Physical Map Of The Bovine Genome Revealed

Main Category: Water - Air Quality / Agriculture
Also Included In: Biology / Biochemistry;  Genetics
Article Date: 22 Aug 2007 - 1:00 PDT

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The recent publication of a paper in Genome Biology describing a physical map of the bovine genome provides cattle researchers with a tool to aid their search to improve cattle production and health and decrease the environmental footprint of the industry. The physical map is like a framework of a house in that it allows all the fine details to be positioned and placed in order. This framework underpins most current and future cattle research, including the genome sequencing project currently underway and new DNA based methods to improve cattle genetics.

The international bovine BAC mapping consortium consisted of contributions from over 20 groups based in 8 countries: Australia, Brazil, Canada, France, Italy, New Zealand, Scotland, and the USA. Lead author, Warren Snelling based at USMARC at Clay Centre Nebraska, said "It is very gratifying to see this project completed as this resource will aid research for all grazing species including cattle, sheep and goats. "These species have the unique ability to convert pasture from extensive uncultivable regions into high quality protein in a low cost energy efficient manner."

One of the challenges of such a large project extending over more than a five year period has been its coordination. Steve Kappes of USDA Agricultural Research Service (ARS) who chaired the consortium was particularly pleased with the way the information was made available rapidly to the community: "As the information became available it was placed into the public domain promptly, it would be fair to say that a lot of the cattle genomics research conducted over the past 5 years has relied on the information provided by this project."

The project serves, also, as an example of how a motivated international group can combine their limited resources to obtain an outcome for the benefit of all. Kellye Eversole from the Alliance for Animal Genome Research is pleased with the progress achieved. "We have advocated for a coordinated, international effort and it is rewarding to see both the end of this step and its success."

The project commenced with the construction of a high quality BAC library with DNA obtained from a linebred Hereford bull bred at the USDA-ARS research station near Miles City, Montana. The BAC library contains random segments of genomic DNA placed inside bacterial cells and propagated. These acted as the resource for the majority of the subsequent work. This work included mapping the genome in 4 different ways. The DNA segments were fragmented into unique patterns using enzymes that cleave at certain short sequences and then the patterns compared to merge the segments into larger units Using information gained by reading or sequencing the actual base pairs for short regions on the ends of the BACs, the size of these units was increased. The sequences were then used to create probes for 2 different types of mapping, one based on inheritance of variants through cattle pedigrees and another based on close physical distance. The combination of methods, each with its own strengths, allowed for the maps to be cross checked against each other and a combined or consensus map created. The map also integrates and builds upon bovine maps created over the last decade. The final version consists of 422,000 end sequences, 291,000 digests and 17,000 markers. It is available at http://www.bovinegenome.org.

This is not the final step for the bovine genome project as the community at large is awaiting eagerly the next assembly and annotation of the bovine genome being done by the Baylor Genome Sequencing Centre. Resources from the physical mapping project were provided to the Baylor team to improve the quality of the assembly. Expected within a year, the next assembly and annotation of the bovine genome will permit the identification of many of the genetic differences that distinguish grazing animals or ruminants from other mammals unable to digest forages containing cellulose.

The project was funded by United States Department of Agriculture, the Alberta Science and Research Authority, Agriculture and Agri-Foods Canada, the Biotechnology and Biological Sciences Research Council, The European Commission, the Commonwealth Scientific and Industrial Research Organization of Australia, AgResearch Ltd, New Zealand Foundation for Research, Science and Technology, EMBRAPA Brazil, CNPq (National Council for Scientific and Technological Development) Brazil, the Roslin Institute Scotland, INRA (the French National Institute for Agricultural Research), AGENAE, Genoscope, the Texas Agricultural Experiment Station, and the Alliance for Animal Genome Research.

The paper in Genome Biology is freely available at: http://genomebiology.com/content/pdf/gb-2007-8-8-r165.pdf

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