Wednesday, December 6, 2017

NCBA Hosts Cattle Genetics Webinars


National Cattlemen's Beef Association (NCBA) is partnering with eBEEF.org to host a series of webinars in 2018. Find more information about the webinars in the series at BeefUSA.org. The first webinar will be Thursday, January 18, 2018 at 7 p.m. CT.

Monday, December 4, 2017

AHA Educational Session 2017: Paving the Genetic Path

Dorian Garrick
Theta Solutions LLC

The Theta Solutions LLC is made up of Dr. Bruce Golden, Dr. Dorian Garrick, and Dr. Daniel Garrick. They have developed the BOLT software for genetic and genomic evaluations.

The American Hereford Association formed an advisory committee to check the new genetic evaluation system. The advisory committee looked at the process during development. The advisory committee included:

  • Joe Ellis
  • Jack Holder
  • Lee Haygood
  • Paul Bennett
  • Mitch Abrahamsen

Suppose we had 100 progeny (i.e. offspring) on 1 bull. You might look at that bull and decide you like him or you don’t like him. But, that bull is just an envelop that carries genetic information. What the bull looks like really doesn’t matter, what matters is what his progeny look like. The way to look at the genetic value, or breeding value, of the bull is to look at his offspring. But, there are lots of environmental effects that influence the performance of the offspring. One example is the age of the dam. We can adjust (i.e. correct) for these effects before we measure his genetic merit. If we had thousands of progeny on a bull, his progeny performance would be his genetic merit. We use a statistical process called BLUP to account for uncertainty in the prediction. This is what produces EPDs.
We have now shifted to using DNA information in animal breeding and genetic prediction. DNA is made of four different molecules, called bases. These four bases are represented by A, C, G, and T. When DNA is copied between parents and offspring, mistakes are made. For example, an A could be replaced with a G. There are proteins that go in and correct these errors. But, some errors still slip through. These are what we call new mutations. The most common mutations are single base pair changes, we call these SNPs.
We can look at associations between SNP types (AA, AB, or BB genotypes) and the predigree based EPD.  When we compare (i.e. regress) the EPD to the SNP genotype, we can estimate the effect of each SNP (which tags a chunk of DNA).
We can test thousands of SNPs at a time using a DNA test called a SNP chip. This SNP technology was developed for human medical research applications. In the BOLT software, they find the effect of thousands of SNPs, and then sum up the SNP effects to produce a genomic prediction.
The AHA has made improvements in genomic prediction between 2010 and 2012. Dr. Garrick pointed out that he called out Hereford breeders for not genotyping more animals. The Hereford breeders stepped up to the plate and genotyped more animals so GE-EPDs could be launched.
Now we had a problem. We had a genetic prediction based on pedigree data and genomic predictions based on DNA data. They could combine these two numbers using a weighted approach. More weight was put on the pedigree EPD if the animal had more progeny information.
We can have a model about how the performance is expressed. Cattle producers may talk about this in terms of breeding and feeding equals the performance. In statistical animal breeding, we use mixed models. We have the phenotype (performance) that is a function of environmental effects such as dam age or contemporary group, the animal effect which is the breeding value and then an unknown effect (the residual).
For a genomic prediction we have the SNP genotypes, the DNA variant effects (i.e. allele effects), and an extra effect that can’t be explained by the SNP DNA markers. This is the model for a genotyped animal. But what do we do for animals that aren’t genotyped?
We can use a process called imputation to infer the genotypes of animals that have not been DNA test based on relatives that have been genotyped. Imputation adds another term for the imputation uncertainty (or error).
In single-step BLUP, they combine genomic and pedigree information to measure relatedness. They get one number out of the evaluation, the estimated breeding value.
In the BOLT model, they explicitly model the SNP effects. This can allow them to better understand and diagnosis how the statistical model is working. This also allows them to create different models, using different SNPs, for different traits.
The BOLT software is based on the super hybrid marker model.
Dr. Mahdi Saatchi was a post-doctoral fellow in Dr. Garrick’s group, when Garrick was still at Iowa State University. They identified a set of SNPs that were predictive in multiple breeds. These are the SNPs that are used in the AHA single-step prediction.
The current PACE evaluation fit all traits simultaneously, which required estimating the relationship between all the different traits. These require a linear relationship between increase in one trait and increases in a different trait.
There are now 9 different models in the Hereford evaluation. Only traits that are related to the same economically relevant traits are grouped together.
There has also been data pruning that has gone on. The evaluation now only uses data that was recorded in the Whole Herd Reporting program. This improves the genetic prediction because only unbiased, complete data is used.
BOLT uses MCMC which looks at multiple plausible values in thousands of iterations of analyses. At the end, we take the average of these plausible values which gives us the breeding value. Through these MCMC interations, we could look at the spread in the plausible values. These gives us the Prediction Error Variance, which is a measure of the uncertainty of the prediction. 

