2002

International consortium to create sequence-ready map of the cattle genome

Jim Barlow, Life Sciences Editor
(217) 333-5802; b-james3@uiuc.edu

3/12/02

CHAMPAIGN, Ill. – An international consortium of U.S., Canadian and French scientists has begun work on a new resource that will enable the rapid and efficient sequencing of the entire cattle genome.

When the $2.5 million project is done by early 2003, scientists will have new tools to genetically improve dairy and beef cattle, to enhance food safety and to protect the cattle industry against bioterrorism. Coordinating the project are Harris Lewin, a professor of animal sciences and director of the W.M. Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign, and Steve Kappes of the U.S. Department of Agriculture-Agricultural Research Service USDA-ARS in Clay Center, Neb.

The effort to create a sequence-ready map is being done by scientists of the UI, USDA-ARS, Children's Hospital Oakland Research Institute (CHORI), British Columbia Cancer Agency (BCCA) and The Institute for Genomic Research (TIGR) in Maryland.

Scientists will create a sequence-ready bacterial artificial chromosome (BAC) map and anchor it to the human genome map by reference points called comparatively-anchored sequence tagged sites, or CASTS. Constructing the map will proceed in three phases.

First, all 280,000 clones of a BAC library produced by Pieter de Jong’s laboratory at CHORI will be fingerprinted by Marco Marra's group at BCCA. Second, sequencing of the ends of at least 100,000 fingerprinted BAC-clones will be done by Lewin's team and by Shaying Zhao at TIGR. The sequence-ready BAC map will be created by merging the BAC fingerprints with the BAC-end sequence data. The entire ordered array of cattle BAC clones, called contigs, will be scaffolded on to specific cattle chromosomes using COMPASS, a bioinformatics tool created at the UI.

The assignment of contigs to cattle chromosomes will be based on a whole-genome cattle-human comparative gene map created by Lewin's group in collaboration with James Womack's Texas A&M University laboratory and published in the December 2000 issue of Genome Research. Reciprocal exchange of BAC fingerprinted and end-sequenced clones with scientists at INRA will be used to create a thorough sequence-ready map.

So far, more than 125,000 cattle BAC clones have been fingerprinted at BCCA and more than 2000 BAC end-sequences have been produced by the UI. Once this initial stage is completed, a new consortium will produce a draft sequence of the entire cattle genome.

Sequencing the cattle genome will help scientists understand the evolution of mammalian genomes and provide powerful new tools for animal breeding and securing the safety of the world’s supply of meat and milk, Lewin said.

"Obtaining the sequence of a mammalian genome from the Artiodactyl (even-toed ungulates) order of mammals will provide an invaluable resource for deciphering the human genetic code," he said. "Already, research has shown that sequenced cattle DNA can be more valuable than sequenced mouse or rat genomic DNA in predicting the location of evolutionarily conserved non-coding gene regulatory elements."

In addition, because of the potential threat of bioterrorism to the nation’s food supply, the use of genome-based technologies to speed the diagnosis of exposure to animal pathogens or chemical agents may be critical to states whose economies are heavily dependent on animal agriculture, he said.

Funding is from the USDA-ARS; USDA Cooperative State Research, Education, and Extension Service; University of Alberta; Alberta Innovation and Science; Alberta Cattle Commission; Canadian Cattlemen's Association; and Biotechnology and Biological Sciences Research Council, United Kingdom. Other scientific contributors include the National Institute for Agricultural Research (France), AgResearch (New Zealand), Texas A&M and Commonwealth Scientific and Industrial Research Organization (Australia).