Reverend Bayes via Wikimedia Commons You are asking yourself, who is Reverend Bayes and what does he have to do with cattle? The answer to this question will answer a major misconception in cattle genetics. Reverend Bayes was an 18th century Presbyterian minister. He was also trained in logic. Due to Bayes’ work on probabilities, an approach to statistics called Bayesian statistics is named after him. In Bayesian statistics, we start with a prior belief (prior probability). As more information and data are gathered, we update this prior belief. We call this new update a posterior belief. We continue this process as we collect additional data. Further, a key tenant of Bayesian statistics is evaluating the methods (i.e. models) used in our analysis. Statisticians and scientists did not frequently use this system of statistics in the early 20th century. But, with increased computing power, Bayesian statistics has become very popular in the 21st century. By Lutz Koch CC BY-NC-ND...

My group is currently recruiting a postdoctoral fellow. We are looking for candidates who are passionate about genetics, genomics, and research. Ideal candidates are creative, hard working (while maintaining a work/life balance), and self starters. Our group is strictly computational, so candidates should enjoy working on computers and analyzing data. Candidates should have programming experience (typically in R, Python, Perl, Julia, etc.) and be familiar  with the command line. Candidates will need to demonstrate  ability to write well and publish research. We currently have access to over 48,000 genotyped beef cattle with phenotypes and breeding values from breed associations (see Decker, 2015 ). We are currently negotiating to obtain access to an additional 300,000 genotyped cattle. These samples are in addition to tens of thousands of animals genotyped by the University of Missouri researchers (see Google Scholar profile for examples of data sets). We also have access...

Bruce Golden Theta Solutions Over the last 50 years we have had evolution of the statistical methods used to calculate genetic predictions, EPDs, for livestock. What drove the evolution of these methods? Knowledge of statistical models? New methods? Data? Enabling computer technology? Golden states that he believes the drive for better models has been a desire to increase the accuracy of prediction. Golden and Garrick had written grants to write genetic prediction software in the past. This avenue appears to have dried up, so they decided to start a company, Theta Solutions, in order to fund the development of genetic prediction. The latest genetic prediction runs contained 46,000 animals with genomic data. Theta Solutions uses graphical processing units, originally built for video gaming, to have a high performance computer at a relatively low cost. The BOLT software focuses on custom turnkey analyses, once the system is set up all one needs to do is feed it data. Using non-G...

My group is currently recruiting people to fill two graduate student positions. We will also be recruiting a researcher to fill a postdoctoral position in the coming year. We are looking for candidates who are passionate about genetics, genomics, and research. Ideal candidates are creative, hard working (while maintaining a work/life balance), and self starters. Our group is strictly computational, so candidates should enjoy working on computers and analyzing data. Candidates should be willing to learn programming (typically in R or Python), or already have some programming experience. We will soon have access to over 200,000 genotyped beef cattle with phenotypes and breeding values. We also have access to whole genome sequencing data from over 2,000 cattle. So, if you like working with lots of data, come join us! Our group uses population genomics to better understand the  history of cattle breeds and to inform future selection decisions. We are interested in local genetic ada...

Dorian Garrick Iowa State University The Pre-Genomic Era In the Pan-American Evaluation there are four countries, US, Canada, Uruguay and Argentina. Agricultural Business Research Institute (ABRI) collects the pedigree and trait data. Then the Animal Genetics & Breeding Unit uses BREEDPLAN to estimate EPDs. To put the number of records turned in to the AHA data in context, we can compare them to other breeds. The 11 breed associations in International Genetic Solutions add 340,000 new animals in each of 2012 and 2013. AGI adds about 300,000 per year. Herefords add a little less than 100,000 animals per year. The Early-Genomic Era Cattle have 30 pairs of chromosomes. There are about 100 million base pairs per chromosome and about 2.6 billion base pairs in the entire DNA (genome). Most errors in chromosome replication are fixed. But, some slip through and are passed down through generations. The EPD of a bull is a sum of the average gene effects he carries. Until the g...

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 ...

Duane Dailey ,  Writer,  University of Missouri Extension COLUMBIA, Mo. – Selecting breeding animals on how they look, by phenotype, worked for centuries. Progress in improving cattle was made just on appearance. Now genotype pushes phenotype back to horse-and-buggy days. It’s data and what’s inside that counts. Arrival of huge computers and sequencing of the bovine genome changed all. “There’s a better way of selecting,” said Jared Decker, University of Missouri geneticist, at a Cattlemen’s Boot Camp, July 14 in Columbia. Training by MU scientists was sponsored by the American Angus Association with MU. The Cattlemen’s Boot Camp is a national program. Things changed in the 1970s with statistical models that predicted EPDs (expected progeny differences). Then software was developed to combine many EPDs into a single economic index number. Indexes help herd owners search a sire catalog to match a bull’s traits needed to improve a farmer’s cow herd profits. “We ...

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...