PG II Meeting Summary

STEPHEN R. HELLER srheller at ASRR.ARSUSDA.GOV
Tue Apr 5 08:27:11 EST 1994


PLANT GENOME RESEARCH BEGINS A NEW VOYAGE OF DISCOVERY 
Brief Summary -- Plant Genome II Conference (San Diego, Calif., 
Jan. 24-27, 1994) 
 
Susan McCarthy, USDA 
National Agricultural Library, 4th Floor 
10301 Baltimore Blvd. 
Beltsville, MD  20705 
 
February 24, 1994 
Applications of genome mapping and analysis to solve existing 
problems and uncover answers to fundamental questions relating to
the plant genome and its evolution were featured in the recent 
Plant Genome II conference (San Diego, Calif., Jan 24-27, 1994).  

The meeting attracted 553 participants from 22 countries.  
According to Steven Oliver, University of Manchester, Manchester,
UK, we are entering a stage where the taxonomy of gene function 
will be essential in efficiently identifying new genes.  This new
age will require a multi-disciplinary approach encouraging the 
collaboration of physiologists, geneticists, biochemists, and 
plant breeders.  He defined this era as a new voyage of the 
Beagle.   
 
The message was reinforced by Dr. James Cook, USDA, ARS and 
Senior Scientist, CSRS, who pointed out that now is the time to 
bring plant breeders together with molecular biologists to 
conduct a gene hunt for agronomically important genes. 
 
New insights 
Understanding plant genome structure and organization can lead to
interesting and relevant discoveries as highlighted by Dr. 
Richard Flavell, Director, John Innes Institute, Norwich, UK.  
Understanding the role of epigenetic regulation, gene order, and 
in situ homology sequence searching will ultimately help in the 
practical application of biotechnology.  Plants have had to 
defend themselves from foreign DNA over the millennia and as a 
result have developed strategies -- including gene silencing -- 
to cope with transposon selection pressures.  The plant's ancient
art of anti-sense technology may take advantage of gene location. 
Gene location would determine epigenetic DNA methylation events, 
which in turn would regulate gene expression.  In all, Flavell 
points out, concerted evolution in the long term helps to 
maintain high levels of conservation across the chromosome both 
in terms of sequence and gene order or synteny. 
 
Evidence of ancient transposon and retrotransposon events were 
detected by Thomas Bureau, University of Georgia.  Extensive 
sequence similarity searches were performed on the GenBank and 
EMBL nucleotide sequence databases.  These "database mining" 
experiments have identified over 100 normal plant gene sequences 
showing evidence for a member of either the "Tourist" or 
"Stowaway" family of transposons.  The location of several 
elements corresponds to previously reported cis-acting regulatory
elements.  Significantly, a "Tourist" element was found to serve 
as the promoter for the maize auxin-binding protein (abp1).  The 
first plant retrotransposon, Bs1, was found to contain a cellular
gene fragment: this provides the first evidence for transduction 
by a retrotransposon in plants.  
 
Progress in rice 
The Japanese rice genome program reported significant advances.  
A genetic map with 1400 RFLP and RAPD markers was described by 
Dr. Nori Kurata, NIAR/STAFF, Japan.  Over 7,500 clones from 
callus tissue at different developmental stages have been 
sequenced.  Of those sequenced 1,800 are clones of known 
function.  Dr. Kurata reports that an expression map has been 
constructed using cDNA mapping as a base.  This map includes 
information on tissue-specificity, distribution of isozyme genes,
gene families, and functionally related genes in the genome, such
as ribosomal protein genes and the histone gene family.   
 

Physical mapping in the Japanese rice genome program will be used

to identify economically important genes.  Two YAC and three 
cosmid clone libraries have been developed, representing about 
20% of the rice genome.  Ordered libraries will be prepared from 
these clone libraries.  To date 120 YAC end-clones have been 
isolated and end-clone mapping is underway.  Typical YAC's have 
400 kb inserts, which when finished the Japanese expect will 
cover the rice genome 6 times over.  Chromosomes 1, 4, 6, and 11 
are being given high priority.  It is known that a number of 
important resistance genes reside on Chromosome 6.  Mapping data 
from the Japanese program have been entered onto two versions of 
an internal database called RiceBase, one version contains mostly
cDNA information while the other version has the physical map 
data.   
 
