Friday, December 19, 2014

GE-EPDs and Genetic Selection
Breed Improvement Session
Angus Means Business National Convention

There was standing room only for the Breed Improvement Session of the Angus Means Business National Convention on November 4th, 2014.

Genomic Recalibration
Dan Moser, Angus Genetics Incorporated
Performance data reported to the American Angus Association has become more important than ever. Not only is this data necessary to get highly precise estimates from sires, but it is the foundation of developing genomic predictions for genomic-enhanced EPDs. In the training or recalibration of genomic predictions, basically an EPD effect is estimated for every DNA variant included in the genomic prediction test. The genomic prediction (also called the Molecular Breeding Value, MBV) is the sum of every EPD effect for approximately 50,000 DNA variants evenly spread throughout the cattle chromosomes.

Initial GE-EPDs in 2010 were based on 2,253 animals. In 2012 the training set increased to  11,756, by 2013 the training set was larger than 38,000 animals, and now in 2014 has reached over 57,000 animals.

Moser said, "No one item by itself gives us the best story." Precision of genetic predictions relies on using pedigree, performance, progeny, and MBV.

MATERNALPLUS™™
Tonya Amen, Angus Genetics Incorporated
MaternalPlus is a voluntary, inventory-based reporting system. This whole-herd reporting program allows the capture of reproductive trait data. This allows improvement of reproductive selection tools.

"If it is important to them, it needs to be important to you," Amen stated to encourage seedstock producers to keep the needs of their commercial customers in mind. While decreasing generation interval is important in a seedstock setting, longevity is vital in commercial operations. For each inventoried female, producers need to report a calf record, disposal code for the cow, or reason the cow did not have a calf reported.

Certain results will only be available to MaternalPlus members. This include:

  • Within herd genetic trend- how do you relate to the breed? 
  • Production records 
  • Calving distribution 
  • Cow-age performance summary 
  • Dam disposal report- why are your cows leaving the herd? 
  • Female age distribution 

New perks coming to the program include:

  • A MaternalPlus logo, 
  • MaternalPlus catalog inserts
  • Other customizable MaternalPlus advertisements 
  • Periodic mention as MaternalPlus participant in the Angus Journal and Angus Beef Bulletin 

Dan Moser pointed out that AAA has been ahead in many instances, but in terms of cow herd reporting and longevity EPDs the Angus Association has been way behind.

Angus $Value Indexes
Dan Moser, AGI
The $F index (SHORT EXPLANATION) originally include rough estimations of feed efficiency as fewer days on feed due to quicker growth rate. But, the relationship between feed efficiency and growth is not 1 to 1. Intake data has accumulated over time and now allows inclusion of feed intake into $F and $B indexes. Feed intake remained fairly level for the early years of $F indexes, but in the past few years, genetic trend for feed intake has changed drastically. Each year the economic assumptions of the $Value indexes are updated, and AGI is taking this opportunity to incorporate feed intake into the $F and $B indexes. The changes in index values will be mostly be due to updated economic assumptions with changes due to feed intake being secondary.

Foot Scores
Moser also discussed foot scoring. Producers are reporting two main issues: shallow heals with long toes and scissor or corkscrew claws, which may be related. What we need is a simple system to score cattle for these two conditions. In a new research program members will provide two scores to AGI, foot angle and claw set. Both scores are on a 1 to 9 scale where 5 is ideal. The AGI scoring system will be similar to parts of the Australian system, but greatly simplified. Breeders are asked to score the worst foot. An ideal angle would be a 45 degree angle between hoof and pastern. EPDs may be calculated in the future, but the soonest impact may be more attention paid to foot structure. Australian data suggests heritabilities around 15% for foot angle and hoof set. Scoring must be done prior to hoof trimming. Producers will need to submit basic information on feed ration when submitting foot scores. EPDs will be provided as soon as sufficient data is available.

See the 2014 Angus Convention Newsroom for more information from the session.


