Monday, January 9, 2017

Brangus Journal: Using Genomics in Your Herd

My second piece on genomic prediction was published in the Brangus Journal back in December.

The Dance Steps of Genomics Part II: Using Genomics in Your Herd

This piece discusses how we get started with genomic testing. What animals should we DNA test and when should we test them?

The first article in the series is available here

What do you think of the article? As always, your feedback is welcome.

Friday, January 6, 2017

Genomic Prediction Patented???

Hat tip to Dr. John Cole, USDA, and Jesse Hoff for bringing this to my attention on Twitter.

I need to make an important point: I am not a patent lawyer. I do not have a deep understanding of patent law and nothing in this post should be considered legal advice or council.

On November 8, 2016 Canada issued a patent to Ben Hayes and Michael Goddard for genomic prediction. Genomic prediction is estimating an animal's breeding value (i.e. genetic merit) using DNA variants. See the Canadian Intellectual Property Office website for more detailed information about the patent.

Meuwissen, Hayes and Goddard first published their work on genomic prediction in 2001.
Hayes and Goddard filed for a patent of the method on December 21, 2007 with the United States Patent and Trademark Office.
About 23 days later, the Illumina BovineSNP50 Beadchip, a DNA test that can test 54,000 DNA variants quickly and cheaply for cattle, was released at the Plant and Animal Genome Conference. This 50K SNP chip was developed, in part, to deploy genomic prediction in North American dairy and beef cattle breeds.
This USPTO patent has not been granted. See https://assignment.uspto.gov/patent/index.html#/patent/search/resultAbstract?id=20120144508&type=publNum. However, the Canadian patent has.

A few points I want to make.
In 1997, Nejati-Javaremi, Smith and Gibson published a method they call total allelic relationship, which is basically genomic prediction by a different name. They even state in their article that genetic markers (not the actual DNA variants responsible for differences, i.e. causal variants) could be used to measure total allelic relationship. This method is basically the single-step genomic prediction that we use today, and in my non-legal opinion this probably represents significant prior art to the work of Hayes and Goddard.

Further, the Hayes and Goddard patent is limited to populations in which the effective population size (a measure of diversity, the size of a randomly mating population) is smaller than 1,000. I believe it could be argued that genomic predictions of multiple-breed data sets could have effective population sizes larger than 1,000.

In related news, Meat and Livestock Australia is fighting a Cargill USA and Branhaven LLC that basically allows them to patent all cattle DNA, see "MLA launches Federal Court bovine genome patent fight" by James Nason. In another article by Sue NealesRob Banks, University of New England, stated the Cargill/Branhaven patent is “intellectually and morally indefensible”. With this patent, the amount of prior art is even more staggering, basically all of modern cattle genetics. I don't know where to start or end with this patent...


Cattle breeders have fought other patents of animal breeding technologies. In 2014, legal battles started between the American Simmental Association versus Leachman Cattle of Colorado, LLC and Verified Beef, LLC. Ultimately, in August of 2016, the American Simmental Association won these cases and the Leachman patents were overturned.

Unfortunately, I worry that the American Simmental Association and their genetic evaluation arm, International Genetic Solutions, may have additional legal battles on their hands. Of the twelve breed associations that are included in the IGS multiple-breed evaluation, five are Canadian associations. International Genetic Solutions recently announced that they have released a multiple-breed single-step genomic prediction of stayability. They will continue to release multiple-breed genomic evaluations for additional traits in the coming months. In Canada, these genomic predictions could be viewed as infringing upon the Hayes and Goddard patent. 

We live in interesting times in the beef breeding world... 

Here is hoping for more patents to be overturned.

UPDATE: 6 January 2016
I received word on Advantage Cattle from JohnD that the US patent on genomic prediction had been rejected just yesterday on January 5th. http://www.advantagecattle.com/forum/topic.asp?whichpage=24.6666666666667&TOPIC_ID=10783#166702 

Most of the US rejection cites a Monsanto patent application titled "Marker assisted best linear unbiased prediction (ma-blup) software adaptions for practical application for large breeding populations in farm animal species." This patent was abandoned as an incomplete application in April of 2012. From the USPTO website, "Abandoned means that the application is no longer pending and, thus, cannot mature into registration."
The examiner referred to the Monsanto patent application as prior art, and rejected the Hayes and Goddard patent application in the US. Perhaps the same arguments can be used in Canada to overturn the granted patent?

Also, I should point out that I believe both dairy and beef industries, especially in the affected countries, should band together to fight these patents. I do not think that the American Simmental Association should be asked to carry the water again on this issue. But, I do fear that they might be a target of litigation. 

