Published in Probe Volume 5(1): February-March 1995
Bruno Quebedeaux, Department of Horticulture
University of Maryland, College Park, MD
Andrew Kalinski, Susan McCarthy
USDA, ARS, National Agricultural Library
Beltsville, MD
Patrick Byrne
University of Missouri, Columbia, MO
The third plant genome international conference on the status of plant genome research was held in San Diego, California, USA, on January 15-19, 1995. Plant Genome III presented the following areas of genome research and development: isolation and transformation of agriculturally important genes, comparative genetic mapping, chromosome structure, and new instrumentation and automation technology. Plenary and general sessions and specific workshops highlighted new computer tools, databases, nomenclature, gene-tagging for abiotic stress, or individual species: pine trees, arabidopsis, barley, tree fruits, maize, legumes, cotton and grass genome integration.
The conference was sponsored and supported by the USDA Agricultural Research Service (ARS), the USDA National Agricultural Library (NAL), USDA Cooperative State Research, Education, and Extension Service, National Research Initiative Competitive Grants Office, John Innes Centre (UK), the Rockefeller Foundation, and the International Society for Plant Molecular Biology. The meeting attracted over 660 participants from 25 countries; there was substantially increased participation from the European Community and Japan.
The plant genome research program is now entering its fifth year. Jerome Miksche, Director, USDA Plant Genome Research Program, commended conference participants for their efforts leading to development of new genomic information, new technologies, and international collaboration. He stressed the need for continued and expanded funding to support ongoing research efforts. He indicated that the program, using molecular genetics to search for genes of agricultural importance and to construct detailed maps, has already yielded a plentiful harvest of new information.
Marker-Based Breeding
Genetic improvement of crop plants depends upon genetic diversity. Intensive breeding for crop improvement has narrowed the diversity of many of our commercially important cultivars. For these crop species, additional genetic improvement will be increasingly difficult to achieve without the new approaches to breeding now under development.
Steve Tanksley (Cornell University, USA) discussed the need to develop new QTLs, and identified a strategy for advanced backcross analysis: nearly elite lines are matched with an exotic, or ancient, donor germplasm. The F1 progeny are backcrossed several times and rapidly screened for advantageous QTLs. Tanksley's approach is to develop QTL isogenic lines for rapid map-based plant breeding.
Marker-facilitated QTL manipulation has been successfully used to transfer traits between elite maize lines, Charles Stuber (North Carolina State University, USA) reported. The marker-assisted backcrossing was used in a complex breeding program which greatly accelerated the development of a new hybrid line. The two highest yielding hybrids afforded an improvement of 1.7 to 1.9 ton/hectare.
A Tree Fruit Workshop, organized for the first time at the conference, also announced accelerated breeding. Norman Weeden (Cornell University, USA) reported that high heterozygosity, characteristic of the apple genomes and related species within the Rosaceae family, permits genetic analysis of isolated genes approximately 9 months after making a cross between two varieties. This technique can accelerate breeding by 5 to 15 years while reducing costs. Future breeding goals aim to develop cultivars with improved fruit quality, as well as insect and disease resistance.
Maps with over 200 segregation markers for several major apple cultivars have already been completed. Weeden indicated that molecular techniques such as RAPD and RFLP markers and bulk segregant analysis are being incorporated into the apple breeding program at Cornell. Genes encoding fruit color, fruit size, columnar growth habit, bud break, scab resistance, powdery mildew, and aphid resistance have recently been isolated. The USDA plant genome mapping program has expanded its mapping efforts from a few species initially to over 45 species.
Genome mapping activities in citrus, peaches, almond, cherry, and grapes by U.S. institutions and the European Community were presented and discussed. Several laboratories reported on the isolation of molecular markers for nematode-resistance. Identification of molecular markers near the nematode resistance gene(s) and generation of high-density maps in this region will enable scientists to develop new resistant plant cultivars.
