Whitepaper
From IGGP
Contents |
Title page
International Grape Genome Program
| July 2002 |
A note about the cover. The images on the cover are from Ampélographie by P. Viala & V. Vermorel published at the beginning of the 20th century between the years 1901-10. These magnificent volumes contained state-of-the-art knowledge on the biology of the grapevine and the varieties. In the 21st century, one hundred years later, a new chapter on the understanding of grapevine biology is about to begin through the use of molecular technologies to unravel the mysteries of the grapevine genome.
Summary
Grapevine (Vitis vinifera L.) is the most economically important fruit crop in the world. Viticulture and wine making have been part of human culture for thousands of years. Increased production efficiency and improved fruit quality has traditionally been based on the modification of management and growing conditions of specific genotypes which have generally been kept constant by vegetative multiplication. Today, the limitations of this approach are obvious with increased input costs and practices, some of which are not sustainable, and include the use of chemicals with potential negative secondary effects on human health and the environment. In contrast, the biology of Vitis is relatively unknown and awaits further exploitation to improve quality and yield.
A genomics approach to discover and determine the function of all grapevine genes is today a feasible strategy to achieve a rapid and thorough understanding of grapevine biology. Vitis is well suited for genomic studies with a genome size of approximately 500 Mbp and has a number of unique features including a novel shoot architecture and non-climacteric fleshy fruit produced from a perennial deciduous woody vine. The fruit also has unique secondary metabolism producing color pigments, tannins, flavor and aroma compounds. Understanding the basic biology of Vitis will allow us to understand how a grapevine plant responds and interacts with the physical environment, management practices, abiotic stresses, as well as pests and diseases.
Vitis genomics research will be able to address current viticulture and enology issues. Envisioned benefits will be; improved fruit and wine quality, resistance to pests and diseases which will reduce the use of chemicals, better adaptation to environmental conditions including improved water use efficiency and salt tolerance as well as an improvement in plant architecture and yield. Furthermore, understanding the biology of grapevine will allow the development of predictive tools for plant health and fruit quality.
The overall benefit of the application of genomics to grapevine will be to increase the precision of genetic improvement and viticultural practices by establishing refined correlations between molecular characters (i.e., genes, proteins and metabolites) and agricultural traits. With the advent of such knowledge, long sought after goals, such as low input viticulture and higher value end products, can be pursued with an increased probability of success. In addition to these ecological and economical relevant benefits, the new knowledge generated from studying the grapevine genome will advance basic plant research into complex biological processes and evolutionary biology.
I. Introduction
Grapevine is the most widely cultivated fruit crop in the world and the most important in economic terms. Contrary to other fruit crops grapevine is not only used as a fruit in its multiple uses (fresh fruit, fruit juice, dried fruit, etc) but it is the basis for the production of high value-added products such as wine and spirits. Because of these multiple uses, the grapevine has been a part of human culture since the establishment of agricultural societies, thousands of years ago. Today, the grapevine is more than an economically valuable crop. It is an important component of Western societies by providing substantial employment through a large number of diverse jobs, and in many cases being associated with a national culture or life style.
Grapevine cultivars dedicated to wine production result from the selection of superior genotypes of ancient origin mostly generated by spontaneous crosses centuries ago. These cultivars are propagated vegetatively and therefore each elite cultivar represents a unique, usually highly heterozygous, genotype. Over the last two hundred years, as viticulture has spread throughout the world, wine grape production improvements have relied mainly on advances in agronomic and management techniques including an increased reliance on chemicals. As a consequence, production costs of modern intensive viticulture are higher and include a large energy cost component. Furthermore, chemical protection from the numerous grapevine diseases is not only expensive but is of increasing concern to consumers due to possible secondary effects on human health and the environment.
