Friday, October 30, 2015

Selection for Improved Feed Efficiency

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant, beefefficiency.org

Meat Animal Research Center, Clay Center, NE

Matt Spangler
University of Nebraska-Lincoln


In poultry, we have seen a 250% improvement in feed efficiency since 1957. We have dramatically improved the efficiency of gain in chickens.

We have not made similar progress in beef cattle. How can we move the needle and start to make progress?

First of all, how do we define feed efficiency?

  • Average daily gain (ADG)
  • Average daily feed intake (AFI)
  • Residual feed intake (RFI) is the difference between what we expected an animal to eat and what they actually ate. In residual feed intake, how we define a contemporary group is very important. For example, think of combining Scottish Highland and Chianina cattle in a group. 


EPDs for feed efficiency

  • Residual gain
  • residual feed intake
  • dray matter intake
  • Days to finish


If a breed publishes multiple efficiency EPDs, which one do I choose?
Hint: The answer comes below! Spoiler alert, economic indexes!

Getting feed intake records can be very expensive. It is probably not feasible for a large number of feed intake phenotypes to enter national cattle evaluation. Genomics helps us collect phenotypes on
a manageable number of animals and use that data to predict feed intake in a much larger population.

With genomic testing, we can account for a large portion of the genetic variation in feed intake and about 30 to 40% of the overall variation in feed intake (phenotypic variation).

The largest effect genes in feed intake

We want to select for the most profitable animals. We don't want the most productive cattle or the most efficient cattle, but the cattle that best combine production and efficiency to be profitable.

Depending on how we measure feed efficiency, cattle rank differently.

Do we want to estimate the relationship between two traits? Such as feedlot efficiency and cow efficiency.
Spangler says, "Collect, record, estimate". If producers want to know the answers to these types of questions, they need to turn the data into breed associations.

We need to think about efficiency in terms of economic returns. An economic index approach is the optimal way to make change in many different traits.

"These large USDA grants are a jumping off point for breed associations," Spangler said.
The breed associations and beef industry will then need to create methods to continue to collect the data.

For a video of this talk see the conference website: http://www.beefefficiency.org/annualmtgoct15.html


Thursday, October 29, 2015

Selection for Cattle that are Less Susceptible to BRD

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant, beefefficiency.org

Meat Animal Research Center, Clay Center, NE
Alison Van Eenennaam
University of California-Davis
Twitter: @biobeef


The long-term goal of this project is to reduce the incidence of bovine respiratory disease (BRD) complex through genomic selection. We would not want to challenge our herd to see if they are susceptible or not; too many would end up dead! Genomics helps us select for traits that are difficult to measure or have a low heritability.

But to create genomic predictions we need large populations, e.g. 1000s of animals, with phenotypes (trait measurements) and genotypes. BRD can be difficult to measure and quantify; the data can be noisy. Part of the focus of the project was a very careful definition of a sick animal. Temperature, cough, nasal drainage, eye scores, and ear scores were used to define whether or not an animal was sick. Each morning a researcher would walk down a row of calf hutches to find a sick animal and would take a blood sample. The researcher would then find a calf in an adjacent hutch who was not sick. A similar approach was done in beef cattle feed lots. In California, over 200,000 calves were screened to obtain 1,003 cases (sick) and 1,003 controls (healthy) diary calves. In the dairy cattle, genetics explained 21% of the variation in BDR susceptibility. In the beef cattle, genetics explained 18% of the variation in BRD susceptibility. Curt VanTassel is working on incorporating BRD susceptibility into the dairy economic index ($NetMerit). A SNP chip with 220,000 variants has been developed to test variants that are functional. These variants affect the amount or sequence of a protein. It is hoped that these functional variants within genes will be more predictive of the genetic differences in BRD resistenance. In order to produce genomic-enhanced EPDs, we will need to collect phenotypic data on which animals get sick, and which do not. The logical place to do this is beef feedlots, as they record which animals gets sick. We need to figure out how to make this a win-win situation for feed lots, breed associations, and breeders. Disease predictions are not necessarily low hanging fruit. But, if genetic and genomic predictions are successful, they will have a significant economic impact.

