Development of Genomics Resources for Molecular Breeding of Drought Tolerance in Cassava

Cassava is an important root crop in unfavourable environments in poor areas of developing countries. As cassava is often cultivated in dry areas, research towards improvement of drought tolerance in cassava is needed. In order to accelerate the advance of genetic improvement of cassava, genomic resources must be made available to the community. A genome sequencing project for cassava has already been initiated at the U.S. D.O.E. Joint Genome Institute (JGI) in Maryland, USA. A partially inbred cultivar generated at CIAT has been selected for genomic sequencing to avoid the problem of heterozygosity.

The CGIAR Generation Challenge Programme has provided funding for a project aimed at developing a panel of single nucleotide polymorphism (SNP) markers on a genome-wide basis to localize favourable alleles in existing mapping populations, generated from contrasting drought tolerance genotypes. For this purpose, a bacterial artificial chromosome (BAC) library from the same genotype being sequenced at JGI is being fingerprinted. A set of minimally overlapping clones or minimal tiling path (MTP) will be selected and the ends of all BAC clones in the MTP will be sequenced for SNP discovery.

In the mean time, SSR markers in the parents of the mapping populations are to be tested to estimate the level of polymorphism. The genome-wide SNP marker set that this project will deliver will allow identification of quantitative trait loci (QTL) associated with drought tolerance by high-throughput genotyping of validated SNPs.

As cassava is a close relative of castor bean, whose genome has been sequenced, once the genome sequence and fingerprint map of cassava are released, it will be possible to conduct comparative analyses within the Euphorbiaceae family. This kind of information will facilitate the elucidation of the evolutionary history and domestication of cassava.

Furthermore, the availability of a fingerprint map and the genome sequence for one genotype of cassava will open the door for genome-wide diversity studies using other cultivated or wild cassava varieties in comparison with the reference genome. Next-generation sequencing technologies will make it affordable to re-sequence different cassava genomes and take full advantage of the broad genetic diversity of cassava for breeding and crop improvement.

This international project is being led by Dr Pablo Rabinowicz of the University of Maryland, involves the University of California, as well as two ACGT partner institutions, the University of Pretoria (Prof Zander Myburg) and University of the Witwatersrand (Prof Chrissie Rey). South African involvement was facilitated through the ACGT’s standing as a consortium member of the Generation Challenge Programme.