KIWI HAND IN
WORLD-FIRST
International scientists including a University of Otago researcher
are the first in the world to use whole genome sequencing to help
diagnose a plant pathogen destroying crops on African farms,
potentially paving the way for preventing crop failures which is vital
to the African economy.
Dr Jo-Ann Stanton, a
senior research fellow
in anatomy, has helped
develop the PDQeX, one
of the two prototype technologies
which have made it possible to carry
out the whole genome sequencing
on remote African farms. “This
achievement opens the way to
rapid and accurate pathogen
identification, permitting immediate
corrective action to prevent crop
failure,” Stanton says. “For the
subsistence farmers of East Africa,
this is the difference between having
food and an income or going hungry.
Crop failure means a loss of food
security and no income for school
fees, supplies, farm improvements
or maintenance.” The team includes
scientists from Mikocheni Agricultural
Research Institute in Tanzania,
the National Crops Resources
Research Institute in Uganda, Jomo
Kenyatta University of Agriculture
and Technology in Kenya and the
University of Western Australia,
who all worked together under the
Cassava Virus Action Project with
cassava growers in three countries
- Tanzania, Uganda and Kenya.
Cassava - a tuberous root of a
tropical tree which produces flour
and a starchy vegetable similar to
potato - is under attack from viral
pathogens that reduce or destroy
the crop. Farmers affected by the
growing viral threat depend on
cassava for their main food source
and yearly income. “Eight hundred
million people worldwide depend
on cassava as their main source
of calories and virus spread is a
significant global threat,” Stanton
says. As a researcher, her vision
is to take complex molecular
diagnostics out of the lab and into
the hands of non-experts to facilitate
rapid, accurate and cost-effective
responses to real-life situations.
Using hand-held molecular
diagnostic devices, Stanton and
the team have been able to carry
out whole genome sequencing on
the farms. A device (PDQeX) from
New Zealand company ZyGEM that
permits on-site DNA extraction was
used together with the MinIT base-
calling mini-supercomputer made
by UK company Oxford Nanopore.
Bringing these technologies together
with the MinION, a portable DNA
sequencer, it has been possible to
select either leaf, stem or insect
samples on the farms, prepare
the DNA for sequencing and then
covert raw data to DNA sequence
reads for data interpretation, all in
real time. Stanton says the whole
process takes less than four hours
from sampling to diagnostic results
and all devices are run on battery
working outdoors at the farms. The
project has significant implications
not only for the African farmers,
she says. “On a broader level, this
breakthrough has applications in
areas of human and animal health,
environmental management and
conservation. The need for accurate,
rapid and on-site diagnosis is
growing as globalisation of human
activity accelerates.”
www.foodtechnology.co.nz 129
/www.foodtechnology.co.nz