International collaboration of rice mapping efforts was 
encouraged by an informal workshop held in conjunction with the 
conference, Dr. Susan McCouch, Cornell University, and Dr. Gou- 
fan Hong, Director, Chinese Rice Genome Program co-chaired the 
workshop.  Dr. Kurata indicated that the Japanese mapping data 
should be made public later this year.  Five prime sequence data 
for several hundred markers is currently available.  Pamela 
Ronald, University of California, Davis, CA,  announced the 
public availability of a variety of libraries including their 
Bacterial Artificial Chromosomes and cosmids. 
 
Physical mapping  
Physical mapping was again highlighted in the Arabidopsis 
workshop.  Caroline Dean (John Innes Institute, Norwich, UK) and 
Howard Goodman (Massachusetts General Hospital) reported that 
chromosomes 4 and 5 are nearing completion in their joint effort 
to integrate the two YAC and cosmid maps.  A new YAC library 
developed by David Bouchez should help in developing the 
integrated physical map.  Several thousand Arabidopsis cDNA's 
have been sequenced by the French EST project.  Michel Delseny, 
(CNRS, Perpignon, France) reported on the project indicated that 
the cDNA sequences have been deposited in the public database 
 
Resources   
Plant Genome II provided participants with information on useful 
technologies and resources.  The latest developments in the plant
genome databases were outlined, as well as computational tools 
for mapping and sequence analysis.  Database demonstrations with 
a live Internet link were available throughout the meeting  
allowing hands-on experience to interested researchers to test.  
Electronic BIOSCI newsgroups were the focus of several workshops 
organized by Dave Kristofferson, (Intelligenetics, Mountain View,
Calif.).    
 
QTL experimental design  
Quantitative trait (QTL) analysis was examined with attention to 
experimental design and analysis.  Dave Webb, Pioneer Hi-Bred, 
Johnston, Iowa, looked at soybean cyst-nematode resistance; one 
soybean introduction was found to have more resistance than any 
other soybean tested to date.  Three resistance loci were 
identified; with this information the effect of population size 
in detecting the traits was tested.  Large sample populations 
were found to be essential in finding and mapping these traits. 
The minimum sample population size is 200.   
 
The need for large sample populations was again emphasized by 
Karl Lark, University of Utah, Salt Lake City.  Lark found that  
specialized statistical methods and graphing were needed to 
identify many important loci.  Specifically, Lark identified 
interacting traits a condition called epistasis.  One trait 
measured on its own had no effect on plant height.  This same 
trait was found to interact with another plant height QTL and 
could explain 25% of the plant height variation.  The basis of 
Lark's technique is to use large population sizes and to conduct 
pairwise comparisons of loci in plants with extreme phenotypes.  

The results are graphed and epistatic interactions are then 
identified.  According to Thomas Cheesbrough, South Dakota State 
University, Brookings, this type of analysis will be essential to
study the genes of such metabolic pathways as oil production, 
because each enzyme is highly interdependent on the gene products
of the entire metabolic chain. 
 
Mapping Technologies  
Mapping technologies were featured in several talks and posters 
throughout the conference.  Perry Cregan, USDA, ARS, Beltsville, 
Md., and others reported on the continued success with simple 
sequence repeats (SSR).  The SSR's are small sequence patterns 
which are repeated at variable lengths.  The variable length of 
the repeats provides a means to identify varieties and 
individuals; tools needed by crop breeders and geneticists.  In 
addition to SSR technology, amplified fragment length 
polymorphism (AFLP), a related new technology, was reported by 
Drs. Pieter Vos and Marc Zabeau, KeyGene, Wageningen, The 
Netherlands.  AFLP will provide markers for those map regions 
which other markers have not successfully bridged.  The AFLP 
technique has the capacity to exploit multiple forms of variation
within the genome.  The new technology described by Vos is still 
a long way from direct application by plant breeders as discussed 
at the International Triticale Mapping Initiative meeting held in
San Diego in conjunction with the Plant Genome II conference.  
 
Plant Genome III 
Plant Genome III will be held January 15-19, 1995, in San Diego, 
Calif.  Sessions will address all aspects of mapping, from QTL's 
to the latest molecular marker technologies, instrumentation, and
gene isolation.  For more information or program suggestions 
contact: Jerome Miksche or Stephen Heller, USDA/ARS, BARC-W, 
Bldg. 005, Room 331-C, Beltsville, MD 20705 USA. 
 
 
 







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