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NRC Calls for More Sequencing, 'Omics' Tool Development for Plant Genomics Initiative

NEW YORK (GenomeWeb News) – A federal cross-agency effort to plumb the secrets of plant life through genomics research should expand its sequencing capabilities and focus on developing new tools for epigenomics, transcriptomics, proteomics, metabolomics, and other so-called “omics” disciplines, according to a report published this week by the National Research Council.
The report, prepared by a committee of 12 experts in plant genetics and other fields, reviews the accomplishments of the decade-old National Plant Genome Research Initiative and recommends a number of future research directions and objectives.
Among those recommendations is a call to “expand plant genome sequencing, plant-associated microbial sequencing, plant-associated metagenome sequencing, and associated high-quality annotation.”
In order to meet this demand, the NRC report, available here, recommends that the NPGI expand its existing relationship with the DOE’s Joint Genome Institute and “empower” researchers “to access and utilize next-generation sequencing technologies for a broad spectrum of genomics and metagenomics discovery.”
The report also encourages the development of “omics” resources for “high-resolution” studies of a “few, carefully chosen plant species,” as well as resources “at a broader, shallower level across a number of additional species.”
Other recommendations include using systems-level approaches to improve US competitiveness for important crop and tree species, to focus studies on plant evolution, and to turn all of this research into plant improvement programs.
NPGI was launched in 1998 as a way to coordinate research funding from multiple federal agencies. It is managed by the Interagency Working Group on Plant Genomics, which includes representatives from the National Science Foundation, the National Institutes of Health, the US Department of Energy, the US Department of Agriculture, the US Agency for International Development, the US Forest Service, and the Office of Management and Budget.
The NRC report concludes that the initiative has been a success so far, but it should aim to broaden, deepen and diversify its efforts to reflect changing demands in the years ahead.
According to the report, the NPGI has awarded a total of 392 grants over the last 10 years totaling $774 million. The report did not provide any recommendations for future funding for the program, however.
The NPGI has provided “a huge bang for the buck” over the last ten years, Jeff Dangl, a professor of plant genetics at the University of North Carolina at Chapel Hill and chair of the review committee, told GenomeWeb Daily News.
He said that the $774 million in funding for NPGI so far is an excellent investment compared to federal spending on human genomics through the National Institutes of Health. By comparison, the National Human Genome Research Institute has received $4.5 billion in federal funds between 1998 and 2008.
When it comes to pitching the government for more funding, Dangl said, greater knowledge of the “three Fs” — food, fiber, and fuel — will be the centerpiece of plant biologists’ arguments.
Dangl said that the challenge now is to “generate the three Fs in an environmentally sustainable way, and plant biology plays a huge role in that.”
In light of the value of these three Fs for civilization and the challenges of the 21st century, Dangl said, “plant biology has been hugely, hugely under-funded.”
Dangl said that in addition to the need for more sequencing and “omics” tools, there also is a need for greater emphasis on bioinformatics in the plant community.
“What we found is the same challenge in all of genomics,” he said. “How do you generate interoperable databases for different kinds of data? We can have really good ones for grasses, [but] how well does it talk to a tomato database? Or what can these say about the ripening of strawberries?”
According to the report, the NPGI’s centerpieces to date have been the sequencing of the Arabidopsis and rice genomes — projects that have led to a number of important discoveries.
In particular, the group said research into plant genomics has led to the discovery of receptor molecules that bind to nearly all of the major plant hormones; a detailed understanding of how these receptors control subsequent plant development programs; knowledge of how to encourage the flowering and fruiting of plants by treating seeds, bulbs or seedlings to induce a shortening of the vegetative period; how the correct light and dark periods leads to flowering; and how leaves, flowers and roots are built and how plant immune systems control pathogen defenses. 
By comparing the genomic data from these studies, researchers have learned much about other important plants, including new information about the molecular events that were involved in the human domestication of maize, rice, tomato, and wheat.
The program has promoted plant biology as a field and has spurred private sector investments, and has helped fuel the education of hundreds of graduate students, creating a wealth of informed human capital in the field that is ready to carry the work into the future, the NRC report said.

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