During the last few decades breeding of new grapevine cultivars has been increasingly successful. Genotypes with improved fungal disease resistance have been selected from the progeny of crosses between Vitis vinifera and wild Vitis species carrying the resistance traits. Recurrent backcrossing with elite grapevine cultivars and selection for both superior wine quality and fungal resistance has led to new cultivars with resistance traits and high wine quality. However, introduction into the market remains difficult. The process generates completely new genotypes, new varieties which have to be introduced into the market and accepted by consumers. Genetic engineering is likely to be one of the most efficient ways to introduce a new trait into existing elite cultivars without altering the unique genetic complexity of the genotype. Many of the elite cultivars and rootstocks are amenable to genetic transformation with either Agrobacterium or biolistics. In spite of the conservative views of some European consumers to this technology, and recalcitrance to change within the wine world, we anticipate that this situation will change in the future if transgenic vines result in environmental and health benefits and if proposed genetic engineering strategies are based on the use of Vitis genes.
The phenotype of a cultivated plant (berry quality, yield, vigor) is the result of complex interactions between the environment, the imposed management regime and the genotype (genes) of the cultivar. An extensive body of knowledge, built up over more than a hundred years, exists about the best environment for growing grapevines and appropriate viticultural management techniques. As a result, it is increasingly difficult to improve grape quality and production through environmental or management manipulations. In contrast, the genetic resources in Vitis are vast, and there is great potential to exploit this untapped potential for traits of importance to both scions and rootstocks. Similarly, there is no substantial information on the structure and function of the grapevine genome or on the gene sequences which, either alone or in combination, are required for each specific trait of interest.
Genetic improvement of grapevine either through classical breeding of new cultivars or genetic engineering of elite genotypes would benefit from a better understanding of the genetics and biology of the species. Having this information will increase the efficiency of current genetic improvement by permitting the identification and evaluation of the genetic variants of interest through the use of intragenic molecular markers. Furthermore, it will allow the design of strategies for the improvement of elite wine cultivars using Vitis genes.
The rapid development of genomic technologies and applications in the last years and the recent completion of the Arabidopsis and rice genome sequences have provided the tools and the comparative information to allow detailed characterization of the grapevine genome. The functional information accumulating in Arabidopsis also offers a model system for the functional analyses of grapevine genes. Altogether, these possibilities provide a framework in which to efficiently identify and functionally analyze important grapevine genes controlling key traits. A genome program can now be envisioned as a highly important tool for grapevine improvement. Such an approach to identify key grapevine genes and understand their function will result in a "quantum leap" in grapevine improvement with key outcomes such as improved disease resistance and berry quality. Additionally, the ability to examine gene expression will allow us to understand how a grapevine responds to and interacts with the physical environment and management practices. This information, in conjunction with appropriate technology, may provide predictive measures of plant health and fruit quality and become part of future vineyard decision management systems.
The grapevine is ideally suited for genomic studies. It is a diploid plant and can be easily crossed and selfed. It has a small genome of approximately 500 Mbp, equivalent to 3-4 times the genome size of Arabidopsis. Vitis can be considered as a representative of a group of deciduous woody perennial plants that produce non-climacteric fleshy fruits containing secondary metabolism compounds responsible for color, flavor and aroma. Furthermore, as a basal eudicot family, with unique shoot, flower and fruit architecture, the Vitaceae are also interesting systems for basic comparative genomic studies.
The advantages of grapevine genome research are recognized by both public and private researchers in many countries of the European Union, Australia, the U.S.A., South Africa, Chile and other grape and wine producing nations. Given the magnitude of the effort required, and in order to ensure rapid scientific advances without unnecessary duplication of effort, full cooperation of all nations involved in grapevine genome research is essential. This document has been developed with the involvement of a multinational community of scientists.
II. General Scientific Goals
The ultimate goal of the program is to understand the genetic and molecular basis of all the Vitis biological processes that are relevant to the crop and, with this goal, to encourage the free exchange of ideas and information through open communication and interactions at the scientific level. This is a fundamental principle to allow efficient exploitation of Vitis biological resources in the development of new cultivars with improved quality and reduced economic and environmental costs as well as new diagnostic tools. Traits considered of fundamental interest are pathogen and abiotic stress resistance, quality traits for table and wine grapes and reproductive traits. This work will be strongly based on the information developed by the functional analyses of other sequenced genomes, especially the Arabidopsis and rice genomes, whenever significant sequence homology is found.