Friday, December 16, 2016

Beef Genetics Education Team Announces National Essay Contest: “What does it mean to be a beef breeder in the 21st century?”

Youth participating in 4-H, FFA, or junior beef breed organizations are encouraged to compete in a national essay contest. Essays should respond to the prompt “What does it mean to be a beef breeder in the 21st century?

The winning essay will be published in one of BEEF magazine’s online newsletters (e.g. BEEF Daily or BEEF Cow-Calf Weekly). The 2nd through 5th place essays will be published on A Steak in Genomics blog. We will award $500 for first, $300 for second, and $200 for third place in the contest. The first place winner will also receive 50 GeneMax Focus or PredicGEN tests.
Essays will be judged by beef genetics extension specialists, breed association staff, and trade publication staff.

Essays will be judged on their ability to encourage best practices and technology adoption by describing:
  • Trust and effectiveness of beef breeding best practices and technologies.
  • Simplicity of using technology.
  • The profit and sustainability outcomes of using best practices and technology.


Essays are required to be at least 600 words long but not longer than 3,000 words. Please submit contest entries at https://missouri.qualtrics.com/SE/?SID=SV_9YwBWK2WvM7Tdsh. Entries are due February 15, 2017.


Thanks to our essay sponsors BEEF magazine, Zoetis, and GeneSeek.

This educational program and essay contest are part of the "Identifying Local Adaptation and Creating Region-Specific Genomic Predictions in Beef Cattle" funded by the USDA-NIFA, Grant No. 2016-68004-24827.

Thursday, December 1, 2016

AHA Educational Forum: AHA Creative Services

Sean Jersett, Christy Bengno, Julie Mais, Alison Marx, Caryn Vaught

Number one piece of advise for an advertiser:
Be aware of your sale dates! You need to have the deadlines for dates to go to the printer and when catalogs will be to the customers. You need to have your ducks in a row before the printing date.

How do you handle photography?
Photos need to be high resolution, print quality photos to look good in the catalog. "We need to have the photos identified so we know how to use them," Bengno said. Dropbox or email is a good way to send in the photos. Make sure that email allows for the photos to be sent as high resolution. If you have a lot of photos, Dropbox is much easier. Put the photos in Dropbox and then share the folder with the AHA staff. Make sure you notify the AHA staff that you have added photos to an existing shared photo.

When using phones, make sure your phone has a high quality camera on your phone and that you have your phone setting to the highest resolution possible (largest file size). If you don't change these settings, your phone will not take a high enough quality picture. If you have a 72 DPI photo, it will appear 4 times smaller than it should be in print.

What about breeders using Photoshop?
The Photoshop images are a great way for a producer to share their vision of the picture, but the actual Photoshop and other processing needs to be done by AHA staff to make sure that the requirements for print are meet. Send the raw photo, and the AHA staff will do the edits. Make sure that there is enough background space around the animal.

Advice for preparing an Hereford Journal ad?
Make sure that there is good communication. If the photos are not going to be ready in time, let the AHA staff know. "Too much information is often better than too little information," Marx said.

If an ad is made by a different publication, have the other organization communicate with the AHA staff to make sure the ad is prepared according to AHA specifications.


If preparing an ad, share colors that you don't like. Share items you would like to be included. Photos help a lot! Communication is key. "Some times I like a blank page, but at least tell me what you hate!" Jersett said.

What is the difference between a ride-along and other catalogs?
Figure out your target audience. If you are marketing to juniors showing heifers, including a ride along with the September issue that focuses on the Junior Nationals. If you are focusing on commercial cattlemen, printing in the tabloid publications is a great way to hit commercial ranchers.

The tabloids printed on paper are a cost savings for the AHA. If the commercial producer will fill in a card and send it back to the AHA, this allows them to send out the tabloid at no cost to the commercial producer.

How many clicks are you getting on banner ads?
Working on the back end, AHA staff can give you data on your specific banner ads.


Ag Teachers can request for a free subscription to the Hereford World. But, they need to request a new subscription each year.



Decker's Take Home Message
Progressive beef producers need to make sure they are doing a good job branding and marketing their cattle. To see a full return on investment in best practices and technology, producers need to be aggressively marketing their cattle. Working with the right creative services can really help.

Tuesday, November 29, 2016

Brangus Journal: Understanding Genomic Prediction

Head on over to the Brangus Journal website to see some of my latest writing on genomic prediction.

