Transcript U.S. Meat Animal Research Center (MARC)

Coming soon to a genetics lab near you!
Marker adjusted EPDs
NBCEC Beef Genetic Workshop
Clay Center, NE
March 27, 2004
Cattle genes affecting carcass traits
Thyroglobulin- marbling
(Gene Star)
Calpastatin- tenderness
(Gene Star)
Calpain- tenderness
(MARC)
Leptin- fat deposition
DGAT- milk fat and protein
Current limitations in genomic research
Single gene selection is worse than single trait
selection
 Need to incorporate with EPDs
We need to rapidly identify sufficient number
of genes that explain the majority of the
genetic variation
 Need for additional laboratory tools
Additional laboratory tools
Large expensive projects - require international
collaborations
Cattle physical (BAC) map
10 labs from US, Canada, UK, France, Brazil,
New Zealand, Australia
 Complete in Summer 2004
Mapping a trait to a gene
Ultimate physical map
Sequence the cow genome
 Funding from NHGRI; USDA; Texas; Genome
Canada; New Zealand; Australia; National, Texas
and South Dakota Beef Council; UK; and Norway $54+ million (6X coverage, 10K full length genes,
SNPs)
 Started Feb 2004- complete 2006?
How do we identify more genes faster?
BAC map and genome sequence will help fine map
QTL
Need more QTL populations to identify more genes
and for more traits
 SNP map will be used to develop low cost, high
throughput genome scans
 Use industry populations?
Implementation of Marker Adjusted
EPDs
 Develop haplotyped markers
TGGCAC
AGGCTC
TGCTTG
TGGCTC
TGCCTC
TGCTTC
TACTTC
Implementation of Marker Adjusted
EPDs
 Develop haplotyped markers
TGGCAC
AGGCTC
10%
14%
TGCTTG
TGGCTC
TGCCTC
25%
17%
21%
Functional alleles
TGCTTC
1) AGCTC, TGCAC, TGCTC
1%
2) TGCTC, TGTTC, TGTTG, TATTC
TACTTC
12%
Implementation of Marker Adjusted
EPDs
 Validate/replicate and estimate effect (different genetics
and environment)
 Evaluate interaction of different markers for the same trait
 Evaluate effect upon additional traits
 Selection pressure for each gene based upon effect of allele
substitution, gene interaction, effects on different traits,
and breeding objectives
 Need some continual phenotyping to estimate effect
Genes affecting additional traits
 Carcass traits- marbling , tenderness
 Growth – bend growth curve
 Milk production- composition
 Feed efficiency – expensive to measure
 Reproduction- dissect components
 Twinning population
 Health traits - difficult to measure
 Utilize genetic diversity- crossbreeding
Additional uses for DNA markers
 Parentage
 Verification system for animal identification
 Same markers used for parentage and animal ID
 Government subsidize genotyping
 Who maintains database and has access???
 Added value with animal records
MARC’s role in advancing cattle genomics
BAC map, genome sequence, pedigree populations
Identify additional markers, QTLs (publicly available)
 Develop haplotype system
Provide GPE cycle 7 as a validating population
 Published or patent submitted
 Not for product development
Work with NBCEC to incorporate
DNA markers with EPDs