Comparative Mapping
Tim Helentjaris (Pioneer Hi-Bred International, Inc., USA) presented insights into the evolutionary origins and the duplication of large segments of chromosome within the maize genome. He described how comparative mapping is distinguishing between alternative hypotheses of duplication: internal duplication with subsequent rearrangement, or by the fusion of two distinctive genomes. The development of comparative maps for individual species is allowing scientists to pool genetic information from related crop species, and is increasing the efficiency of molecular-marker and gene isolation technologies applied to crop improvement.
Comparative mapping applied to divergent taxa and to divergent chromosomes within a particular taxon can provide a better understanding of the evolution of a phenotype. Andrew Paterson (Texas A&M University, USA) showed that comparative mapping provides an opportunity to use chromosomal rearrangements as phylogenetic tools. A comparative approach to this problem will increase the number of available markers in any grass crop and will be useful for construction of a framework map of conserved regions in the genomes of the Gramineae family.
Mark Sorrells (Cornell University, USA) identified 150 anchor probes that hybridize to most of the targeted genomes; many of these probes were mapped in at least 5 species of the Gramineae family. Katrien Devos (John Innes Centre, Norwich, UK) showed the comparative maps of wheat, barley, and rye and concluded that arrangement of genes along the chromosomes of those cereal species is remarkably conserved. Devos predicts, on the basis of current data, that grass comparative genetics will use rice as the pivotal genome.
Comparative mapping is bringing scientists together who would otherwise have little in common: an international cross-species collaboration has been proposed for the Gramineae. The effort is being spearheaded by Jeff Bennetzen (Purdue University, USA) and Mike Gale (John Innes Institute, UK). The International Grass Genome Integration (IGGI) Program will, as noted above, use rice as the central genome for comparative mapping. Anchor probes will link genomes to map across species. Anchor probes are currently available for wheat vs. rice comparisons. Significant progress in identifying genes and rapidly transferring biochemical and physiological information is expected when mutants are mapped.
Mapping of Legume Genomes
Gary Kochert (University of Georgia, USA) compared the genomes of peanut and soybean. Several probes were tested in genomic blots of pea, alfalfa, soybean, and peanut for their usefulness in comparative mapping. Comparative mapping, Kochert said, will provide new and useful tools to locate genes encoding valuable agronomic traits. Norman Weeden (Cornell University, USA) reported considerable conservation of gene linkage of the agriculturally important pea subfamily. Detailed genetic maps consisting of hundreds of molecular markers are needed for positional cloning of genes and map-assisted breeding approaches. Peter Gresshoff (University of Tennessee, USA) showed the usefulness of DNA amplification fingerprinting (DAF) in the generation of appropriate markers; DAF technique results in highly reproducible profiles in soybean.
Graphical Representation of QTLs
The Maize Workshop focused on the theme of reporting, displaying, and utilizing complex data from quantitative trait loci (QTL) studies. Ed Coe (USDA, Columbia, USA) commented on the crucial importance of integrating quantitative trait information with molecular genetic data in working toward the goal of understanding the structure and function of the maize genome, and applying this information. Diego Gonzalez de Leon from the Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT, Mexico) showed methods for concise graphic representation of QTL results across different traits and environments. When using QTL data in marker-assisted selection (MAS) at CIMMYT, Gonzalez' group takes into account the size and effects of QTL regions, as well as economic thresholds that must be targeted.
Mathilde Causse from the International Network for Religion and Animals (INRA, France) explained research underway in her unit on using QTL methodology to understand early growth, carbon metabolism, drought tolerance, and variation in protein quantities in maize. She explained her location's in-house database, which has numerous options for managing and visualizing QTL data. Clare Nelson (Cornell University, USA) demonstrated QGENE, a software package he developed for analyzing and viewing QTL data and for applying such data to MAS. Pat Byrne (USDA, Columbia, USA) provided an on-line demonstration of accessing and searching QTL information in USDA's Maize Genome Database.
