Tuesday, March 17, 2015

"Why Do Many Reasonable People Doubt Science?"
Discussing the National Geographic Article

“Science is not a body of facts,” says geophysicist Marcia McNutt ... “Science is a method for deciding whether what we choose to believe has a basis in the laws of nature or not.”
One of the attitudes I try to help beef producers embrace is a scientific, data-driven mindset. This applies to all phases of their operation, from reproduction, nutrition, health, genetics, and other management practices. In the March issue of the Missouri Angus Trails magazine, I encourage producers to take a science-based approach to farming and ranching. If you are a Missouri producer who uses Angus genetics, I encourage you to subscribe to the Missouri Angus Trails. (Also, watch for an article by me in the Missouri Hereford News.)

Joel Achenbach wrote an interesting piece in National Geographic asking "Why Do Many Reasonable People Doubt Science?" With the recent measles outbreak, this topic has been in the news recently. I suggest you make some time to read it. Here are some of my favorite quotes:
The idea that hundreds of scientists from all over the world would collaborate on such a vast hoax is laughable—scientists love to debunk one another. 
I have been on the giving and receiving end of this debunking, and I can attest that scientists love to prove each other wrong! Science truly is self-correcting.

“Science will find the truth,” Collins says. “It may get it wrong the first time and maybe the second time, but ultimately it will find the truth.”

Doubting science also has consequences.

Being right does matter—and the science tribe has a long track record of getting things right in the end. Modern society is built on things it got right.

I strongly believe that a technology-driven attitude is part of what made the United States special. I hope we never abandon that philosophy.

What were your favorite quotes or ideas from the article? What questions did you have from the article? Please share in the comments section.

Friday, March 13, 2015

A Big Number for a Little Calf
MU’s dairy program produces a genetically outstanding animal

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 efficiency, dairy herd health, nutrition, and milk quality. Foremost plays a key role in the Division’s teaching mission, providing experiential learning opportunities through laboratory courses, undergraduate independent study, the dairy club, and graduate student research projects. The farm is also an essential resource for Mizzou’s College of Veterinary Medicine, supporting clinical training of veterinary students and research in animal health.

John Denbigh, dairy farm manager, with Pastel, Amanda Fischer, animal science major, Ann Callahan, pre-veterinary medicine, and Eric Adkins, research specialist. Photo by CAFNR.

Students Help Create Something Unique

About a dozen MU dairy students work at the Foremost Dairy Center each semester, learning the operation of a working dairy farm.

Pastel was part of that learning experience. In fact, as a new management strategy, she was one of the first 20 calves at the farm tested using a genomic DNA panel to increase the reliability of her TPI. It was then her high genetic rating became apparent, said John Denbigh, dairy farm manager.

“We didn’t fully appreciate the significance initially of the high rating,” he said. “When we started getting numerous inquiries about her purchase, it was then we knew she was something unique.”

TPI, or total production index, is a guideline created by Holstein Association to rank Holstein cattle and assist dairy producers worldwide in identifying superior cattle with high production potential, and desirable health and fertility characteristics. TPI also measures an animal’s potential for superior feed efficiency and ability to produce milk. The index also measures the genetic ability to reproduce superior and healthy offspring.

An average Holstein’s TPI is around 1800. Pastel’s $25,500 price will go into the farm’s operating account. The farm’s previous best-selling cow sold for $5,000.

Pastel’s superior lineage came about by the suggestion of a pair of dairy students, Denbigh said. The students had attended a national dairy show and were impressed by the genetic characteristics of a bull named Mountfield Mogul. The students suggested he mate Mogul with a Mizzou heifer named Shameless Patty.

“Mountfield Mogul and Shameless Patsy both have superior genetics,” Denbigh said. “The students’ suggestion to use Mogul as a mating sire turned out to be good advice.” When additional data is not available a calf’s genetic merit is estimated as the average between the sire’s and mother’s ratings. But, with additional data from a genomic test, more precise ratings are achieved, and stars like Pastel can be found. Denbigh continued, “We didn’t expect the result we got. It was one of those things where the moon and stars aligned.”

Pastel’s 2007 Origins

Finding Pastel’s true genetic potential is an example of genomic research going back more than a decade at Mizzou. It was Jerry Taylor, curators’ professor and Wurdack Chair in Animal Genomics, and Robert Schnabel, research associate professor, who helped create the technology used to identify Pastel’s superior potential. In conjunction with USDA researchers, the pair created the Illumina BovineSNP50 BeadChip, an inexpensive and easily used device that investigates variant positions in the DNA of cattle and is used to evaluate genetic merit in both dairy and beef cattle.
SNP chips. Photo by CAFNR

Often referred to as a SNP chip, it allows scientists to obtain information concerning the DNA bases present in an animal at over 50,000 predetermined positions within the genome (the genome is the entire DNA of an animal). Since its 2007 introduction, this assay has been applied internationally within the dairy and beef industries to improve genomic selection options, said Jared Decker, assistant professor of beef genetics extension and computational genomics. This approach allows the estimation of an animal's genetic merit at birth from a DNA sample that may be obtained from hair roots, blood sample or even a nose swab.