As a way to achieve this final goal, the immediate goals of the Program will be focused on the identification and characterization of Vitis vinifera genes and the understanding of their function both at the molecular and the organism level. This approach will also include those genes for disease resistance, stress tolerance, nematode resistance and other traits of relevance in viticulture which are present in other Vitis species. With this purpose the following specific objectives have been developed:
III. Specific Objectives
Genome Analysis
The complete analysis of the grapevine genome will be approached through several complementary strategies with the final goal of having full integration of the genome sequence and the genetic map. These strategies include the generation of saturated genetic maps, the construction of BAC libraries and a physical map and the sequence identification of all Vitis genes through both EST and genome sequencing approaches. As mentioned below, these approaches will generate common resources that will require the establishment of stock centers and databases to make information and material accessible to all interested research groups.
Genetic Maps
Several genetic maps, built with different molecular marker types, are already available for several genotypes and many more are being generated with different purposes. However, it is essential to generate a common reference map and to select a common set of molecular markers and common chromosome nomenclature to integrate all the genetic maps generated and speed up the process of genetic mapping. A working group is currently investigating the options.
Short term goals:
1. Develop a framework genetic map using microsatellite (SSR) markers, which covers the complete genome.
2. Establish a reference F1 segregating population from a Vitis vinifera cross for the production of a consensus map and develop a mechanism for the distribution of DNA and plant material to all interested researchers.
3. Determine a common marker set for germplasm assessment, variety identification and genetic relationship studies.
4. Initiate mapping studies of non-vinifera species for localization of disease and pest resistance genes.
Long term goals:
1. Develop fine scale genetic maps based on new marker types (e.g. EST based SNPs) for the localization of genes in both vinifera and non-vinifera species responsible for berry quality traits, fruitfulness, yield, pest and disease resistance, tolerance to abiotic stresses, and plant architecture.
2. Apply the information in marker assisted breeding programs to rapidly advance the breeding of new varieties.
3. Apply the information in conjunction with EST and physical mapping research to identify and isolate genes responsible for traits of agronomic importance through positional cloning approaches.
BAC Libraries, Physical Maps and Genome Sequence
Several BAC libraries for cultivars of Vitis vinifera and related Vitis species are already available in different laboratories and for different purposes. Construction of a physical map by ordering one of these Vitis vinifera BAC libraries is an essential task that needs to be undertaken and will speed the process of gene identification in forward genetic approaches. Given the current development of sequencing technologies, undertaking the sequencing of the Vitis vinifera genome can be an efficient approach for gene identification, once current EST programs reach saturation redundancy. Taking into account the poor knowledge of the grapevine genome, sequencing of shotgun clones of the whole genome seems to be a realistic strategy. Sequencing of the grapevine genome will complement EST sequencing, physical mapping and the development of functional analysis tools. A working group has been formed to advance this area of research.
Short term goals:
1. Selection of a common reference BAC library corresponding to one of the parental cultivars of the reference segregating population.
2. Initiate physical map construction based on a combination of BAC fingerprinting and STS analysis.
3. Sequence BAC ends as a complement to physical map construction.
4. Integrate the physical map with the genetic map obtained for the reference segregating population using SSRs, EST derived SNPs and AFLP markers.
5. Construct BAC libraries for non-vinifera species, resistant to pests as a tool for comparative mapping and gene identification
Long term goals:
1. Sequence the complete genome of Vitis vinifera.
2. Sequence homologous genomic regions in both parents of the reference population and other cultivars to generate additional molecular markers and learn about genetic variation in Vitis vinifera.
3. Sequence homologous genomic regions from different members of the Vitaceae family as a tool for the identification of variant gene and regulatory sequences.
EST sequencing
ESTs are partial gene sequences which have been generated or are in the process of being produced in several laboratories using different species and cultivars as well as varied tissues and developmental stages. This represents an important step towards the identification of all expressed genes in grapevine. EST sequences are also an important resource for identifying single nucleotide polymorphisms, localizing and isolating gene sequences and for producing cDNA microarrays for expression profile analyses. EST sequencing efforts will be greatly improved by sharing the information held by different laboratories and designing strategies to avoid duplication and extend the coverage of all expressed genes. This is the task of a specific working group.