Dr. Bruce Golden
Theta Solutions LLC
Dr. Golden addressed five topics:
  • Using Genomic Data
  • Date Cutoff
  • Effects of Accuracy Calculation
  • New and Improved traits
  • Genetic Trends

There are 26,154 genotypes paid for by producers. There are about 50,000 total genotyped animals in the evaluation.
In the evaluation, they have to do marker selection (which SNPs to include in the model). For a lot of SNP effects, if the birth weight effect goes down, the weaning weight effect also goes down. However, there are markers that have an effect on birth weight but have no predicted effect on weaning weight.
In Theta Solutions analyses, single-step BLUP is more accurate than pedigree estimates. However, doing marker selection in the super hybrid models gives you an increase in accuracy over the single-step BLUP model.
Genotype information can give you the same amount of information based on 3 to 15 progeny, depending on the heritability of the trait.
Accuracy is simply a measure of the certainty of the prediction. Zero is bad, one is perfect. Accuracy is harder to calculate and harder to understand. Accuracy is really a measure of risk that the EPD will change with more data.
Breeders are accustomed to full sibs not having very different EPDs. However, with genomic EPDs we can see full siblings to be very different.
Between two full sibs with very different EPDs, they see that 35% of their SNP genotypes are different. They got very different gene samples from their parents (see eBEEF fact sheet for more information).
There is now a new accuracy calculation. There is now no approximation bias in the accuracy calculation. They now use an exact method to estimate the prediction error variance. Because of the evolution in hardware and the MCMC approach, they can now directly measure accuracy (problem is now tractable). The accuracies reported in the new system are going to be lower. The evaluation is not worse, we have done a better job of measuring accuracy. Old accuracy values were approximations and were biased to be larger than they should have been. New accuracies are unbiased, lower, and direct measures.
The new evaluations only uses whole herd Total Performance Records data. They only used observations from January 1, 2001 and forward. They are using pedigree through great-grand parents.
New method is a better measure on accuracy. Breeders will need to recalibrate their eyes to these new accuracy numbers.

Cow Fertility
Cow fertility test to be lowly heritable. However, cow fertility has a big impact on economic selection indexes because it is a huge driver of profitability. Genomics solves the lowly heritable problem. We can now make genetic progress for cow fertility.
There have been lots of measures of cow productivity

  • Days to Calving
  • Calving Interval
  • Cow Longevity
  • Stayability
  • Random Regression Sustained Cow Fertility

We now use the random regression Sustained Cow Fertility. In this analysis, we use all of the available data, cows of any age contribute to the analysis. There are now simultaneous solutions to all ages of cows. There is handling of missing values, such as cows becoming donors (rather than a cow becoming a donor being a “failure” it is now treated as missing).
The Hereford data has observations from 3 years-of-age to 12 years-of-age. A disposal code (reason cow was culled) allows the Hereford Sustained Cow Fertility to focus on fertility and not other reasons for failure.
Hereford is also going to use a new calving ease EPD. This now uses a random regression model, which allows contemporary groups with no variation to be used in the analysis. This evaluation uses scores from all ages of dam and all birth weight records. It predicts EPDs for females as 2 years old. The comparison of the genetic trend between the old model and the new model were very different for Calving Ease Direct. The trends for Calving Ease Maternal were very similar.

Dorian Garrick 
If the sire has an AA genotype at a SNP, and the dam has a BB at a SNP, the calf must be AB (A from sire, B from dam). If the calf is AA, then the dam's genotype doesn't match the calf. If we find lots of these, then the parentage is not verified.
In the past we used blood types to verify parentage. We then used microsatellites, which are lengths of DNA repeats. In cattle, we first used 12 microsatellites, which was later updated to 24 markers. We then switched to SNPs, first using 100 SNPs, which was later updated to 200 SNPs. Theta Solutions genotype pipeline uses all possible markers that animals are genotyped for. They look for animals where the genomic data doesn't match the pedigree data.