More information about the Bovine Respiratory Disease Coordinated Agriculture Project (BRD CAP) can be found at http://www.brdcomplex.org/.

For a video of this talk see the conference website: http://www.beefefficiency.org/annualmtgoct15.html

Wednesday, October 28, 2015

Selecting for More Fertile Females

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant, beefefficiency.org

Meat Animal Research Center, Clay Center, NE

Jared E. Decker
University of Missouri


Introduction

It has frequently been stated that reproductive traits have low heritabilities, meaning little of the variation in reproductive traits is due to genetic differences. Due to this catchphrase, producers may not emphasize reproductive traits in their breeding decisions. Further, cows and heifers may sometimes receive a “Get Out of Jail, Free” card when their reproductive performance is lacking.
Let us reconsider the amount of variation in reproductive traits due to genetics. First consider the Heifer Pregnancy EPD reported by the American Angus Association. They report a heritability of 14% for Heifer Pregnancy (https://www.angus.org/Nce/Heritabilities.aspx ). At first, this may seem like a very small percentage. But, to put it in further perspective, we can compare it to other traits that receive more attention. Weaning weight, the most consistently selected trait in Angus cattle from 1955 to 2007 (Decker et al., 2012), only has a heritability of 20%. The American Hereford Association reports a heritability of 27% for their Heifer Calving Rate EPD. Thus, there is sufficient genetic variation present to make sustained genetic progress for reproductive traits. Due to the economic importance of reproductive traits, beef farmers and ranchers should consider putting more emphasis on reproduction when making selection decisions. Below, some of the tools available to accomplish this are discussed.

Breed Association EPDs

Expected progeny differences (EPDs) and economic indexes are the preferred method of selection, as they are the most accurate and unbiased tools. Although they are newer than traditional growth EPDs, several breed associations publish fertility EPDs. These can be broadly characterized as heifer success or repeated success EPDs. Selecting for fertility EPDs will increase the reproductive performance of herds, assuming appropriate management practices are used.


Heifer Reproductive Success EPDs


Breed Association
EPD
Units
Description
American Angus Association
Heifer Pregnancy
Percent
Probability of daughters becoming pregnant.
American Hereford Association
Heifer Calving Rate
Percent
Probability of daughters to calve as heifers.
American Gelbvieh Association
Heifer Pregnancy
Percent
Probability of daughters becoming pregnant in a regular breeding season.
Red Angus Association of America
Heifer Pregnancy
Percent
Probability of heifers conceiving to calve at two years of age




Repeated Reproductive Success EPDs

Breed Association
EPD
Units
Description
American Hereford Association
Sustained Cow Fertility
Risk Ratio, lower number favorable
*Now defined as percentage, higher number favorable
Risk of daughter not achieving a calving interval of 425 days or less.
American Gelbvieh Association
30-month pregnancy (Pg30)
Percentage, higher number favorable
Given that a daughter calved as a first-calf heifer, probability that daughter will calve at three years of age.
American Gelbvieh Association
Stayability
Percentage,
higher number favorable
Percent of daughters staying in the cowherd at 6 years of age.
American Simmental Association
Stayability
Percentage,
higher number favorable
Percent of daughters staying in the cowherd at 6 years of age.
North American Limousin Federation
Stayability
Percentage,
higher number favorable
Percent of daughters staying in the cowherd at 6 years of age.
Red Angus Association of America
Stayability
Percentage,
higher number favorable
Percent of daughters staying in the cowherd at 6 years of age.


Phenotypic Selection

In some situations, such as selecting commercial replacement females, EPDs are not available. And, of course, all EPD predictions are based on sound phenotype records. Below, we discuss some of the traits that have been beneficial to measure in the Missouri Show-Me-Select Heifer Replacement Program. In the program, a prebreeding evaluation is required 4 to 6 weeks prior to breeding for all yearling-age heifers, and includes animal identification, weight, pelvic area measurement and reproductive tract score. We also require a pregnancy examination within 90 days from the start of the breeding season.

Culling Open Females

One of the most common selection practices to improve herd fertility is to simply cull open cows. For herds looking to improve reproductive performance, this will continue to be an effective strategy.