Short term goals:
1. Develop a framework for the sharing of EST sequence information.
2. Reduce duplication and increase EST coverage.
3. Develop an EST UNIGENE set.
4. Develop microarrays using the UNIGENE set for gene expression studies.
5. Provide a gene EST resource for genetic and physical mapping research.
Long term goals:
1. Discovery of all the expressed genes in the grapevine genome.
2. Development of a common complete UNIGENE microarray for expression studies.
3. Significantly increased understanding of grapevine biology and how the plant responds to the environment and management practices.
4. Application of this information in vineyard and winery decision management systems to monitor plant health and fruit quality.
5. Application to grapevine improvement in conjunction with genetic and physical mapping research to identify key genes responsible for berry quality traits, fruitfulness, yield, pest and disease resistance, tolerance to abiotic stresses, and plant architecture.
Functional Analysis
A fundamental objective that should have a continuous emphasis during the course of the grape genome program is the development and use of methods to define gene functions at the molecular and organismal level. The identification of specific genes involved in significant grapevine biological processes is a prerequisite for interpretation of molecular information on the structure and organization of the Vitis genome. Tools need to be developed that allow both forward and reverse genetics in Vitis as well as the elucidation of gene molecular functions, gene regulation and gene interactions. These tools include the requirement for simpler genetic systems more adapted to laboratory requirements, the generation of collections of mutants and natural variants, the development of efficient transformation systems in transient test systems and stable models, and gene knockout tools such as transposon tagging, RNAi or virus induced silencing. The development and use of EST microarrays is considered to be one of the first important steps to correlate gene expression with specific biological processes. This gene expression information will be further complemented with the use of two-hybrid libraries for studying protein-protein interactions, systematic proteome analyses, and metabolic profiling studies.
Short term goals:
1. Development of rapid cycling laboratory lines to facilitate genetic analyses in Vitis.
2. Development of efficient protocols for grapevine genetic transformation.
3. Development of technologies for reverse genetic approaches in grapevine.
Long term goals:
1. Functional determination of grapevine genes and their interactions using genomic, proteomic and metabolomic approaches.
2. Understanding the molecular basis of agronomically relevant pathways.
3. Understanding gene regulation in genotypes with different traits.
Resource Centers
Currently there are several grapevine germplasm centers that hold reference collections of grapevine cultivars. However, the International Grape Genome Program will require the establishment and distribution of collections of molecular tools (e.g. EST collections, BAC libraries, DNA markers, etc.) as well as genetic stocks required for functional analyses (pure lines, mutant and natural variants, transgenic lines, transposon lines, introgression lines, etc). Having a central repository center is an efficient and simple system for the distribution of various resources to researchers. The resource center should function as:
- A center for collection, maintenance and cataloging of plant samples, genetic stocks, mapping stocks, etc.
- A holder of DNA libraries and pooled DNA samples.
- A source of information about the biological collections.
For security reasons it is advisable to create at least two similar resource centers. Alternatively, a distributed resource center model could be more feasible with different centers holding different resources but one center acting as the portal for all.
Short term goals:
1. Investigate the feasibility of various resource center models.
2. Initiate establishment of genomic stocks.
3. Initiate establishment of plant genetic stocks.
Long term goals:
1. Improvement of conservation technologies to allow maintenance of thousands of genetic stocks in a small space and with minimum maintenance and distribution costs.
2. Genomic and genetic stock resources available to the research community.
Bioinformatics
The Grape Genome Program will generate a large amount of data that will require processing, storage and distribution to the multinational research community. The data will include not only sequence information, but information on mutations, markers, maps, functional discoveries, etc. Genome projects in other organisms have already generated a wealth of information about the processing of this type of data and the way to make it available to the scientific community in a user-friendly manner. Three key objectives for grape bioinformatics include: (1) to encourage the submission of all sequence data into the public domain, through repositories such as EMBL and NCBI, and (2) to provide rational annotation of genes, proteins and phenotypes, and (3) to elaborate relationships both within the grape data and between grape and other organisms. Such information would likely be served to the grape community by a combination of a centralized bioinformatic activity(ies) and individual groups with interests in specific tools and tasks within the framework of bioinformatics. A specific working group is in charge of identifying these informatic requirements of the program as wells as the possible location of the databases.
