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By Fred Miller U of A System Division of AgricultureAug. 2, 2017
Related Video: Rice Breeding and Researchhttps://www.youtube.com/watch?v=infKOyhd2FE
(1,231 words)(Download this story in MS Word here.)
FAYETTEVILLE, Ark. — Rice scientists are developing advanced gene editing tools for
the University of Arkansas System Division of Agriculture crop breeding toolbox.
Rice breeders today develop improved varieties from genetic breeding stock that has
been advanced through thousands of generations and over many decades with conventional
crossbreeding techniques, said Vibha Srivastava, professor of crop, soil and environmental
sciences for the Division of Agriculture.
Since rice breeding began at the division’s Rice Research and Extension Center near
Stuttgart in the 1930s, more than 40 rice varieties — oftened referred to as “cultivars”
— have been released, helping propel Arkansas to the lead in U.S. rice production.
The state accounts for half of the nation’s rice production.
“Variety development is an important core effort in Division of Agriculture research,”
Srivastava said. The continual need for new varieties is driven by nature’s tendency
to change growing conditions.
Such changes include plant diseases that mutate to overcome resistance and insects
that eventually adapt to defeat a plant’s natural defenses. Environmental changes
can include climate changes that affect air temperature or water availability, or
the invasion of new weeds or insects.
In order to keep up with the demand for improved cultivars, breeders may soon have
to look far afield — outside available breeding stock — in order to find new genetic
traits for improved rice varieties, Srivastava said.
A lot of useful genetic traits are available in wild relatives of rice, Srivastava
said. But to move those traits into available breeding stock by conventional means
would require hundreds or thousands of crossbred generations that would take decades
Advancing the process
Gene editing makes that process faster, easier and more precise by providing a means
to recreate such traits in existing breeding stock, Srivastava said.
She is adapting a technology called “CRISPR,” scientific shorthand for “clustered
regularly interspaced short palindromic repeats.” These are segments of DNA that contain
short, repetitive base sequences.
The Division of Agriculture recognized the importance of gene editing technology,
Srivastava said, and invested in a research program to develop it for use in Arkansas
rice breeding. The program teams Srivastava with two other division scientists — plant
pathologist Ken Korth and weed scientist Nilda Burgos.
She emphasizes that gene editing is not the same as genetic modification, in which
genetic code from one organism is inserted into another organism.
Under current USDA policy, CRISPR and other gene editing techniques are not considered
genetically modifying technology. Srivastava recently received a USDA grant to further
“A plant’s genetic traits are developed through mutations that occur naturally in
response to environmental stresses,” Srivastava said.
Those mutations could be viewed as naturally occurring gene editing that results in
new information being stored in the plants’ genes. As a tool for plant breeders, Srivastava
said, gene editing provides a way to copy and paste that information from rice plants’
wild or distant cousins into available breeding stock.
“We use the information from the wild plant to try to induce the same mutation in
breeding stock,” Srivastava said.
Srivastava said gene editing is not currently being used in Division of Agriculture
crop breeding programs. Division plant breeders in rice and other crops use available
breeding stock developed by conventional methods.
Gene editing technology was developed in 2012 and has been studied more broadly by
Srivastava and other scientists around the world since then. Building on her background
in biotechnology development, Srivastava is learning how to apply the technology to
rice and testing its effectiveness.
The goal is to have the technology and proven methods for using it ready when plant
breeders need it. “If you’re not working on this, you’re already out of date,” she
Applications in crop breeding
In her research, Srivastava is applying gene editing to tackle a persistent problem
in rice grain quality — chalkiness.
Under certain environmental conditions, including high nighttime air temperatures,
starch formation in the seed can take on a chalky texture that lowers the grain quality.
Chalky rice heats unevenly during processing or cooking, leading to broken kernel
or undesireable food texture.
Srivastava is targeting a gene that controls the development of chalkiness in rice.
The gene is a regulator of processes that lead to chalky texture that responds to
A naturally occurring mutation in a Chinese rice variety changes how that regulator
gene responds to stress and reduces the inclination to form chalky texture. Srivastava
is using gene editing techniques to take the information from that Chinese rice and
try to induce that same mutation in Arkansas rice.
“The reference (mutated) gene is only used to understand how it works,” Srivastava
said. “No genetic material is actually being transferred from one plant to the other.”
In another application of the technology, Korth is working with senior graduate assistant
Kathryn Haydon to turn off a gene that controls production of enzymes that cause rancidity
in the bran layer of the rice seed.
The bran layer is removed when processing white rice, but is left in place to make
brown rice. Korth said white rice will last virtually forever on store shelves or
in kitchen pantries, but brown rice goes rancid in a matter of months.
If Haydon’s efforts can result in gene-edited rice that turns off or reduces that
enzyme production, the shelflife of brown rice may be extended, Korth said.
Nilda Burgos …
Burgos is applying CRISPR technology to generate herbicide resistance in crops, using
rice as the model.
“We intend to use information on herbicide resistance traits from weeds to endow rice,
or other crops, with the same traits,” Burgos said. “I am looking for genes in weeds
that are not already used by the chemical companies for crop improvement.”
“I’m in an exploratory phase, using a well-known PPO- inhibitor-resistance trait
in Palmer amaranth,” Burgos said.
PPO refers to protoporphyrinogen oxidase, an enzyme that is targeted by some herbicides
such as Aim, Blazer, Goal Tender, Reflex/Flexstar, Ronstar, and Spartan Charge.
Burgos said Patrick Tranel, a weed scientist from the University of Illinois at Champaign-Urbana,
first discovered the gene mutation in tall waterhemp. The same mutation occurs in
PPO-resistant Palmer amaranth.
Burgos’ Lab also found other mutations in the PPO gene of PPO-resistant Palmer amaranth, which may be useful for editing in rice or
A crop with such a trait would allow farmers to use PPO-inhibitor herbicides “over
the top” to control weeds even while the crop is growing in the field.
Once she works the kinks out of the technique in rice, Burgos wants to apply the technology
to other traits and other crops.
CRISPR technology, Burgos said, gives plant breeders a way to develop useful herbicide
resistance in commercial crops without introducing foreign genes.
When perfected, gene editing will prove a valuable tool for plant breeders working
to develop new varieties with improved disease-resistance, plant health and cultivation,
and post-harvest quality, Srivastava said.
The techniques they’re developing for rice can also be applied to soybeans, wheat
and other crop breeding programs, she said.
For now, Srivastava said, their gene editing work stays in the Arkansas Agricultural
Experiment Station’s labs and greenhouses in Fayetteville. “We’re not developing breeding
material at this stage,” she said. “None of these plants will leave the lab.”
“Our aim is to have the technology ready for when it is the right time to use it to
help keep the Arkansas rice industry competitive in world rice markets,” Srivastava
About the Division of Agriculture
The University of Arkansas System Division of Agriculture’s mission is to strengthen
agriculture, communities, and families by connecting trusted research to the adoption
of best practices. Through the Agricultural Experiment Station and the Cooperative
Extension Service, the Division of Agriculture conducts research and extension work
within the nation’s historic land grant education system.
The University of Arkansas System Division of Agriculture offers all its Extension
and Research programs to all eligible persons without regard to race, color, sex,
gender identity, sexual orientation, national origin, religion, age, disability, marital
or veteran status, genetic information, or any other legally protected status, and
is an Affirmative Action/Equal Opportunity Employer.
# # #
Media Contact: Mary HightowerDir. of Communication ServicesU of A Division of AgricultureCooperative Extension Service(501) email@example.com