October 2013

Using Genomics to Thwart Two Plant Viruses
Decimating a Source of Dietary Carbohydrates
Illumina sequencing is enabling BecA-ILRI Hub researchers to better understand two viruses
responsible for infecting cassava crops throughout Africa.

Recognizing that its technology could
play a critical role in alleviating global
hunger, malnutrition, and poverty, Illumina
created the Agricultural Greater Goodinitiative. Each year, Illumina awards
Greater Good grants to agriculturalresearch organizations that are focusedon identifying and breeding plants and animals that will increase
the sustainability, productivity, and nutritional density of crop andlivestock species. Under the grants, Illumina sequencing andgenotyping reagents are provided free of charge.

BecA-ILRI Hub
2013 Illumina Greater Good
Initiative Award Winner

Introduction
People living in sub-Saharan Africa have learned to make the mostof plants that can survive the environmental extremes of the region.
Cassava, a woody flowering shrub that grows well in poor soil andrequires little water, is one such plant. Introduced to Africa from Brazil
in the 16th century by Portuguese traders, every part of the plant has
a use. The leaves are eaten as vegetables. The leaves and branches
are processed into biofuel and animal feed. The tuberous roots are anexcellent source of carbohydrates and can be eaten fresh, cooked,fried, or processed into syrup, flour, or powder, forming the basis of avariety of culinary dishes.
Cassava is a staple food in Africa, providing more than 200 million
people with 50% of their daily carbohydrate intake. It’s the third-largest
source of food carbohydrates in the tropics, after rice and maize.
While it can withstand the withering heat and drought-like conditionsof the region, cassava is susceptible to several viral infections thatdamage its tubers, making them inedible. The Biosciences Easternand Central Africa (BecA) Hub is managed by the International
Livestock Research Institute (ILRI) and possesses world-classresearch facilities where genomics tools, such as the Illumina
MiSeq® sequencing system, are used to understand and combat
these diseases.

BecA-ILRI Hub Supports Genomics Researchand Innovation“The BecA-ILRI Hub1 is ten years old,” said Appolinaire Djikeng, Ph.D.,
Director of the BecA-ILRI Hub. “We’ve refurbished and upgraded ourlaboratory infrastructure, established a world-class research program
and revolutionary capacity-building activities, and now want to drive
research innovation to support agricultural development in Africa.”
All of the BecA-ILRI Hub’s projects are in collaboration with national
agricultural research institutions and universities in Africa. “The natureof that collaboration helps us to have a conduit for transferring theknowledge and data back to people who can use it,” Dr. Djikeng
said. “We created the Africa Bioscience Challenge Fund to identify

Cassava is harvested not only for its roots, which resemble sweet potatoes,
but also for its leaves, trunk, and branches.
Appolinaire Djikeng, Ph.D., is Director of the BecA-ILRI Hub which isheadquartered in Nairobi, Kenya.

October 2013
scientists from universities and research institutions who are inneed of integrating one aspect of the technology into their research
programs. We host them at the BecA-ILRI Hub up to 9 months,
during which they can learn genomic techniques and apply them tocurrent projects.”

Sequencing Ellucidates Cassava Virus SpreadHigh-throughput sequencing has enabled the BecA-ILRI Hub to better
integrate genomics and support projects in the region. “We now offer
a subset of genomic strategies, mainly SNP-based genotyping andsequencing,” Dr. Djikeng said.
Receiving the Greater Good Initiative award provided support for Dr.
Djikeng and his team to investigate the causes and transmission ofcassava mosaic begomoviruses, the causal agents of cassava mosaic
disease (CMD), and cassava brown streak viruses that cause cassava
brown streak disease (CBSD). These diseases are transmitted by thewhite fly (Bemisia tabaci), which is responsible for their spread fromplant to plant and field to field in Tanzania (the country of origin) andother parts of Africa.
“Statistics from 2005 indicate that CMD alone has spread to ninecountries in eastern and central Africa, covering a region of about
2.6 million square kilometers,” said Dr. Djikeng. “It’s caused an
estimated 47% loss in cassava production. Cassava isn’t widelyexported, so lower production rates negatively impact local
populations that depend upon it as a food source.”“We’re in the early stages of a third project to interrogate cassava
viruses in circulation in different agro-ecological zones,” Dr. Djikeng
added. “We’re looking primarily at mixed crop systems. We want
to see if there is any indication of CMD or CBSD host tropism—amechanism that enables viruses to adapt and establish either an
infection or the ability to live in a different host, causing the disease tospread even further.”
The BecA-ILRI Hub team is also using the MiSeq system to look at
the transcriptomes, as well as the microbial populations within thesecrops. “The MiSeq is a simple system to use and the running costis low,” said Dr. Djikeng. “It’s the type of technology we need in thisregion to perform genomic analysis.”
According to Dr. Djikeng, his team is also fortunate to be collaboratingwith Dow AgroBiosciences, and have access to their expertise andan Illumina HiSeq® system. “We’re dividing the work between the two
facilities, with any high-throughput sequencing jobs being performedat Dow AgroBiosciences,” Dr. Djikeng said. “We hope to complete
most of the sequencing by the end of this year, with analysis and data
integration to follow.”

References1.

http://hub.africabiosciences.org/

2.

http://www.ari-mikocheni.org/home/mari-information/staff-profiles/

3.

http://www.iita.org/

Greater Good Award Supports Multiple
Genomics Projects
According to Dr. Djikeng, the Greater Good Initiative award is funding
three projects. “The first is in support of Dr. Joseph Ndunguru[Mikocheni Agricultural Research Institute (MARI)2] and focuses on
disease diversity and using deep sequencing to assess viral diversity,”
Dr. Djikeng said. “The second project supports Dr. Morag Ferguson’sresearch [International Institute for Tropical Agriculture (IITA)3 andBecA-ILRI Hub] to resequence the genomes of different cassava
varieties, looking for genome differences, and associating markers withphenotypic characteristics. Some of those phenotypic characteristics
are for resistance or susceptibility to CMD and CBSD.”

Illumina, Inc. • 1.800.809.4566 toll-free (U.S.) • +1.858.202.4566 tel • techsupport@illumina.com • www.illumina.com
FOR RESEARCH USE ONLY
© 2013 Illumina, Inc. All rights reserved.
Illumina, illuminaDx, BaseSpace, BeadArray, BeadXpress, cBot, CSPro, DASL, DesignStudio, Eco, GAIIx, Genetic Energy,
Genome Analyzer, GenomeStudio, GoldenGate, HiScan, HiSeq, Infinium, iSelect, MiSeq, Nextera, NuPCR, SeqMonitor, Solexa,TruSeq, TruSight, VeraCode, the pumpkin orange color, and the Genetic Energy streaming bases design are trademarks or registeredtrademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.
Pub. No. 1370-2013-004 Current as of 18 October 2013