Predictions of genetic merit made through SNP data are now actively being used by Holstein breeders to make selection decisions on bulls. The industry received immediate benefits from substantial gains in the accuracies of predicted genetic merits early in an animal's life, allowing easier identification of superior animals at a lower cost. This permits more rapid genetic progress, Decker said. The SNP chip is now part of the criteria that identified Pastel’s superior traits.

Research is also continuing today at MU in improving dairy and cattle traits in other ways. The MU animal genomics group is involved in research to utilize DNA technology for the prediction of genetic merit for economically important traits in cattle, including disease susceptibility, feed efficiency, milk production, reproduction, and growth.

Results of the bovine respiratory disease research should conclude in about two years with the testing of a genomic tool to help identify animals with a prevalence to this disease.

“We have so much more information now,” Decker said. “The possibilities for profit are exciting.”

Monday, March 9, 2015

Articles of Note: Drovers CattleNetwork

There are two articles in the February issue of Drovers CattleNetwork by Mary Soukup that you should read. First, "The tale of the missing homozygotes" describing Mizzou's USDA funded sequencing project looking for DNA variants responsible for early pregnancy losses. Second, "Genomic Gains: Bringing value to seedstock and commercial herds" describing adoption of genomic technologies in the beef industry.

As always, don't hesitate to contact me if you have questions.

Monday, February 9, 2015

Register for NCBA Cattlemens Webinar:
New Tools in Bull Selection
Understanding and Using Selection Indexes

NCBA has recognized the changing face of selection in the seedstock industry. In order to help commercial producers make wiser selection decisions during the upcoming bull sales this spring, they are hosting a webinar at 7:00 pm CST on February 19th. Space is limited, so sign up soon. For those who can't catch the session live, it will be recorded and a link posted on the NCBA webpage.

The seminar will feature Dr. Dan Moser from the American Angus Association, Jack Ward from the American Hereford Association, and Dr. Wade Shafer from the American Simmental Association.

For more information and to register, visit the NCBA website.

Monday, February 2, 2015

2015 Angus Convention to Host International Genomics Symposium

The American Angus Association® and Angus Genetics Inc. (AGI) will host the first-ever International Genomics Symposium as part of the 2015 Angus Means Business National Convention and Trade Show.

The event takes place Nov. 3 in Overland Park, Kan., and will provide cattle producers with cutting-edge information about advancements in genomics technology – and how these advances impact their businesses.

The symposium is sponsored by GeneSeek, a leading provider of comprehensive genomics solutions to the cattle industry, including the GeneSeek Genomic Profiler (GGP-HD).

“We are excited about the symposium and what it will mean for the cattle business,” says Dan Moser, AGI president. “Genomics is rapidly reshaping the way we produce livestock, and providing producers with the best information available will not only help us improve quality and consistency, but also make our industry more competitive.”

Genomics researcher and entrepreneur Richard Resnick (previously featured on this blog) will be the event’s keynote speaker. Resnick serves as CEO of GenomeQuest, a company that builds software to support genomic medicine, research and individualized treatments. Before becoming a bio-entrepreneur, Resnick was a member of the Human Genome Project at the Massachusetts Institute of Technology. Resnick will be one of several widely acclaimed experts on genomics technology to be speaking at the event.

“GeneSeek has partnered with the Angus breed since 2009, and our sponsorship of the symposium is a natural extension of our long-standing commitment to the breed and the cattle industry,” says Dr. Stewart Bauck, general manager of GeneSeek/Neogen Agrigenomics. “There is intense interest among cattle producers about genomics – and this event will go a long way in serving GeneSeek’s mission not only to advance the use of genomics technology, but also show the positive impacts it will have on producers.”

The rise of genomic testing and evaluation is reshaping the Angus business at an accelerating pace. In fiscal year 2014, genomic testing increased by 32%, and AGI recently reported that genomic testing in the first quarter of fiscal year 2015 grew by more than 56%.

The 2015 Angus Means Business National Convention and Trade Show takes place Nov. 3-5 at the Overland Park Convention Center in Overland Park, Kan. The first-ever convention last year attracted nearly 2,000 progressive producers from across the country. For more information about the convention, visit www.angus.org.

Avoid the Headache: Properly Submitting DNA Samples
Breed Improvement Session
Angus Means Business National Convention

DNA sampling
Tonya Amen, AGI
During the second portion of the Breed Improvement session, Dr. Amen answered the question "How can we avoid sample failure when DNA testing animals?" She gave four points:

  1. Have proper collectors on hand. Blood samples are preferred, as the process can be automated. Blood samples can also be archived, whereas tissue samples cannot be. Contact your DNA service provide or see the Angus website. Have samples properly identified. "You cannot invent your own collection system!" said Amen. A business card, airline barf bag, and other home-remedies won't work!
  2. Practice good sampling technique. Make sure you have a nickel sized spot that has soaked completely through the card. Do not send wet samples-mold will grow like crazy! Make sure samples dry overnight in a safe place (not the dash of your truck!).
  3. Package well. Padded envelopes work well.
  4. Consider shipping method. How long will the sample be in transit?

