At the National Western Stock Show, I had a great discussion with the American Angus Association board and members. Angus Media put together a nice summary of that presentation.

Allen Moczygemba, CEO of American Angus Association announced in a memo  Monday August 14, 2017 that the price for Neogen GGP-LD and Zoetis i50K tests would be reduced to $37, effective immediately. The motivation for this price reduction is even more notable. In November of 2017 Angus Genetics Inc. (AGI) and Neogen will launch a new genomic test (SNP panel) called AngusGS™. This test will use 50,000 (50K) DNA variants, designed specifically for Angus cattle. DNA variants are included based on their frequency in the Angus breed, rather than across many breeds like most DNA panels currently used in the industry. Further, AGI has increased the number of DNA markers in stretches of DNA believed to be involved in fertility, feed efficiency and tenderness. The more detailed genotyping of these chromosome segments will enable more refined research of these important traits. For example, AGI could include increased markers in regions believed to harbor embryonic lethal DNA vari...

It is the time of year to once again record and report hair shedding scores. This fact sheet on eBEEF.org should come in handy. Participants in our hair shedding genomic research project should have received an email from Harly Durbin. This email contained an Excel file to report hair shedding scores on enrolled cattle. If not, please get in touch with us as soon as possible. We must receive 2017 data in these Excel files! It is important that we receive data on our target goal of 8,000 cattle. If your cattle are enrolled in the research program, we should have received DNA cards and 2016 data from you by now. If we have not yet received your data, you are in danger of being removed from the program. If we have not received your data, please get in touch with Harly and I by email or by phone . We know receiving genomic-enhanced EPDs is very important to hair shedding study participants. This is also a priority to us. We have worked with breed associations and GeneSeek to m...

This fact sheet goes through the fundamentals of how and when producers might use DNA testing in beef cattle production.  It covers the different types of tests that are available, how to submit samples and to whom, and what to do with the results. For more information, see the eBEEF.org factsheet " How to Get Started with DNA Testing ".

Tonya Amen Consultant for Illumina, Inc. One dairy operation was making $35 per year progress for net merit. After using genomics in late 2009, they were making $50 per year in progress for net merit. After they started testing females, this rate increased to nearly $80. This dairy herd is now seeing $340 more in life time production by using genomics. From 2005 to 2008, $B was increasing by $3.77 per year. From 2009 to 2015, $B increased by $5.62 per year. From 2013 to 2015, $B increased by $9.31 per year. A 146% increase in genetic trend. We have seen more rapid genetic improvement in Angus, Hereford and Simmental, all of which line up nicely with the deployment of GE-EPDs. Thus, it is possible (likely?) that this improved genetic improvement is due to the benefit of genomics. In the dairy industry, genomics is equivalent to 25 production records, 25 conformation records, and 140 fertility records. Genomics is saving the Canadian dairy industry $111 million dollars ann...

Breeding objectives indicate value of genomics for beef cattle Dr. Mike MacNeil DeltaG Is genomic testing a good value to seedstock producers? The answer to this question requires several different lines of thought. To answer this we need a system based approach. What makes up a genetic prediction? Information from relatives Molecular breeding value Correlated phenotypes Phenotype No individual animal in a genetic prediction ever has an accuracy of prediction of zero. The information from the calf's relatives brings in substantial amount of information. What are the advantageous of genomic prediction? 1) Increase accuracy of evaluation 2) More exciting is the opportunity to incorporate additional traits costly or difficult to measure measured late in life (after the time of selection decisions) sex-limited 3) Avoid prolonged generation intervals. For many selection decisions in beef cattle, we make many selection decisions around a year of age. 4)...

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...

Photo by Lana Eaton, Eaton Charolais, Lindsay, Mont. Cover by Molly Schoen The June/July issue of the Charolais Journal contained an article I wrote. Click this link to download a copy of the article. In the article I discuss trends I see coming in the development of genomic prediction. Please provide feedback in the anonymous survey below. Loading...

Meat Animal Research Center, Clay Center, NE Matt Spangler University of Nebraska-Lincoln  Why are we working on these novel traits?  Because they have great economic importance.  Further, they have heritable genetic variation.  We do have EPDs for feed intake and fertility, but they are not as pervasive as other (weight and carcass) traits. Continued phenotypic data collection and recording is critically needed. But, the breed associations have to do something with the data. Otherwise, progressive seedstock producers will look outside breed associations for genetic evaluations. This will not be a great outcome for commercial cattle producers. Nine breeds are already incorporating genomic information into EPD, with many other breeds right on the cusp of releasing genomic-enhanced EPDs. As genotyping becomes more common and more animals are genotyped, many of the current limitations are eliminated. But, there is continued room for statistical approaches...