Reproductive Tract Score

Reproductive tract scores are used to access the puberty status of heifers for selection decisions and timing of estrous synchronization. Based on rectally examining the uterus and ovaries, heifers are given a 1 to 5 score corresponding to prepubertal/infantile tract, prebubertal/greater than 30 days to puberty, peripubertal/less than 30 days to puberty, pubertal, pubertal/has already ovulated.


Pelvic Area

Pelvic measurements can be used successfully to identify abnormally small or abnormally shaped pelvises.  These situations, left unidentified, often are associated with extreme calving difficulties. Because pelvic growth is strongly influenced by puberty, pelvic area may also be an indicator of puberty status.


Ultrasound Pregnancy Diagnosis

An initial pregnancy examination should be performed within 90 days from the start of the breeding season.  Individual animal identification, pregnancy status and fetal age (in days) should be recorded.  Herds utilizing artificial insemination should report breeding dates.  Pregnancy determination at this point relative to the start of the breeding period enables the veterinarian to more accurately determine fetal age and success of the heifer’s first breeding period.

Future Research

Opportunities exist to research the genetics and genomics of heifer fertility. Reproductive tract scores may be an important indicator trait to more reliably predict heifer pregnancy or heifer calving rate EPDs. A Beef Improvement Federation committee has also been formed to improve the recording and reporting of female reproductive data.


Selecting for More Fertile Females - Dr. Jared Decker, University of Missouri from Iowa Beef Center on Vimeo.

*Post updated on 10 November 2015 to reflect new definition of Sustained Cow Fertility.

Speaker Sensation at the National Angus Convention

Entertaining and educational, an impressive line-up headlines Angus events Nov. 3-5 in Overland Park, Kan.



The complete program for the 2015 Angus Means Business National Convention & Trade Show, which takes place Nov. 3-5 in Overland Park, Kan., features an incredible slate of speakers.

Highlights of the week’s events include an International Angus Genomics Symposium on Tuesday, Nov. 3, sponsored by Neogen®’s GeneSeek Operations, during which keynote speaker and genetics pioneer Richard Resnick will discuss the evolving progress of genomic technology. The afternoon will provide hands-on Genomics Innovation Workshops sponsored by Zoetis.

On Wednesday, Nov. 4, Angus University, sponsored by Merck Animal Health, returns to follow “A Story of a Steak” and share insights on increasing quality in the nation’s beef production chain. Ken Schmidt, former Harley-Davidson communications director is the morning keynote speaker. The afternoon will feature 21 educational breakouts with emphasis on management, animal health, advertising and marketing, commercial cattle production, ag markets, social media training and low-stress cattle demonstrations.

In response to attendee feedback, there will be a few repeated sessions so there is a better chance of attending all desired sessions.

“We are incredibly proud of the slate of education and entertainment available at the 2015 National Angus Convention,” says Becky Weishaar, Creative Media director and lead contact for the event. “We encourage cattle producers to reserve their place in advance of the early registration deadline of October 2 for only $75 per person. Hotel reservations are also made on the convention website, and the hotel block features a variety of price points and amenities on a first-come, first-serve basis.”

Registration increases to $125 per person from Oct. 3 to Oct. 16. After that date, advance registration will be closed and participants may register onsite for $150 per person. Delegates elected to represent their state during the Association’s Annual Convention may attend the Association business meetings for free; however, participation in convention education, meals, entertainment and trade show requires a full convention registration.

Go online to www.angusconvention.com to access a convention schedule, trade show map and more information on travel arrangements to Overland Park, Kan.

Listed below is a summary of featured education at the 2015 Angus Means Business National Convention & Trade Show.



ANGUS MEANS BUSINESS. The American Angus Association is the nation’s largest beef breed organization, serving nearly 25,000 members across the United States and Canada. It provides programs and services to farmers, ranchers and others who rely on the power of Angus to produce quality genetics for the beef industry and quality beef for consumers.

For more information about Angus cattle and the American Angus Association’s programs and services, visit www.ANGUS.org.