Shane Bedwell 
AHA Director of Breed Improvement
Stacy Sanders
AHA Director of Records Department 
Hereford now has a lower DNA price. For $38, breeders get profile, parentage, abnormalities and genomic profile. They can get a combo test for $58, which includes profile, parentage, abnormalities, genomic profile, and Horn/Polled status (previously $85). An add-on Horn/Poll test costs $30, so buying the combo test saves $10. Animals that have previously been tested for parentage can be upgraded to GE-EPDs for $20.
Testing bulls is important from a marketing standpoint. It allows a seedstock producer to sell bulls with more confidence to their commercial customers. From a breed improvement standpoint, it is important to genotype heifers and cows.
Hereford producers can now be paid for using the Allflex TSU Tissue Sample Unit. The unit costs $2 to buy and the producer gets a $4 credit after the animals have been DNA tested.
Dr. Mike MacNeil has updated the AHA Economic Indexes. These updated indexes have been reviewed by Matt Spangler, Larry Kuenen and Bruce Golden.
There are two maternal indexes. The older indexes were driven largely by scrotal circumference. However, scrotal circumference was not a direct measure of female fertility, but only an indicator.
The new maternal index will now have a fertility/longevity trait. Sustained Cow Fertility will now drive the bus.
There has been significant progress in the genetic trend of Hereford. The index will now include Dry Matter Intake (DMI) and Carcass Weight (CW). Ribeye Area (REA), Marbling (MARB), and Back Fat (BF) will be included in the index for balance. The index is now accounting for inputs through the DMI EPD.
[Residual Feed Intake, and other efficiency measures, can rerank animals based on how you look at it. Feed intake is the economically important trait. The appropriate way to do this is through an index.]
The plan is to update economic indexes as the new BOLT evaluation is launched.
The American Hereford Association has been running both evaluations in parallel. The AHA is planning to switch to single-step and new indexes hopefully in mid-November.
Today it takes 20 to 50+ days for progeny records to influence their parent’s EPDs. Going forward, there will be no interim evaluations. There will now be full parent evaluations weekly. Evaluations will be launched midnight on Saturdays. Results of these evaluations will be released Sunday nights. It will now take 9 to 15 days for data to impact an evaluation. Ultrasound scan data now needs to be done 4 weeks or more before a sale. DNA samples for GE-EPDs need to be submitted 6 weeks or more before a sale.
Jack Holden was part of the advisory board and felt the BOLT numbers much better tracked with the performance in his herd. Calving ease has a lot more spread and better matches.
Joe Ellis felt the new numbers and indexes would be more relevant in the commercial industry. Some animals will look better and some will look worse.
Paul Bennett says genetic evaluation has never been perfect, and never will be perfect. But, the analysis has improved. There will be some cattle that are surprised winners. This evaluation has had its day in court and the questions have been answered.

Thursday, November 30, 2017

KOMA Beef Cattle Conference in Springfield, Mo. on January 16th; Preregister by January 12th

Stockton, Mo. – The KOMA Beef Cattle Conference begins at 4 p.m., January 16, 2018, at the Springfield Livestock Marketing Center in Springfield, Mo.

The KOMA (4 – State) Beef Cattle Conference is a joint effort by the Extension Services in Kansas, Oklahoma, Missouri and Arkansas.  It is designed to provide the latest information on beef cattle production, marketing, economics, nutrition and forage utilization. 

Presenters and presentations at the meeting include:
  • Dr. David Lalman, Professor – Harrington Chair Extension Beef Cattle Specialist Oklahoma State University, will be discussing “matching genetic potential to forage resources”
  • Dr. Jared Decker, Assistant Professor of Beef Genetics Extension and Computational Genomics at the University of Missouri – Columbia, will be discussing “genetics for cow efficiency and profit”
  • Dr. Craig Payne, University of Missouri – Columbia Associate Extension Professor Veterinary Medicine, will be discussing “current thinking on parasite control in cattle”


The evening meal will be catered by Mingles in Springfield, Mo.

“That same evening, agriculture businesses that have supported the event will have booths set up. Attendees can visit and learn how their products can help improve your beef cattle operation,” said Dr. Patrick Davis, county program director for Cedar County Extension.