Short term goals:
1. Establish the bioinformatic needs of the working groups developing genetic maps, physical maps, ESTs, functional data and resource centers.
2. Encourage submission of raw or annotated sequence data to public repositories, such as EMBL and NCBI.
3. Identify and evaluate bioinformatic solutions to improve annotation and elaborate relationships inherent within the data.
4. Initiate web based community forum for issues related to grape genomics (http://www.vitaceae.org).
Long term goals:
1. Accessible grape bioinformatic solutions serving the needs of the research community.
Workshops and Symposia
Research Workshops and Symposia are a very important part of the Program. In previous years there have been periodical meetings focused around Grape Genetics and Breeding as well as Physiology and Biotechnology. These almost yearly meetings should in future include a specific component, such as a workshop, for discussions about the progress of the Grape Genome Program and the individual projects. It is also recognized that more specific Workshops and Symposia will also be required either within the frame of these meetings, at the annual Plant and Animal Genome Meeting in San Diego, or independently organized by the Steering Committee.
Short term goals:
1. Establishment of a calendar of events for the International Grape Genome Program.
Long term goals:
1. Regular annual International Grape Genome Program meetings
Social and Legal Issues
Success of the International Grape Genome Program strongly depends on the participant’s agreement to share the results of their individual efforts. As the number of participants increase, the benefits of sharing results will increase as well as the availability of public information. As a rule, the matter of intellectual property rights should be handled according to the legal convention of the country that provides for the individual research project in question. If there are any restrictions which potentially prevent free exchange of ideas, information and materials for research purposes, they should be identified and made widely known so that rights of individual investigators to intellectual property will not be inadvertently violated. When research projects are conducted under official joint agreements between nations, such agreements should contain clauses on the intellectual property rights in accordance with the international agreement on intellectual property rights.
Participation in this International Grape Genome Program does not necessarily require the exchange of funds between cooperating countries. Each country or entity will provide financial support to the activities of its own scientists.
Release of genetically engineered plants into the environment for research purposes should follow the guidelines and applicable regulations of the country where the field tests are being conducted.
Organization and Implementation of the Multinational Grape Genome Research Program
A structured approach to coordinate and foster collaboration and participation within the International Grape Genome Program is required, as it has been done in other species. In June 2001, at the University of California, Davis, a meeting of scientists representing most of the major wine countries formed an interim Multinational Organizing Committee. This committee created six working groups to foster discussions on topics such as Markers and Genetic Mapping, BAC libraries and Physical Mapping, ESTs and transcriptional profiling, Functional Analysis, Bioinformatics, as well as the development of a White Paper to define the objectives and vision of the Program. The working groups report their recommendations to the Steering Committee.
The International Grape Genome Program was formally announced in January 2002 at the Plant, Animal, and Microbe Genome X Conference, San Diego, California. To coordinate the program a Steering Committee was formed representing scientific experts from the major grape and wine regions of the world. Specific responsibilities of the Multinational Steering Committee include:
1. Coordination of the Grapevine Genome Program.
2. Facilitate exchange of information and collaboration with the wider viticulture and enology research communities.
3. Monitor, summarize and communicate progress of scientific activities of participating laboratories.
4. Identify research areas of benefit to grapevine improvement and plant biology and communicate them to funding agencies of participating nations.
5. Periodically up-date the goals of the program.
6. Serve as a primary contact with other plant genome projects.
7. Interact with an Industry Advisory Committee to ensure relevance of the research to industry problems.
8. Act on recommendations received from the various working groups.
The members of the Steering Committee are listed on the Steering Committee page of the wiki.
Participation in the International Grape Genome Program working groups is open to all interested researchers and the contacts for each working group are listed in Appendix 1.
The current status of grapevine genome analysis at the international level is reported in Appendix 2.
