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.

Saturday, October 4, 2014

American Gelbvieh Association Releases Genomic-Enhanced EPDs

The American Gelbvieh Association (AGA) has released genomic-enhanced EPDs with the fall 2014 international cattle evaluation. Genomic-enhanced EPDs (GE EPDs) combine pedigree, individual performance and genomic information to save time and money, reduce risk, and accelerate the rate of genetic progress.

GE EPDs provide more precise EPDs based on a combination of both phenotype and DNA. One major benefit of these EPDs is risk reduction through increased accuracies. These increased accuracies save time when assessing young breeding stock as well as deliver commercial customer confidence when buying seedstock. Herd improvement is accelerated when breeders can more accurately identify young individuals with the best genetics.

GE EPDs also give the chance to collect data on economically important traits, which are expensive or difficult to measure.

The information from the genomic data can be as informative as a bull's first calf crop or a cow's lifetime production record. Since the genomic data is incorporated directly into the EPDs, cattle producers will not have to learn how to interpret the new data.

Development of GE EPDs for Gelbvieh and Balancer® animals has been in progress at the AGA since 2012, starting with the Genomic Pioneers project. This project helped to build a diverse panel of Gelbvieh and Balancer genetics to be the foundation genetics for the calculation of the GE EPDs.

"The AGA has been working closely with the scientific community over the past couple years to build the training population for developing GE EPDs for the Gelbvieh breed," says Susan Willmon, director of breed improvement at the AGA. "Implementing genomic-enhanced EPDs is a high-priority goal in the AGA's strategic plan and we are excited to be able to offer this tool to our breeders and their commercial customers."

EPDs that are genomically-enhanced will show up on the new American Gelbvieh Association Registry Service as highlighted in yellow. All animals with these enhanced EPDs will also have the AGA GE EPDs logo on their registration certificate.

For more information on GE EPDs visit Gelbvieh.org or contact Susan Willmon at susanw@gelbvieh.org or call 303-465-2333.

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Be sure to click on the links for more A Steak in Genomics content!

Wednesday, September 24, 2014

North American Limousin Foundation and American Shorthorn Association Move Genetic Evaluations to International Genetic Solutions

Cavans Waterloo Serene S171
Photo by Robert Scarth
Stier
Photo by LID
In a blog post by Kris Ringwall I became aware that the American Shorthorn Association has moved its genetic evaluations to International Genetic Solutions, the genetic evaluation arm of the American Simmental Association. The North American Limousin Foundation (NALF) has also announced that it is  joining a growing group of breeds that use International Genetic Solutions (IGS) as their service provider for the estimation of EPDs. NALF joins Red Angus Association of America, American Maine-Anjou Association, American Chianina Association, American Simmental Association, American Gelbvieh Association, Canadian Simmental Association, Canadian Angus Association, Candadian Gelbvieh Association, and most recently American Shorthorn Association. The new Shorthorn evaluations were released this fall; the first release of Limousin IGS evaluations will be released in the Spring of 2015.
As Kris Ringwall points out, this is good news for commercial cattlemen as EPDs from these evaluations will be directly comparable across the partner breeds. This also provides a larger quantity of data backing these genetic evaluations. And, in the prediction of EPDs data is the name of the game.

Thursday, September 11, 2014

BEEF Editor's Blog:
Will Quality Beef Be The Industry’s Nirvana?

Learn More at Thompson Research Center Field Day

Burt Rutherford recently reported on a presentation by Mizzou's Scott Brown. Dr. Brown challenged beef producers to identify a strategy to remain profitable when beef prices come down in the next decade. Brown's solution is to target more cattle that grade Prime on the rail. He presented data from the Thompson Research Center, where 30% of the steer calves consistently receive a Prime grade. The genetics used at Thompson Research Center has allowed the herd to meet those levels.

To here more about the genetics and changes that have occurred at the Thompson Reseach Center, watch this blog or attend the 2014 Thompson Research Center Field Day where both Scott Brown and I (among others) will be speaking.

