Golubovskaya, Yasuo
Hotta
June B. Nasrallah, Mikhail E. Nasrallah Maize Desynaptic Mutants: Chromosome Pairing,
A Structural and Transcriptional Analysis of the S-Locus Synapsis and Recombination Nodules
Region of Brassica University of North Dakota
Cornell University
Stephen M. Stack, Nora L.V. Lapitan
Kathleen Newton Physical Mapping of Genes and RFLP Markers on
J.
Transcriptional Regulation in Zea Mitochondria Tomato Pachytene Chromosomes
University of Missouri Colorado State University
Brent L. Nielsen James L. Starr, M. Burow, A.H. Paterson, C.E. Simpson
DNA
Detailed Characterization of Tobacco Chloroplast Genetic Study of a Multigenic System for Nematode-
Replication Initiation Sites Resistance in Peanut-Utility in Gene Management
A&M
Auburn University Texas University
Basil J. Nikolau, Patrick S. Schnable Thomas Dermot Sullivan
Molecular Analysis of Meiotic Recombination Genetic and Biochemical Analysis of Maize Brittle-1 and
Iowa State University