Published in Probe Volume 4(1-2): July 1993-July 1994
Susan McCarthy, Coordinator
Plant Genome Data & Information Center
National Agricultural Library, USDA
Beltsville, MD 20705
Plant Genome II featured applications of genome mapping and analysis to solve existing problems and uncover answers to fundamental questions relating to the plant genome and its evolution. The meeting attracted 553 participants from 22 countries.
According to Steven Oliver, University of Manchester, Manchester, United Kingdom, we are entering a stage where the taxonomy of gene function will be essential in efficiently identifying new genes. This new stage will require a multidisciplinary 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 also Senior Scientist at 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, United Kingdom. According to Flavell, 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.
Thomas Bureau, University of Georgia, detected evidence of ancient transposon and retrotransposon events. 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. Dr. Nori Kurata, NIAR/STAFF, Japan, described a genetic map with 1,400 RFLP and RAPD markers. 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 YACs have 400 kb inserts, which, when finished, the Japanese expect will cover the rice genome six 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 session. Highlights included Dr. Kurata's announcement that the Japanese mapping data should be made public later this year. Five prime sequence data for several hundred markers are currently available. Pamela Ronald, University of California, Davis, CA, announced the public availability of a variety of libraries, including those on 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 cDNAs have been sequenced by the French EST project. Michel Delseny, (CNRS, Perpignan, France) who reported on the project, indicated that the cDNA sequences have been deposited in the public database EMBL.
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 handson experience for interested researchers. Electronic BIOSCI newsgroups were the focus of several workshops organized by Dave Kristofferson (Intelligenetics, Mountain View, CA).
QTL Experimental Design
Quantitative trait loci (QTL) analysis was examined with attention to experimental design and analysis. Dave Webb, Pioneer Hi-Bred, Johnston, IA, 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 in 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 studying 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 SSRs 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, CA. Sessions will address all aspects of mapping, from QTLs 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. (See Announcing Plant Genome III in this issue.)