 

Wednesday, December 17, 2014

Feed Intake, $F, $B and You



In October, we reported that Angus Genetics Inc would be including feed intake data into $F and $B indexes. On December 5th, 2014 those changes took effect. In our October poll, 91% of the respondents indicated that they considered including feed intake data as an improvement to the $B index. And, the data backs this up (see here for more about our data-driven philosophy). Since 2004 the American Angus Association has seen an increasing genetic trend for feed intake. This means Angus producers have been indirectly selecting for increased feed intake, which is a negative when we are striving for more efficient cattle.

Figure 1. Deregressed estimated breeding values for birth and weaning weight plotted against birth date. Deregressed estimated breeding values plotted against birth date for 3,570 Angus animals. The blue lines represent fitted linear and red lines represent fitted quadratic regressions. a. Deregressed birth weight EBV, and b. Deregressed weaning weight EBV.
Decker et al. BMC Genomics 2012 13:606 doi:10.1186/1471-2164-13-606
One of the best examples of moderating one trait while improving others is the relationship between birth weight and other production traits. Since the mid-1980s Angus producers have been decreasing birth weight and the associated calving problems while increasing correlated traits such as weaning weight and carcass weight. This is perhaps one of the great accomplishments of modern animal breeding—the ability to break apart negative relationships between traits. Including feed intake into $B will allow Angus breeders to break the negative relationship between production and feed intake.

The USDA funded Beef Feed Efficiency Project has provided many of the phenotypes used in the Angus feed intake EPD calculation. The Beef Feed Efficiency Project will continue to work with breed associations and producers to provide tools and resources for the improvement of feed efficiency.

For more information on changes to $B and $F see this FAQ sheet by the Angus Association.

Monday, November 17, 2014

Data-Driven Extension Education and Research



As you know, I started in my current position at the University of Missouri Beef Genetics Extension Specialist in March of 2013. Check out the first A Steak in Genomics video to see how I describe my approach to extension education and research. (Excuse the ums and uhs, I was a little more nervous than usual as it was a job interview!)

Have you ever wondered why polls started appearing at the bottom of these blog posts? It is an effort to have a data-driven extension program in which we measure and respond to feedback from you, the Steakholders.

In order for us to really make progress in using genomic technologies and animal breeding best practices in beef production, there needs to be an open and honest conversation about these topics. If you ever are concerned there is an inaccuracy in my writings or presentations, please bring it to my attention as a comment on the blog, in an email, or a phone call. But please bring the data! Don't bring fallacies or antidotes to a data-driven conversation.

In God we trust.
All others bring data.
– W. Edwards Deming


Thursday, November 6, 2014

Piecing the Puzzle
Story By Rebecca Mettler for Cattlemen’s News

Rebecca Mettler wrote a story for the Joplin Regional Stockyards Cattlemens News. Mettler talked to Dr. Megan Rolf of Oklahoma State University and me about the use of DNA testing in the beef industry with a focus on commercial operations. Check out the article on page 18 of the November issue!

Wednesday, October 22, 2014

Food Babe Visits University of Florida


Post at Illumination Blog

For those that have experienced the clarity and beauty of viewing the world through the lens of science, interacting with those who choose opinion and fear over facts and evidence can be very frustrating. But Kevin Folta, at the University of Florida didn't even get to interact with or question Ms. Hari about the misinformation she shares to a large audience. Head over to the Illumination blog to read Kevin Folta's thoughts. 

Wednesday, October 8, 2014

Brown Bagger EPD Updates

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 Genetic Summit presentation.

Wade Shafer
For the first training of Simmental genomic predictions, there were 2,800 animals with genotypes (DNA information) and phenotypes (trait measurements) available. This resulted in genomic predictions that gave the same amount of information as 1 to 9 progeny; which depends on the correlation between the genomic prediction and the trait, and the heritability of the trait. To avoid confusion, Shafer emphasized that they do not provide the genomic predictions to the producer only the genomic-enhanced EPD, which combines the genomic prediction and the traditional EPD. This is done to avoid confusion.