Staff at AGI have a mantra about blood card sampling—Donor Dams Die. Collect samples on your animals, even if you think you will never DNA test that animal. Better to be safe than sorry.
When sampling twins, hair samples are required due to twins sharing blood in the cows uterus.
If blood cards are stored at home, store in a cool dry place and do not store in plastic.

Friday, January 30, 2015

Angus Only No More!
Maternal Edge Female Profile, Igenity Gold and Silver Profiles Are Released

Previously, when I spoke with commercial producers about genomic predictions for their heifers, I talked about two products, the GeneMax Focus and the GeneMax Advantage tests marketed by Zoetis. This has now changed.

GeneMax Focus and GeneMax Advantage

Of course, genomic predictions for seedstock cattle have been available for a large number of breeds, including Angus, Red Angus, Simmental, Hereford, Limousin, Gelbvieh, Santa Gertrudis, and Charolais. But, genomic predictions for commercial cattle where only available from Zoetis for high-percentage (greater than 75%) Angus cattle.

GeneMax Focus was the first commercial cattle genomic prediction test released. It provides predictions on a 5 point scale for marbling and gain, and an index called a GMX score on a scale from 1 to 100. These scores are percentile ranks where 50 is average, 1 is the bottom of the heap, and 99 is top of the class. This test cost $17. From my conversations, it explains about 20% of the variation in marbling and gain. This test is most appropriate for commercial producers who retain ownership of their cattle in the feedlot.

In March, 2014 Dr. Kent Anderson said Zoetis was working on a "complete game plan." Zoetis is leveraging data and information from the seedstock level to build products for the commercial level. At that time they released the Zoetis GeneMax Advantage test. This test reports three indexes, a Cow Advantage index focused on cow-calf production, a Feeder Advantage index focused on performance in the feedlot and on the grid, and a Total Advantage index which ranks animals on performance from conception to carcass. These indexes are also reported as a percentile ranks from 1 to 100. The GeneMax Advantage test also reports SMART Outliers. This flags animals that have extreme values for cow size, milk, docility, marbling, and tenderness. This test explains approximately 65% of the variation in dozens of traits and then combines these predictions into indexes based on economic importance. Those who have talked with a beef genetics extension specialists know indexes are the preferred way for commercial cattlemen to make selection decisions. This test costs $44 and is appropriate for anyone with high-percentage Angus.

Maternal Edge by American Gelbvieh Association and GeneSeek

In November of 2014 the AGA and GeneSeek release the Maternal Edge Female Profile. This is a commercial heifer genomic prediction for high-percentage Gelbvieh females. The Maternal Edge Female Profile returns scores for calving ease, maternal calving ease, weaning weight, yield grade, marbling, and carcass weight. Scores are from 1 to 10, with 5 being average, 1 being worst, and 10 best compared to the American Gelbvieh Association animals with genomic predictions. Kari White of the American Gelbvieh Association stated that simplicity was a priority in the design of this test. This test cost $26 and is appropriate for anyone with high-percentage Gelbvieh cattle.

Igenity Gold and Silver

On their website, Neogen GeneSeek announced the release of Igenity Gold and Igenity Silver profiles. They will introduce the product at the National Cattlemen's Beef Association convention on February 4th and the tests will be available March 1st.

Dr. Stewart Bauck said, "Previously we screened for hundreds of gene markers. Now we target thousands, and are focusing on the most powerful genes that affect profits in commercial cow herds." The new Igenity Gold profile ranks cattle on 12 categories of maternal, performance, and carcass traits, while the Igenity Silver profile ranks animals on 6 categories. Both tests offer free parentage verification. The profiles can also be combined with BVD-PI and pregnancy testing. The profiles will also test for the presence of male Y chromosomes in females, which research at USDA-MARC suggests reduces fertility. Igenity is also improving its website to provide producers with tools to manage their selection decisions.


As part of the Show-Me-Select Replacement Heifer Program, we have created a new designation for heifers with genomic predictions called Show-Me-Plus. In the past, the Show-Me-Select program created a designation for heifers that were out of high-accuracy AI sires called Tier II heifers. Buyers had more information about these heifers and consistently paid a premium for them. To capitalize on the increased information provided by genomic predictions, the Show-Me-Select program created the Show-Me-Plus designation. These are either registered heifers with genomic-enhanced EPDs or commercial heifers with a prediction from an approved genomic test. The GeneMax Advantage and Maternal Edge Heifer Profiles are currently approved for use in the program. Watch this blog or the Show-Me-Select website for more information about Show-Me-Plus heifers.

Take Home Messages

The GeneMax Focus, GeneMax Advantage, and Gelbvieh Maternal Edge Heifer Profile are all built on genomic prediction best practices and are designed with the breed-specific nature of genomic predictions in mind. We also expect that other breed associations will be releasing breed-specific commercial heifer predictions in the future. I will pass along more information about the new Igenity profiles as I gather it. As more commercial heifer genomic predictions are released a greater number of beef farms and ranches will have access to the benefits of genomic technology.