Tuesday, June 30, 2015

Red Angus Releases Herd Navigator DNA test

The Red Angus Association of America has enabled more particular selection of Red Angus commercial females. The Herd Navigator reports breed percentile ranks for the RAAA HerdBuilder and GridMaster indexes, plus 13 EPD traits. The percentile ranks mean a score of 50 is average, a score of 1 is in the top 1 percent (cream of the crop) and a score of 99 is in the bottom 1 percent (bottom of the barrel). The interpretation of these percentile rankings is the same as Red Angus EPDs but is opposite to other commercial heifer panels. The test is marketed for $25 per female. The producer is required to own at least one registered Red Angus bull and the registration must be transferred to the producer (or show involvement with RAAA, such as large semen orders). If the possible sires of the females have been genotyped at GeneSeek for genomic-enhanced EPDs, then the parentage of the females will also be reported to the commercial producer. This is helpful if the commercial producer has used a combination of A.I. and a clean-up bull or multiple-sire pastures.
The HerdBuilder and GridMaster indexes allow a producer to select for profit, i.e. the producer selects to increase revenue and decrease costs. The HerdBuilder index is used if replacement females will be retained from the calf crop. The GridMaster index is used if the entire calf crop will be feed out for beef. Even though the HerdBuilder index accounts for raising replacement females it uses all available traits from conception to slaughter and weights each trait by its economic importance. Economic indexes are the optimal method of multiple trait selection. While the producer can set cutoffs for a small number of traits, such as calving ease or milk, the animals that meet those cutoffs should be ranked by the appropriate economic index.
Although the Herd Navigator is based on several thousands of DNA variants, through a process called imputation, the producer gets basically the same amount of information as the Red Angus RA50K genomic prediction test.
Previously, commercial breeders selected heifers based on age, weight, or perhaps the genetics of the sire. Now, commercial producers using Red Angus genetics can select heifers based on a variety of traits that match their production goals. The Red Angus Herd Navigator test joins a growing list of commercial heifer genomic prediction panels.

For more information see:
Herd Navigator Guiding Commercial Female Selection
Guiding Commercial Female Selection - Red Angus Association of America Releases Herd Navigator

Wednesday, June 17, 2015

eBEEF.org launched at BIF

A new website dedicated to beef cattle genetics has been launched at the 2015 Beef Improvement Federation Conference. eBEEF.org is part of the national eXtension program with the goal of being a one-stop site for beef cattle genetics and genomics information. Beef cattle specialists from six land grant institutions have joined forces to provide educational materials that are pertinent to today’s beef cattle producers, without searching multiple sites or filtering through countless hits on a search. The site contains factsheets, short frequently asked question (FAQ) video clips, relevant conference recordings and webinars, a blog and links to other useful beef sites.
One of the developers of the new site, Dr. Darrh Bullock at the University of Kentucky said “Often beef producers get frustrated when they search for information online and get information overload. We wanted to develop a user friendly site that provides information in a concise, understandable way without having to sort through enormous amounts of information.”
The team plans to achieve this goal by including only selected, peer-reviewed publications on the website. Additionally, a list of FAQs will be available and easily accessed in short videos. Archived recordings of webinars and conference presentations can be accessed through the video library. The “Ask the Expert” section of the site can be utilized to find custom answers to specific problems and covers all aspects of beef cattle production.
Another goal of the eBEEF.org website is to archive the information generated from current and future beef genetics integrated grants funded by USDA-NIFA. All eBEEF.org team members are a part of one or more of the three current grants (Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef andDairy Cattle; National Program for Genetic Improvement of Feed Efficiency inBeef Cattle; and Identification and Management of Alleles Impairing Heifer Fertility While Optimizing Genetic Gain in Beef Cattle). Another team member, Dr. Alison Van Eenennaam from the University of California – Davis, stated “A large investment has been made to develop tools to genetically improve health, feed efficiency and reproduction in cattle and we need to ensure that the information gained is available to beef producers for years to come.”

For more information or to make suggestions please contact any of the eBEEF.org team members. The other team members are Dr. Jared Decker, University of Missouri; Dr. Megan Rolf, Oklahoma State University; Dr. Matt Spangler, University of Nebraska; and Dr. Bob Weaber, Kansas State University.

Thursday, June 11, 2015

Cow Lifetime Productivity Task Force

Dr. Mike MacNeil
Delta G

In my opinion, this is the best talk of the conference so far. MacNeil gave an in depth look at the estimation of genetic potential, focusing on cow efficiency. My notes are too sparse to do the talk just, so I suggest that you visit the BIF Newsroom to read the proceedings paper, look at the PowerPoint, and listen to the audio (available in a day or so).

