Friday, November 13, 2015

Hereford Education Forum: AHA Developments in National Cattle Evaluation

Dorian Garrick
Iowa State University

The Pre-Genomic Era

In the Pan-American Evaluation there are four countries, US, Canada, Uruguay and Argentina. Agricultural Business Research Institute (ABRI) collects the pedigree and trait data. Then the Animal Genetics & Breeding Unit uses BREEDPLAN to estimate EPDs.

To put the number of records turned in to the AHA data in context, we can compare them to other breeds. The 11 breed associations in International Genetic Solutions add 340,000 new animals in each of 2012 and 2013. AGI adds about 300,000 per year. Herefords add a little less than 100,000 animals per year.

The Early-Genomic Era

Cattle have 30 pairs of chromosomes. There are about 100 million base pairs per chromosome and about 2.6 billion base pairs in the entire DNA (genome).

Most errors in chromosome replication are fixed. But, some slip through and are passed down through generations.

The EPD of a bull is a sum of the average gene effects he carries. Until the genomic era, we progeny tested a bull to see how his progeny performed, and thus the gene effects he carries. In genomic prediction we try to use DNA information to estimate the gene effects the bull carries. A good bull has more of the favorable gene effects, and fewer unfavorable gene effects. A bad bull has fewer favorable gene effects and more unfavorable gene effects. But the good bull still carries unfavorable gene effects and can produce bad progeny, based on the chromosomes and genes that progeny inherits.

We tend to think of EPDs associated with an animal. But in genomics we associate an EPD (breeding value) with a segment of DNA to predict the genetic merit of the bull.

In current genomic prediction, we don't test the actual DNA variants causal or responsible for the variation in the trait. We use DNA variants spread throughout the genome. There are relationships between DNA variants on SNP chips and the actual causal variants. We call this relationship linkage disequilibrium. So, even though we are not testing the causal variant, we can use the linkage disequilibrium to predict the causal variant inherited based on the DNA variants in the same chromosome neighborhood.

Using the DNA variants on the SNP chip, Garrick's group came up with a prediction equation. Each SNP gets an effect in this model. The animal's DNA is then tested at GeneSeek, the prediction equation is applied, and a molecular breeding value is calculated. This molecular breeding value is then combined with pedigree and trait data to produce a genomic-enhanced EPD. The American Hereford Association now has over 20,000 animals genotyped. In the last month, 2,000 Hereford animals were genotyped.

Usually a very small portion of a contemporary group was genotyped (usually one or no animals are genotyped per contemporary group). When a larger portion of the contemporary group is genotyped many of the issues (statistical difficulties) with genomic prediction go away.

Make sure an animal has a registration number before doing DNA testing. Make sure the registration number is correct when submitting samples.

If the genotyped sex does not match the recorded sex, Garrick's group doesn't use these genotypes.

Also, we can't use duplicate genotypes. If an animal has multiple DNA tests run, either the failed test is removed, matching genotypes are merged, or if the genotypes don't match, both sets of genotypes are thrown out.

Garrick's group can also do breed verification.

We can also do parentage verification. If the Dam has an AA genotype at a DNA variant, then the calf cannot have a BB genotype at that DNA variant (calf can be AB or AA). Breeds should begin considering testing all animals in the herd. This would allow us to identify unknown parentage, not just verify the reported parentage.

The first SNP test widely used in cattle was the Illumina 50K SNP chip (the earlier Affymetrix chip was not widely adopted). In a hope to use genomic predictions across breeds, a 700K SNP chip was created.

GeneSeek then created a 25K and a 30K chips (GGP LD chips).

GeneSeek also created a 70K chip and later a 150K GGP uHD chip.

Initally, when implementing genomic selection reduced marker panels were created. Pfizer (now Zoetis) recognized they could get a bulk discount on 50K and never released a low density product.

Next step forward

Garrick gave a list of developments he is working on, namely:

  • Single step analyses (no blending or interms).
  • Actual rather than Approximated Accuracies.
  • More regular runs.
  • Readily incorporate new traits.

Bruce Golden and Garrick are creating a new evaluation system called BOLT CUDA evaluation system. At this point in the presentation, Garrick took off his ISU hat and put on his Theta Solutions hat (private company). The difference in this evaluation is the use of graphics cards (GPUs) instead of CPUs. Water cooling systems are also used in GPU systems.
Theta Solutions is currently using computers with 4 graphics cards.

Using a traditional computing, it would take an hour and a half to run an analysis. Using parallel computing, can get this down to 25 minutes. But, with graphic cards, can do this in 1 to 2 minutes.
Using 4.5 million animals can solve genetic predictions for Herefords in less than 12 minutes. It takes another hour to calculate the real accuracies.


