A team of international scientists that has been studying DNA sequence information from cassava varieties grown all over the world have provided clear evidence on the ancestry of cassava. They have also published a high-quality genome assembly of the hardy crop which will be very useful in efforts to improve cassava.

Cassava is a very important food staple in sub-Saharan Africa, yet its yield and quality are compromised by two damaging virus diseases: cassava mosaic disease (CMD), causing disfiguration, curling, and yellowing of leaves, and cassava brown streak disease (CBSD), causing severe browning in the storage roots. The new DNA sequence resources will help scientists develop varieties that are resistant to these virus diseases.

The team comprised scientists from the International Institute of Tropical Agriculture (IITA), the University of California, the United States Department of Energy Joint Genome Institute (DOE JGI), and from National Agricultural Research Organizations of Tanzania, Nigeria, Fiji, and Micronesia, among others.

The team sequenced 58 wild and cultivated cassava varieties including related species such as Caera or Indian rubber (Manihot glaziovii), and genotyped 268 African cassava varieties. The team has published the results in the April issue of the journal Nature Biotechnology. The paper is titled “Sequencing wild and cultivated cassava (Manihot esculenta) and related species reveal extensive interspecific hybridization and genetic diversity”.

“The development of genomic resources, such as this chromosome scale reference sequence, has increased understanding of the genetic diversity of cassava and its wild relatives, and given insights into its population structure. It is expected this will accelerate progress in basic biological research and genetic improvement,” says Morag Ferguson, Molecular Geneticist at IITA-Kenya and one of the scientists in this effort and co-author of the paper.

The study also provided clear evidence to support the hypothesis that cassava was domesticated from a wild species, known asM. esculenta subspecies flabellifolia, in the western part of the southern Amazon region in Brazil, and went through a “genetic bottleneck”, restricting the amount of genetic diversity in cassava.

This reduction in cassava genetic diversity, especially in Africa, was a result of the use of a limited number of parents in the development of new varieties. This is important knowledge to guide breeding decisions to restore lost variation.

“We are excited about the results of this study. As a clonally propagated crop, genetic improvement of cassava through conventional breeding is a complicated and lengthy affair. Therefore understanding the genetic diversity of cassava and its wild relatives will support genome-enabled breeding efforts,” says Peter Kulakow, Head of IITA’s cassava breeding program, based in Ibadan, Nigeria.

History of the cassava breeding program in Africa

The study also provided useful insights into cassava varieties in Africa and their breeding history. The scientists studied varieties from a past cassava breeding program in Amani, Tanga Province, in Tanzania, which was started under the Germans, closed during World War II, and later reopened by the British. It focus was on breeding cassava for resistance to cassava mosaic disease, and later, cassava brown streak disease.

After screening cassava from many parts of the world, these early breeders were unable to find varieties with high levels of resistance to these diseases and therefore resorted to making crosses with wild species including M. glaziovii and “tree cassava”. Introduced to Tanzania during the time of German colonization for rubber production, M. glaziovii and their inter-specific hybrids “tree cassava” now grow in the wild, particularly in coastal areas of Tanzania. The cassava tree leaves are used as a vegetable.

Sequence information revealed that some of the popular cassava varieties in Tanzania including Namikonga and Muzege, still contain sections of M. glaziovii in their genomes. These varieties are also among the most tolerant to CBSD. Other popular varieties are related and are likely to have been derived from the Amani program; these include Nachinyaya, Albert, and Kibaha.

Following the closure of the Amani breeding program, many of the varieties were transferred to the Moor Plantation in Nigeria. The cassava breeding program at IITA has extensively used these inter-specific hybrids from Moor Plantation to produce a large number of high-yielding improved varieties with resistance to pests and diseases. Evidence of this is shown by trace sections of M. glaziovii DNA that were found in many IITA developed varieties. These sections are rare, however, in farmer varieties from Southeast and Central Africa.

Other institutions involved in the study included Koronivia Research Station (Fiji); French agricultural research and international cooperation organization (CIRAD) (Vanuatu); Mikocheni Agricultural Research Institute (Tanzania); Naliendele Agricultural Research Institute (Tanzania); Donald Danforth Plant Science Center (USA) Cornell University (USA), Monash University (Australia); and Dow AgroSciences (USA)

Originally published by IITA as Scientists use DNA sequence information to unravel the origins of cassava and provide resources for its genetic improvement. Photo: D. Dufour/Roots, Tubers and Bananas