Wednesday, August 27, 2014

Smithsonian's Genome Unlocking Life's Code exhibit coming to St. Louis, Mo.

For a little over a year, the Smithsonian has housed the Genome: Unlocking Life's Code exhibit at the National Museum of Natural History. This fall, that will change as the exhibit makes a cross country tour visiting several U.S. cities. The exhibit will be housed at The Saint Louis Science Center from May 15 to September 10, 2015.

The exhibit was designed to celebrate the 60th anniversary of Watson and Cricks discovery of the structure of DNA. The exhibit allows visitors to learn about the human genome and genomics, and how DNA codes for the diversity of life on Earth.

I wonder if the exhibit discusses cattle... ☺

Friday, August 22, 2014

Applying new technologies to investigate ancestry in cattle


Article from Fall 2011 "Lincoln Letter"
Newsletter of the North American Lincoln Red Assocition

Jared E. Decker and Jeremy F. Taylor

Animal breeding can be viewed from the perspective of three basic categories: recording matings, predicting the outcome of matings, and planning future matings.  Thus, ancestry is a central and integral part of animal breeding, and breeders have had an inherent interest in ancestry since at least the time of Robert Bakewell (1725-1795).  Until recently, we could only trace ancestry as far back as we had pedigree records.  But, with the advent of DNA technologies we are now able to infer the extent of relationships among individuals separated by hundreds, thousands, and even millions of years – i.e., the individuals are from different species.
In 2009, we published research that describes the relationships between 48 different breeds of cattle and the relationships between cattle and other ruminant species. We used a recently developed DNA analysis kit, called the Illumina BovineSNP50 BeadChip, to survey approximately 50,000 sites among the entire 3 billion DNA bases present in cattle (referred to as the genome).  By genotyping a sample of individuals from each breed we can use this information to identify which breeds of cattle are most similar and which must have the most recent common ancestor.  One example of a group of breeds that share recent common ancestry is the descendants of the Durham Shorthorn.  In the “family tree” of cattle breeds (Figure 2 of our PNAS publication and close-up as Figure 1 of this article), we see that the Belgian Blue, Maine-Anjou, American Shorthorn and Lincoln Red breeds all share a recent common breed ancestor (point A in Figure 1).  From our knowledge of breed histories, we can infer that the related ancestors in breed A are Durham Shorthorns.  Furthermore, this figure also shows that Lincoln Reds and American Shorthorns are more similar to each other than they are to the Maine Anjou and Belgian Blue breeds (point B in Figure 1).

Figure 1. Family Tree of Durham Shorthorn descendants. Branches are not drawn to genetic distance scale.
Using DNA markers we can also examine relationships between animals within a breed.  The American Shorthorn Association registers animals that have at least 15/16 Shorthorn blood.  Animals with a smaller faction of Shorthorn ancestry can be registered in the ShorthornPlus registry.  Some Shorthorn breeders have designated the term “Native Shorthorn” to indicate animals whose entire ancestry can be traced back to the 1822 Coates herd book or the 1830 Clay importation into the USA without any other outside influence.

