What will mapping What will mapping the genome mean to the genome mean to
the industry?the industry?
Clare A. Gill, Ph.D.Department of Animal Science
Texas A&M University
OutlineOutline Current Status of the Bovine Genome Current Status of the Bovine Genome
MapMap International Bovine BAC Map ConsortiumInternational Bovine BAC Map Consortium
Strategy for Genome SequencingStrategy for Genome Sequencing
Industry ApplicationsIndustry Applications
30 pairs of chromosomes
10-30m
Bovine Genome
30 pairs of chromosomes
3,000,000,000 base pairs
30,000 - 50,000 genes
Genes make up less than10% of the genome
Base changes can affectphenotype
Bovine Genome
Mapping
Sequencing
Bioinformatics
Genetic Linkage map of bovine chromosome 1
BM6438
BM4307
TGLA57
RM95
BL28
BM1312
TGLA49
BM6506
CSSM32
MAF46
INRA117
DIK70
URBO14
http://www.marc.usda.gov/genome/htmls/LinkageMap
Grisart et al. (2001) Genome Res. 12: 222-231
BAC FingerprintsBAC Fingerprints http://www.bcgsc.bc.ca/projects/bovine_mapping/http://www.bcgsc.bc.ca/projects/bovine_mapping/
The current database contains 294,652The current database contains 294,652 clonesclones 45,000 Angus BACs contributed by TAMU45,000 Angus BACs contributed by TAMU >1000 loci mapped using TAMU library>1000 loci mapped using TAMU library
280,000 BACs will be end sequenced280,000 BACs will be end sequenced 100,000 BAC ends will be contributed by TAMU100,000 BAC ends will be contributed by TAMU
Cattle is the only animal species that will have the BAC Cattle is the only animal species that will have the BAC Map completed prior to genomic sequencingMap completed prior to genomic sequencing
BAC End SequencingBAC End Sequencing
International BAC Map International BAC Map Consortium MembersConsortium MembersUSDA-MARCUSDA-MARC INRAINRA
BCGSCBCGSC AgResearchAgResearch
TIGRTIGR Roslin InstituteRoslin Institute
Baylor College of MedicineBaylor College of Medicine CSIROCSIRO
Texas A&M UniversityTexas A&M University
University of AlbertaUniversity of Alberta plus researchers fromplus researchers from
University of IllinoisUniversity of Illinois Brazil & JapanBrazil & Japan
DNA Markers = DNA Markers = BookmarksBookmarks
Sequence = Words on Page
The Bovine Genome Project
From Green (2001) Nat. Rev. Genet. 2: 573-583.
Bovine Genome Sequencing Initiative
White Paper submitted to NIHGibbs, Weinstock, Kappes, Schook, Skow & WomackHIGH PRIORITY STATUS
Objectives:• Sequence the bovine genome to 6x coverage. • Identify 100,000 single nucleotide polymorphisms (SNPs)• Use comparative information from cattle to identify new genes and novel regulatory elements in humans, mice and rats.
• Understand how genetic variation contributes to diverse phenotypes and disease• Understand genetic interactions with environmental factors
COMPARATIVE TRIANGULATION
Informing Human Biology• Cattle have already played an extensive role in physiological and biochemical research pertaining to human health
• Understanding reproductive and pituitary hormones• Bovine insulin to treat human diabetes (Sanger et al. 1955)• Anticoagulant, Warfarin, in cattle with sweet clover disease (Stahmann et al., 1941)• Identification of parathyroid hormone (Collip, 1925)• Demonstration of leuteotrophic effect of leutinizing hormone (Wiltbank et al., 1961)• Growth promoting effect of growth hormone (Evans & Long, 1921)• Lactational effects of GH demonstrated in dairy cattle
• Reproductive Techniques• superovulation, oocyte culturing, in-vitro fertilization• embryo maturation, transfer and freezing
Benefits to Human HealthBenefits to Human Health
The bovine model is relevant to human health research The bovine model is relevant to human health research priorities such as obesity, female health, osteoporosis, and priorities such as obesity, female health, osteoporosis, and communicable diseases.communicable diseases.
Will be invaluable to study host-pathogen interactions for Will be invaluable to study host-pathogen interactions for food safety (e.g. E. coli O157-H7, Salmonella and Listeria) food safety (e.g. E. coli O157-H7, Salmonella and Listeria) and agents that affect food security and human health (e.g. and agents that affect food security and human health (e.g. Foot and Mouth Disease, Mad Cow Disease)Foot and Mouth Disease, Mad Cow Disease)
Benefits to the Cattle IndustryBenefits to the Cattle Industry
• Availability of the genome sequence will significantly reduce the time needed to develop genetic tests
• Novel therapeutics or management strategies could be developed to leverage the underlying genetic information for improved production efficiency
• Will ultimately allow us to understand how networks of genes interact with each other and the environment to affect animal physiology (e.g. reproductive efficiency, bone structure, growth rates, fat deposition, heat tolerance, pathogen resistance)