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BGI and CIAT announce collaboration for large-scale genome sequencing of cassava

Cali, Colombia and Shenzhen, China -- The International Center for Tropical Agriculture (CIAT) and BGI, the world's largest genomics organization, announced a collaborative agreement to sequence 5,000 cassava genotypes, including landraces, improved varieties, experimental populations and related wild species of the crop. Cassava is the fourth most important provider of dietary calories in developing countries (after maize, wheat and rice.) Results of this research project will enable a major advance in applying modern genomics technology and analytics to improving this orphan crop. CIAT and BGI invite the cassava research community to join in this collaborative effort.

Barely known outside the tropics, cassava is a critical source of food and income for more than 200 million families in the developing world. Over half the production is in Africa, with 30 percent in Asia and 16 percent in the Americas. Because it is not grown in the developed world, investment in research to improve the species has lagged behind many other crops. And because the crop is clonally propagated, and farmers save stem pieces for planting from one generation to the next, the private seed industry has not invested in cassava improvement. This initiative promises to allow modern genetics tools to contribute to the improvement of cassava for the benefit of the world's poor and help cassava scientists worldwide "catch up" with other crops.

454 LifeSciences and Joint Genome Institute(JGI) produced the first draft of the cassava genome from a CIAT accession at the end of 2009. The assembly remains highly fragmented (12,000 scaffolds) but is believed to contain 97% of known coding loci ( CIAT is currently planning to employ Illumina paired-end sequencing to attempt to join some of these scaffolds. The University of Arizona is sequencing selected genotypes. The Chinese Academy of Tropical Agricultural Sciences (CATAS) is undertaking the sequencing of an additional four genotypes.

Dr Joe Tohme, Director of CIAT's crop research area, noted the significance of this partnership toward meeting the center's mission of alleviating hunger and poverty in the tropics through research on eco-efficient agriculture.

"This collaboration represents an unprecedented opportunity to boost cassava research and accelerate crop improvement for millions of smallholder farmers," he said. "This work will also help to establish the importance of cassava, giving it the recognition and research support that it rightly deserves."

The current initiative will increase scientists' understanding of the crop's evolution and distribution from its origins in the Americas to Africa and Asia, information necessary for breeders to seek new traits to adapt the crop to new production systems, new markets, and to climate change.

The combination of sequences from both wild as well as domesticated species will give researchers the opportunity to discover genomic regions and individual genes which have played a role in the domestication of cassava. Having whole genome sequences allows the exploration of genomic variations associated with different characteristics of interest. A large number of genomic sequences from a variety of genotypes for a given region will enhance marker-assisted breeding in cassava, and boost breeding activities to develop more desirable breeding lines in a shorter space of time.

Dr. Gengyun Zhang, Director of Life Science Division, BGI, noted, "Genetically improved cultivars are the key output of cassava breeding research. The rapid advance of genomics, especially large scale genome re-sequencing technology, will accelerate the improvement of cassava yield, quality and resistance to pests and diseases."

Benefits of Cassava Sequencing

Full genome sequencing of a broad array of genotypes will contribute immensely to the basic knowledge of the crop and the potential for further improvement. Three main areas of interest include evolutionary and phylogenetic studies, understanding of the basic genetics of the crop and of the genus, and development of tools for breeding.

The availability of sequenced genomes, phenotypic data and improved molecular tools will allow the development of molecular markers for traits that offer clear advantages such as improved post-harvest storage and resistance to whiteflies.

There will be a much better understanding of the potential contributions of the wild species to cassava improvement, both in terms of trait identification and the methodologies for transferring those traits to grower-accepted varieties.

Finally, this initiative will stimulate broad partnerships among molecular biologists, genebank curators, geneticists, plant breeders, pathologists, entomologists and other disciplines. A multi-partner collaboration will accelerate an integrated approach to the application of modern and traditional breeding tools, for the benefit of small cassava producers. BGI has a similar agreement with the International Rice Research Institute (IRRI) and CAAS to sequence up to 10,000 rice accessions. CIAT and BGI welcome partners to collaborate in the research and share the results.

Contact: Jia Liu
BGI Shenzhen

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