With the help of Roy Lovaas we collected 108 DNA samples from 5 different populations and genotyped these samples with the BovineSNP50 BeadChip to evaluate how distinct Native Shorthorns are from other Shorthorn populations and breeds commonly used to generate ShorthornPlus cattle.  We used a statistical procedure called Principal Component Analysis to identify components (unobserved factors which measure similarity and differences among individuals) that represent, in decreasing order of importance, the greatest amount of variation between the animals’ genotypes.  We can then plot the first two principal component values for each genotyped animal to examine how the animals cluster according to the sources of variation within their genomes (Figure 2).  The American Shorthorn samples (blue dots) are spread throughout the plot, indicating the large amount of variation within the group, likely due to the presence of DNA from other breeds within these animal’s genomes resulting from an open herd book.  Within the Native Shorthorns (purple dots) and Lincoln Reds (red dots) individuals are clustered much more closely together indicating that the individuals within these groups are more closely related than are individuals within Shorthorns in general. Also notice that the Native Shorthorn and the Lincoln Red clusters lie physically close to one another indicating genetic similarity and a relatively recent common ancestry.  While the BovineSNP50 DNA markers primarily represent the common variation within the cattle genome and the sample sizes are small for some of the groups, it is still possible to identify patterns of relationship within these data.  Due to the closed breeding programs, Native Shorthorns and Lincolns Reds form distinct populations of cattle, but they are both closely related and trace their ancestry to Durham Shorthorns.
Figure 2.  Plot of the first two Principal Component values for each animal.
While breeds may share a recent common ancestry, they can be quite different phenotypically.  The descendants of Durham Shorthorns provide a very good example of closely related individuals which substantially differ phenotypically.  In this group there are double-muscled Belgian Blues and light-muscled Milking Shorthorns.  Lincoln Reds are solid colored and Shorthorns can be white, red, roan or a combination of the three.  Shorthorns may be horned, polled or scurred.  Milking Shorthorns produce large volumes of milk, while Beef Shorthorns have moderate amounts of milk. These are just some of the examples of phenotypic differences that result from the forces of artificial selection.  Thus, even though two populations may be closely related, they may differ phenotypically because a relatively small number of genes of large effect cause the divergence. Rapid genetic progress has been made in many breeds through the process of artificial selection using phenotypic selection and estimated breeding values to improve economically important traits.

This brings us to another important application of the new genetic marker technologies- the implementation of Genomic Selection.  While the details of Genomic Selection are far beyond the scope of this article, a brief explanation is beneficial.  In traditional breeding value calculations, the pedigree relationship matrix is used to represent the extent to which two individuals share genes that are identical by descent. Or another way to look at this is that the pedigree relationship coefficient represents the extent to which the genomes of two individuals are identical because they were inherited from common ancestors.  Cattle, like all animals, receive half of their genetic material from their sire and half from their dam.  So, on average, they also receive one quarter of their genetic material from each of their paternal grandsire, paternal granddam, maternal grandsire, and maternal granddam.  However, as a consequence of the random shuffling of chromosomes during the formation of eggs and sperm, the actual contribution from each of the grandparents may vary considerably from these averages.  With the use of the new DNA marker technologies we can precisely identify the actual fractions of the animal’s genetic material that were received from each grandparent.  This actually facilitates a much more accurate prediction of genetic merit at a much earlier age.  By taking a DNA sample at birth and genotyping the sample with the BovineSNP50 BeadChip, we can immediately estimate the genetic merit of the animal for the traits that are routinely recorded and possibly also for traits that have been recorded in experimental populations such as for feed efficiency and meat tenderness. Genomic Selection has been fully implemented in the U.S. dairy industry and is slowly gaining traction in the beef industry.

Applying these new DNA marker technologies has increased our ability to more precisely establish ancestry all the way from the species level down to familial relationships between grandparents and their grandprogeny.  This information is not only interesting from an historical perspective, but it informs the design of new Genomic Selection programs.  These technologies also allow us as animal breeders to more accurately identify relationships arising from previous matings, estimate genetic merit of progeny from current matings, and more precisely plan future matings.

