Last week’s publication of the indica and japonica subspecies of the rice genome by the Beijing Genomics Institute and Syngenta, respectively, was heralded as a milestone for agricultural genomics. The nearly complete sequence is an ideal model for other cereals, scientists said, and should go a long way toward easing world hunger through the development of better crops.
But the rice genome wasn’t the only news in agricultural bioinformatics last week. A number of private and public research groups offered updates on their progress while the genomics spotlight was on the farm rather than the clinic:
Myriad Genetics, one of Syngenta’s collaborators on the rice genome, will next apply its bioinformatics expertise in a $25 million research collaboration with Pioneer, a subsidiary of DuPont.
One area the companies will partner on will be maize development. Bill Niebur, maize production development director at Pioneer, told BioInform that the company has been collecting phenotypic data on different varieties of maize for over 75 years. The partnership with Myriad will enable the company to link genotypic data to that information, resulting in “a database that’s radically different than anything we’ve had in the past.”
Genoptera, a joint venture between Bayer and Exelixis aiming to discover new insecticide targets, said it has identified and partially sequenced approximately 90 percent of the estimated genes of the moth Heliothis virescens, a pest also known as the tobacco budworm. The sequencing project took a year to complete, said Darren Platt, a senior manager of Exelixis’ bioinformatics group.
Rather than sequencing the entire genome, the scientists combined EST sequencing and genomic shotgun sequencing to obtain partial gene sequences, followed by extensive comparisons with the known Drosophila genome.
In what Platt described as a novel approach, the researchers used proprietary simulation tools to predict that 0.5x genomic shotgun sequencing, combined with the EST data, would suffice to tag a recognizable fragment of 90 percent of all genes. “All of that simulation was put into finding the optimum way to get the information we need,” Platt said, predicting that this approach might become more widespread as the number of sequencing projects increases. He also mentioned that they had sequenced ESTs of about half a dozen other insects and constructed a “virtual insect” from the results.
After four years of work, the Maize Mapping Project — a collaboration between researchers at the University of Missouri, Clemson University, and the University of Georgia — has released iMap, an integrated genetic and physical map of the maize genome.
The goal of the resource, available at www.maizemap.org, is to allow easy cross-referencing between the position of a gene or genetic trait on the genetic map and its corresponding location at the DNA level on the physical map.
The National Science Foundation funded the Maize Mapping Project with a five-year, $11 million grant in 1998. Project director John Davison of the University of Missouri said that the integrated map might serve as a suitable framework for a maize genome sequencing project, although no plans for such a project have been announced.
Another publicly available bioinformatics resource for agricultural research, Gramene, is described in a recent article in Comparative and Functional Genomics (April 2002). Gramene, a comparative mapping tool for rice and other monocots available at www.gramene.org, is a collaboration between researchers at Cold Spring Harbor Laboratory and Cornell University. The article describes the project’s use of three related controlled vocabularies to facilitate comparison across various databases. Gramene researchers are working with both the Plant Ontology Consortium and the Gene Ontology Consortium to develop controlled vocabularies for the resource.