The cost of the event for those who pre-register and pay prior to January 12, 2018, is $20 per person. No refunds if cancellation after the registration date.  Mail payments to the Cedar County MU Extension Center at 113 South Street, Stockton, Mo. 65785. Payment at the door will cost $30 per person.


To register or for details on this event, contact the Cedar County MU Extension Center at (417) 276 – 3313 or send an email to davismp@missouri.edu.  Also contact the office immediately if you need accommodations because of a disability, need to relay emergency medical information or need special arrangements if the building is evacuated.

Monday, November 27, 2017

eBEEF announces webinar series

eBEEF is partnering with National Cattlemen's Beef Association to present a series of webinars in 2018. Please mark your calendars and watch for more information!

January 18, 2018 "Fake News: EPDs Don't Work", Dr. Alison Van Eenennaam and Dr. Matthew Spangler

February 22, 2018 "Show me the money! Are there EPDs for profit?", Dr. Darrh Bullock and Dr. Jared Decker

March 22, 2018 "The 4 S's of crossbreeding: simple, structured, successful, and sustainable", Dr. Robert Weaber and Dr. Megan Rolf

April 19, 2018 "Putting the tools to use: buying your next bull", the eBEEF team

These webinars will include opportunities for audience participation and will be an engaging series.

Monday, November 13, 2017

Show-Me-Plus™ Heifers to Sell in Fruitland, MO

On December 2, 2017 at 11:00 am at the Fruitland Livestock Auction, 80 bred heifers will be available for sale in the Southeast Missouri Show-Me-Select™ Replacement Heifer Sale. Seven of these heifers are Show-Me-Plus™ heifers. A Show-Me-Plus™ heifer is a registered or commercial heifer that has genomic predictions. For a registered heifer, this means she has GE-EPDs. For commercial heifers, it means she has been tested with a DNA panel providing genomic predictions.

The following lots contain Show-Me-Plus™ heifers.


Glen Birk Farms

1036 Co. Rd 341
Jackson, MO 63755
573-243-4874

12 Angus Heifers

  • 7 Registered Angus
  • 5 Commercial Angus
  • 4 Show-Me-Plus
Registered heifers:
  • 1 is sired by KM Broken Bow 002, AI bred to Quaker Hill Rampage 0A36, bull calf due 2/8/18. This heifer qualifies as Tier II and has been i50K tested.
  • 3 are sired by Birks O’Reilly Factor 83, AI bred to AAR Ten X 7008 SA, bull calves due 2/8/18.
  • 1 is sired by GBF Upshot 4436, AI bred to AAR Ten X 7008 SA, bull calf due 2/8/18.
  • 2 are sired by Birks O’Reilly Factor 83, natural bred to GBF Discovery 5429, due 2/27/18 to 3/4/18.
4 heifers sell as Show-Me-Plus and have genomic enhanced EPDs provided by an i50K test.

Commercial heifers:
  • 1 is sired by Birks Iron Mountain 102; 1 is sired by Birks Upward 500; 3 are sired by Birks O’Reilly Factor 83
  • All are natural bred to GBF Discovery 5429, due dates starting 2/8/18
Birth dates and sire information on the individual heifers will be available sale day.
All are bred for carcass quality with marbling genetics stacked for multiple generations. 95% of their steer mates grade CAB, Prime or choice at US Premium Beef or National Beef at 11 to 13 months of age.
Heifers that are called AI bred were pregnancy checked safe to the AI date, but are pasture ex-posed to the natural service sire.
If the buyers want registration papers for the registered heifers they should contact Glen Birk and provide information for transferring the papers.



AI SERVICE SIRES
CED
BW
WW
YW
Milk
Mrb
REA
Fat
$B
$W
Quaker Hill Rampage 0A36
Angus 16925771
+9
.86
+2.3
.96
+84
.95
+143
.90
+19
.41
+.52
.54
+1.40
.52
-.047
.54
$182
$87
AAR Ten X 7008 SA
Angus 15719841
+9
.94
+.6
.98
+64
.97
+124
.96
+23
.91
+.97
.79
+.70
.76
-.009
.79
$164
$70
NATURAL SERVICE SIRES
CED
BW
WW
YW
Milk
Mrb
REA
Fat
$B
$W
GBF Discovery 5429
Angus 18433287
+13
.35
-.1
.51
+64
.48
+119
.44
+31
.31
+.82
.38
+.80
.38
-.051
.34
$143
$70


