US-AUSTRALIAN ACADEMIES JOINT WORKSHOP

US-AUSTRALIAN ACADEMIES JOINT WORKSHOP ON VERTEBRATE COMPARATIVE GENOMICS
Beckman Conference Centre, Irvine, California, 23-25 May 2007

Application of the bovine whole genome sequence to SNP discovery in Toll-like receptor genes
by Jim Womack

Dr Jim Womack received his PhD from Oregon State University in 1968 and has been employed by Texas A&M University since1977. He holds the title of Distinguished Professor in the Department of Veterinary Pathobiology and on the Faculty of Genetics. His interests are comparative gene mapping with emphasis on genes for disease resistance in cattle and other bovids.

Toll-like receptors (TLRs) play a crucial role in innate immunity in vertebrates as well as in insects where they were discovered.  The recognition of microbial elements by different members of the gene family initiates signal transduction pathways leading to the expression of specific genes important to the innate immune response and to direct paths to antigen-specific acquired immunity.  A large body of data is emerging suggesting roles of single nucleotide polymorphisms (SNPs) in human TLR genes in susceptibility to infectious and inflammatory diseases.

We, along with others, have mapped the bovine TLR family of 10 genes to their respective chromosome positions which correspond to expected locations relative to conserved synteny in humans.  We have begun a search for bovine SNPs in coding regions of TLR genes, utililzing data available from the bovine genome sequencing project and also by resequencing the coding regions of all genes in 10 animals representing 10 different breeds of cattle. 

We sequenced approximately 35 kb of coding sequence in eight of the ten bovine TLR genes from 10 animals.  More than 250 SNPs were revealed, 49 of which account for non-synonomous coding.  SNP distribution is not uniform with TLR-4 and 10 revealing 13 SNPs per kb of coding sequence.  As expected, most SNPs were discovered in Bos Taurus/Bos Indicus comparisons. 

We compared SNP discovery from genome sequence databases and resequencing animals from diverse breeds.  As expected at this early stage of the bovine SNP project, most SNPs for TLR genes are not yet available from the databases.

Contact details:
Department of Veterinary Pathobiology, ms 4467
Texas A&M University
College Station, TX  USA 77843-4467
Phone: (1) 979 845 9810
Fax: (1) 979 845 9972
Email: jwomack@cvm.tamu.edu
Web: www.cvm.tamu.edu/womacklab/