Garrick gave five take home points for producers:

  • Genomic analyses are developing rapidly
  • New statistical models
  • New marker panels
  • More animals genotyped
  • New computing resources

Wednesday, November 11, 2015

Hereford Educational Forum: New Traits

Bill Bowman and Sally Northcutt
Method Genetics LLC

Bowman and Northcutt discussed several new EPDs either in development or released by AHA, including:

  • Dry Matter Intake
  • Sustained Cow Fertility
  • Heifer Calving Rate
  • Udder Quality (Teat Size and Udder Suspension)

Heifer Calving Rate, Sustained Cow Fertility, and Dry Matter Intake are currently released as prototype evaluations and can be accessed as a downloadable Excel file.

"One of the things you all have going for you is the foresight to begin a TPR program," said Bowman.

Heifer Calving Rate

Heifer Calving Rate (HCR) is a categorical trait, they either calved or they didn't. Method Genetics reports a heritability of 15% for Heifer Calving Rate. They analyzed 98,000 records, of which 73% had calved by 800 days of age, 27% had not calved. Contemporary grouping for heifers is based upon their herd, yearling weigh date, calf birth year and season.

"This EPD goes beyond a traditional heifer pregnancy EPD." said Northcutt.
Bowman added, "This follows through to calving, which is really what we want."

The higher value is more favorable for the Heifer Calving Rate EPD. If Sire A has a HCR EPD of 8% and Sire B has a HCR EPD of 2%, we would expect 6% more of Sire A's heifers to calve.
The benefits of this EPD include improvement for a lowly heritable trait, provides an opportunity for selection pressure to improve calving, and can now directly include fertility (Heifer Calving Rate) into AHA indexes in the future.

Sustained Cow Fertility

Whole Herd TPR allows a spring board for Heifer Calving Rate, which acts as a first step in looking at Sustained Cow Fertility. Sustained Cow Fertility is a survival analysis that is different from a typical longevity EPD. It uses the Heifer Calving Rate evaluation as the starting point. After this point contemporary groups become dynamic; after calving as a heifer females exposed together make up a contemporary group. Calving intervals and age at calving are calculated. The model accounts for milk and total maternal calving ease EPDs.

A cow is "Successful" until she fails to have a calf. But, some records are "Censored", i.e. the data is handled carefully for exceptions like a cow being sold as a breeding female (registration transferred) or becoming a donor dam. Sustained Cow Fertility has a heritability of 20%.

A higher value is more desirable for sustained cow fertility.

Dry Matter Intake (DMI)

This EPD starts with a multi-trait animal model including:

  • Individual feed intake (standardized)
  • National Cattle Evaluation weaning and yearling weights
  • Four-generation pedigree

Feed intake has a heritability of 40%.
Weaning records are included for contemporaries of calves with an individual intake record to account for selection bias (sending the best calves to feeding test to measure feed intake).

In Dry Matter Intake (DMI) lower values are predictive of less intake. When you begin looking at feed intake, cattle that gain well tend to be more efficient, but they tend to eat more. We want to find outliers who eat less feed but gain more weight. Downloadable Excel spreadsheets contain both DMI EPDs and Yearling Weight EPDs to allow breeders to look at this. Single trait selection should be avoided. Incorporation of Dry Matter Intake genetic values into the AHA indexes will be the greatest benefit.

As we have discussed in the past, depending on how you slice it, feed efficiency rankings can be different and the most effective strategy is an economic index.

Think about the entire system, not a single trait!

Challenging traits are now more accessible from a genetic standpoint. Reproductive traits with lower heritability are addressed. A foundation is established for genomic-enhanced EPDs in these traits.

Udder Quality

In the current udder quality evaluation, it is a standalone evaluation, meaning no other traits are fit in the model, only Udder and Teat scores. Currently there is no genomic component. Since 2008 the genetic trend for udder and teat scores have increased dramatically.

Genetic Trends for breed averages in udder suspension and  teat size EPDs. Data from Fall 2015 AHA Sire Summary.

The genetic correlation between Udder and Teat EPDs is about 0.8. But, this does not mean the udder score should always equal the teat score; in fact we should see many instances where this is not the case.
Higher scores are more favorable for both Udder Suspension and Teat Size EPDs.

This is an example of publish it and they will come; from the Spring 2015 and Fall 2015 evaluations 25,000 records were added to the Hereford udder and teat data set.

Repeated measures on females are included in this analysis. Scoring system is designed for characterizing udder quality - not milk production levels.
[My question, is there an optimal level for udder suspension? If the udder is too tight, will milk production suffer?]
The contemporary group records account for subtle differences between how different farmers and ranchers score the udders and teats.

The purpose of scoring udders is to provide commercial producers with problem-free genetics. Producers are encourages to score udders when taking calf's birth weights.
When scoring, 9 is favorable and 1 is unfavorable. Be consistent in scoring within your cow group and herd. In scoring, suspension is always the first number and teat score is the second number.