Appendix 1: List of Current Working Groups and Contact Person
1. Markers and Genetic Mapping
- M. Stella Grando
- email:stella.grando@mail.ismaa.it
- Fax:39-0461 650956
2. BAC libraries and Physical Mapping
- Anne-Francoise Adam-Blondon
- email:adam@evry.inra.fr
- Fax:33 1 60 87 45 49
3. ESTs and transcriptional profiling
- Mark Thomas
- email:Mark.R.Thomas@csiro.au
- Fax:61 8 83038601
4. Functional analysis
- Eva Zyprian
- email:e.zyprian@geilweilerhof.suew.shuttle.de
- Fax:49-6345-919050
5. Bioinformatics
- Douglas Cook
- email:drcook@ucdavis.edu
- Fax:530-754-6617
6. White paper
- José Martinez Zapater
- email:zapater@cnb.uam.es
- Fax:34-915854506
Appendix 2: Status of Grapevine Genome Analysis in Several Countries as of January 2002
Australia
Grapevine molecular research was initiated in the late 1980’s and today involves several groups. Current research involves a wide range of techniques including functional characterization of single genes to genomic approaches including genetic mapping, physical mapping, gene discovery using ESTs and gene expression analysis using microarrays and transgenic plants. A transformation system has been developed for introducing genes into the major world wine cultivars. Beneficial outcomes from this research are expected to be new knowledge of grapevine biology, improved berry and wine quality, plants resistant or tolerant to powdery mildew, botrytis, nematodes and phylloxera, new varieties through marker assisted breeding strategies and diagnostic technologies for vineyard and winery decision management systems for monitoring plant health and fruit quality.
Chile
Molecular biology and genetics of grapevine is poorly developed in Chile. Some investigators from the National Institute for Agricultural Research (INIA) have participated in the Vitis Microsatellite Consortium (VMC) in 1998 generating molecular markers for fingerprinting of table grape, wine grape, genetic maps and for studying germplasm genetic diversity. In the last few years, other groups have started working with grapes and established grape transformation systems for introducing genes into wine and table grapes. Recently, a group of scientists from different Chilean universities have submitted a proposal to the national government for funds to support a national initiative for implementing the basic capacities for working in grape functional genomics. The proposal will establish tools to obtain EST libraries as well as transcriptome profiles of berry development and grape pathogen interactions.
France
Eight groups have been coordinating their efforts towards the development of genetic resources and knowledge on grapes since the 1950s. A great influx for the development of grape genomic resources has been given since 1999 through financial support of the Génoplante consortium (www.genoplante.org) and of INRA (www.inra.fr). Recently the accent was put on the development of microsatellite markers and of a reference genetic map as a tool for QTL detection of traits of agronomic interest such as berry traits and resistance to pathogens. BAC libraries have been constructed with the intention to participate in the development of a physical map of the genome of Vitis vinifera in collaboration with members of the IGGP. ESTs are also under production and will contribute to the development of microarrays that will be helpful for the studies on the expression, regulation and signaling control of berry developmentally related genes. In parallel, INRA has been developing methods for grapevine transformation (transient & stable). A database for grape genetic resources is available at INRA and at the European level and several other databases are under development (EST management and processing, genetic maps, BAC). All this knowledge should help in the development of high quality grapevine varieties resistant to pathogens and also lead to a better understanding and management of grape-environment interactions.
Germany
In Germany grapevine genomics started in the early 1990s with the application of molecular marker technology to address questions of cultivar identification, pedigree analysis, evaluation of genetic resources and genetic mapping. The major focus is on localization and long-term molecular characterization of genes involved in pest resistance and quality traits with the aim to understand their complex genetic basis. Various test populations segregating for agronomically valued traits are currently under investigation. Different marker systems are being employed, including the SSR markers developed by the VMC consortium with the aim to achieve transferable data for the construction of a consensus map by integrating the results with other mapping projects on an international scale. In addition, an EST program has been initiated to gather genes expressed in different tissues from fungus-disease resistant cultivars. These ESTs are to be used for SNP marker development for mapping of functional genes as well as expression studies. Physical mapping studies are planned to follow the genetic approaches. Several groups are doing research in the frame of transformation assays that are already well established, together with the required tissue culture techniques. The major focus of these studies is to achieve viral or fungal disease resistance by transgene inactivation of the pathogen. Investigations of genes related to pathogen resistance and their regulatory regions are also under way.
