Tuesday, September 18, 2018

Neogen launches upgraded Igenity® Beef Profile

Commercial beef producers will get more traits and selection index tools in the upgraded Igenity® Beef profile.
The Igenity Beef Profile will offer 16 traits for $29, replacing Neogen’s 13-trait Igenity Gold ($40) and 6-trait Igenity Silver ($25) tests. The upgrade includes new predictions for weaning weight, yearling weight and hot carcass weight for a total of 16 traits scored on a 1–10 scale, plus two new selection indexes.
“Our customers will be getting a powerful new profile at even greater value,” said Dr. Stewart Bauck, vice president of agrigenomics at Neogen. “The Igenity profile was designed and validated for crossbred or straightbred cattle with backgrounds of Angus, Red Angus, Simmental, Hereford, Limousin and Gelbvieh.
“Most DNA profiles are breed-specific,” Bauck continued. “The novel design of Igenity Beef allows for the accurate prediction of performance in both crossbred or straightbred cattle among the target breeds. This lets cow-calf producers use a DNA profile to select the best replacements from their crossbred heifers as well as their straightbred heifers.”
Using DNA testing in a crossbreeding program helps producers leverage the advantages of both practices. “The practices are complementary and can have a positive impact on the bottom line,” he said.
“The Igenity Beef Profile offers a more complete set of traits and tools for traditional weaned-calf marketing, retained feeder production or quality-grid programs,” Bauck said. “Producers also have a greater ability to customize the criteria they use to select the replacement heifers that will fit their marketing system,” he added.
Result reports include more how-to information and integrate with the Igenity Beef Dashboard to streamline decision making. “You can use the standard Igenity indexes, or in seconds you can create your own custom index and sort your heifers online,” he said.
“Using DNA to predict the merit of traits heifers will express — and pass on to their offspring — helps you manage risk and reduce the rate at which you replace cows. Each replacement heifer represents an investment of about $2,000 per head in cost of development and lost sale opportunity,” he said.
For many producers, a key economic driver is cow-replacement rate. “Igenity offers stayability predictions, which reflect the likelihood that a heifer’s offspring will calve over six seasons. A one-point increase in Igenity stayability score for a 250-cow herd represents an expected 48 fewer replacement heifers and gross savings of up to $96,000 over six years,” he said.

Igenity was introduced in 2003 and over its 15-year history has steadily improved in power and cost-efficiency, Bauck said. Neogen is also marking the 20th anniversary of its GeneSeek genomics operation. Neogen purchased GeneSeek in 2010 and the Igenity portfolio of products in 2012. Neogen’s world-leading position in animal genomics has led to investment in new labs, automation, capacity, work force and product diversity across the Americas, Europe and Australasia.

Wednesday, September 5, 2018

ARSBC 2018: Practical Application of Genomic Tests in Beef Production

Megan Rolf
Kansas State University

What is genomic testing?
We are looking at single base changes (SNPs) at thousands of locations across an animals DNA. We can use these DNA markers to predict genetic merit differences. We can also use these DNA markers for parentage.

Other DNA test don't use markers, but they directly test the variant responsible for the phenotype. Examples of this are genetic defects or coat color testing.

Genotyping in seedstock
We collect a DNA sample, send it off to the breed assocation, and the data is incorporated into EPDs. DNA testing for genomic-enhanced EPDs is a breed improvement strategy. It is a way to make genetic progress faster. For a seedstock producer, it also provides customer service by providing more accurate EPDs.

We can used DNA to improve EPDs using two approaches. First, we can use a DNA to create a prediction of the trait and blend this prediction with the EPD. Or, we can use the DNA to better estimate the relatedness between the animals in our pedigree.

Even a low accuracy EPD is our best tool to make selection decisions. DNA tests don't predict all of the genetic variation in the trait. When we combine the performance and pedigree information with a DNA test, we get our best source of information. As we get more data on a bull he can become a high accuracy sire and very proven.

Parentage testing can help us figure out if a calf is sired by the AI bull or the clean up bull.
Parentage testing can help identify which bulls are frequent breeders and producing lots of calves, and which bulls are breeding very few cows. We are spending money maintaining a bull when he is not working very hard breeding cows.

