Dorian Garrick Theta Solutions LLC The Theta Solutions LLC is made up of Dr. Bruce Golden, Dr. Dorian Garrick, and Dr. Daniel Garrick. They have developed the BOLT software for genetic and genomic evaluations. The American Hereford Association formed an advisory committee to check the new genetic evaluation system. The advisory committee looked at the process during development. The advisory committee included: Joe Ellis Jack Holder Lee Haygood Paul Bennett Mitch Abrahamsen Suppose we had 100 progeny (i.e. offspring) on 1 bull. You might look at that bull and decide you like him or you don’t like him. But, that bull is just an envelop that carries genetic information. What the bull looks like really doesn’t matter, what matters is what his progeny look like. The way to look at the genetic value, or breeding value, of the bull is to look at his offspring. But, there are lots of environmental effects that influence the performance of the offspring. One example is the age ...

Hat tip to Dr. John Cole, USDA, and Jesse Hoff for bringing this to my attention on Twitter . I need to make an important point: I am not a patent lawyer. I do not have a deep understanding of patent law and nothing in this post should be considered legal advice or council. On November 8, 2016 Canada issued a patent to Ben Hayes and Michael Goddard for genomic prediction. Genomic prediction is estimating an animal's breeding value (i.e. genetic merit) using DNA variants. See the Canadian Intellectual Property Office website for more detailed information about the patent. Meuwissen, Hayes and Goddard first published their work on genomic prediction in 2001. Hayes and Goddard filed for a patent of the method on December 21, 2007 with the United States Patent and Trademark Office. About 23 days later, the Illumina BovineSNP50 Beadchip, a DNA test that can test 54,000 DNA variants quickly and cheaply for cattle, was released at the Plant and Animal Genome Conference. This 50K ...

Photo by Robert Scarth Photo by LID In a  blog post  by Kris Ringwall I became aware that the American Shorthorn Association has moved its genetic evaluations to International Genetic Solutions , the genetic evaluation arm of the American Simmental Association. The North American Limousin Foundation (NALF) has also  announced that it is  joining a growing group of breeds that use International Genetic Solutions (IGS) as their service provider for the estimation of EPDs. NALF joins Red Angus Association of America, American Maine-Anjou Association, American Chianina Association, American Simmental Association, American Gelbvieh Association, Canadian Simmental Association, Canadian Angus Association, Candadian Gelbvieh Association, and most recently American Shorthorn Association. The new Shorthorn evaluations were released this fall; the first release of Limousin IGS evaluations will be released in the Spring of 2015. As Kris Ringwall points out, this is go...

by David Dodge Psst ... Can I let you in on a secret? All EPDs are accurate. That's right all EPDs are accurate. EPDs are calculated using a statistical procedure called BLUP. BLUP stands for Best Linear Unbiased Prediction . Because BLUP estimates are unbiased , they are all accurate. So, if all EPDs are accurate what is this accuracy we always talk about? Calling this measure an accuracy is a misnomer . What EPD accuracy actual measures is precision. The EPD accuracy measures how precise the EPD estimate is. All EPDs are on the top row of the grid above. What is reported as the accuracy is a measure of the precision or reliability. When animals have lots of data, the estimates are precise and there is a small difference between the true value and the estimated prediction. When animals have little data, the estimates are not precise, but the EPD estimates average out to the true values. This is why using many low accuracy sires (rather than a single proven sire) is an ...

Yesterday my cows got turned out on grass. Despite it being a cloudy day, I think they were pretty happy! Let me tell you the story of these three cows. Last August my mother brought three of her two-year-old cows to Missouri. In New Mexico they have been struggling with drought, so the cows would benefit from some extra feed. And they did. In the first three months their  body condition score  increased by one (almost two) units. But, then my pastures ran out of grass, so I started feeding hay, and I started to observe big differences between the cows. I started to notice their feet were sore, and I soon realized I was dealing with fescue toxicosis . Two of the three responded rapidly to 20% protein cube supplementation, but the third one never did. So, I have made a selection decision, and this fall after she weans her calf, the fescue sensitive cow will be culled from my herd. In a previous post, one commenter mentioned gene-by-environment interactions. In my case, ...

The Beef Improvement Federation (BIF) will host a Genetic Prediction Workshop in Kansas City, MO on December 12-13, 2013 at the Holiday Inn KCI Airport and KCI Expo Center, 11728 NW Ambassador Drive. The conference is designed to give academic, allied industry, breed association staff and cattle producers a forum to learn about and discuss the latest developments in beef cattle genetic evaluation strategies. The implementation of genomics technologies in national cattle evaluation systems will be the focus of discussion.  Speakers will highlight the experiences and current status of technology deployment at several major US breed associations, experiences developing genomic predictions of genetic merit and alternate strategies for computation of genomically enabled EPDs. The conference will also feature discussion of planned modifications to the system used to compute the Across Breed EPD adjustment factors at the US Meat Animal Research Center. A USDA multi-state project ...

This past summer Hereford , Simmental , and Limousin breed associations announced genomic-enhanced EPD programs, following the lead of the Angus Association.  Two strategies have emerged, which I will call the commercial model and the genotype model. The Commercial Model In the commercial model, cattle producers send hair or other tissue samples to their breed association.  The association enters the identification information into its database, and sends the tissue sample to the DNA testing company (typically Pfizer or GeneSeek).  The DNA testing company extracts DNA from the tissue and runs a SNP assay.  These SNP tests contain hundreds or thousands of SNP markers, depending on the company.  The company then computes molecular breeding values (MBVs) based on the animals SNP genotypes.  A MBV is an estimated breeding value based solely on molecular markers.  The company then returns the MBVs to the breed association.  The breed associa...

Two different paradigms have existed regarding the use of DNA markers in animal breeding. The first strategy is gene tests, also referred to as marker assisted selection (MAS).  The second is genomic selection. Gene Test Gene tests attempt to predict a trait or breeding value based on the results (genotypes) of a small number of DNA markers. These tests are either developed using a candidate gene approach or from genome-wide analyses.  In a candidate gene approach, a scientist assumes which genes influence a trait and investigates variants within those genes for an association with the trait of interest.  These assumptions can be wrong and a scientist may identify an association by random chance.  In a genome-wide approach, a scientist makes no assumptions about which genes influence the trait, but analyzes markers evenly spaced throughout the genome. Genomic Selection In genomic selection, thousands of evenly spaced DNA markers are genotyped in a large po...