Coming soon to a genetics lab near you

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 (6 X coverage, 10 K 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 T G CT T G TGGCTC TGCTTC TACTTC

Implementation of Marker Adjusted EPDs ! Develop haplotyped markers TGGCAC AGGCTC 10% 14% Functional alleles T G CT T G TGGCTC TGCCTC 25% 17% 21% TGCTTC 1) AGCTC, TGCAC, TGCTC 1% 2) TGCTC, 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