Parentage testing uses patterns of inheritance. The genotype of the calf has to be possible based on genotype of sire and dam.

Link to video of Rolf's presentation: https://www.facebook.com/AngusJournal/videos/1070121819820475/

See ARSBC Newsroom for more information. http://www.appliedreprostrategies.com/2018/newsroom.html

Note: this post was live blogged and may contain errors.

ARSBC 2018: EPDs and How to Use Them

Darrh Bullock
University of Kentucky

Crossbreeding should always be a consideration for commercial cattlemen. Crossbreeding has the greatest benefit for reproduction and other lowly heritable breeds.

Practical Guide to Bull Buying
Determine marketing strategy. Will heifers be retained? Make breeding decisions based on specific marketing plan. But, change marketing plan based on current situations.

It's pretty easy to find a bull that will give you great feeder calves and market animals. When we are keeping replacement females, we are now asking a bull to create females and feeder calves. We've given him a new job.

Determine your management level.
What is your labor? How frequently do you visit your cattle? How much attention do you give to them?
What is your level of nutritional management?
Assure that bulls are reproductively sound with a BSE.
Check for structural soundness. This is doubly important if you are retaining females.

The tough one is to set performance levels based on resource availability.

Select for performance using EPDs and indexes.
Determine other factors included horn/polled, color, tempermant, visual attractiveness.

"For trait for which EPDs are available that is the single piece of information you should be looking at," Bullock said. The other pieces of information including actual measurements, ratios, and genomics feed into the EPDs. Don't try to outsmart the system!

If you are looking at actual weights and EPDs together, you are reducing your ability to make accurate decisions. Just look at the EPD!

Environment is muddying the water. If we take it out we are improving the tool to make selection decisions.
EPDs is the best tool. Uses all information actual measurements, relatives, environment and genomics. EPDs are a risk management tool, they are not perfect.

One bull has an EPD of 65 lbs. Another has a 50 lbs EPD. The first bull's calves on average will weigh 15 pounds more.

Prior to EPDs, we basically had no opportunity to select for maternal traits. Maternal traits are predictions on the daughters of the bull.

American Angus Association started publishing EPDs in the early 1980s. Prior to EPDs there was success in increasing growth. Before EPDs you couldn't select for milk. The rate at which growth was increasing was faster with EPD selection. EPDs allowed us to select for increased growth and decrease birth weight (decreased calving problems).

All breeds have upward pressure for weaning weight. This increased growth is also increasing the mature size of cows. Mature height is under control, it has stayed flat. However, mature weight continues to increase. Mature height does not dictate nutrional requirements. Mature weight is what drives feed needs.

The trait we need to focus on is calving ease, not birth weight. Birth weight is simply an indicator of calving ease.

We need to be careful with selecting for more milk, or we will run into issues like we did with the frame race in the 1980s. Too much milk can lead to reproductive failure.

Most DNA variants (SNPs) have very small effects. But, when we add them all together they can have large effects.

Without a genomic test, accuracies are low. But, if we send in a DNA sample and do the DNA testing, it is the same as having 24 calving ease records out of that bull.

Calving Ease Direct is the tool to look for bulls that have calves that come easy. Calving Ease Maternal tells us if the heifer has the potential to calve unassisted.

Use EPD closest to marketing endpoint (weaning weight, yearling weight, carcass weight). Keep in mind correlated responses in calving ease, milk, and mature weight.

For maternal traits, watch for too much milk. There are Heifer Pregnancy, 30-Month Pregnant, Stayability and Sustained Cow Fertility for selection for reproduction.

Carcass traits are highly heritable and can make a lot of progress in first year of selection.

Selection indexes allows for comparison on a single value. Look for an index that matches what you are trying to do.

EPDs are breed specific. Different breed associations are continuously updating EPDs. Others are still updating on a twice a year basis.

Percentile rankings are one of the most under utilized tool in cattle selection. It is a great tool to find where in a breed a bull ranks.

Summary
Commercial bull buyesr should be practiciing crossbreeding
Best tools for selection are EPDs and indexes.

