Wednesday, July 23, 2014

Look in the Mirror:
What do We Need to Change?

For those of you who follow my Twitter feed, you know I have been a little disgruntled about a paper that appeared in PNAS earlier this week. I think this paper may be the motivation behind a new documentary called "Cowspiracy" that Amanda Radke reported about on Monday. Jude Capper (a.k.a Bovidiva) really takes this paper to tasks and points out some serious flaws in the analysis. In addition to ignoring beef's benefits as a source of nutrients such as iron and B vitamins, the habitat that ranches create for livestock, and the ability to turn arid rangeland into food, the authors also miss that cattlemen can be an ally to conservationists.

But, Jude Capper and other have sufficiently defended the beef industry. In this post, I want to take this opportunity for us as a beef industry to collectively take a look in the mirror. What do we need to learn from this research?

Despite errors in the analysis, should the beef industry decrease its use of feed grains? People such as John Wood, of US Wellness Meats, would probably say so. If we are interested in producing beef for a ground beef nation, do we need to grain finish cattle? If cattle can reach 90% of their mature mass on pasture at a young age, do we need feedlots to produce hamburger? One of beef's advantages over swine and poultry is the ability to use a rumen to turn grass into protein. As Scott Brown pointed out at the recent Cattlemen's Boot Camp, whether you are trying to succeed in the commodity or quality market, you need to be all in, not half way. Is a move away from feed grain a way to be all in for ground beef? I don't claim to be on expert on this, just throwing out ideas.

One of the things I do know is that the beef industry has been a slower adopter of technology compared with the dairy, swine, and poultry industries. How much does this contribute to the differences in efficiencies? Perhaps this is a wake up call to more aggressively embrace new technology and correctly use older technologies (I'm looking at you birth weight EPD).

But, rest assured, there is already research underway to address feed efficiency in beef. Visit to learn more. In addition to evaluating differences in gene expression, microbial populations, and mitochondrial differences in efficient and inefficient cattle, the research has produced genomic predictions for feed efficiency. These genomic predictions should be release to the beef industry in the next year, allowing beef producers to make genetic progress for feed efficiency. The team has already produced decision support tools to help cattle producers improve their herd's efficiency (more on this in a future post). With economic pressures from within the beef industry,and growing pressures from outside the industry, cattle producers need to latch on to these technologies. As a fan of beef cattle, one of the domesticated species that lead to my ancestors success over hunter gathers, I hope beef will be on dinner plates for a long time.

Monday, July 21, 2014

Simmental to Host 1st Annual Educational Session September 8-11

Join the American Simmental Association September 8-11, to kick off the first annual educational session held in conjunction with the Fall ASA Board meeting.

Join us September 8, for a free daylong symposium on applied information in beef cattle genetics with the following key speakers:

Click here to read full bios.

Dorian Garrick, PhD
Jay Lush endowed Chair in Animal Breeding & Genetics, Iowa State University

Bruce Golden, PhD
Department Head and Professor, Dairy Science Department, Cal Poly

Matt Spangler, PhD
Associate Professor, Extension Beef Genetics Specialist, University of Nebraska

After the educational seminar, stay for the Fall ASA Board meeting. Since all ASA meetings have an open format this will give you an opportunity to also attend committee meetings, as well as the official meeting. Join the ASA for a barbecue at the ASA headquarters, and a chance for ASA members to share ideas and learn about new programs in the ASA. To register, find more information, and see any updates to the program, as the dates get closer, visit or call us at 406-587-4531.

For Hotel Reservation
Holiday Inn Bozeman
5 East Baxter Lane | Bozeman, MT 59715
Phone | 406.587.4561
Reference "ASA" or "American Simmental" for the special $85 rate

Register here

Click for tentative schedule
There is no fee, but the ASA needs you to register so they can plan for meals.

