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 ...

Daniela Lourenco The University of Georgia Before genomics, we were fairly happy with genetic prediction. Traditional evaluation combined pedigree, individual performance and progeny information. This was equal to summing all of an animal's genetics effects and dividing by 2. SNPs are used as markers for genes, or regions of the genome that impact production. The color of a banana peel (green vs. yellow) is a marker for banana ripeness. SNP markers are used in the same way. Marker assisted selection did not work. Why? Most traits are polygenic, meaning they are controlled by hundreds or thousands of genes. Trying to predict quantitative traits with a small number of DNA markers doesn't work well. What is 100,000 times cheaper now than in 2001? Airline flights are 2 times cheaper. Computers are 5 times cheaper. DNA sequencing is 100,000 times cheaper now than in 2001. A Holstein bull named Freddy was the best bull according to genomic predictions in 2009. In 2012, ...

Angus Genetics Inc will switch to single-step genomic prediction on July 7th. Since 2010 they have been using multi-step genomic prediction. In multi-step, genomic predictions are treated as correlated traits to produce GE-EPDs. In single-step, all genomic, pedigree, and performance data is analyzed in one model. The key to calculating EPDs is measuring genetic similarity. Traditional EPDs used pedigree data to estimate genetic similarity. In single-step, genomic data more accurately measures relatedness, i.e. genetic similarity. The pedigree and genomic relationship measures are combined. Since November, AGI has evaluated multi-step vs single-step. They have seen very similar accuracies between the two methods. But, single-step tends to have slightly higher accuracies. Further, there are several advantages to single-step. These advantages include removing the need to recalibrate and using all of the data simultaneously. Watch for further information from Angus about the switch t...

Steve Miller AGI Angus Genetic Services provides evaluations for AAA, CAA, and Charolais breed associations. "The ship has sailed on using genomics. Breeders are using it now, and seeing the benefits of it," said Miller. Previously at AGI, they have been using a two-step approach. In this method, a genomic prediction is created and then is used as an indicator trait for EPD estimation. The calibration data set size has increased dramatically as Angus breeders have used genomic-enhanced EPDs. The orgininal method of incorporting genomic predictions as correlated trait. In the future, we will stop referring to genomic-enhanced EPDs. We don't refer to EPDs as pedigree-enhanced or performance-enhanced, we simply refer to them as EPDs. In the future use of genomic data in genetic prediction will become so routine that we will simply call them EPDs. Is the Animal Model Obsolute? In single-step genomic prediction, we combine the measures of relatedness from pedig...

Dr. Mahdi Saatchi International Genetic Solutions IGS performs genetic evaluations for 12 breed associations from North America. IGS has over 16 million animals in their database and is adding over 400,000 animals per yer. IGS has 84,197 animals with genotypes. Simmental makes up about 40,000 of these genotypes. Currently at IGS they blend the molecular breeding value (MBV, the genomic prediction) with the multi-breed international cattle evaluation. This is more like the blending that occurs with selection indexes. Single-step genomic prediction allows information from genotyped animals to be spread to related animals in the data set. Also, multiple-step genomic predictions were often trained on breeding values, and any errors in the estimation of the breeding values influenced the genomic prediction. There are two approaches to single-step genetic evaluation. Single-step BLUP uses a breeding value model. Single-step Bayesian Regression uses a marker effects model. In Si...

Here are videos from the American Simmental Association's Facebook livestream of my presentation titled "Taking Technology Home to the Farm and Ranch." Tradition Intuition Legacy Seedstock Producers as Educators Decker's Rants EPDs and Environment  Q&A Loading...

Jack Ward, Wade Shafer, and John Genho presented during todays NBCEC Brown Bagger seminar. They gave updates about how their breeds are utilizing genomic information. Jack Ward The American Hereford Association will release an Udder EPD in the Spring 2015 update, which is typically published in late December. They are also working on a Feed Efficiency EPD which could be released in December, but will more likely be in the Summer of 2015. In the Summer of 2015 the AHA will also publish a Sustained Cow Fertility EPD (similar to other breed's longevity EPDs) and a Heifer Calving Rate EPD (a measure of heifer fertility). Ward also presented a nice analysis of price differences between bulls with and without genomic-enhanced EPDs. He set an upper limit of $15,000 to avoid high priced bulls that would skew the numbers. Bulls with traditional, low accuracy EPDs averaged $5,325. Bulls with genomic-enhanced EPDs averaged $7,475 at sale. More results can be seen in Ward's Hereford ...

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 ...

Dorian Garrick Henderson originally described breeding values (EPDs) as sums of gene effects. Meuwissen, Hayes, Goddard re-expressed this as sums of effects estimated for genotyped DNA variants.   In current selection we have two models for genetic prediction, one for genotyped animals and a separate model for animals not genotyped. You can combine a pedigree based relationship matrix with a genomic based relationship, we call this single-step BLUP or HBLUP ( Aguilar et al., 2010 ). There is a second approach which Garrick refers to as a hybrid approach. Now breeding values for nongenotyped animals are expressed as the part explained by genotyped relatives and the part not explained by genotyped relatives. This is similar to the animal model where we have the breeding value explained by relatives and the breeding value due to the random shuffle of genes across generations. This model is in press and should be out later this summer (Fernando, Dekkers and Garrick 2014 GSE). I...