AgSeq comes to Texas A&M AgriLife Research

Texas A&M, PerkinElmer create leading public agriculture, life sciences genome platform

Writer: Kay Ledbetter, 806-677-5608,
Contact: Dr. Charlie Johnson, 979-862-3287,

COLLEGE STATION – Texas A&M AgriLife Research and their internationally recognized Genomics and Bioinformatics Service are poised to change the face of agriculture-focused genomics.

Dr. Charlie Johnson, director of the Texas A&M AgriLife Research
Genomics and Bioinformatics Service facility,
shows off the new equipment. (Texas A&M AgriLife photo)

“We are excited to make this significant announcement on National DNA Day, which celebrates the 15th anniversary of the Human Genome Project,” said Texas A&M University System Chancellor John Sharp.

“On a day designed to demonstrate to the public the advances in genetics and genomics, it is fitting we open the doors to a revolutionary, one-of-a-kind public agriculture and life sciences genome facility,” Sharp said. “This facility will impact the health of every Texan by empowering our Texas A&M researchers to develop healthy foods that are good for you, taste great, high yielding and sustainable.”

Masoud Toloue, vice president and general manager for applied genomics for PerkinElmer in Waltham, Massachusetts, said, “It is a great pleasure to expand upon our long history of collaboration with Texas A&M and AgriLife Genomics and Bioinformatics Service.

Matthew Stull, left, and Dr. Shichen Wang, standing,
Texas A&M AgriLife scientists,
discuss with Taylor Appleberry, seated right,
PerkinElmer field applications specialist,
the new Sciclone G3 NGS Workstation.
(Texas A&M AgriLife photo)

“PerkinElmer is a leading provider of innovative detection, imaging, informatics and service  capabilities,” Toloue said. “We offer solutions spanning the genomics workflow, including nucleic acid extraction, liquid handling, sample preparation, DNA/RNA quantitation, library preparation, data analysis and applications expertise.

“We look forward to working with Texas A&M in the future to bring genomic technology to agriculture researchers around the world,” he said.

The new Sciclone G3 NGS Workstation and JANUS G 3R NGS Express Workstation have been installed at the AgriLife Research Genomics and Bioinformatics Service at 101 Gateway Blvd, College Station.

“This will be a magnet for public and private agriculture researchers from around the state, country and world to come to Texas A&M to take advantage of this revolutionary advancement in DNA genotyping,” said Dr. Patrick Stover, vice chancellor of agriculture and life sciences at Texas A&M in College Station.

“The major limiting factor to scientists around the world striving to improve the healthy attributes and other advancements in crops and livestock has been the expense of genetic improvements,” Stover said. “Without genetic improvements, change through traditional breeding methods takes an extensive amount of time.”

Dr. Yanni Lun, front, and Prativa Gautam,
standing, exam the new JANUS. (Texas A&M AgriLife photo)

Dr. Craig Nessler, director of AgriLife Research in College Station, said AgriLife Research has been able to attract extremely qualified individuals to work in the areas of genomics.

“They have only been limited in capabilities by the equipment they were able to work with,” Nessler said. “This collaboration is putting the scientific knowledge with the state-of-the-art equipment.”

Dr. Bill McCutchen, executive associate director of AgriLife Research, College Station, said this combined effort is creating a whole new capability that did not exist before because of the high cost associated with DNA sequencing.

“Genetic researchers who were previously limited to screening handfuls of individuals due to extreme costs will now be able to screen tens of thousands of samples,” McCutchen said. “In combination with our new gene-editing tools, the ability to process greater numbers will result in faster improvements to crops and livestock, which is needed to meet the demands of the growing world population.”

Dr. Shichen Wang, left, and Dr. Joshua Hill,
right, unpack the Sciclone G3 NGS Workstation.
(Texas A&M AgriLife photo)

Dr. Charlie Johnson, director of the Genomics and Bioinformatics Service lab in College Station, said, “We have been striving for the last eight years toward a goal of becoming a world-leading center of agriculture genomic excellence. Now, with a capability of processing 50,000 samples per year with the ability to grow to 100,000 in the coming years, empowered by PerkinElmer’s state-of-the-art robotics systems, we are there.

“This has allowed us to launch our one-of-a-kind high throughput multimillion-dollar genomics research lab,” Johnson said. “We are very excited about the possibilities this will provide for Texas A&M and agricultural research around the world.”

He said the collaboration’s first output will be the development of an exclusive first-of-its-kind academic genotyping pipeline called AgSeq, which combines Illumina’s latest sequencing technology, PerkinElmer’s automation in library preparation, proprietary sample bar-coding system with capability to provide low cost genotyping-by-sequence using low coverage whole genome sequencing.

“Our service faculty will be the sole source for access to PerkinElmer’s custom high throughput DNA preparation kit designed for agriculture applications,” Johnson said. “In terms of research and development, our public-private team strives to develop solutions that will allow scientists to take full advantage of genomics across agricultural and life science applications in ways that have been impossible until today.”

He said through economies of scale, process optimization, robotics and new biochemistry, the laboratory will be able to slash the cost per sample by 600 percent for large-scale DNA genotyping projects.

“Previously, these larger projects were done using technologies that all had significant drawbacks – the biggest when it comes to whole genome sequencing based genotyping was cost,” Johnson said. “As an example, a human genome cost between $1,500-$2,400 to be sequenced in a commercial lab. Using all the tools we are developing, using low coverage sequencing, we can obtain 85-95 percent of the same information for 33 times lower cost.

“This puts the price point of sequencing-based genotyping at the same level or below DNA microarray,” he said. “One of the great limiting factors for large-scale agriculture and life science genome research has been cost, which limits the size of studies.

“Today we have made great strides to remove that barrier and expect over the next year as new technologies under development are launched we will see an even greater use of genomic technology in agriculture,” Johnson said.

To facilitate the utilization of this technology, AgriLife Research is providing funds to create population genetic maps in corn, cotton, sorghum, wheat and pepper, he said. The focus of this program will be to develop molecular markers to improve plant water use efficiency.

“This program ties into our new Gene Editing and Crop Transformation labs, so that as new discoveries are made, we can help accelerate the creation of new varieties for the farmers of Texas,” Johnson said.

To access more information on the technology, contact Johnson at or go to