Wednesday, July 16, 2014

Genomics enhance beef cattle breeding

Duane DaileyWriter, University of Missouri Extension

COLUMBIA, Mo. – Selecting breeding animals on how they look, by phenotype, worked for centuries. Progress in improving cattle was made just on appearance.
Now genotype pushes phenotype back to horse-and-buggy days. It’s data and what’s inside that counts.
Arrival of huge computers and sequencing of the bovine genome changed all. “There’s a better way of selecting,” said Jared Decker, University of Missouri geneticist, at a Cattlemen’s Boot Camp, July 14 in Columbia.
Training by MU scientists was sponsored by the American Angus Association with MU. The Cattlemen’s Boot Camp is a national program.
Things changed in the 1970s with statistical models that predicted EPDs (expected progeny differences). Then software was developed to combine many EPDs into a single economic index number.
Indexes help herd owners search a sire catalog to match a bull’s traits needed to improve a farmer’s cow herd profits.
“We must still look at bulls and cows,” Decker assured his audience of mostly Angus breeders. “Phenotype still counts, as there’s no EPD for feet and legs in beef cattle.”
Genomics tells a lot about calving ease, weaning weight, carcass weight or carcass grade. But there is no index for feet and legs.
The eye of the stockman still plays a role in breeding. However, on traits of economic value, there are genetic tools.
Plain EPDs will fade away as breeders learn more from the DNA of individual animals. A calf’s genes at birth predict much of what that animal will do in a lifetime.
New tools provide genomic-enhanced EPDs. A GE-EPD cuts time spent waiting for EPDs from data collection.
EPDs are based on production records of offspring from a sire, for example. Those require recording weights at various stages of life. A growing calf is weighed and data collected. Not on just one offspring, but hundreds.
If a thousand calves are tested, accuracy goes up for EPD predictions for a sire. A thousand tests are better than a hundred.
Proven EPDs enhance breeding selections, but take time and money.
A bull might be 20 years old before it gains high-accuracy proof, Decker said.
Some EPDs—meat tenderness, marbling of rib-eye or carcass grade and yield—can only be collected after harvest. “Some data collection is very invasive,” Decker said. “You can’t collect and use semen to breed from that slaughtered steer.
“You buy a young sire, with few records, expecting high growth rate, but find after a year of use that actually it’s a low-growth bull.”
EPDs on young animals have low accuracy. There are no or few progeny to test. However, genomics improve accuracy on the young. Such a DNA test is like having 20 offspring to start.
Available tests range in price from $17 to $75, depending on depth of data.
Genomic tests five years ago tested one gene on one trait. Those were misleading, but new tests are useful, Decker said. “One trait, such as weaning weight, may be influenced by tens of thousands of genes.”
With today’s genomics, DNA can be collected and tested at birth for new herd replacements. DNA in a drop of blood can be tested with a chip called a “snip” or SNP (single nucleotide polymorphism). That gives more accurate answers from the whole genome.
A new University of Missouri SNP chip has 50,000 genetic markers.
Researchers at the MU College of Agriculture, Food and Natural Resources study three areas in cattle: embryonic death, feed efficiency and resistance to bovine respiratory disease.
Decker told producers: “It’s not all genetics. Environment and management still count. Genomics offer much for herd improvement to meet consumer demands.”

Friday, June 20, 2014

Opportunities and challenges for a new approach to genomic prediction

Dorian Garrick
Henderson originally described breeding values (EPDs) as sums of gene effects. Meuwissen, Hayes, Goddard re-expressed this as sums of effects estimated for genotyped DNA variants.  
In current selection we have two models for genetic prediction, one for genotyped animals and a separate model for animals not genotyped.
You can combine a pedigree based relationship matrix with a genomic based relationship, we call this single-step BLUP or HBLUP (Aguilar et al., 2010).
There is a second approach which Garrick refers to as a hybrid approach. Now breeding values for nongenotyped animals are expressed as the part explained by genotyped relatives and the part not explained by genotyped relatives. This is similar to the animal model where we have the breeding value explained by relatives and the breeding value due to the random shuffle of genes across generations.
This model is in press and should be out later this summer (Fernando, Dekkers and Garrick 2014 GSE).

If everyone is genotyped, this hybrid approach reduces to the genomic selection models such as BayesA, BayesB, and BayesC. If no one is genotyped the model reduces to the traditional models used to calculate pedigree EPDs. Garrick also states that HBLUP is a special case of their hybrid model, but HBLUP has certain assumptions not needed in the hybrid model.

