|The American Simmental Association’s 2004 Fall Sire Summary
Featuring the Industry's First Marker Assisted EPDs
The 2004 Fall Sire Summary represented yet another groundbreaking event for ASA's genetic evaluation program. It contained the first Marker-Assisted EPDs (MA-EPDs) ever published. Calculated by Dr. Richard Quaas of Cornell University, these Shear Force MA-EPDs were the result of a far reaching collaboration between the ASA, Cornell University, the National Beef Cattle Evaluation Consortium and NCBA's Carcass Merit Project. This cutting edge technology blended the outcomes from DNA marker tests with tenderness data on sires' offspring to arrive at slightly more accurate EPDs, particularly on low-accuracy animals, than with tendernedd data alone. Dr. Quaas offers up a brief overview on the technology below:
Explaining Marker-Assisted Expected Progeny Differences for WBSF. Traditional EPDs are calculated using phenotypic data – Warner-Bratzler Shear Force measurements – and pedigree to evaluate the merit of the average of a sire’s genes. With the advent of DNA marker tests, however, we can now look more closely at particular segments of a sire’s DNA. In particular, the US Meat Animal Research Center found two polymorphisms(a) in calpain1 gene that are associated with beef tenderness; these have been validated by the Nation Beef Cattle Evaluation Consortium utilizing data on Simmental-sired cattle provided by ASA. There are at least three commercial labs providing genotyping for these markers under a variety of names. Our genotypes all came from Frontier Beef – TenderGENE. Each marker has two alleles (forms): C and G for marker “316” and A and G for “530.”
Procedures for calculating Marker-Assisted Expected Progeny Differences (MA-EPDs) are somewhat like multibreed EPDs that take into account the breed composition of a sire. In MA-EPDs we account for the expected composition of a typical gamete (sperm) in the region (QTL) marked. An MA-EPD is the sum of the effect of expected haplotype(b) transmitted to a sire’s progeny, plus a polygenic (multiple gene) effect. The first is an evaluation of the marked region; the latter quantifies all the other genes affecting WBSF.
In validation studies, the DNA for marker genotype and WBSF come from the same animal. In MA-EPDs, the genotype comes from the sire, the WBSF from progeny. Because the sire transmits only one of its two copies of the QTL, the effect of sire genotype is not as large as seen in the validation studies. Furthermore, the validation studies indicate the “best” genotype to include CC for 316. The 316 CC genotype is absent in the 63 genotyped sires. This further reduces the impact of marker information on ranking these sires for WBSF. The tendency was for the best to look better and the worst to look worse. A few sires moved from the middle of the pack toward one extreme or the other.
(a)A polymorphism refers to alternate DNA sequences for a short stretch of DNA that exist in a population. Red vs. black alleles at the color gene is an example.
(b)A haplotype refers to closely linked alleles that tend to be inherited together.