April 2015

Genomics Powers Development of Higher Yielding,More Nutritious Orphan Crops in Africa
Illumina sequencing accelerates gene function studies and plant breeding programs.
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 cropand livestock species. Under the grants, Illumina sequencing
and genotyping reagents are provided free of charge.

2015 Greater Good
Initiative Award WinnerIntroduction
A child malnourished during its first 1000 days of life will often
succumb to the effects of stunting, a form of growth failure. An
irreversible syndrome, stunting reduces a child’s chance of survival
and impairs cognitive ability. In Sub-Saharan Africa, 35–40% ofchildren under 5 years old are stunted. The long-lasting effects include
a reduction in school and work performance, which impacts thedevelopment potential of nations1.

Allen Van Deynze, PhD, is technical lead for the AOCC program andDirector of Research for the Seed Biotechnology Center at UC Davis. He
specializes in applying genomic technologies to plant breeding.

Chronic malnutrition in Africa is caused primarily by insufficientamounts of 5 nutrients in the diet: vitamin A, vitamin C, iron, zinc, andiodine. The species of crops grown by African smallholder farmers
have not been bred for high yield, increased nutritional value, or theability to adapt to abiotic and biotic stress from the environment orpests. Neglected by researchers and industry because they are noteconomically important on the global market, these “orphan crops”
form the basis of diets in many African countries.
The African Orphan Crops Consortium (AOCC) wants to change this.
AOCC is an open collaboration with a mission to curb malnutrition
and the incidence of stunting in African children. The consortium wasconceived in 2011 by Howard-Yana Shapiro, PhD, Chief Agricultural
Officer at Mars Corporation and Ibrahim Mayaki, CEO of the New
Partnership for Africa’s Development (NEPAD). Its goal is to identify
robust species of orphan crops, and to train African plant breeders indeveloping new varieties that improve African diets and health. Allen
Van Deynze, PhD, Director of Research at UC Davis and member ofthe AOCC Steering Committee, is a leader in applying genomics toidentify traits rapidly that breeders can use to select for higher yielding,more nutritious crops.

Combining Plant Breeding with Genomics“Through AOCC, we’re combining genomics and breeding to makecrops more productive,” explains Dr. Van Deynze. “Illumina sequencingand genotyping technologies enable us to essentially skip the 10–15
years of basic breeding used to select for traits in the field. Using
DNA markers, we can advance the breeding process and reduce thetimeline to 5–10 years depending on the crop’s life cycle.”

The Greater Good Award will support RNA sequencing of 50 orphan crop
plant species, including finger millet (left) and the leafy spider plant (right),
with the HiSeq® System.

April 2015
The AOCC program will sequence 101 species, and 100 plant lines
per species. Crops include trees, vegetables, and legumes, which
produce the fruits, nuts, leaves, and seeds used as food. One of thefirst species that will be sequenced is finger millet (Eleusine coracana),
a highly nutritious methionine-containing grain used to make a foodsimilar to grits, but with more texture. The leafy spider plant (Cleomegynandra), which resembles spinach and is eaten cooked, will also
be sequenced. The varieties of these plants that exist in Africa are
not improved or selected to grow well in areas such as Kenya orBenin. The idea is to select crops and use genetic selection andcrossbreeding to produce varieties that deliver the best yield andnutritional traits for specific geographies.

A Multi-Phase Sequencing Program to Optimize
Orphan Crops
There are several phases to the AOCC’s sequencing program, withthe first focused on DNA sequencing of each species to establish
reference genomes. The reference genome is used to compare
plant species. “Of the 101 crops we’re working on, only 15 havebeen sequenced or have a completed genome published by othergroups,” said Dr. Van Deynze. The next phase of the program
involves resequencing at least 100 varieties to reveal genetic diversityand define the alleles useful for breeding. Breeders will grow these
100 plant lines in the field to identify which ones have the desired
traits. They’ll use crossbreeding to combine these plant lines into
better varieties.
The Greater Good Initiative will support the annotation and genediscovery phase of the program. In this phase, transcriptome
sequencing (RNA-Seq) of 50 species will be used to analyze gene
expression. RNA-Seq using Illumina HiSeq® Systems will be performedin Dr. Jasper Rees’ laboratory at the Agricultural Research Council
in Pretoria, South Africa. “Illumina jump-started the program,” Dr.
Van Deynze said. “With expression data, we’ll know which genes
are expressed in these 50 species as the plants grow. We’ll haveexpression data for half of our species in about a year. The Greater
Good Initiative is making a vital contribution and is a perfectcollaborator for this project.”Training and Funding for a Sustainable FuturePart of the AOCC is a plant breeding academy where 120 of the best
African breeders will be trained to integrate the sequence information
into their breeding programs. “We have a grant that will support ourwork with breeders, helping them to introduce new plant varieties
using the genomic tools that we’re creating,” Dr. Van Deynze said.
“Yet, our real long-term goal is to make the African Plant Breeding
Academy obsolete within the next 4 years. Because most African plant
breeding programs are not well funded, the AOCC is also working
with participants to obtain long-term funding and persuade African
governments to invest in breeding of their country’s crops.”
The program has already been successful. “This year, 1 of ourplant breeding academy students, Dr. Firew Mekbib, convinced his
government to provide funding,” Dr. Van Deynze added. “They’veopened a center focused on 38 crops indigenous to Ethiopia, which isa global center of orphan crop diversity. They’re funding PhD students’
education and the breeding programs to develop these crops. We’repleased that the AOCC plant breeding academy has already replicateditself in less than a year through the efforts of 1 of our own students.
That’s our biggest success right now.”

References
1.

Improving Child Nutrition: The achievable imperative for global progress,2013. UNICEF. data.unicef.org/corecode/uploads/document6/uploaded_
pdfs/corecode/NutritionReport_April2013_Final_29.pdf

Learn more about the Illumina system mentioned inthis article:•HiSeq Systems, www.illumina.com/systems/hiseq_2500_1500.
html

Follow the Illumina Agrigenomics Community“The advantage with Illumina sequencing systems is throughput,”
Dr. Van Deynze said. “We can obtain genome and genome annotation
data quickly and with good quality. While we want a very strong
reference genome, we also need to sequence it over and over tosample genetic diversity. One sequence is interesting, but the practicalpart of genomics and plant breeding is diversity. To capture diversity
we have to be able to sequence things quickly and affordably,something Illumina systems enable us to do. We need data from tensof thousands of plant lines in weeks, not years, or even months. That’s
how fast a breeding program works.”

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© 2015 Illumina, Inc. All rights reserved. Illumina, HiSeq, and the pumpkin orange color are trademarks of Illumina, Inc. and/or its affiliate(s) inthe U.S. and/or other countries. Pub. No. 1370-2015-003 Current as of 01 May 2015