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.

Tuesday, August 5, 2014

A Note on EPD Accuracy

The Mac Innon girls-- Twins
by David Dodge
Psst... Can I let you in on a secret?

All EPDs are accurate.

That's right all EPDs are accurate. EPDs are calculated using a statistical procedure called BLUP. BLUP stands for Best Linear Unbiased Prediction. Because BLUP estimates are unbiased, they are all accurate. So, if all EPDs are accurate what is this accuracy we always talk about? Calling this measure an accuracy is a misnomer. What EPD accuracy actual measures is precision. The EPD accuracy measures how precise the EPD estimate is.
All EPDs are on the top row of the grid above. What is reported as the accuracy is a measure of the precision or reliability. When animals have lots of data, the estimates are precise and there is a small difference between the true value and the estimated prediction. When animals have little data, the estimates are not precise, but the EPD estimates average out to the true values. This is why using many low accuracy sires (rather than a single proven sire) is an effective way to hedge against changes in EPD estimates.

EPD precisions are a measure of risk. If you are very conservative and risk-adverse, use EPDs with high reliabilities (high accuracies). If you are more progressive and risk-tolerant, EPD reliabilities will be less important in your decisions.

Hopefully breed associations can begin to update their EPD reporting practices. Dropping the misnomer of EPD accuracy and replacing it with EPD reliability (dairy breeders use this word) or EPD precision would be a great change to make EPDs easier to discuss and understand.

For more information on EPD reliabilities see:
How Risk Adverse are You?
You Would be Crazy Not to Test!
Adapting Breeding Practices to Genomic Technologies


Wednesday, July 23, 2014

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

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


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

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

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

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