Scientists use DNA sequence information to unravel the origins of cassava, provide resources for its genetic improvement

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, causing disfiguration, curling, and yellowing of leaves, and cassava brown streak disease, 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, Berkeley, 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 as M. 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.
Many of the common cassava varieties in many countries were found to be nearly identical. 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 cassava breeding program, Ibadan, Nigeria.
History of the cassava breeding program in Africa
The study 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 re-opened by the British. It focused on breeding cassava for resistance to cassava mosaic disease, and later, cassava brown streak disease.
After screening cassava from many parts of the world, they were unable to find varieties with high levels of resistance to these diseases, so they started making crosses with wild species including M. glaziovii and “tree cassava”.  M. glaziovii, was introduced to Tanzania during the time of German colonization for rubber production. These trees now grow in the wild, particularly in coastal areas of Tanzania and are an ancestor of “tree cassava” found in many homesteads and on the edge of fields where their 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.
When the Amani program closed, many of the varieties were transferred to Mtwapa in Kenya and Moor Plantation in Nigeria. IITA have used the varieties from Moor Plantation extensively in their breeding programs. 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.

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