Garrick then transitioned to discussing improvements in computing. He showed that memory continues to improve according to Moore's Law. But, he showed that clock speed has stopped increasing since 2004 due the heat produced by fast processors. Super fast processors were producing as much heat as a rocket nozzle. But, we have have seen increased use of multiple core processors and graphical processors.

Garrick has been working to improve parallel computing of genetic . The data available on genotyped animals is not large enough to see speed ups of genomic predictions by use of parallel computing. But, single-step BLUP and hybrid models are a perfect size for speed up with parallel computing.

Breed Updates on Genomic Prediction

Several of the breed associations gave reports on their progress to implement genomic-enhanced EPDs. When a breed is small it is difficult to obtain genotypes of animals with reliable EPD estimates. More on this later.

The American Gelbvieh Association has implemented and released genomic-enhanced EPDs. See page 30 of the April 2014 Gelbvieh World for more information. Gelbvieh has implemented a solution unique to beef breeds in which a beef producer can either purchase a low density or high density SNP test. The SNPs not genotyped on the low density tests are implemented based on inheritance patterns in the populations. This process is referred to as imputation.

This September, the American Hereford Association will be adding a low-density SNP test that will be marketed at half the cost of the complete SNP test. The SNPs not genotyped on this assay will be imputed from the genotyped DNA variants, the same as the Gelbvieh strategy. When first introduced, AHA genomic predictions had a correlation of 0.33 with calving ease. Now, after training with 10,000 animals across multiple continents, the correlation is now up to 0.84. This means 70% of the variation in calving ease will be explained by the genomic predictions.

John Genho of Livestock Genetic Services reported on the development of genomic-enhanced EPDs for Santa Gertrudis. Because small breeds have a significant challenge in obtaining enough genotypes and phenotypes to implement a genomic prediction, Santa Gertrudis Breeders International has implemented a single-step genomic BLUP where a genomic relationship matrix is merged with a pedigree relationship matrix. Because SNP effects are not estimated, genomic-enhanced EPDs can be produced when many fewer animals are genotyped. Genho looked at ultrasound data from the King Ranch to evaluate the value of the genomic BLUP. Without genomics, correlation between pedigree EPDs and the actual ultrasound intramuscular fat measurements was 0.22. When genomics were added to the genetic estimate, the correlation between EPD prediction and ultrasound measurements increased to 0.34.

Things that Annoy Thallman About National Cattle Evaluation

Mark Thallman
Mark Thallman recently attended a bull sale with his farther-in-law to help him buy a bull. He was annoyed to find out the embryo transfer calves only had parent average EPDs. This annoyed Thallman because his masters thesis had been focused on calculating EPDs using data from embryo transfer calves.
Thallman also speculates that herds using within herd genetic evaluations are due to frustrations with the genetic evaluations published by breed associations.
Thallman also points out that we need better fertility EPDs. Stayability EPDs were a good first step, but we can do better. He suggests implementing fitting Days to Calving and Pregnant/Open as separate traits. He also envisions fitting each parity as separate pairs of traits in a 6-trait model. Thallman also sees a "build it and the data will come" strategy working best.
We have also failed to implement and use visual scores such as structural soundness, udder soundness, and sheath scores.
Should we score breeders on how biased their submitted data is? We could then regress their EPDs back to the breed average based on the quality of their data.
We also need better decision support software. Unfortunately, as funding for national cattle evaluation research dried up, the development of decision support software lost steam.

It is possible to genetically change the nutrient profile of beef

Raluca Mateescu
What do consumers want? First taste, second price, and a close third healthfulness. In the last 30 years obesity rates have increased, but beef consumption has decreased. Beef is not causing the rising obesity rates. Previously heart disease has been linked to saturated fat consumption but recent research has questioned this link. On average Americans are overweight and undernourished, in particular their diets are low in iron and B vitamins. Beef can help fix this lack in dietary nutrients!

Iron deficiency is the most common and widespread nutritional disorder, and in aging adults we see an increased risk of sarcopenia (muscle loss likely due to iron and zinc deficiency). We can use genomic predictions to increase the amount of iron in the beef we produce. Increased iron also helps color stability and beef flavor. Genomic prediction of iron content is another example of novel traits that we can tackle with the help of genomic predictions.