Link to video of Bullock's presentation: https://www.facebook.com/AngusJournal/videos/2146961142208480/

See ARSBC Newsroom for more information. http://www.appliedreprostrategies.com/2018/newsroom.html

Note: this post was live blogged and may contain errors.

ARSBC 2018: Impact of fly control on cattle performance

Brandon Smythe
New Mexico State University

Three species Smythe works on:

  • Horn flies
  • Stable flies
  • House flies


House flies become an issue when we upset our neighbors. Dairy in New Mexico dealt with litigation from their neighbors.

Everyone knows that flies are horrible.

Both horn fly males and females feed on blood. Horn flies feed 30 to 40 times a day. Stable flies feed once or twice and then find a place to rest. Horn flies almost never leave a cow. Only time they leave is to lay eggs on a manure patch.

There can be 200 to 1000 flies per animal. Flies are reproductively efficient. Flies lay 10 to 200 viable eggs per female. This reproduction efficiency allows for population surges.

Horn flies are a warm weather pest, thus during cattle breeding and growing. Flies go dormant in winter months.

Horn flies reduce performance in feed efficiency, growth and milk production. Horn flies are number one in causing production losses.
We see a $5 to $8 return for every $1 we spend on fly control.
We need to interven when we see >200 flies per animal.

Horn flies don't affect reproductive outcomes.

We need to rotate fly control methods. Need to have seasonal rotations, and even better is intra-seasonal rotations. If you notice that flies are coming back earlier than the previous year, you probably need to rotate fly control method.

Thursday, August 30, 2018

ARSBC 2018: EPDs and Reasonable Expectations in Commercial Crossbred Operations

Jared Decker, PhD
University of Missouri

One point must be clear from the very beginning: EPDs work. When we select parents based on EPDs the genetic merit for that trait increases in our herd. When we select the parents using EPDs the performance of the next generation improves.
EPDs Defined
EPD stands for Expected Progeny Difference. These three words are loaded with meaning, thus the need to define them here. The most loaded word is Expected. Here we use Expected the way a statistician would use the word. Expected means we are making a prediction of a future value. But, in this context, Expected also means we are describing the average of a group. What is the group for which we are predicting the average? We are predicting the average performance of the Progeny or calves out of an animal. An animal’s own performance and its EPD can be quite different, because that is not the purpose of an EPD. The EPD is predicting the average performance of that animal’s calf crop. Finally, EPDs are used to measure Differences. A single EPD profile is useless. We must compare the EPD between two animals or compare the EPD to the breed average.
Imagine for a moment that we have two bulls, “Black Bull” and “Gold Bull”. Black Bull has a Weaning Weight EPD of 2 and Gold Bull has a Weaning Weight EPD of 22 (Figure 1). A Weaning Weight EPD of 2 does not tell us much about the weaning weight of the Black Bull. However, we can see that the difference between the Black Bull’s EPD and the Gold Bull’s EPD is 20 pounds. In this example, we produce 100 calves out of the Black Bull and 100 calves out of the Gold Bull. These calves are born and raised at the same ranch with the same environment and management. When we weight these calf crops, the average of the Gold Bull’s calves would be 20 pounds heavier than the average of the Black Bull’s calves. This difference in average weaning weight of the bull’s calf crops is predicted by the EPDs. This is how EPDs work. However, we should note that some of the Black Bull’s calves outperform the Gold Bull’s average. Some of the Gold Bull’s calves underperform the Black Bull’s average. This is due to the randomness of inheritance. (See “The Random Shuffle of Genes: Putting the E in EPD” at http://articles.extension.org/pages/72650/the-random-shuffle-of-genes:-putting-the-e-in-epd for more information.)
Figure 1. Example of Weaning Weight EPDs, calf crop weaning weight averages, and weaning weight distribution of two hypothetical bulls.