The International Brangus Breeders Association Selects New DNA Testing Provider

SAN ANTONIO, TX- The International Brangus Breeders Association (IBBA) has selected GeneSeek, a division of Neogen Corporation, as the association’s new DNA services provider.
The partnership will allow Brangus breeders to submit DNA samples to GeneSeek for parentage determination and lay a foundation for Genomic-Enhanced EPDs for the breed association.
“IBBA’s agreement with GeneSeek moves us closer to conducting all Brangus parentage testing using Single Nucleotide Polymorphism (SNP) genetic markers versus previously used technologies,” said Dr. Tommy Perkins, IBBA Executive Vice President.
Samples will be tested with the GeneSeek®Genomic Profiler™ GGP HD 80K (tests approximately 80,000 DNA variants) and the GeneSeek®Genomic Profiler™ GGP LD 30K (tests approximately 30,000 DNA variants) for eventual incorporation into genomic-enhanced EPDs for the Brangus breed. The GGP 80K is finding a role as a premium genomic profiler, while the GGP LD 30K is a highly accurate, affordable option for routine testing of herd bulls and other seedstock.
The arrangement allows Brangus breeders to request parentage as either a stand-alone SNP test or as part of their GGP HD 80K or GGP LD 30K results. Both profilers provide parentage verification along with a wealth of information on animal potential. Testing turn-around time is dependent on the type of testing requested.
Brangus breeders should be pleased with the innovative direction they are going, said Ryan Ruppert, National Sales Director for Neogen GeneSeek.
“Profiling is a much faster and affordable way to learn about the merit of bull calves. The profiles also help you confidently represent your seedstock at shows and sales,” Ruppert said. “Plus, a genomic profile on a bull calf or yearling may identify a potential A.I. sire, so if you are fortunate to experience this you can retain and showcase that animal.”
Genomics will have a growing impact on seedstock and commercial cow-calf operations, due to bottom-line benefits that matter to producers, he said.
Some “lowly heritable” traits have a big impact on a rancher’s bottom line. An example is reproductive performance. This is partly inherited and is also affected by management and nutrition. Knowing more about maternal traits of seedstock bulls helps ranchers buy the right young bulls and then select and invest in heifers that will breed and calve efficiently. Using genomic profiles, seedstock producers can measure maternal traits in young bulls and market them on that basis.
“Genomics helps you get the advantage of reliable EPDs without having to do years of progeny testing,” Ruppert said.
While maternal traits help ranchers raise great mother cows, in other cases the seedstock operators’ customers are looking for terminal bulls that will pass along growth efficiency. Genomic profiles also predict performance factors for feed efficiency and feed conversion, as well as carcass quality and composition. The information puts added power in the hands of seedstock breeders and their customers.
When IBBA members order tests from GeneSeek, results will be emailed or mailed. Contact Rosanne Sralla, IBBA Registry Specialist, by email or at 210-696-8231 with questions. For more information, visit www.GoBrangus.com.

This article was adapted from a press release provided by The International Brangus Breeders Association.

Wednesday, August 20, 2014

Charolais Association Reaches Genotyping Milestone

In their efforts to develop genomic predictions and genomic-enhanced EPDs, the American-International Charolais Association announced today that they have surpassed the 1,000 samples suggested to develop genomic predictions. Now that this level has been reached the association can prepare to release a commercially available genomic prediction test. As we have seen in other breed associations, once the genomic prediction test is commercially available, the amount of data available for retraining can grow. As new animals are tested they can also be used in future rounds of retraining (also called recalibration).

This is an exciting day for the AICA. Congratulations Charolais breeders! Now, what will you do with genomics?


Vache de race charolaise avec son veau.jpg
"Vache de race charolaise avec son veau" by Forum concoursvaches.fr - http://www.concoursvaches.fr. Licensed under CC BY-SA 3.0 via Wikimedia Commons.

Tuesday, August 19, 2014

Eureka Genomics Receives USDA Grant For Bovine Genotyping Project

Management aims to raise additional capital to commercialize range of high-value targeted genotyping assays for clinical, animal health, and agriculture.

HERCULES, CA, August 18, 2014 — Eureka Genomics, a leader in Next Generation Genotyping (NGG), announced that it has been awarded a $450,000 grant from The National Institute of Food and Agriculture. The Institute is an agency of the U.S. Department of Agriculture (USDA). Eureka Genomics was awarded this grant to commercialize a second generation NGG assay focused on bovine genotyping known as the Sparse Genome Scan (SGS).

Eureka Genomics’ SGS is a technology platform that produces commercially relevant data, currently generated from micro arrays, at less than half the cost.

This most recent USDA grant awarded to Eureka Genomics follows an ongoing cooperative research and development agreement with the USDA’s Meat Animal Research Center.

