About IITGS

ORIGIN OF PROPOSAL

On November 3, 2003 researchers, from more than 10 countries, representing academic and government research labs, industry and extension/outreach specialists with interest in the Solanaceae met for a full day in Washington DC to kick off the 10 year initiative entitled “The International Solanaceae Genome Project (SOL)”. The forum united around a common set of tools, populations and concepts with a firm commitment to work together to elevate our level of understanding of the network of interactions that lead to population diversity and adaptation. The agreed upon course of action for the first stage of this initiative was: 1) to obtain high quality sequence of the tomato genome as a reference for Solanaceae plants as well as plants from other related taxa, 2) to display all data generated from around the world via a single virtual entry point for Solanaceae genomics, and 3) to establish a Steering Committee that will facilitate and coordinate research and funding for projects under the virtual umbrella of SOL. It is proposed that over the coming 10 years the International Solanaceae Genome Project (SOL) will integrate diverse disciplines and research groups from around the world to create a coordinated network of knowledge about the Solanaceae family aimed at answering two of the most important questions about life and agriculture:

(i) How can a common set of genes/proteins give rise to such a wide range of morphologically and ecologically distinct organisms that occupy our planet?

(ii) How can a deeper understanding of the genetic basis of plant diversity be harn
essed to better meet the needs of society in an environmentally-friendly and sustainable manner?

The long-term goal of the SOL program is to create a network of map based resources and information to address key questions in plant adaptation an
d diversification. This will be done using the tools and philosophy of systems biology which is a multidisciplinary approach to tackle the complex interactions that occur at all levels of biological organization and their functional relationship to the organism as a whole. Moreover, these studies would provide a new outlook to how we value and utilize natural variation to impact the health and well being of humans in a more environment friendly and sustainable manner. The international effort will be expected not only to impact Solanaceae biology but will also set the road map for implementing rational strategies for improvement of other crop species that are important to human nutrition. Therefore, it is proposed that India should actively participate in SOL program. Keeping this in view, DBT has already organized two meetings for discussion. In addition, Prof. R. P. Sharma (Central University Hyderabad) and Prof. J. P. Khurana (University of Delhi, South Campus) attended 1st Solanaceae Genome Workshop 2004 in the Netherlands, for scientific interactions and present Indian viewpoint regarding SOL.

DEFINITION OF PROBLEM


Solanaceae family includes many economically important plants. Some of the plants are most valuable in terms of vegetable crops. These crops are quite diverse in terms of their agricultural utility. Solanaceae includes the tuber-bearing potato (very important vegetable crop and source of industrial starch), a number of fruit-bearing vegetables (e.g. tomato, eggplant, peppers, husk tomato), ornamental flowers (Petunia, Nicotiana), edible leaves (Solanum aethiopicum, S. macrocarpon), and medicinal plants (e.g. Datura, Capsicum). Some of the fruits and tubers from this family provide us vitamins, fiber, carbohydrates, and phyto-nutrients in our diet. The World Health Organization and the United Nations Food and Agriculture Organization (FAO) recently launched an effort to enhance fruit and vegetable consumption worldwide as low consumption is considered one of the top ten contributing factors to human mortality. Solanaceae members are unique in that multiple crop species in this family are major contributors to fruit and vegetable consumption and thus to our quality of life.

Solanaceae family plants are models for a number of biological studies important to agriculture. Some of the areas of research where Solanaceae members have been in focus are fruit development and ripening, tuber development, physiology and biochemistry, disease resistance and quantitative trait loci.

Fruit development is a phenomenon unique to plants. In addition to affecting the yield of fruit plants it also affects the nutritional quality of edible plant products. Tomato is one of the most widely studied plant to understand fruit ripening. Potato tubers form an important component of the human diet throughout the world, particularly for people in parts of Africa, the Americas, much of Europe and Russia. Potato is the primary model organism for understanding tuber development.