Validation of EPDs
Top Dollar Angus, Inc., Gardiner Angus Ranch, Triangle H Grain & Cattle Co., and Zoetis, Inc. conducted a field test of the $BEEF economic selection index in Angus cattle. (See https://www.cabpartners.com/articles/news/3213/FieldTesting$BeefJan2017.pdf for more information.) An economic selection index is simply a genetic prediction of profit differences. The economic selection index predicted a profit difference of $187.38 per head between the High $B group and the Low $B group in their trial. The actual profit differences were $215.47 per head between the two groups. Thus, the economic selection index accurately predicted profit differences between the two groups. The Zoetis GeneMax Feeder Advantage Scores (genomic predictions) also predicted the genetic differences between the two groups.
Along with several other traits, we analyzed weaning weights records from the University of Missouri’s Thompson Research Center commercial cowherd. For every 1 pound increase in a sire’s WW EPD, we observed a 0.94 pound increase in the average of his calf crop. This is not statistically different from the expected value of 1. In other words, a sire’s EPD predicts the performance of his calf crop.
We also validated Zoetis GeneMax Advantage tests at Thompson Research Center. GMX scores are on a 1 to 99 scale, with 50 being average. The GMX score of the cow significantly predicted the calf’s performance for Weaning Weight, Milk, Marbling, Carcass Weight, and Fat Thickness. For example, a 1 point increase in GMX Score predicted a 0.57 pound increase in the calf’s weaning weight. A cow with a Weaning Weight GMX score of 99 would wean calves that on average weight 55 pounds heavier than a cow with a Weaning Weight GMX score of 1.
At the Thompson Research Center weaning weight performance has been increasing by 1.5 pounds per year. This is not the genetic trend, but the actual change in performance. While a 1.5 pound difference between 1996 and 1997 is not a big deal, a 30 pound difference between 1996 and 2016 is substantial. Add this to improvements in calving ease, marbling, carcass weights, all while moderating mature cow size, and the impact of selection using EPDs becomes evident.
Considerations for Using EPDs
There are a few issues to be aware of when using EPDs in commercial operations, including: traits without EPDs available, selection for optimal performance, multiple trait selection, and environmental stressors.
Traits Without EPDs Available
While the number of traits for which there are EPDs available is growing, not all important traits have EPDs. One example is structural soundness. Currently, farmers and ranchers must use visual appraisal when selecting for structural soundness. However, this does not have to be the case. What is needed is data collected and analyzed to produce soundness EPDs. For example, the American Angus Association has published a research Foot Score EPD. Other breed associations have conducted research projects related to structural soundness. Some breed associations now publish EPDs for Heifer Pregnancy and Stayability/Reproductive Success. We do not have predictions for male fertility.  For most traits that are economically important, but lacking EPDs, what we need is simply more data collection.
Selection for Optimal Performance
Unfortunately, when using EPDs a common mistake is selecting for extremes. For many traits this is not a problem. However, there a few traits that we need to watch. Milk EPDs are one trait farmers and ranchers should watch. This is especially true in environments where forage resources are limited, such as the Southwest. Cows with high Milk EPDs often fail to perform at their genetic potential. Further, high Milk potential leads to larger internal organ size, which increases the maintenance requirement of these cows. So, not only do these cows fail to reach their genetic potential, they also underperform compared to cows with more moderate Milk EPD levels.
Another drain on maintenance is mature cow size. We do not want cows that are too large, require extra resources for maintenance, and struggle to become pregnant. We also do not want cows that are too small and sacrifice the growth potential of their calves. One of the most under used traits is the Mature Weight EPD. Just as we have breed cattle who bend the beginning of the growth curve from birth to weaning, we also need cattle who bend the end of the growth curve from yearling weight to mature weight.
We are also receiving reports of extreme birth weights, specifically calve that are too small. Birth weight is an indicator of calving ease. We want calves that are small enough to be born without difficulty. But, we do not want calves so small that they struggle to thrive once born. One way to avoid this trap is to select on Calving Ease Direct for bulls and Calving Ease Maternal for females, and not use actual birth weight and Birth Weight EPD in selection decisions.
Multiple Trait Selection
Another challenge for commercial producers is identifying which traits are most important and placing proper emphasis on the various traits. We have all learned that single trait selection causes major issues. But, for many the question remains, what traits should be emphasized and how much focus should I put on different traits? In other words, how do I use the information to make a decision? What is the most important trait in beef cattle production? The answer, if given a friendly hint, is quite simple. The most important trait in cattle production is profit. Economic selection indexes are genetic predictions (i.e. EPDs) for profitability. Economic selection indexes weight each EPD trait by its economic importance and combine them into one number. Economic selection indexes allow us to use multiple trait selection, focusing on our economic wellbeing. Selection indexes also simplify our decisions because they combine all of the information into one number on which to rank cattle.
Environmental Stressors
Cattle performance at commercial farms and ranches can suffer when there are interactions between genetics and environment. These interactions between genetics and environment can cause cattle to re-rank between environments. In other words, the most profitable bull who produces the best calves in one environment may not be the most profitable bull in a different environment. Cattle in challenging environments may see re-ranking compared with national cattle evaluations. These challenging environments may include the Gulf Coast with heat and humidity, Desert Southwest with heat and limited feed, Fescue Belt with toxic fescue, and the Rocky Mountains with altitude stress. Until selection tools that consider these environmental stresses are published, producers in these regions may want to purchase genetics raised in a similar environment to theirs. Two USDA-NIFA funded research projects are investigating environmental stressors, one lead by the University of Florida and the other lead by the University of Missouri. The goal of the University of Missouri research is to prototype the use of environmental region-specific EPDs. These region-specific EPDs will allow us to match a cow’s genetics to the environment she is producing in.
Conclusion
Farmers and ranchers who manage beef operations, whether seedstock or commercial, need to fully embrace the use of EPDs. Genetic evaluations and the EPDs they produce are old technologies that are firmly on the plateau of productivity. However, far too many producers fail to use the technology. Some of this blame lies on academics and industry professionals. We have failed to explain EPDs in a way that the average farmer and rancher can understand and trust. We continue to work to publish EPDs for all traits that are important to beef producers. Further, we have failed to account for environmental stressors that reduce the predictive ability of EPDs. Academics and industry professionals are currently working to remedy these issues. However, beef producers are independent and take responsibility for their own operations. For the beef industry to be successful and sustainable, independent-minded producers must realize the value of EPDs. We value the traditions that have been handed down to us. But for there to be a vibrant beef industry for the next generation, we must use genetics properly to be more profitable and sustainable.