Define "Efficiency": ability to produce output without wasting inputs. Evaluations shouldn't look at residuals, i.e. measure outputs holding inputs constant or measure inputs holding outputs constant. Inputs and outputs are strongly correlated, thus improving efficiency is rather hard.

Cow efficiency is an incomplete picture, though it is a valuable picture. Hopefully indexes take all of the traits into account.

The current suite of genetic evaluations is lacking important traits.

In terms of replacement female costs reproductive traits are important and two traits are currently evaluated, Heifer Pregnancy by AAA and Heifer Calving Rate by AHA.
The benefit from the number of offspring is currently measured by stayability or  sustained reproductive success.

Research suggests there is more variation for maintenance than for performance (Merlyn Nielsen's work in mice).  We need work on the genomics of cow maintenance.

Every time you make a selection decision, you employ an index! Using an analysis technique called index in retrospect, research can look at your selection decisions and can infer the mental weights you use in your selection decisions. Humans aren't consistent in mental decisions from the beginning of a sale catalog to the end of a sale catalog. Have to use indexes to be consistent.

Number of offspring marketed (NO)
  • probability of producing an offspring each year
  • longevity
  • Binary, assumes producers are culling open cows (may not be true based on value of the cow!)
  • inefficient use of contemporary groups
  • partial records
Survival Analysis
  • time dependent contemporary groups (contemporary group changes every year, compare cow to different sets of females over time, weather and environment changes year from year)
  • allows data to be censored
Replacement cost (Rd)
  • opportunity cost of weaning weight not marketed - well evaluated
  • postweaning growth and feed intake - adequately evaluated
  • pregnancy (calving) rate and culls - not reporting data on the culls causes problems with evaluating the replacements.

Report EPDs on economically relevant traits, calculate EPDs on indicator traits but roll them into economically relevant traits. Create contemporary groups on what actually happened on the farm.

Successful evaluation of efficiency
  • Requires capture of the full range in variation of underlying component traits
  • Let's not make data capture too onerous (think through what data should be reported)
  • Whole-herd reporting should include information about females that "fail" and leave the system
  • Lets be explicit about who leaves and why.

*Note: Dr. MacNeil made a note about a project that we collaborate on in which we have proposed to look at local adaptation. Dr. MacNeil stated that the DNA genotype doesn't change, so how would the EPD/breeding value change. This is not accurate. While the DNA genotype doesn't change, the allele substitution effect of the genotype (the "breeding value" of the genotype) does change depending on the population or context. This is the definition of a gene-by-environment interaction. See Falconer and Mackay "Introduction to Quantitative Genetics" for more information on the framework I am proposing.

*Update: Dr. MacNeil and I spoke in the hallway at BIF. Dr. MacNeil was considering the true breeding value (unknowable, can only be estimated) and I was considering the estimated breeding value. The true breeding value is independent of the environment. But, when gene-by-environment interactions exists (and we know they do) they would influence the estimation of region-specific breeding values. This does not pertain to national cattle evaluations or national EPDs, only the analysis of local adaptation. 

Wednesday, June 10, 2015

How Do Current Market Incentives Affect Genetic Selection Decisions?

Dr. Lee Schulz
Iowa State University

Genetic selection should focus on long term profitability, but cattle producers live in a short-term price world.

"The market signal is pretty clear; more calf production is needed and will be rewarded." -Peel

We need to increase the pounds of calf weaned per exposed female. Need to increase conception rate, increase calving percentage, decrease pre-weaning calf death loss, and increasing weaning weight.

The beef industry operates as a textbook commodity industry. Long-run economic (not accounting) profits are zero. Profit levels lead producers to 'bid away' margins.

The inventory cycle has become more variable, e.g. longer troughs.

Beef replacement heifers now make up 20% of the national beef cow herd. Growth has been largest in Great Plains.

Because of short-term price fluctuations, we should us management to address short-term price changes.

How much expansion should be expect? FAPRI and USDA projects vary greatly.

Should you buy or raise replacement females?

  • Does it cost you less to raise than buy?
  • Is Genetic base acceptable? (Calving ease, milk, weights, quality, etc.)
  • Your environment is not stressful to "imported" heifers


  • Cost you less to buy than raise
  • Value alternative uses of money or time

If you buy heifers, rather than raise, you need to have increased performance from the progeny of the purchased female. Typically, this means you need heavier weaning weights from that purchased heifer.
Expanding is very expensive now. Risk management becomes a priority.

