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Showing posts from 2012

Lower Prices, More Genotypes

I was really happy to see that 23andMe has lowered prices in an effort to genotype 1,000,000 people. Luckily the effective population size (a measure of genetic diversity) is much smaller in cattle breeds, so many fewer animals are needed to design genomic selection programs!
But, in an effort to increase the number of animals in its training population with high accuracy EPDs (genetic predictions), the American Hereford Association is offering a cost-sharing program to offset DNA test cost for breeders. If I was a breeder with a bull who meet the AHA's criteria, I would be jumping at the opportunity. (And, if I can scrounge up the money during the holidays, I will be taking advantage of 23andMe's deal!)
See message from the AHA below. 

High Accuracy Bulls Sought, Cost-Share Option Available During the American Hereford Association (AHA) Board meeting the Board discussed its continued commitment to DNA testing more high accuracy sires. Hereford breeders who have a bull that d…

Beef Genomic Selection strategies

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 association then uses these MBVs as an indicator trait to p…

Birth Date Selection Mapping

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My advisor, Jerry Taylor, and I recently developed and published in BMC Genomics a new method to identify ongoing selection on complex or quantitative traits (A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits). Previous methods identify selection which has reached completion (or nearly reach completion) on novel mutations affecting Mendelian traits. A well known example of this type of selection is the adaptation of human populations to digest milk as adults. But, these sweeping selection events are the exception.
Selection often acts in an incremental fashion on variants already present in populations, and this selection is often on complex traits influenced by a large number of genes. By analyzing birth date as the dependent variable in a genome-wide association analysis our method is able to identify these more subtle selection responses.


In our BMC Genomics paper we analyzed 3,570 Angus animals…

Doctor Bovine Genome
or: How I Learned to Stop Worrying and Fix the Assembly

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I know, this is a very strange title for a post.  More about that later...

USDA Fellowship In this post I want to introduce you to part of my day-to-day research.  In August of this year, I was awarded a USDA NIFA Postdoctoral Fellowship.  I was awarded this fellowship for two reasons: to prepare to become a leader in agricultural science and to complete a specific project.  My project is reassembly of the bovine reference genome sequence.

Motivation: Why are we reassembling the bovine genome? The completion of the draft human genome sequence was announced to much fanfare in 2000.  But, the work of finishing the human genome still continues.  Two versions of the bovine reference sequence, by the Baylor College of Medicine and the University of Maryland, were published in 2009.  At that time the bovine genomics community began discussing how to improve the draft assembly.  Key players suggested that more sequence data on L1 Dominette 01449, the cow on whom the reference sequence is bas…

Take Care When Collecting Hair Samples

I received this reminder from the American Hereford Association this morning:
Take Care When Collecting DNA GeneSeek Inc., Lincoln, Neb., is the new American Hereford Association (AHA) DNA lab (learn more). The switch has not been without its challenges and one of those is that the new technology, SNP based, requires a lot more DNA than the previous technology. In other words, we have had several requests that have not fully been reported because the lab will not have enough DNA for each of the tests. Assays are different for the abnormalities, parent verification, horned/polled and 50k GE-EPD. The bottom line is the lab needs a minimum of 80 hairs with the follicles and the best place to pull is right above the switch on the tail. This technology is also very sensitive to contamination due to pour-ons and other insecticides, so please keep that in mind. If you have any questions, contact Jack Ward at 816-842-3757. SNP assays require large amounts of high quality DNA. From GENESEEK…

Asking the Right Questions...

Drovers Cattle Network recently shared this video in which they discussed the recent changes at Igenity.  The conversation continued by discussing strategies (and products) to reduce risk and select the best replacement heifers and cows during drought conditions.  So, that got me interested in the products referred to by Dr. Jim Gibb.  A quick search lead me to here and here on Igenity's website.  At the end of the second link it says:
Have more questions?Let an expert give you the inside information — igenity.support@neogen.comSo, what questions should beef producers be asking?  As we previously discussed, some beef genomic technologies return valuable information (tests for traits with genes of large effect, genomic selection) and some do not (gene tests predicting a complex trait with a small number of markers).  Following are some questions (and suggested actions) to get you started:

1. Has the test been validated by the NCBEC?
    (If it is a new test the process of NCBEC valid…

Quality Beef:
A result of reproductive technologies and genetic selection

I recently came upon this post about Cattlemen's Evolution on the Bridging the Cattle Gap blog.  I loved that he explained the link between reproductive technologies and genetic selection.  In addition to the points raised in his post, artificial insemination also increases the selection intensity.  As we use a smaller number of elite sires that are further from the average of the breed or population, genetic change becomes more rapid.

On August 30th 2012, the College of Agriculture, Food and Natural Resources at the University of Missouri will be launching a new program called Quality Beef-By the Numbers.  This program aims to assist commercial cattle operations to realize increased income as a result of utilizing reproductive and genomic technologies.  Previously, progressive cattle operations have not been rewarded for producing a higher quality product.  This program aims to change that situation.  I encourage you to check it out.

Scott Brown, one of the organizers of Quality …

Gene Tests vs Genomic Selection

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 population of animals (more th…

Manuscript submitted

I submitted a manuscript to BMC Genomics this morning.  I can't wait till the manuscript has made it through the peer review process and is published so I can tell you all about it!

Accuracy improvement from Genomic-Enhanced EPDs expressed as progeny equivalents

There is a great article in the Drovers CattleNetwork expressing the improved accuracy from genomic-enhanced EPDs in the number of progeny required to see the same increase in accuracy.  The big gain is in yearling weight, where genomic information provided as much information as 20 progeny.  As the article states, most dams will never have this many progeny in a lifetime, and now producers can have that same level of accuracy at birth.

These results are for Pfizer's 50K product.  I would be interested in seeing the results for Igenity's product as well.  I'll talk more about the differences between the two products in a future post.

Better breeding through cow genetics

Welcome to A Steak in Genomics!

A few weeks ago I was fortunate to be featured in a story on KBIA, Better breeding through cow genetics, by Sarah Redohl.  The story began by describing how I became interested in animal genomics.  It continued by explaining the Animal Genomics Group's genomic selection research.  It concluded with a somewhat skeptical assessment of genomic markers by an Angus breeder.

So, I decided to write this blog to inform farmers, ranchers, and scientists about the use of genomic technologies in animal breeding.