Link to video of my presentation: https://www.facebook.com/AngusJournal/videos/234774267187325/

See ARSBC Newsroom for more information. http://www.appliedreprostrategies.com/2018/newsroom.html

ARSBC 2018: Pregnancy Diagnosis

Ky Pohler
Texas A&M University

Pohler will discuss many different methods of pregnancy diagnosis. Producers need to find a method that works for them.

When do cows experience pregnancy loss?
95% of time fertilization occurs.
By day 28, pregnancy has dropped to 70%, a 25% loss of pregnancies. This is referred to as early embryonic loss.
By day 42, we lose 8% more pregnancies, the pregnancy rate is now around 62%. This is late embryonic loss.

Cows all cost the same to manage. If they don't have a calf or have a calf born late in the calving season, they cost us money.

Knowing pregnancy status of the herd helps make management decisions. They can help with drought management (sell open cows) and marketing decisions. Pregnancy diagnosis also helps us evaluate bull or semen fertility and breeding program success.

Pregnancy diagnosis doesn't cost a lot, but provides a great economic benefit.

What is the ideal pregnancy test?

  • High sensitivity (correctly identify pregnant animals)
  • High specificity (correctly identify open animals)
  • Simple
  • Cost effective


If a cow calves, we know she was pregnant. There are manual diagnosis, ultrasound, and chemical based diagnostics.

Rectal palpation of pregnancy looks at presence of fluid, may be able to identify amnion, fetus, placental junctions, or membrane slip.

Ultrasound pregnancy diagnosis requires a skilled professional. There is nearly 100% accuracy of ultrasound at >27-28 days of gestation. The difference between rectal palpation and ultrasound is feeling versus seeing.