Decker's Take Home Message:
Using genetic and genomic selection to focus on increased performance, efficiency, and quality can be an effective risk management tool.

*Note, Dr. Schulz often referred to reproduction as lowly heritable. This is not actually born out by the data. Genetics influences 14% of the variation in pregnancy; for comparison, genetics influences 20% of the variation in weaning weight. We can make substantial improvement in reproduction using genetics!

Sustainability: What Does the Data Say About the Beef Industry

Dr. Kim Stackhouse-Lawson
National Cattlemen's Beef Association

Sustainability is now seen as responsibility. Sustainability is now continuous improvement.
Sustainability is about feeding people; doing more with less.

Zero impact is not possible. Start the conversation with this point.

Over the last 6 years, we have improved sustainability by 5%. How is this possible when we weren't even thinking about sustainability 6 years ago? Any technology improvement we have implemented has improved sustainability. Stackhouse-Lawson's father-in-law thought her sustainability research project was a complete waste of Beef checkoff dollars to define a word, sustainability, that outsiders created. When she thanked him for helping her project, he was completely taken aback. She then explained that the new sprinkler system he had installed improved the sustainability of his operation.

To meet the growing demand for beef by meeting environmental, economic and social concerns.

Food waste is responsible for more greenhouse gases than all of beef production.

Since 2005 emissions to water have been reduced by 10%. Consumers love this improvement.

Since 2005 beef production has reduced its water use by 3%.

Since 2005 there has been a 32% reduction in occupational accidents and illness.

Sustainability is a great opportunity for beef producers. We have a great story to tell.

  • Sustainability research has several benefits
  • Tell our story
  • Good science leads to a baseline
  • Supply chain focus in the right areas, e.g. food waste, for improvement

Sustainability is a journey, not a destination. We have multiple generation operations. This is sustainability!

Decker's Take Home Message:
By focusing on profit and new technologies, we can improve sustainability of our cattle operations. Breeding objectives and economic selection indexes help our operations be focused on profit, an important component of sustainability. Are you accepting of new technologies? 

Sustainability: What is it and why does it matter?

Dr. Sara Place
Oklahoma State University

Took human civilization from 10,000 BC to 1804 AD to reach a billion people. We are now projected to reach 9 billion people by 2045. Human population growth is exponential.

Sustainability is a "wicked" problem. Such a problem has the essential characteristics that it is not solvable, thus it can only be managed. There is no clear definition of the problem, different stakeholders have different definitions, and the beef production system is very complex.

Place's working definition entails economic, environmental, and social solutions to create to sustainability.
Most of the pressure has come from environmental groups. The biggest concern is global warming. Climate has fluctuated over time. The problem is that carbon dioxide levels are increasing more rapidly than before. Previous high was 300 parts per million, but we are now over 400 parts per million.

Why are animal rights and environmental groups focusing on beef production? Movies like Cowspiracy get their statistics from the UN's Livestock's Long Shadow report. The land use change used in the life cycle analysis refers to desertification and deforestation linked to cattle production. These land use changes are happening in developing world, like South America and southeast Asia. Thus, a third of the report does not apply to U.S. beef production. To address these points, a report titled "Clearing the Air: Livestock’s Contribution to Climate Change" addressed these concerns. Livestock's Long Shadow is a global assessment and should not be applied regionally. In the U.S. 3.65 of greenhouse gas emissions come from livestock. Most importantly, transportation industry was not evaluated using a life cycle analysis. The new UN FAO report shows that cattle production using modern practices has a smaller environmental footprint.

Less than 1% of solar energy is used by photosynthesis. Cellulose is the most abundant organic compound on the planets. Cattle are basically bioreactors that allow humans to utilize cellulose. Without cattle, this would not currently be possible. Today we produce the same amount of beef with 30% fewer animals. The beef industry is using 33% less land.

Food insecurity was the spark of the Arab Spring. Food insecurity in the U.S. is defined as not knowing from where your next meal will come.

Public perception of intensive systems is not positive. But, the public is favorable of pastoral cow-calf production. This is more than just an "educate the public" issue. There are differences in values and trust. We need to close the communication gap between public, research, and food industry.

Drought Was Just One Reason the US Cow Inventory Declined

John Paterson
National Cattlemen's Beef Association

What are the causes of the change in cow numbers?
1. Drought
2. High feed prices
3. High operating costs
4. Age of beef producers
5. Competition with crop production for better income
6. Price of cull cows
Reduction in cows numbers has been due to more factors than just drought.

We have seen an 18% drop in producers from 35 to 55 years old. Sixty-five percent of the land is owned by producers over 55 years old.