The Dance Steps of Genomics Part I: Understanding Genomic Prediction

Personally, it is probably my favorite of the articles I have written, so I would encourage you to make the time to read it.

What do you think of the article? As always, your feedback is welcome.

Wednesday, November 23, 2016

AHA Educational Forum: myHERD services

Stacy Sanders and SyAnn Foster
AHA

"When we do things electronically, we are no longer waiting on the postal service," said Stacy Sanders.

He also noted that electronic reporting did not require any handling or processing by the association staff.

The electronic recording also eliminates paper work and automatically uses semen certificates that have been released to the breeder.

In addition to the AHA myHERD.org service, the association also allows you to use Genetic and Economic Management (G.E.M.) and CattleMax. AHA is also working with the smart phone app CALF BOOK. "We want to give you options, we want to give you something that works for you," Sanders said.

The myHERD service is also switching to a different system to enable a faster web interface, which will also work better on smaller screens like tablets and smartphones.

AHA has a goal of 80% of records turned in electronically. Weaning and yearling data is currently above 80% reported electronically, other data points, such as registrations or payments are increasing.

When using a third party software, make sure that you are creating animals in the software, not in myHERD. Once the initial extract is made to go into the third party software, the AHA does not send data to the software. This is a one-way street of the data going from the software into the AHA system.

The easiest way to transfer animals is to make sure you get the buyers member ID. This is the best way to identify a member in myHERD. myHERD is also able to search for nonmembers that are already in the AHA database.

You can also release AI certificates to customers and to see which certificates have been released to you.

myHERD also displays information which producers you have done business with. You are able to download this list to get addresses and other contact information for your customers. This list can also be extend to 5 years. The download is a CSV file which can be easily opened in Microsoft Excel, or other spreadsheet software.

In myHERD you can also update incorrect data, see adjusted weights, and other reports. Breeders can also order DNA tests through myHERD, see the status of currently ongoing tests, and see previous DNA test results.

There is now a new button to get calf crop data. First, go to the TPR Whole Herd Reporting screen. Click on the calf crop you want to retrieve. You can then click on the "Calf Crop" button to download the data on that calf crop. This data includes data records such as weights, chute scores, dam weights, etc. This report also contains EPD and EPD accuracy data. This report will also contain any genetic defect testing.

AHA has held "School of myHERD.org" webinars. They now have 23 myHERD tutorials on the AHA website at http://hereford.org/content/schoolofmyherdtutorials. There are two ways to view myHERD tutorials.
The first method tells you step by step and tells you where on the screen to click.
Second, you can have all steps shown or printed at once.

When ordering DNA tests, it automatically shows you active animals. But, if you need to DNA test a deceased or disposed animal, you can simply click on "All Animals" to show all your animals. After selecting the animal, you click the primary reason for DNA testing the animal. You will then choose the type of test you want to use (parentage, GE-EPD, horn-polled, etc.). When doing parentage, if one of the parents does not have a DNA test on file, it will automatically create a field to order a DNA test for that parent. myHERD will also check for duplicate DNA testing, which saves the association money.

Another new feature in myHERD is to look at the status and results of previously purchased test.

Allflex tag products are now available directly from AHA. Allflex has a Tissue Sampling Unit (TSU) that will take a sample for DNA testing. These ear tags can be various combinations of visual, EID, and TSU Allflex products. The TSU sample can be kept at room temperature for a year, and if kept in a freezer can be kept indefinitely (a long time).
PI testing can also be done with TSU sample. AHA is investigating offering PI testing at the same time as DNA testing. One way to simplify DNA testing and PI testing at the same time is to collect two samples.

Thursday, November 3, 2016

Road Warrior: First Week of November Addition

This weekend I get to cross the state to visit with several producer groups.

Friday November 4th I will be speaking at 3pm at the Joplin Regional Stockyards during the Central States Beefmaster Breeders Association field day. The CSBBA will be having a performance bull sale at the Joplin Regional Stockyards the next day at 1 pm. I will be discussing the how and why of genomics.

Saturday, at 8am I will be speaking as part of the Pearls of Production Program at the University of Missouri South Farm Research Center in Columbia, MO. I will be discussing bull selection, and the South Farm herd bulls will be on display for viewing.

Saturday at 7 pm I will be speaking at the 2016 Beef Producers Seminar in Maryville, MO. The trade show will start at 2pm with demonstrations and presentations to follow.  I will be discussing genomic prediction, and we will have a live animal demonstration with a set of heifers that have commercial heifer genomic predictions.

Google says this will be 942 miles on the road for me...

Hope to see you at one of my stops this weekend!