###

National Angus Convention & Trade Show

Schedule at a Glance | Nov. 3-5, Overland Park, Kan.



Tuesday, Nov. 3



7 a.m.-7 p.m. — Registration open



9 a.m.-Noon — International Angus Genomics Symposium sponsored by Neogen’s GeneSeek Operations

Keynote, Richard Resnick

Future of Angus Genomics panel: Brian McCulloh, Bill Rishel, Michael Bishop, Illumina; Dan Moser, moderator Ronnie Green

Featured Speaker, Mitch Abrahamsen, Cobb-Vantress



Noon-1:30 p.m. — Trade Show Grand Opening featuring Certified Angus Beef® (CAB) lunch



1:30-5:30 p.m. — Innovation Workshops: Technology & Scientific Advancements for Cattlemen



1:30-3 p.m. — Purebred Angus Genomics Cattle Demonstrations sponsored by Zoetis Animal Health

HD50K, Kent Andersen, Zoetis, and Mark McCully, Certified Angus Beef LLC



3-4 p.m. — Innovation Workshops sponsored by E.I. Medical Imaging, Merial, Angus Genetics Inc. and AAA Login



4-5:30 p.m. — Commercial Angus Genomics Cattle Demonstrations sponsored by Zoetis Animal Health GeneMax® Advantage™ and GeneMax Focus™

Kent Andersen and Mark McCully



5-7 p.m. — Trade Show Social



6:30 p.m. — Cat® 262D Skid Steer Giveaway



Wednesday, Nov. 4



7 a.m.-7 p.m. Registration open



7:30-8:30 a.m. — Angus Auxiliary Breakfast (optional — additional $25 registration)



8:30-10 a.m. — American Angus Association Board of Directors candidate forum



10 a.m.- 7 p.m. — Trade Show open



10 a.m.-12:30 p.m. — Angus University sponsored by Merck Animal Health

Emcee, John Stika, Certified Angus Beef LLC

Keynote, Ken Schmidt

Individual Branding panel: Bob McClaren, 44 Farms, Cameron, Texas; Jonathan Perry, Deer Valley Farms, Fayetteville, Tenn.; Eric Grant, Angus Media; John Stika, moderator



12:30-2 p.m. — Lunch in trade show featuring CAB



2-5 p.m. — Angus University Workshops sponsored by Merck Animal Health



Management

2-2:50 p.m. Maternal Plus

Richard Tokach, Tokach Angus Ranch; Matt Perrier, Dalebanks Angus; Tonya Amen, Angus Genetics Inc.; moderator Dan Moser

3-3:50 p.m. Maternal Plus (repeat)

Richard Tokach, Tokach Angus Ranch; Matt Perrier, Dalebanks Angus; Tonya Amen, Angus Genetics Inc.; moderator Dan Moser

4-4:50 p.m. Succession and Estate Planning

Bill Sheets, Colorado State University



Animal Health

2-2:50 p.m. Healthy Bulls & Females for Your Customers

Mark Spire, Merck Animal Health; Randall Spare, Ashland Veterinary Center Inc.

3-3:50 p.m. Start them off right. Healthy cows raise healthy calves

Kevin Hill, Merck Animal

4-4:50 p.m. Start them off right. Healthy cows raise healthy calves (repeat)

Kevin Hill, Merck Animal



Marketing

2-2:50 p.m. Data-driven Marketing

Eric Grant, Angus Media

3-3:50 p.m. Data-driven Marketing (repeat)

Eric Grant, Angus Media

4-4:50 p.m. Adding Value to Your Customer’s Commercial Herd

Art Butler, Spring Cove Ranch; Dave Rutan, Morgan Ranches; moderator, Ginnette Gottswiller, American Angus Association



Commercial Cattle Production in 21st Century

2-2:50 p.m. How to Build the Perfect Steer

Paul Dykstra, Certified Angus Beef LLC

3-3:50 p.m. Top 10 Things I Learned from Feeding My Cattle

Justin Sexten, Certified Angus Beef LLC; Jimmy Moore, Moore Cattle Co.; Darrel Busby, Tri-County Steer Carcass Futurity; Shane Tiffany, Tiffany Cattle Co.; and Paul Dykstra, Certified Angus Beef LLC

