Angus tackles tenderness, genomics provide more, better data on more traits
— New genetic tools to better measure important traits
Breed associations are always trying to leverage genomics to objectively describe traits. One of these traits is tenderness. Simmental was the first in the industry to produce a genomically-enhanced expected progeny differences (GE-EPD) when they came out with a tenderness EPD in 2006. Simmental worked hard to collect phenotypes in their carcass progeny test to go with their genomics, but in more recent years has relied on gene markers to add additional information.
Angus is now on the path to calculate their own tenderness EPD as early as this fall. Unlike normal genetic predictions, which are based on phenotypes, Angus’ tenderness EPD will be based primarily on genomics. They do have a phenotypic baseline from the early 2000s when the National Cattlemen’s Beef Association (NCBA) conducted the large and comprehensive tenderness project from which to work. Gelbvieh is also actively exploring the calculation of a tenderness EPD, and Santa Gertrudis is considering one.
Tenderness has long been included in the seedstock commercial panels offered by Zoetis and GenSeek. Both companies now offer both low-density and high-density panels for the breeds they service. Zoetis’ low-density panel has approximately 20,000 markers while its highdensity panel is marketed as a “50K” but in reality has approximately 60,000 markers. The low-density panel provides approximately 98 percent of the same information as the high density but is much more affordable.
GenSeek too offers a low-density panel with approximately 30,000 markers and a high-density panel with about 150,000 markers. Given the price/ benefit ratio, it appears that for most producers, the low density panel is the way to go, reserving the use of high density panels for artificial insemination (AI) sires and donor dams.
Angus recently completed their fifth recalibration of their genomic information with their phenotypic database, which was implemented April 1. Included in this recalibration were 108,000 genotypes. Most of the traits saw little change with the exception of heifer pregnancy, which had had a significantly higher correlation, meaning the genomic panel will now add more accuracy to their heifer pregnancy EPD then it did before the recalibration.
The reason for this increase in correlation was they had significantly larger heifer pregnancy phenotypic database, which the recalibration was based upon. It appears that their needs to be a critical mass of phenotypes to fully leverage genomics, and the submission of phenotypes is still critically important especially when it comes to new and novel traits. Red Angus has also completed their second recalibration, but has yet to implement it.
All breeds that compute GE-EPDs are in the process of incorporating the full marker panels into EPD models in a process called “One Step” instead of the two-step method of using markers as correlated traits. This will erase the need for future recalibrations. One Step has already been implemented in some of the American (Bos Indicus-influenced) breeds and is expected to implemented by the rest of breeds later this year.
A full explanation of this development will be covered in the article, “Entering a new era in objective selection,” that will appear in the upcoming Western Livestock Journal’s special Commercial Cattle Issue later this month.
One of the more exciting genomic research projects regards fertility and is being conducted by Dr. Jerry Taylor at the University of Missouri using a 250K chip. This chip has 250,000 markers also known as SNPs (Single Nucleotide Polymorphism), and he is exploring markers associated with fertility by finding those out of equilibrium.
By being out of equilibrium, it is thought that the absence or low frequency of certain markers will be associated with lack of fitness. Examples of their absence or low frequency could be a general lack of fertility, embryonic death and lethal conditions. Once these markers are identified, they will be included in the panels currently used by producers and will add a great amount of information to fertility EPDs such as Stayability and heifer pregnancy. Interestingly, a number of these fitness markers have also been found to be associated with feed efficiency.
Genotyping embryos is also being developed, and appears practical and implementable. This will allow breeders to determine parentage, sex, genetic conditions and production trait genomic values. How this will be handled by breed associations needs to be considered, and potentially allows for GE- EPDs to be produced on embryos before being implanted. Coming up with policy on how each breed association will handle this new technology will be a challenge to the industry.
The world of genomics and their use is rapidly changing. As traits like tenderness are added where the collection of phenotypes is very difficult and cost prohibitive, genomics will play an even bigger role. For most all other traits, genomics will continue to add a significant amount of accuracy to genetic predictions, but in no way substitute the need for aggressive collection of phenotypic performance data. As was demonstrated by the increased correlation for heifer pregnancy in Angus’ latest recalibration, the collection of phenotypes is especially important as new traits are added to EPD suites. — Dr. Bob Hough, WLJ Correspondent
(Dr. Bob Hough has served as the Executive Vice President of the Red Angus Association of American and more recently as Executive Vice President of the North American Limousin Foundation from 2009 to early 2011. He is now a consultant, freelance writer and semiretired.)