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Bioinformatics Evolves With Expansion And Partnerships at Pioneer Hi-Bred

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JOHNSTON, Iowa--Agricultural genetics company Pioneer Hi-Bred International announced last month that it will expand its research and training facilities here. A 130,000-square-foot expansion at the Reid Research Facility will allow more room for, among other activities, Pioneer's genomics efforts.

The company said the facility will enable Pioneer to expand research programs related to quality grain, agronomic, and industrial use traits. Research staff will focus on genomics and enabling technologies for developing seed, grain, grain products, plant materials, and other crop improvement products for corn, soybean, and other selected oilseed crops.

Pioneer also announced it is doubling funding of its gene discovery collaboration with CuraGen from $2.5 million a year to a minimum of $5 million. Pioneer Vice-President and Director of Trait and Technology Development Tony Cavalieri called the agreement "an affirmation of Pioneer's commitment to genomics."

Bob Merrill, who heads Pioneer's 18-month-old bioinformatics department, and Lisa Lorenzen, a computational biologist, spoke with BioInform recently about the direction their bioinformatics program is taking as the company expands its genomics efforts.

Agricultural genomics pioneer

Within the agriculture industry, Pioneer is a genomics pioneer. While life sciences companies such as Monsanto and DuPont are investing heavily in genomics research, Pioneer claims to be the only true agriculture company with a genomics program.

"We come at agricultural genetics and genomics from a different perspective," Merrill explained. "What Pioneer has always been about is providing advanced genetics for development of agriculture products. So we view the genomics effort as another key tool in our ability to continue our company's mission of providing genetics to help feed the world's population."

In fact, Pioneer's genomics informatics efforts are really an extension of the informatics program the company has had for 20 years. Pioneer's extensive breeding programs around the world are completely computerized, Merrill explained. "We can do data collection and analysis for over 2 million agricultural field research plots per year," he said.

"In terms of informatics, because of the genomic sciences that are being brought together with it, this is a new area for us. But we have a lot of experience managing information around the genetic processes of plant breeding. So we view this as just another set of technologies to apply to Pioneer's processes involved with product development," Merrill said.

Strategic partnerships

The commercialization of genomics technologies has rapidly changed the competitive landscape for Pioneer and other agriculture companies, Merrill pointed out. Pioneer aims to develop strategic partnerships with genomics technology providers. "Our approach has been to identify useful technologies, develop them in-house or partner with the organizations that have them, and integrate these technologies into Pioneer's development efforts for agricultural genetics," said Merrill.

Pioneer has gotten a jump start on partnership opportunities. For instance, Pioneer is entering the third year of a collaboration with Human Genome Sciences--from which it received a proprietary sequence database and associated software--and is approaching the first anniversary of its agreement with CuraGen. "Where HGS is providing information regarding expressed sequence tags, CuraGen is a partner in collecting expression information," Lorenzen said.

In a collaboration formed less than a year ago, DuPont bought a 20 percent equity stake in Pioneer and set up a broad research alliance for genomics and gene trait quality improvement. "Researchers in both organizations are just beginning to realize the value of that alliance," Merrill said. "It has the potential of opening up large areas of DuPont's research organizations to Pioneer researchers and allows DuPont's researchers access to a lot of the technology research at Pioneer."

Those alliances fit with the direction of Pioneer's bioinformatics department. "We see the role of the bioinformatics effort at Pioneer as one of integrating all the various technologies from a number of different sources, such as our partners," said Merrill. "Our job is taking all those information sources and integrating them into Pioneer's system so we can combine information about sequence, expression, and function together with our large phenotypic database of field trial results. That way we can figure out how the genes work in the organisms of interest--for us, primarily corn and soybean," said Merrill.

The partnerships also serve to leverage Pioneer's bioinformatics capabilities. Lorenzen said that Pioneer taps into the knowledge and experience at HGS, CuraGen, and DuPont. "It's very much an interactive scientific collaboration with our partners," Merrill said. "It's not a cash and carry application development relationship."

Bioinformatics integrated with product development

The same goes for in-house relationships. Pioneer's five-person bioinformatics team, integrated tightly with a 35-person research and computer application development group, doesn't operate outside the fray. "Everything that we do needs to tie in to how we develop products," Merrill said.

"The key is to be able to integrate genomics technologies and related computer software into our product development process. Pioneer has a strong commitment to product development and we see the genomic and advanced laboratory technologies as tools that allow us to improve our product development process."

Genomics has brought several different scientific technologies together and shown the value of combining this information," said Lorenzen. She said the bioinformatics group looks at four areas: sequencing, expression, mapping, and functional data. "Bioinformatics ties these four pieces together so that the scientists can go to one place and locate everything they want to know about the gene of interest," she explained.

Lorenzen said, "We don't look at genomics as being the end of the story. It's the beginning of the story. That's where we identify the genes we want to enhance the product. We have a long testing process to make sure the gene consistently behaves as expected."

Added Merrill, "Part of that testing feeds into our large field trial evaluation effort which we have informatics set up to run and manage. Bioinformatics is feeding new information into our product development process with the hope of providing better products for our customers."

Despite appearing to be ahead of the curve on that front, Merrill is cautious. "The technology of genomics and informatics is evolving rapidly and a lot of financial resources are being spent for research in genomic and bioinformatic technologies. No one should feel safe or comfortable whether or not they're ahead of the competition. It changes so fast."

--Adrienne Burke

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