Solanaceae members have been used for pioneering research on cell wall and storage polysaccharide synthesis and metabolism, volatile production, vitamin biosynthesis, biosynthesis and action of the hormones ethylene and brassinosteroids and biosynthesis of flavonoids and carotenoids. Many disease resistance (R) genes have been characterized from Solanaceous species. Tomato was the first plant from which a "gene-for-gene" class of R gene was cloned. More than 12 R genes have since been isolated from tomato, including genes conferring resistance to fungi, nematodes, aphids, bacteria and viruses. Several QTLs for traits of agronomic importance including yield mating behavior, fruit characteristics, heterosis, and molecular breeding have been identified. Tomato genome sequencing will help in cloning of genes involved in conferring these traits.

In plants, the use of comparative genetic molecular mapping has revealed a high level of conservation of gene content and order within the grasses, crucifers, legumes and Solanaceae species. There have been no large-scale duplication events (e.g. polyploidy) in Solanaceae family early in its evolution, as a result, micro-synteny conservation amongst the genomes of tomato, potato, pepper and eggplant is very high. This can be exploited to predict regions between genomes that are similar to each other and study the evolution of sequence and function of orthologous genes – a key to understanding diversification and adaptation. The high degree of conservation in genome organization, both at the macro- and micro-syntenic levels, would allow the information generated with one species to be extended beyond the individual species thus creating a common map-based framework of knowledge for related species also. Hence, the first goal of SOL is to determine, with great precision, the nucleotide sequence of the tomato genome and link it to the Solanaceae map. The tomato map-based genome will provide a reference to interpret the sequence organization of other Solanaceae crops and their wild relatives as the basis of understanding how plants diversify and adapt to new and adverse environments.

Tomato fruits are rich source of carotenoid pigments. These pigments with beta-ring are known as provitamin A. They are the only source of vitamin A in the human diet. Epidemiological studies indicate carotenoids to be preventive agents against specific diseases such as prostate cancer (lycopene) and age-related muscular degeneration (lutein/zeaxanthin). Carotenoids show protective activity in vitro and in vivo against a variety of degenerative diseases, possibly through their activity as antioxidants.

Tomato has been selected as a reference since it provides the smallest diploid genome (950 Mb). Homozygous inbred lines of tomato are available. Further, an advanced BAC based physical map, which is required for map based sequencing, is available. Tomato has been studied intensively for its genetics. Tomato has short generation time, efficient transformation technology. Tomato is suitable because of the availability of rich genetic and genomic resources. The tomato genome encodes approx. 35,000 genes, which are largely sequestered in contiguous euchromatic regions corresponding to less than 25% of the total DNA in the tomato nucleus (220-250 Mb of gene rich regions). Presently, the Solanaceae Genome Network (SGN; http://www.sgn.cornell.edu/) hosts multiple informations from diverse sources around the world in a (MySQL) relational database. SGN currently contains approximately 200,000 gene/EST sequences from tomato, potato, eggplant, pepper and petunia.

OBJECTIVES

University of Delhi, South Campus
1.
To produce a high quality sequence of the gene rich 5 Mb euchromatin of the chromosome 5 of tomato.
2.
To process and annotate this sequence in a manner consistent and compatible with similar data from Arabidposis, rice and other plant species.
3.
Submission of sequence information to an international bioinformatics portal for comparative Solanaceae genomics to make the information available to research community.
4.

To identify agronomically useful genes from tomato genome.

NRCPB-IARI

1.
To produce a high quality sequence of the gene rich 5 Mb euchromatin of the chromosome 5 of tomato.
2.
To process and annotate this sequence in a manner consistent and compatible with similar data from Arabidposis, rice and other plant species.
3.
Submission of sequence information to an international bioinformatics portal for comparative Solanaceae genomics to make the information available to research community.
4.

To identify agronomically useful genes from tomato genome.

National Centre for Plant Genome Research, New Delhi

1.
To produce a high quality sequence of the gene rich 2 Mb euchromatin of the chromosome 5 of tomato.
2.
To process and annotate this sequence in a manner consistent and compatible with similar data from Arabidposis, rice and other plant species.
3.
Submission of sequence information to an international bioinformatics portal for comparative Solanaceae genomics to make the information available to research community.
4.

To identify agronomically useful genes from tomato genome.

The work related to Bioinformatics and submission of sequences to international portal for NCPGR will be done in collaboration with UDSC.