And where are we going next? Data via  http://www.genome.gov/sequencingcosts/ . Code for generating the plot at  https://missouri.box.com/SequencingCost . This graph never ceases to amaze me. On the horizontal axis we have dates from September 2001 to July 2015. On the vertical axis we have the cost to sequence a million base pairs of DNA, with the axis having a logarithmic scale  (each tick mark is multiplied by 10, e.g. change from 10 to 100 to 1000). The blue line describes what is called Moore's Law  which describes the increase in purchasing power as computer costs come down. The rate of improvement in DNA sequencing easily outpaces the improvement in computing. Since September 2001, the price of DNA sequencing has dropped 6 orders of magnitude  from $5,292.39 to $0.015. From more than $5,000 to less than 2 cents!!! Same data as above by with the vertical cost axis  on a normal scale, not logarithmic. What caused the drop in sequencing f...

The Thompson Research Center Field Day will be held on Tuesday September 15, 2015 at the research center in Spickard. I will be discussing the use of genomics predictions in registered and commercial heifers. In addition to my talk and demonstration, there will be information on reproduction, nutrition and forages, antibiotic labeling, economics, and timber sales. In the survey below, let me know what topics or questions you would like addressed in my presentation. For those of you in Northwest Missouri, I would love to see you there. Loading...

Written by Randy Mertens If it wasn’t for genomic testing, Mogul Pastel would be just another heifer calf valued around $750. But her Holstein Association’s USA’s Genetic Total Performance Index (GTPI) is so far beyond average – at 2561 – she’s now recognized as the second highest rated red carrier Holstein calf in the country. That number, in turn, led to another figure — $25,500 – the price she sold for at the Missouri State Convention Sale in January. She now lives in a New York dairy where she will improve their breeding program. Pastel is a Holstein heifer born Sept. 9, 2014 at the Foremost Dairy Research Center , one of the research farms of the College of Agriculture, Food and Natural Resources, University of Missouri. The Foremost Dairy Center is the Division of Animal Sciences’ 820 acre research and teaching farm west of Columbia. The center supports 425 cattle, including Holstein and Guernsey breeds. Its research aims to improve milk production and reproductive efficien...

SAN ANTONIO, TX- The International Brangus Breeders Association (IBBA) has selected GeneSeek , a division of Neogen Corporation, as the association’s new DNA services provider. The partnership will allow Brangus breeders to submit DNA samples to GeneSeek for parentage determination and lay a foundation for Genomic-Enhanced EPDs for the breed association. “IBBA’s agreement with GeneSeek moves us closer to conducting all Brangus parentage testing using Single Nucleotide Polymorphism (SNP) genetic markers versus previously used technologies,” said Dr. Tommy Perkins, IBBA Executive Vice President. Samples will be tested with the GeneSeek®Genomic Profiler™ GGP HD 80K (tests approximately 80,000 DNA variants) and the GeneSeek®Genomic Profiler™ GGP LD 30K (tests approximately 30,000 DNA variants) for eventual incorporation into genomic-enhanced EPDs for the Brangus breed. The GGP 80K is finding a role as a premium genomic profiler, while the GGP LD 30K is a highly accurate, affordabl...

In their efforts to develop genomic predictions and genomic-enhanced EPDs, the American-International Charolais Association announced today that they have surpassed the 1,000 samples suggested to develop genomic predictions. Now that this level has been reached the association can prepare to release a commercially available genomic prediction test. As we have seen in other breed associations , once the genomic prediction test is commercially available, the amount of data available for retraining can grow. As new animals are tested they can also be used in future rounds of retraining (also called recalibration ). This is an exciting day for the AICA. Congratulations Charolais breeders! Now, what will you do with genomics ? Loading... " Vache de race charolaise avec son veau " by Forum concoursvaches.fr - http://www.concoursvaches.fr . Licensed under CC BY-SA 3.0 via Wikimedia Commons .

Management aims to raise additional capital to commercialize range of high-value targeted genotyping assays for clinical, animal health, and agriculture. HERCULES, CA, August 18, 2014 — Eureka Genomics, a leader in Next Generation Genotyping (NGG), announced that it has been awarded a $450,000 grant from The National Institute of Food and Agriculture. The Institute is an agency of the U.S. Department of Agriculture (USDA). Eureka Genomics was awarded this grant to commercialize a second generation NGG assay focused on bovine genotyping known as the Sparse Genome Scan (SGS). Eureka Genomics’ SGS is a technology platform that produces commercially relevant data, currently generated from micro arrays , at less than half the cost. This most recent USDA grant awarded to Eureka Genomics follows an ongoing cooperative research and development agreement with the USDA’s Meat Animal Research Center. "The USDA’s financial and research support is part of Eureka Genomics’ strategy to ...