There are currently two types of chemical based pregnancy diagnostics. Pregnacy associated glycoproteins (PAGs) are produced by pregnant or recently postpartum cows. PAG testing works through an ELISA assay. There are a series of washes and incubations that look for the presences of PAGs.

IDEXX, bioPRYN, and Genex sell PAG-based tests. All available tests are accurate and recommended for use.

PAGs are low in the first two months. They start to increase at the third month. Accuracy of PAGs ranges from the low 90s to the high 90s.

How early can we detect PAG and successfully diagnosis pregnancy? The earlier we move pregnancy detect, the more possiblity we have for pregnancy loss after the pregnancy check.

PAGs are first at high enough levels to detect at day 24. About 11% of heifers identified as pregnant at 24 days lose their pregnancy by day 32.

Heifers that successfully maintain a pregnancy have higher levels of PAGs than those that eventually loss the pregnancy.

Conclusions:

  • Rectal palpation, ultrasound, andPAG testing are effective methods of pregnancy diagnosis in cattle. 
  • Embryonic mortality between day 17 and 31 of gestation provides a major challenge for early pregnancy diagnosis.
  • No matter what... Use a proven method of pregnancy diagnosis!

Link to video of Pohler's presentation: https://www.facebook.com/AngusJournal/videos/1895412887429420/

See ARSBC Newsroom for more information. http://www.appliedreprostrategies.com/2018/newsroom.html

Note: this post was live blogged and may contain errors.

ARSBC 2018: Predicting and promoting fertility in bulls

Joe Dalton
University of Idaho

Sperm attributes necessary for fertilitization:

  • Acceptable morphology
  • Metabolism for production of energy
  • Progressive motility
  • Capacity for hyperactive motility
  • Stabilization of plasma and acrosomal membrane lipids
  • Acrosomal enzymes
  • Chromatin integrity


More is not always better. 1/2 cc straws are not better than 1/4 cc straws.
How many sperm cells are needed to get a female pregnant? It depends. Different bulls have different sperm fertility.

There are compensable semen traits, such as mis-shaped sperm, that compromise sperm quality. Increasing sperm number can compensate for this.

There are incompensable semen traits, such as genetic inviablity, that compromise sperm quality. Increasing sperm number cannont compensate for these traits.

They used Angus bulls on Nelore cows to look at the effect of sperm dose. They used 10 million, 20 million, 20 million, and 40 million sperm per straw. They put each of these treatments in different colored straws. There was no fertility differences between the number of sperm in a straw. By comparing the pregnancy outcomes between the two 20 million dose treatments they could show the random variation that happens in breeding programs.

They then looked at computer assisted sperm analysis (CASA) and flow cytometry at the bulls used in the study. There were differences between bulls in CASA and FC, but these differences did not explain fertility differences between bulls. There are things going on affecting fertility that we have not discovered yet.

We need to use Breeding Soundness Exams to promote fertility. Only 27% of producers are semen testing bulls. There is a difference between a BSE and a semen test. The spermatagenic cycle takes 60 days to create new sperm. BSE should be performed 60 days before the start of the breeding season.
BSE includes physical examination looking at eyes, feet, legs, testes, epididymides, penis, prepuce, seminal vesicles, etc. There is also a semen evaluation.
The minimum criteria for satisfactory potential breeder are scrotal circumference, sperm motility and morphology,and free of physical problems. There are unsatisfactory potential breeders and deferred breeders. Unsatisfactory breeders will not improve, deferred breeders may improve with time and a new spermatagenic cycle.

Based on reviews of BSEs, anywhere from 18% to 37% of bulls will fail a BSE. The BSE benefit to cost ratio is $20 for each $1 invested.

All sperm attributes necessary for fertilization and embryonic development are not known.

To reduce the risk of uncompensable seminal traits:

  • Use semen from AI studs where morphology is a routine part of quality control.
  • Use multiple sires.
  • Perform BSE on natural service sires.

Link to video of Dalton's presentation: https://www.facebook.com/AngusJournal/videos/242679089923465/

See ARSBC Newsroom for more information. http://www.appliedreprostrategies.com/2018/newsroom.html

Note: this post was live blogged and may contain errors.