The American Simmental Association has created a collaborative genetic prediction service called International Genetic Solutions, which computes EPDs for 11 breed associations. The database contains records for over 15 million animals. During their last round of genomic prediction training they used 5,240 Simmental, 2,164 Angus, 1,604 Red Angus, 999 American Gelbvieh, 571 Maine-Anjou, and 85 Canadian Gelbvieh. For every trait the correlations stayed the same or increased. Progeny equivalents ranged from 1 to 28 progeny, Simmental specific weaning weight genomic predictions gave the same information as 5 progeny. The multiple-breed genomic predictions gave the same information as 8 progeny. For marbling, Simmental-specific genomic predictions gave the same information as 4 progeny, multiple-breed predictions gave the same information as 8 progeny.

In the current round of retraining they are using 56,116 animals from Simmental, Angus, Gelbvieh, Limousin, Red Angus, Maine-Anjou, and Shorthorn. They are currently looking at different ways to approach this training.

Researchers at Iowa State University have created a new approach to combine DNA genotypes and pedigree information in a single step. International Genetic Solutions is planning on using this method in the Spring of 2016. They are working with Bruce Golden and Dorian Garrick to completely rebuild the software used for EPD estimation. This software will use the new single-step method to incorporate DNA information, more robust accuracy estimates, and utilize modern computer hardware which allows multiple processes and faster calculations.

John Genho
Genho discussed the use of single-step  BLUP which simultaneously combines DNA genotypes and pedigree information. Every animal receives half of its chromosomes from its sire and half from its dam. On average an animal receives a quarter for it chromosomes from each grandparent, but these fractions can be quite different from a quarter in individual animals. Single-step BLUP uses DNA information to more precisely calculate relationships between animals rather than simply relying on averages. Genho's company Livestock Genetic Services, LLC uses this method for the Santa Gertrudis Association and several herd-specific genetic evaluations.

Monday, October 6, 2014

Angus Association Refines Genetic Evaluation


Expect Changes in $B Index Rankings

thompson research center_0265
*UPDATED 7 October 2014

I had a brief meeting with Dan Moser of Angus Genetics Inc today in which he informed me of several updates to the American Angus Association's genetic evaluations.

First of all, heifer pregnancy EPDs, which were not estimated this summer, are once again being successfully estimated. When the dataset became large the analysis would no longer run properly. Previously, the heifer's service sire was fit as a fixed effect in the EPD equations. This means sires were forced to have the same conception rate in every herd. In the new model, the service sire's conception rate is fit as a random effect, meaning that we do not perfectly measure the conception rate and allow for factors that influence conception, such as differences in semen handling, to vary between herds. The base year of the heifer pregnancy EPD was also changed from 2000 to 2005 due to 2005 being the earliest year with a large amount of pregnancy data.

Second, the fourth recalibration of Zoetis' genomic predictions was completed this summer. Very few changes were seen. The only trait that saw some movement was carcass weight. With over 60,000 animals genotyped most of the diversity within U.S. Angus has likely been sampled. Further, the effects of the approximately 50,000 SNPs have likely been accurately estimated.

Lastly, feed intake data will be incorporated into the $B (dollar beef) economic index this December. This is done to account for feed efficiency differences between animals. The cost of feed is a major driver of profit in the feed yard. The Angus Association now has sufficient data to include this important economically relevant trait in the $B index. Many sires that previously ranked high for the $B index will continue to rank high because they have excellent feed efficiency. But, many sires that have excellent growth, marbling, and yield, yet because their progeny inefficiently use feed will rank lower for the $B index. So, if your favorite $B sire drops in the rankings come December you now know why. This knowledge will allow you to make corrective matings in the future to increase the feed efficiency of your herd.

*My apologies to AGI staff for inaccuracies that appeared in the first version of this post.