Udder scores should be collected within 24 hours of calving. Udders should be scored annually. Contemporary groups account for herd, year, and season difference in scoring.
Keep scoring independent of milk production levels.

See the Udder Scoring Fact Sheet for more information.

Northcutt encouraged Hereford breeders, saying "You have some exciting new traits."

Tuesday, November 10, 2015

Angus Genetics Inc. Updates to EPD/Pedigree Lookup

Based on input and requests from breeders, we’ve been working on some updates to the information displayed on the Animal Search feature on These new features went live this morning [10 November 2015], and I want to take a minute to highlight and explain these enhancements.
  • Genomic Progeny 
  • EPD percentile ranks
  • Progeny 
For complete post, please visit Angus Genetics Inc blog, and read the post by Dr. Tonya Amen.

Decker's Take Home: I always love to see breed associations changing and innovating. I think these changes will allow producers to more quickly evaluate an animal's genetic merit. Plus, I'm sure breeders appreciate AGI responding to requests.

Thursday, November 5, 2015

The Power of the Genome: Weighing Opportunities, Dangers and Responsibility

Angus Convention 2015

Richard Resnick
CEO of GenomeQuest

One can not impede scientific progress.
- Mahmoud Ahmadinejad 
Resnick gave a series of examples of how genomics is changing society.

Resnick put a nice spin on the typical sequencing cost figure. He overlays Illumina's ($ILMN) stock price on top of the figure.

He went on to explain that the only real differences between humans, cattle, corn, and other species is the proteins they make. The amino acids, the building block of proteins, are actually the same between species.

Resnick used cystic fibrosis as an example of a disease in which genetics has been very important. One DNA variant that causes the disease is called ΔF508. When a person has this variant, the gene produces the protein, but a check and balance in the cell recognizes the protein as not correct and destroys it. A different variant, G551D, is not so severe that the protein is destroyed, but the protein does not function properly. A drug called Kalydeco alters the mis-shaped protein coded by the G551D variant and allows it to function again.

Cancer is a disease of the genome. What we need is molecular names for these cancers. This will allow more individualized treatments of what is biologically wrong.

With these advances in medicine, humans will be living longer and there will be more demand for food. We need to keep in mind, when we digest food, we take the proteins and shred them back up into amino acids.

Genomic prediction allows you to the predict the future with accuracy. This, of course, is not genetic modification in the GMO sense. But, other agricultural species cannot benefit the same from genomic prediction as sexually reproducing organisms.

Bananas don't have sex. The trees are clones of other trees. But, if a disease comes along, you can't breed for the disease resistance in bananas. Oranges face similar disease issues. Most corn has a gene transfected from bacteria that produces a toxin that stops bugs from eating the plant. Most soybeans are now Roundup Ready, meaning we can spray the plant with pesticides, the crop lives and the weeds die. So, we just need to wash the soybeans, and there are no problems with eating these soybeans.

There is actually a gene for apple browning. Scientist took this gene and duplicated it multiple times in the apple genome. When the apple cells see too much of the protein coded by this browning gene, the cells shut down all copies of this gene. Thus, no browning protein, so the apple does not brown!
Aquabounty salmon, is a modified salmon that grows to its mature size in 18 months.

By Kevin586  via Wikimedia Commons
For writers, they moved from pen and paper, to type writers, to word processors, and now to computers with Google and all the other Internet tools. Today in genomics we have the "word processor" figured out. What will happen when we move past the "word processor" of genomics and get to the "Google" stage of genomics?

Many people (20%) find cilantro disgusting, it tastes like soap to them. This disgust is caused by genetics. If you go to a high-end restaurant, wouldn't the chef want to know that you hate cilantro? In fact, a certain food company is doing lots of sequencing in Europe to figure out what foods people like or is more nutritional for them.

The baby's entire genome is circulating in the mother's blood. This means we can test the baby's DNA from the mother's blood. What is the line between aborting a baby for the presence of a horrible disability and aborting a baby for the lack of a preferred trait?

There is a patent for DNA testing to identify sperm donors. "Is this a problem? Certainly not in bovines, but what about humans?" Resnick asked. Previously when we did gene modification, we used a sledge hammer, now with CRISPR technology we can use a precise scalpel. Dehorning is a bad public perception issue, takes time and labor, and is an animal welfare issue. Recombinetics has technology to take an animal with the variant that causes horn growth and to replace it with the gene that causes the animal to be polled.

In the United States, we don't do gene editing in humans due to ethical concerns. But, scientists in China have already worked on altering nonviable human embryos.

"Have I scared you a little bit? Hopefully." Resnick stated. But, he hopes that you now understand the difference between DNA testing (like we do for genomic-enhanced EPDS) and genetic modification, that you understand the impacts genetic modification can have, and that you can intelligently discuss these topics with the rest of society.