There still remains unused capacity in the packing plant sector.
There is $65 return for acre for crop production, but only a $16 return for beef production. The switch from pasture to crop has reduced cow inventory in crop producing states.

Chandler Keyes stated that seventy percent of our beef comes from thirty percent of our producers.
Currently, the beef herd is expanding faster than expected.

Dr. Pete Anderson says the beef industry must produce big, high quality cattle to maximize revenue.

Decker's Take Home Message:
We know prices will come down once supply increases. What is your strategy to remain profitable? Using genetic tools to produce a high-quality product may be an effective risk management strategy.

Temperament and Acclimation to Human Handling Impact Productive and Reproductive Efficiency in Bos indicus-Influenced Cattle

Dr. Reinaldo F. Cooke
Oregon State University

AI causes some extra work in the summer, but saved a lot of extra work in the winter during calving season.

Temperament is the behavioral response of cattle when exposed to human contact. Temperament is a heritable trait, up to 50% of the variation is due to genetics.
How do we assess temperament? Currently we use the chute score, a 1 to 5 scale:
1. Calm with no movement
2. Restless movement
3. Frequent movement with vocalization
4. Constant movement, vocalization, shaking of the chute
5. Violent and continuous struggling

Breed type was the greatest source of variation, and sex, age, and production system were also factors affecting temperament.
What is the interaction of temperament and production? Animals with excitable temperament are more paranoid, thus they have their head up looking for threats rather than in a feed bunk eating.
As temperament worsens, cortisol increases. How does this affect reproduction?
Increased cortisol limits LH levels which impairs ovulation. In addition, pubertal heifers had lower cortisol levels compared with pre-pubertal heifers. As temperament score increases, pregnancy rates decrease in bull bred cows (no human intervention). Cows with an excitable temperament had an 8% lower pregnancy rate.
Excitable temperament is detrimental to overall productivity of beef operations.

Decker's Take Home Message:
Selection tools are available to select for appropriate temperament. Avoiding excitable cattle not only improves handler safety, but also improves production and reproduction.

Assessing the Economic Impacts of Estrus Synchronization and Fixed-Timed AI in Beef Production

Dr. G. Cliff Lamb
University of Florida - North Florida Research & Education Center

"We know how to synchronize the cows!" Cliff Lamb stated to start his talk at the NAAB symposium at the 2015 Beef Improvement Federation Symposium.
Fixed timed AI methods make inseminating cattle much simpler.
Lamb discussed the University of Florida North Florida Research and Education Center case study. From the onset of taking leadership of the center, Lamb set certain rules that cows had to meet to stay in the herd. This is motivated by the fact that pregnancy has 4 times greater economic impact than any other production trait. Because of its importance, shouldn't fertility be a focus?
Cows must meet certain standards, e.g. keep certain rules, to stay in the center's herd.
This include:

  • Must calve by 24 months of age
  • Cow must have a calf every 365 days
  • Cow must calve without assistance
  • Cow must provide sufficient resuource for the calf to reach its genetic potential
  • Calf must be genetically capable to perform
  • Cows must maintain their body condition score for the center's conditions
  • Disposition problems leave.

At the NFREC, heifers must conceive in the first 25 days. Heifers are pregnancy checked 28 days after the end of 25 days.

Lamb listed complicated protocols, bull selection, facilities, labor, and time as primary reasons people do not to AI.

The cost of semen and the cost of AI supplies is not increasing as quickly as the costs of natural service bulls. Thus, economics is not a valid reason not to use AI.

By synchronizing and putting selection pressure on heifers to conceive earlier, calves have been born earlier and earlier in the calving season, independent of AI conception rate. This has resulted in a $169 increase in per calf prices. This has been a $50,700 increase for the center.

In an FDA trial, 5 of the 8 herds had pregnancy rates below or at 50%, and 3 of the 8 herds had much better pregnancy rates. The difference between the successful and disappointing herds was the 3 herds had been artificially inseminating consistently for the last 8 years.

In the bull bred herds, 44% of the calves are born in the first 30 days of calving season. But, 43% of the cows are less than 50 days post partum at the beginning of the breeding season. But in an AI herd, 88% of the calves are born in the first 30 days of the calving season and only 8% are less than 50 days post partum at the beginning of the breeding season. This increases reproductive success dramatically. From synchronizing cows, 8% more calves were weaned and calves were 38 lbs heavier. Just by exposing cows to synchronization, they saw a $49 increase in income. The biggest costs in reproduction are the cost of bulls and the cow-to-bull ratio.

AI Cowculator, a smartphone app, is available to evaluate the benefits of using artificial insemination.