Mapping and Tagging Genes
A workshop on mapping and tagging abiotic stress genes, including drought resistance, water stress, high temperature, winter hardiness and salinity tolerance, identified the genetic complexity of these traits and the laborious mission of traditional plant breeding. Henry Nguyen, John Mullet, and their colleagues at Texas Tech (USA) and Texas A&M Universities (USA) have tagged the "stay green" gene, a post-flowering drought- resistant QTL in sorghum, by using molecular markers. Three major regions on the chromosome have been found to control the stay green trait in different environments. This trait is also linked to enhanced Nicotinamide adenine dinucleotide phosphate (NADP) reducing power, higher chlorophyll content and increased NADP malic enzyme activity. In addition to relieving drought stress in sorghum, the stay green gene may have application in improving turf grasses.
Inventory of Expressed Genes in Plants
The Arabidopsis Sequencing Project (Michigan State University, USA) is generating approximately 1,000 Expressed Sequence Tags (ESTs) per month. These ESTs provide not only a new source of very useful molecular markers but cDNAs also can be used to constitute a genetic map of expressed genes. Anonymous cDNA clones randomly selected from cDNA libraries of roots, etiolated seedlings, leaves, stems and flowering structures and from various developmental stages were sequenced. Thomas Newman (Michigan State University, USA) reported that approximately 35 percent of the ESTs show significant similarities to previously characterized genes in the public databases from plant and non-plant organisms.
The use of EST technology permits the rapid identification of new coding regions in plant genes, especially those whose isolation would otherwise be difficult or impossible. Plant biologists can directly use knowledge about proteins and genes from non-plant sources. Newman expects that tens of thousands of arabidopsis ESTs will be deposited in the public databases during the next several years. Marc van Montagu (Ghent, Belgium) announced the addition by the European consortium of 4,500 ESTs to the public databases through November 1994.
In addition to the arabidopsis program, the Japanese Rice Genome Program (Tsukuba, Japan) has developed rice libraries from calli, root, shoot, and developing seeds, and has generated approximately 20,000 analyzed cDNAs. Craig Venter (The Institute for Genome Research (TIGR), USA) presented results of sequencing ESTs from human cDNA libraries as an approach to quickly finding new genes. This strategy results in a tripled rate of new gene identification in both human and plant species. TIGR scientists are currently sequencing approximately a half-million base pairs of DNA per day and expect to analyze 35,000 new ESTs by the end of 1995. The Expressed Gene Anatomy Database (EGAD) was developed to integrate DNA sequences and mapping data with corollary biological information as gene expression, biochemical function, or cellular role.
Plant Gene Nomenclature
Ellen Reardon and Carl Price (Rutgers University, USA) organized a workshop focusing on the challenges in collection, collation and dissemination of nomenclature for sequenced plant genes. Nomenclature of genes across the plant kingdom is based primarily on the function of the gene products and secondarily on sequence similarity.
Brian Smith-White (Michigan State University, USA) related that the application of appropriate nomenclature to related sequences provides the framework for bringing order out of chaos. Smith-White's shibboleth in applying new terminology is "be conservative." Copies of genes encoding proteins of similar function exist in organelles and in the nucleii of many plants. David Lonsdale (Norwich, UK) discussed the potential for problems replacing terms that no longer convey current understanding. Specifically, the replacement of nads and ndhs with nuos in chloroplast, mitochondrial or E. coli genomes offered an opportunity to establish common nomenclatures across multiple genomes.
Paul Staswick (University of Nebraska, USA), associate editor of Plant Physiology, addressed the problem of converting gene designations in submitted publications to the common nomenclature. Authors would be encouraged to use the common nomenclature, but no worthwhile paper would be rejected for failure to do so.
Finally, Doug Bigwood, (NAL, USDA, Beltsville, USA) announced that CPGN databases are available on the World Wide Web at:
http://probe.nal.usda.gov:8300.html
An approved gene name can provide the springboard to identifying the location of specific loci across the plant kingdom.