For more information on Resnick's talk see Troy Smith's article at and Resnick's presentation slides.

Monday, November 2, 2015

Forty-Nine Performance Bulls Average $4581 at the 86th Southwest Missouri Beef Cattle Improvement Association’s Bull Sale

Eldon Cole, Livestock Specialist

The 86th Southwest Missouri Beef Cattle Improvement Association’s bull sale averaged $4581 on 49 bulls.  Leading the average were the 46 Angus bulls that made $4684.  Three Polled Herefords were harder to get bids on and each received a $3000 bid.

The consignment had outstanding performance data behind them and the knowledgeable bidders on the seats found the top prospects throughout the sale.  One thing that stood out again was the reluctance of buyers to go very high on bulls that had calving ease direct expected progeny differences (EPD) that were poorer than breed average.

The sale top of the evening was a May, 2014 Angus consigned by Truman L. Wiles, Willow Springs.  The bulls calving ease, weaning weight and yearling weight ranked him in the first percentile for Angus non-parent bulls.  His $Wean was also in the first percentile.  The 7-framebull brought $7000 from Kevin and Cheryl Dill of Niangua.

Close behind at $6750 was the entry from Blue Mound Angus, Fred Swartzentruber, Eldorado Springs.  Also a 7-frame score bull with EPDs for calving ease, weaning weight, yearling weight, milk $Wean and $Beef in the top 15 percentile or better was claimed by Travis Eck, Pierce City.

Two Angus bulls were sold for $6500 each consigned by Wiles and Norman Garton, Nevada.  The successful buyers were Brackenridge Brothers, Eldorado Springs and Charles Whisman, Shell Knob.  Each of the buyers regularly purchase bulls from this sale.

The three Polled Herefords were consigned by Bonebrake Herefords, Springfield.  The buyers were Two Bar D, Niangua, White’s Bar W Ranch, Ozark and Brian and Tara Wilson, Neosho.

The sale was held on October 26 at the Springfield Livestock Marketing Center.  Auctioneer was Jerry Lehmann, Lake Ozark.  Pam Naylor, Buffalo serves the SW MO BCIA as sale manager.

The next sale will be the last Monday of March.  Consignments for it will begin in late December.  For details on that you may contact Pam at 417-345-8330 or contact your nearest University of Missouri Extension livestock specialist.

More details on the BCIA may be found at 

Sunday, November 1, 2015

Summary of the DNA Technology: Where we've been, where we are, and where we're headed Conference

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 to be refined.

 Genotyping entire cohorts (groups) fixes many of the problems.

Many groups are rapidly expanding the amount of cattle genomic sequence data. But, substantial effort will be required to turn this data into deliverables and information for the beef industry.

Please check out for more information from the DNA Technology Conference.

Friday, October 30, 2015

Selection for Improved Feed Efficiency

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant,

Meat Animal Research Center, Clay Center, NE

Matt Spangler
University of Nebraska-Lincoln

In poultry, we have seen a 250% improvement in feed efficiency since 1957. We have dramatically improved the efficiency of gain in chickens.

We have not made similar progress in beef cattle. How can we move the needle and start to make progress?

First of all, how do we define feed efficiency?

  • Average daily gain (ADG)
  • Average daily feed intake (AFI)
  • Residual feed intake (RFI) is the difference between what we expected an animal to eat and what they actually ate. In residual feed intake, how we define a contemporary group is very important. For example, think of combining Scottish Highland and Chianina cattle in a group. 

EPDs for feed efficiency

  • Residual gain
  • residual feed intake
  • dray matter intake
  • Days to finish

If a breed publishes multiple efficiency EPDs, which one do I choose?
Hint: The answer comes below! Spoiler alert, economic indexes!

Getting feed intake records can be very expensive. It is probably not feasible for a large number of feed intake phenotypes to enter national cattle evaluation. Genomics helps us collect phenotypes on
a manageable number of animals and use that data to predict feed intake in a much larger population.

With genomic testing, we can account for a large portion of the genetic variation in feed intake and about 30 to 40% of the overall variation in feed intake (phenotypic variation).

The largest effect genes in feed intake

We want to select for the most profitable animals. We don't want the most productive cattle or the most efficient cattle, but the cattle that best combine production and efficiency to be profitable.

Depending on how we measure feed efficiency, cattle rank differently.

Do we want to estimate the relationship between two traits? Such as feedlot efficiency and cow efficiency.
Spangler says, "Collect, record, estimate". If producers want to know the answers to these types of questions, they need to turn the data into breed associations.

We need to think about efficiency in terms of economic returns. An economic index approach is the optimal way to make change in many different traits.

"These large USDA grants are a jumping off point for breed associations," Spangler said.
The breed associations and beef industry will then need to create methods to continue to collect the data.

For a video of this talk see the conference website: