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.