Italy
Although grape genomics is relatively young in Italy, since the early 1990’s molecular biologists were already using several molecular tools for variety characterization, diagnostic, phylogenetic studies and genetic transformation of Vitis species. In the last few years, the interest in grape genomics increased enormously and research involves marker assisted selection, molecular mapping, large EST sequencing, establishing BAC libraries for map positional cloning of genes of economical interest, pest resistances and fruit quality. Beside a wide interest of several Universities and Research Institutions on molecular markers and molecular breeding, Italy has essentially two large genomic projects. A genomic project, headed by a public Institution focussed on developing tools for molecular breeding and map positional cloning approaches, a second one headed by several Universities, focussed on functional genomics of berry maturation phases. Recently, two other smaller projects, one regarding functional genomics of grape secondary metabolism and a second one on structural genomics have been established in order to have a firm base for a whole grapevine genome sequencing approach.
South Africa
Grapevine genomics research in South Africa started with the participation in the Vitis Microsatellite Consortium (VMC) in 1998. This has since expanded to include other primer sets available to consortium members, which we have tested on a grapevine germplasm collection from one of the big grapevine propagators in South Africa. A group at the University of Stellenbosch, including the Genetics Department, the Institute for Wine Biotechnology (IWBT) and the Institute for Plant Biotechnology (IPB) is the major site for grape genomic research in South Africa. Stellenbosch is also the only University in sub-Saharan Africa to teach Viticulture and Enology.
Our grapevine genomics efforts also include regeneration of transgenic plants and the generation of a number of grapevine genomic and cDNA libraries. The IWBT generated genomic libraries for the cultivars Sultana and Pinotage, and cDNA libraries from young expanded leaves of the same two cultivars. Genomic libraries for Chardonnay and Merlot as well as cDNA libraries from early and late berry developmental stages of the same two cultivars were made at the IPB. A project to study the molecular interactions between grapevine and some of its most important virus pathogens is also in progress and will utilize microarray technology. A consortium including the Genetics department, the IWBT, the department of Molecular and Cellular Biology at the University of Cape Town and the Biotechnology department of the University of the Western Cape, have an interest in studying molecular interactions between grapevine and fungal pathogens using microarray technology.
Spain
Genetics and molecular biology of grapevine is presently poorly developed in Spain. A few groups have cooperated in the development of microsatellites within the Vitis Microsatellite Consortium and are now taking advantage of current table grape breeding efforts to generate genetic maps allowing the localization of major QTLs for grape berry quality traits. Table grape breeders have also developed segregating populations derived from crosses between Spanish wine cultivars, which will be the base of the Spanish grapevine program. This program is currently being organized by a small group of researchers representing most of the grapevine producing regions. The common biological interests are the understanding of the genetic components of wine quality as well as disease resistance and environmental stress tolerance. The proposed tools to be developed are EST libraries, ordered BAC libraries as well as the development of protein and metabolic profiles. Other laboratories are developing efficient protocols for the genetic transformation of Spanish wine cultivars, which will be required for functional analyses. A proposal will be submitted to national and regional agencies in 2002 to find funds to support this initiative.
USA
Researchers are taking several approaches toward gaining a more complete understanding of the grapevine genome. Since the early 1990s, several groups have developed molecular marker based maps in both vinifera and interspecific hybrid populations. Markers were located for flower sex, disease and nematode resistance. EST libraries are under development or have been developed in several labs with the intention of studying wine quality, disease resistance, and abiotic (cold and salt) stress tolerance. BAC libraries were developed in cooperation with an Australian group. Several groups have an interest in functional genomic analysis via transcription profiling, and molecular studies as an aid to Vitis systematics are also underway. Work underway is expected to contribute not only to improved breeding efficiency, but should also enhance our knowledge base of the grapevine’s genetic response to stress. With several labs in the United States proficient in grapevine transformation technology, it will be possible to do basic studies on newly discovered genes as well as studies designed to produced transgenic vines with improved traits.