4-4:50 p.m. Fitting Angus Genetics Into Your Environment

Megan Rolf, Oklahoma State University; Mark Enns, Colorado State University; Jared Decker, University of Missouri; moderator Dan Moser



CattleFax

2-2:50 p.m. Market Outlook

Lance Zimmerman, CattleFax

3-3:50 p.m. Market Outlook (repeat)

Lance Zimmerman, CattleFax

4-4:50 p.m. Risk Management

Lance Zimmerman, CattleFax





Responsible Beef

2-2:50 p.m. Farming Your Social Community?

Michelle Payn-Knoper, Cause Matters

3-3:50 p.m. Championing Agriculture

Michelle Payn-Knoper, Cause Matters

4-4:50 p.m. Championing Agriculture (repeat)

Michelle Payn-Knoper, Cause Matters



Creating Connections: Working together for cattle well-being cattle demonstrations

2-2:50 p.m. Stockmanship at Work

Tom Noffsinger

3-3:50 p.m. Low-stress Cattle Acclimation

Tom Noffsinger

4-4:50 p.m. Low-stress Cattle Acclimation (repeat)

Tom Noffsinger



5-7 p.m. — KC Blues & BBQ Social Hour & Dinner featuring Jack Stacks BBQ



7 p.m. — Entertainment: Sammy Kershaw



Thursday, Nov. 5



7 a.m.-Noon — Registration open



7:30-9 a.m. — Awards Breakfast (optional – additional $25 registration)



10 a.m.-2 p.m. — 132nd Annual Meeting of Delegates





For a complete schedule of events at the National Angus Convention, please visit www.angusconvention.com and click on “Schedule.”

Wednesday, October 14, 2015

What have we learned from sequencing efforts to date?

And where are we going next?

Data via http://www.genome.gov/sequencingcosts/.
Code for generating the plot at https://missouri.box.com/SequencingCost.

This graph never ceases to amaze me. On the horizontal axis we have dates from September 2001 to July 2015. On the vertical axis we have the cost to sequence a million base pairs of DNA, with the axis having a logarithmic scale (each tick mark is multiplied by 10, e.g. change from 10 to 100 to 1000). The blue line describes what is called Moore's Law which describes the increase in purchasing power as computer costs come down. The rate of improvement in DNA sequencing easily outpaces the improvement in computing. Since September 2001, the price of DNA sequencing has dropped 6 orders of magnitude from $5,292.39 to $0.015. From more than $5,000 to less than 2 cents!!!

Same data as above by with the vertical cost axis
 on a normal scale, not logarithmic.
What caused the drop in sequencing from April 2015 to July 2015? This is due to the release of the Illumina HiSeq X Ten system. Previously this system was only licensed for human sequencing. But on October 6th, this restriction was lifted and this system is now available for livestock genomics (and other applications). This means we can now sequence cattle genomes for a little more than a $1,000.


What do we plan to do with this decreased sequencing cost? Sequence a lot of bulls and cows of course! As we started to look at this sequence data, what have we found? First of all, we find a lot of DNA variants. In fact, we find similar numbers of variants to when we sequence human genomes. But in cattle we find many common variants (at a moderate frequency in the population) whereas in humans we find many rare variants (very low frequency in the population). This is because humans had a very small number of parents in the past (small effective population size) and a growing number of parents since that time (increasing effective population size). 
Cartoon of changes in population structure of humans
and cattle.
Cattle have the opposite pattern. The wild ancestors of cattle (aurochs) had a very large population in the past with a large number of parents (large effective population size), and through the processes of domestication, selection, and breed formation the effective population size has decreased. Think about how many times you find the same popular bulls in your cattle's pedigrees; this makes the effective population size smaller. This small effective population size with a large number of common variants is what makes downstream uses, like genomic-enhanced EPDs, of genomic data so effective in cattle.

