New Delhi, May 31, 2012
The genomes of the cultivated tomato (Solanum lycopersicon) and its closest wild relative, Solanum pimpinellifolium, have been decoded by the Tomato Genome Consortium (TGC), a group of over 300 scientists from 14 countries. This important result, which will reduce costs and streamline efforts to improve tomato production, combating pests and drought, is published this week as a cover story on the journal Nature
India’s Contribution: India contributed sequencing of the gene-rich region of the tomato chromosome 5 (tomato has total 12 chromosomes) and provided further support to generate 5-fold sequence coverage of the entire tomato genome by Next Generation Sequence (NGS) technology. Indian Team also participated in performing annotation of all predicted proteins using international databases as a part of the International Tomato Annotation Group (ITAG). Simultaneously, Indian researchers have taken up analysis of specific genes/gene families related to disease resistance, abiotic stress tolerance and ripening based on transcriptome (RNA sequence) data and comparative genomics. The outcome is expected to greatly accelerate improvement of tomato varieties by molecular breeding.
Indian Initiative on Tomato Genome Sequencing (coordinator Prof. A. K. Tyagi) was a part of the TGC. It involved 24 scientists from three institutions, namely University of Delhi, South Campus (Principal Investigator- Prof. J. P. Khurana); National Institute of Plant Genome Research (Principal Investigator- Dr. D. Chattopadhyay); and ICAR’s National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (Principal Investigator- Prof. Nagendra Kumar Singh). The Indian project was funded by the Department of Biotechnology, Government of India and supported by the ICAR.
The sequence provides a detailed overview of the functional portions of the tomato genome and its closest relative, revealing the order and structure of their 35,000 genes. The tomato belongs to the Solanaceae family, which includes potatoes, peppers and brinjal, as well as ornamental and medicinal plants, such as petunia, tobacco, belladonna and mandrake. The members of this family have adapted to different ecosystems, from tropical rainforests to the Atacama Desert.
The sequence shows that the genome of tomato has "triplicated" suddenly about 60 million years ago, close to the mass extinction that led to the disappearance of the dinosaurs. Subsequently, most of the triplicated genes were lost, while some of those surviving one have specialized and now control important features of the plant, such as those controlling fruit characteristics, including ripening time, firmness, and red pigmentation.
The sequence will serve as a reference for other Solanaceae species and for comparative genomic studies both within the Solanaceae and with other higher plant taxa. The TGC was founded in 2003 in Washington, and includes scientists from Argentina, Belgium, China, France, Germany, India, Israel, Italy, Japan, Korea, Netherlands, Spain, UK and USA. The genome sequence and related resources are freely accessible on the websites http://solgenomics.net and http://mips.helmholtz-muenchen.de/plant/tomato/index.jsp.
Earlier, ICAR scientists have completed decoding of the rice genome as part of international consortium and the first draft of Arhar (pigeonpea) genome entirely through indigenous efforts. Presently, ICAR scientists are working on the decoding of wheat genome (chromosome 2A) as part of another international consortium. Genome decoding is expected to accelerate the development of improved crop varieties. New rice varieties developed using genome information have already reached the farmers.
(Source and ICAR contact: Prof. Nagendra Kumar Singh, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi-12 Email: nksinghnrcpb [dot] org)