cassavaCassava is one of the most important crops in unfavorable environments in developing countries, where poverty is common and severe. Because of its high productivity, even in extreme conditions, cassava constitutes a source of food and income for poor farmers in Africa, Asia and Latin America. Although cassava is fairly resistant to water stress, the molecular basis for this tolerance is poorly understood. Several traits have been associated with its drought tolerance, such as regulation of stomata activity, changing leaf expansion rates due to decrease in cell proliferation, and modifications of photosynthetic pathways to maintain high photosynthetic activity. Improving cassava's tolerance to drought is important to help increasing yields in the semi-arid Sub Saharan African regions where cassava as an essential crop. Cassava's natural stress tolerance can be substantially improved by breeding, especially by marker-assisted selection of key physiological traits associated with drought tolerance.

Under this project we have constructed a BAC-based fingerprint map of an inbred cultivar of cassava. A BAC library of 70,000 BAC clones has been fingerprinted and a minimum tiling path (MTP) of clones has been selected. The ends of the BACs in the MTP are being sequenced and selected low-copy sequences spread throughout the genome will be re-sequenced in a panel of 10 cassava genotypes to identify single nucleotide polymorphisms (SNPs) and a linkage map will be constructed using two mapping populations generated at the Center for Tropical Agriculture (CIAT). This project will deliver SNP markers for uniformly distributed around the genome that will be useful for identifying quantitative trait loci (QTL) associated with drought tolerance.


Generation Challenge ProgrammeA project funded by the Generation Challenge Programme of the Consultative Group on International Agricultural Research

GCP Project G3007.03: "Development of Genomics Resources for Molecular Breeding of Drought Tolerance in Cassava"

Quick Links

The GMOD Generic Genome Browser showing the FPC fingerprint map of cassva inbred AM560-2, generated at UC Davis

A BLAST server including databases of Cassava ESTs from GenBank, assembled ESTs using DFCI's TGICL tool, and WGS reads from inbred AM560-2 generated by DOE-JGI

Download BAC End fasta, Assembled Cassava ESTs or SNP information from the downloads section.


Principal Investigator

Pablo Rabinowicz Institute for Genome Sciences, Department of Biochemistry and Molecular Biology University of Maryland School of Medicine Baltimore MD, USA


Alexander Myburg African Center for Gene Technologies Department of Genetics Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria, South Africa

Jane Morris African Center for Gene Technologies University of Pretoria Pretoria, South Africa

Chris Rey African Center for Gene Technologies School of Molecular and Cell Biology University of the Witwatersrand Johannesburg, South Africa

Mingcheng Luo University of California Davis CA, USA