"The USDA’s financial and research support is part of Eureka Genomics’ strategy to accelerate the development of our novel NGG assays for animal health. We are looking at providing a low-cost, NGG alternative platform for the AgBio, clinical and research markets in the very near term," said Didier Perez, COO of Eureka Genomics.

More broadly, management also announced that it will be raising additional capital from investors to fund and bring to market new targeted assays for clinical, animal health and crops markets. The Company continues to seek additional commercial partnerships for its clinical and agricultural products.

Genetic testing options for animal health and livestock management are typically limited in scope and prohibitively expensive, compromising the ability for routine or en mass genotyping of animals. Eureka Genomics’ existing NGG technology offers a low-cost solution for genetic testing of production and research animals. The technology can be used for determining parentage, genetic defects, quantitative traits and marker-assisted management of feedlots. Eureka Genomics envisions a number of additional applications of its low-density and medium-density assays in the $1 billon global, animal health market focused on genetics traits and early detection of infections.
 

Monday, August 18, 2014

Dan Moser to Lead Angus Genetics Inc.

Angus announces new AGI president and director of performance programs.

The American Angus Association® welcomes Dr. Dan Moser as its new president of Angus Genetics Inc. (AGI) and Association director of performance programs.

A unanimous selection of the AGI board of directors, Moser brings more than 15 years experience in genetic research and education to the Association’s 25,000-plus members and their commercial partners.

“We are excited for Dr. Moser to join our team of talented professionals and for what he represents to the future of genetic evaluation for the Angus breed,” says Kevin Yon, chairman of AGI and Angus breeder from Ridge Spring, S.C. “Dan not only is one of the industry’s most respected geneticists, but also possesses a common touch, a rare ability to communicate complex concepts into actionable and beneficial information for producers. Along with our talented team of scientists and customer service providers, we are looking forward to him taking our genetic evaluation programs and services into the future.”

Dr. Moser has 15 years of experience in genetic research and teaching in animal breeding and genetics. He served as the faculty coordinator for the K-State Purebred Beef Unit for the past six years, and as the breed association liaison for the NCBA Carcass Merit Project, working directly with 13 breed organizations, including the American Angus Association. He has also served as a director of the National Beef Cattle Evaluation Consortium and the Ultrasound Guidelines Council, and as an advisory board member for the $5 million USDA-NIFA feed efficiency grant led by the University of Missouri. Moser has been a frequent speaker at industry events and has made presentations at 11 Beef Improvement Federation annual meetings.

“Angus has a long and storied tradition for its commitment to providing the industry with innovative genetic-evaluation programs,” Dr. Moser says. “I am proud to be joining that tradition, and look forward to working with Association members and the industry to develop new and innovative technologies and services for Angus breeders.”

As AGI president and Association director of performance programs, Dr. Moser will oversee the organization’s genetic research and development efforts, as well as further the advancement of genomic-enhanced selection tools and the weekly National Cattle Evaluation.

A native of Effingham, Kan., Dr. Moser received his bachelor’s of animal sciences and industry from Kansas State University in 1991, then earned his master’s and doctorate degrees in beef cattle genetics from the University of Georgia. Dr. Moser will begin his new role on Sept. 1.

He remains active in his family’s cattle operation, and he and his wife, Lisa, have two sons, Justin and Ryan, and a daughter, Allison.

Friday, August 15, 2014

Improving Feed Efficiency: Feed Efficiency Project Releases Decision Support Tool

The Beef Feed Efficiency Project has released a new decision support tool. The tool is an Excel spreadsheet in which producers can enter data on a group of cattle with growth and feed intake data. Click here to download the Excel file.

The spreadsheet is pre-loaded with some example data. Depending on how you define efficiency, the animals rank quite differently. Let's consider the example data in the "Many Wts +fatRFI" tab. (See the "notes" tab for further explanation about the traits reported or this factsheet released by the project.)

If we look at Feed:Gain ratio (F:G) Ear Tag 3 is top ranking animal.