Turner Farms
Jon and MaryAnn Turner
10511 State Hwy JJ
Belgrade, MO 63622
573-766-5361

3 Registered Angus Heifers
  • All Show-Me-Plus
  • All AI Bred
  • 2 Tier II
All three heifers are Registered Black Angus. All have been GGP-LD genomic tested. All have been AI’d then pasture exposed to Briarwood Mr Bismarck 5014, a son of SAV Bismarck 5682. All three pregnancy checked AI bred.
  • One Tier II daughter of Connealy Comrade; AI bred to Deer Valley All In; due 2/6/18; fetal sexed bull calf.
  • One Tier II daughter of Plattemere Weigh Up K360; AI bred to MCR Horizon 081; due 2/20/18; fetal sexed heifer calf.
  • One daughter of SydGen Forward 1568; AI bred to Deer Valley All In; due 2/6/18; fetal sexed heifer calf.

AI SERVICE SIRES
CED
BW
WW
YW
Milk
Mrb
REA
Fat
$B
$W
Deer Valley All In
Angus 17307074
+12
.89
+.3
.96
+74
.95
+128
.93
+21
.71
+.65
.75
+.71
.72
-.032
.75
$143
$70
MCR Horizon 081
Angus 17076135
+12
.68
-.8
.84
+62
.81
+115
.69
+26
.44
+.99
.57
+.71
.54
+.002
.55
$172
$63
NATURAL SERVICE SIRES
CED
BW
WW
YW
Milk
Mrb
REA
Fat
$B
$W
Briarwood Mr Bismarck
Angus 18281356
+10
.26
+.6
.35
+63
.31
+111
.30
+26
.19
+.45
.24
+.61
.28
+.015
.24
$145
$59

Friday, November 10, 2017

Show-Me-Plus™ Heifers to Sell December 8, 2017 in Farmington

The Show-Me-Select™ Replacement Heifer program will host a sale December 8, 2017 at the Farmington Livestock Auction starting at 7:00 p.m. At the sale, 3 Show-Me-Plus heifers will sell. 

A Show-Me-Plus™ heifer is a registered or commercial heifer that has genomic predictions. For a registered heifer, this means she has GE-EPDs. For commercial heifers, it means she has been tested with a DNA panel providing genomic predictions.


Below is information about the Show-Me-Plus™ heifers selling in Farmington, Missouri.

Turner Farms
Jon & Mary Ann Turner
10511 St. Hwy JJ
Belgrade, MO 63622
(573) 766-5361
https://turnerangus.farm/

  • All three heifers are Registered Black Angus and have been GGP-LD genomic tested.
  • All have been AI'ed and then pasture exposed to Briarwood Mr Bismarck 5014, a son of S A V Bismarck 5682.
  • Two pregnancy checked AI bred; on natural service bred.
  • One Tier-2 daughter of Connealy Courage 25L; natural bred to Briarwood Mr Bismarck 5014; due around 4/17/2018.
  • Two daughters of SydGen Forward 1568; AI bred to Deer Valley All In; due 2/6/2018 and 2/8/2018; fetal sexed heifer calves.

AI Service Sire
CED
WW
YW
Milk
Marb
REA
Fat
$W
$B
Deer Valley All In
11 (.89)
74 (.95)
128 (.93)
21 (.72)
.65 (.75)
.71 (.72)
-.031 (.75)
70.05
141.5
Natural Service Sire









Briarwood Mr Bismarck 5014
10 (.26)
63 (.31)
112 (.30)
27 (.20)
.45 (.24)
.61 (.28)
.015 (.24)
59.47
145.6


Thursday, November 2, 2017

Food Evolution Screening at Mizzou

The movie Food Evolution will show November 8, 7 p.m., Middlebush Auditorium, University of Missouri.
Join Mizzou's Food Science Association for a screening of the fascinating and controversial documentary, Food Evolution. Amongst all this conflict and confusion around food, how do we make the best decisions about how we feed ourselves? Food Evolution, from Academy Award®-nominated director Scott Hamilton Kennedy (The Garden, Fame High, OT: Our Town), explores the controversy surrounding GMOs and food. In the GMO debate, both pro- and anti- camps claim science is on their side. Who’s right?