So what are the downstream analyses of genomic data? Well there are lots, too many to mention in this post. But one of the first techniques we use in livestock genomics is a process called imputation. I know imputation is another one of those fancy jargon words, but it simply means that we can infer the genotypes at untested DNA variants based on the patterns of tested DNA variants. Now, instead of running our analyses with tens of thousands of DNA variants spread across the DNA like "mile markers", we can analyze millions of variants and get closer to our "points of interest". Using millions of variants we find important regions that we missed in earlier analyses and more precisely identify the regions of DNA that contain the important genes and causal variants that influence our production traits.

Using genomic sequencing data, scientists have identified causal variants for things like genetic defects, variants responsible for pregnancy losses (embryonic lethals), coat color, and horned vs polled. But finding these causal variants is not easy. Rather than being a simple base pair substitution (SNP), these causal variants are frequently structural variants, meaning large chunks of DNA are inserted, deleted, or rearranged.

As we generate more and more whole genome sequence data, we will have new SNP tests (a.k.a. SNP chips or SNP assays) developed. But instead of these SNPs (DNA variants) being evenly spaced like mile markers, they will be concentrated in genes and other functionally important regions. We will see SNP tests that genotype hundreds of thousands of SNPs, which will be mostly used in research settings. The valuable or interesting variants from these research studies can then be put on low density SNP tests. These low density SNP tests will then be more valuable and predictive as they will be focused on functional content, the points of interest.

Another interesting idea is for breed associations to develop programs to sequence the entire DNA of important or popular sires (idea originated with Jerry Taylor). I call this genomic "surveillance." For example, members would pay an extra $1 every time they registered a calf. When a bull has 1,500 registered progeny, he has now earned $1,500 in fees, and the breed association has enough money to sequence his entire genome. This allows breed associations to discover and keep track of new DNA variants that are rising to high frequency in their population. 

The explosion of genomic data will only continue in beef genetics (watch for more on this soon). What an exciting time to be a beef breeder!

See my extension website to download a copy of my PowerPoint, What have we learned from sequencing efforts to date?

Wednesday, October 7, 2015

2015 NBCEC Brown Bagger Series Kicks Off

by Jeffrey Beall
The 2015 National Beef Cattle Evaluation Consortium Brown Bagger series kicked off today. The Brown Bagger is a webinar discussing beef cattle genetics every Wednesday in October at 12:00 Central time. While we've already missed today's webinar, no fear there are more great presentations coming up. Plus, recordings of today's webinar will be available online in the coming weeks.

The theme for this year's series is "Advancing genetic selection in beef cattle: Improving current tools and developing new ones."

The following presentations are scheduled:

Oct 7 Advancements in National Cattle Evaluation Strategies
Host, Dr. Matt Spangler

  • Latest changes to national cattle evaluation systems—Dr. Bob Weaber, Kansas State University
  • Across Breed EPD and multi-breed genetic evaluation developments—Dr. Larry Kuehn, USDA-ARS-US-Meat Animal Research Center


Oct 14 Beef Cattle Fertility Project and Sequencing Effort Update
Host, Dr. Darrh Bullock

  • Update on USDA Fertility Project—Dr. Megan Rolf, Oklahoma State University
  • What we have learned from sequencing efforts to date—Dr. Jared Decker, University of Missouri


Oct 21 New Beef Improvement Federation Guidelines: Development Update
Host, Dr. Matt Spangler

  • Beef Improvement Federation Feed Intake Guidelines Update—Dr. Mark Enns, Colorado State University
  • Beef Improvement Federation Bovine Respiratory Disease Guidelines Update—Dr. Alison Van Eenennaam, University of California-Davis


Oct 28 Genomically Enhanced EPD Evaluations and New Genetics Educational Resources
Host, Dr. Bob Weaber

  • Status update on genomically enhanced genetic evaluation by breeds—Dr. Matt Spangler, University of Nebraska-Lincoln
  • eBEEF: a beef cattle breeding and genetics resource for producers on eXtension—Dr. Darrh Bullock, University of Kentucky
  • 2016 Beef Improvement Federation Annual Meeting Invite—Dr. Bob Weaber, Kansas State University


If you will be watching the live webinars (not the recordings) please register online via https://kstate.qualtrics.com/SE/?SID=SV_etHw1WTZttuldIx.