Ear Tag
ADG
Met.Mid Wt.
DMI
Fat
F:G
3
5.24
207
21.0
0.30
4.01
5
5.06
205
23.0
0.25
4.54
1
4.62
179
22.0
0.20
4.76
6
4.52
213
23.0
0.23
5.09
4
4.81
203
26.0
0.15
5.40
7
4.30
208
24.0
0.30
5.59
8
3.16
190
23.0
0.31
7.27
2
3.29
159
24.0
0.25
7.30

But, these rankings are strongly driven by average daily gain (ADG).

We could also rank the animals by Adjusted Feed:Gain ratio (Adj. F:G).

Ear Tag
ADG
Met.Mid Wt.
DMI
Fat
Adj. F:G
3
5.24
207
21.0
0.30
3.79
5
5.06
205
23.0
0.25
4.33
6
4.52
213
23.0
0.23
4.67
4
4.81
203
26.0
0.15
5.20
1
4.62
179
22.0
0.20
5.21
7
4.30
208
24.0
0.30
5.26
8
3.16
190
23.0
0.31
7.46
2
3.29
159
24.0
0.25
8.98

These rankings are very similar, except that Ear Tag 1 dropped from 3rd to 5th. This adjustment accounts for the size differences between animals. Ear Tag 1 was smaller compared with 6 and 4 during the test, thus it required less feed.

If we rank by residual average daily gain (RG), again Ear Tag 3 and 5 top the list. But, Ear Tag 7 and 2 move up on the list because they gained more weight than we would have predicted based on their feed intake, body weight, and fat thickness.

Ear Tag
ADG
Met.Mid Wt.
DMI
Fat
RG
3
5.24
207
21.0
0.30
0.39
5
5.06
205
23.0
0.25
0.37
7
4.30
208
24.0
0.30
0.24
2
3.29
159
24.0
0.25
0.15
4
4.81
203
26.0
0.15
0.11
1
4.62
179
22.0
0.20
-0.07
6
4.52
213
23.0
0.23
-0.59
8
3.16
190
23.0
0.31
-0.60


If we rank by residual feed intake (RFI) now Eag Tag 6 is top ranking.

Ear Tag
ADG
Met.Mid Wt.
DMI
Fat
RFI
6
4.52
213
23.0
0.23
-1.2
1
4.62
179
22.0
0.20
-1.2
8
3.16
190
23.0
0.31
-0.6
3
5.24
207
21.0
0.30
-0.2
5
5.06
205
23.0
0.25
0.5
2
3.29
159
24.0
0.25
0.7
4
4.81
203
26.0
0.15
0.9
7
4.30
208
24.0
0.30
1.2

The animals at the top of the list ate less than we would have predicted based on their ADG, body size, and fat thickness. An issue with selecting on RFI is that under-performing animals can rank well for RFI. An example of this is Ear Tag 8 which ranks third for RFI but only gained 3.16 pounds per day.


point of view
"point of view" by Chris Blakeley 
Depending on whether we look relative to feed intake or growth, we get different answers. The rankings depend on our point of view. So which measure should we use? 

Theory and profit motivations point us to the economic index. In this index feed intake and growth are weighted by their economic importance. So, rather than a breeder arbitrarily deciding which trait is most important, we let the market and profit dictate the weighting of each trait. The index in the decision tool is based on the work of Rolfe et al. 2011.

Ear Tag
ADG
Met.Mid Wt.
DMI
Fat
FE Index
3
5.24
207
21.0
0.30
-$114.66
5
5.06
205
23.0
0.25
-$23.14
1
4.62
179
22.0
0.20
$41.69
6
4.52
213
23.0
0.23
$51.46
4
4.81
203
26.0
0.15
$111.09
7
4.30
208
24.0
0.30
$122.41
8
3.16
190
23.0
0.31
$282.59
2
3.29
159
24.0
0.25
$328.56

Watch for more updates from the Beef Feed Efficiency Project as they work to improve the genetic prediction of efficiency.