New way to detect Palmer amaranth in contaminated seedlots
Sources:
Patrick Tranel, 217-333-1531, tranel@illinois.edu; Diane Plewa,
217-300-3441, dplewa@illinois.edu
News
writer: Lauren Quinn, 217-300-2435, ldquinn@illinois.edu
URBANA, Ill. – Last summer, farmers in the
Midwest got an unwelcome surprise after planting native seed on
Conservation Reserve Program acres. Palmer amaranth, the aggressive and
hard-to-kill weed, had established in droves. As a possible solution, some
states declared Palmer a noxious weed, which prohibits its sale and transport.
“I’ve
had seed growers call me,” says Pat Tranel, molecular weed scientist in the crop sciences
department at the University of Illinois. “Their businesses are up in the air
because of this. Unless they have a way to certify their product is Palmer-free,
they can’t sell it.”
The
typical testing method involves growing a sample of seeds until the plants are
large enough to be identified, but this is a slow and potentially unreliable
process.
“It
all takes a long time, and sometimes the seeds don’t germinate during the
test,” Tranel says. “Alternatively, there’s a company that will test individual
seeds using DNA sequencing, but they’re charging $100 per seed. It’s not
cost-effective.”
Tranel
and graduate student Brent Murphy developed a way around these issues. Their
low-cost method can identify Palmer amaranth DNA from within a mixed sample
without having to grow the plants. The assay, which uses a method known as
quantitative PCR, can detect genetic variations unique to Palmer even when
flooded with samples from closely related species, including waterhemp.
“Palmer,
redroot pigweed, waterhemp – they all have tiny black seeds that basically look
the same. We needed a way to efficiently extract DNA from pooled seed samples
and, if it’s present, identify Palmer,” Tranel says.
Once
Tranel and Murphy developed this assay, they worked with U of I
Extension’s Plant Clinic to optimize the test for mixed seed
samples. Diagnostic outreach Extension specialist Diane Plewa and Plant Clinic
technician Elizabeth Phillippi began trying different methods to extract DNA
from seed. The assay is very sensitive, but if DNA is not correctly extracted
from a lone Palmer amaranth seed in a mixed sample, it won’t be detected.
“The
trick,” Plewa says, “is to make sure every seed is ground up during the
extraction process.”
The
researchers were able to consistently detect a single Palmer amaranth seed when
mixed with 99 waterhemp seeds, and they believe the assay could achieve even
greater sensitivity with additional refinement.
The
Plant Clinic has optimized a protocol for commercial testing of seed lots. “We
have a test that we feel very confident in,” Plewa says. “We are offering the
service now, for $50 per sample.” For more information, call 217-649-3941 or
visit the Plant Clinic website.
The article, “A quantitative assay for Amaranthus
palmeri identification,” is published in Pest Management
Science. Authors Brent Murphy and Pat Tranel are housed in the Department
of Crop Sciences at U of I, and Diane Plewa, Elizabeth Phillippi, and Suzanne
Bissonnette are from U of I Extension’s Plant Clinic. The work was supported by
a USDA National Institute of Food and Agriculture Hatch grant.
