A Steak in Genomics™

by Eldon Cole, Livestock Specialist Headquartered in Lawrence County, MO
The skidding cattle market the past few months resulted in considerable pessimism prior to the 33rd Show-Me-Select (SMS) Bred Heifer Sale at Joplin Regional Stockyards on November 20.  However, when the last of 293 heifers left the ring, the average price of $2477 brought smiles to most of the sellers.
The previous 32 sales results predicted an average heifer price just under $2000 per head.  That forecast is based on the week’s average price per head for a 550 pound, Medium and Large Frame, Number 1 Muscle steer at the Joplin and Springfield markets.  That average amounted to $1011 per head according to the Missouri Market Summary.
The SMS heifer average of $2477 divided by the steer average resulted in a 2.45:1 figure.  In the previous sales the highest ratio was 2.4:1.  Since the SMS sales began in 1997 at Joplin the smallest ratio was 1.65:1 in 1999.
There was a standing room only crowd at the sale along wit…

Dorian Garrick
Iowa State University

The Pre-Genomic Era In the Pan-American Evaluation there are four countries, US, Canada, Uruguay and Argentina. Agricultural Business Research Institute (ABRI) collects the pedigree and trait data. Then the Animal Genetics & Breeding Unit uses BREEDPLAN to estimate EPDs.

To put the number of records turned in to the AHA data in context, we can compare them to other breeds. The 11 breed associations in International Genetic Solutions add 340,000 new animals in each of 2012 and 2013. AGI adds about 300,000 per year. Herefords add a little less than 100,000 animals per year.

The Early-Genomic Era Cattle have 30 pairs of chromosomes. There are about 100 million base pairs per chromosome and about 2.6 billion base pairs in the entire DNA (genome).

Most errors in chromosome replication are fixed. But, some slip through and are passed down through generations.

The EPD of a bull is a sum of the average gene effects he carries. Until the genomic era, we …

Bill Bowman and Sally Northcutt
Method Genetics LLC

Bowman and Northcutt discussed several new EPDs either in development or released by AHA, including:

Dry Matter IntakeSustained Cow FertilityHeifer Calving RateUdder Quality (Teat Size and Udder Suspension)
Heifer Calving Rate, Sustained Cow Fertility, and Dry Matter Intake are currently released as prototype evaluations and can be accessed as a downloadable Excel file.

"One of the things you all have going for you is the foresight to begin a TPR program," said Bowman.

Heifer Calving Rate Heifer Calving Rate (HCR) is a categorical trait, they either calved or they didn't. Method Genetics reports a heritability of 15% for Heifer Calving Rate. They analyzed 98,000 records, of which 73% had calved by 800 days of age, 27% had not calved. Contemporary grouping for heifers is based upon their herd, yearling weigh date, calf birth year and season.

"This EPD goes beyond a traditional heifer pregnancy EPD." said Northcutt…

Based on input and requests from breeders, we’ve been working on some updates to the information displayed on the Animal Search feature on Angus.org. These new features went live this morning [10 November 2015], and I want to take a minute to highlight and explain these enhancements.
Genomic Progeny EPD percentile ranksProgeny  For complete post, please visit Angus Genetics Inc blog, and read the post by Dr. Tonya Amen.
Decker's Take Home: I always love to see breed associations changing and innovating. I think these changes will allow producers to more quickly evaluate an animal's genetic merit. Plus, I'm sure breeders appreciate AGI responding to requests.

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Angus Convention 2015
Richard Resnick
CEO of GenomeQuest

One can not impede scientific progress. - Mahmoud Ahmadinejad Resnick gave a series of examples of how genomics is changing society.

Resnick put a nice spin on the typical sequencing cost figure. He overlays Illumina's ($ILMN) stock price on top of the figure.

He went on to explain that the only real differences between humans, cattle, corn, and other species is the proteins they make. The amino acids, the building block of proteins, are actually the same between species.

Resnick used cystic fibrosis as an example of a disease in which genetics has been very important. One DNA variant that causes the disease is called ΔF508. When a person has this variant, the gene produces the protein, but a check and balance in the cell recognizes the protein as not correct and destroys it. A different variant, G551D, is not so severe that the protein is destroyed, but the protein does not function properly. A drug called Kalydeco alters the…

Eldon Cole, Livestock Specialist
The 86th Southwest Missouri Beef Cattle Improvement Association’s bull sale averaged $4581 on 49 bulls.  Leading the average were the 46 Angus bulls that made $4684.  Three Polled Herefords were harder to get bids on and each received a $3000 bid.
The consignment had outstanding performance data behind them and the knowledgeable bidders on the seats found the top prospects throughout the sale.  One thing that stood out again was the reluctance of buyers to go very high on bulls that had calving ease direct expected progeny differences (EPD) that were poorer than breed average.
The sale top of the evening was a May, 2014 Angus consigned by Truman L. Wiles, Willow Springs.  The bulls calving ease, weaning weight and yearling weight ranked him in the first percentile for Angus non-parent bulls.  His $Wean was also in the first percentile.  The 7-framebull brought $7000 from Kevin and Cheryl Dill of Niangua.
Close behind at $6750 was the entry from Blue M…

Meat Animal Research Center, Clay Center, NE Matt Spangler
University of Nebraska-Lincoln
 Why are we working on these novel traits?
 Because they have great economic importance.
 Further, they have heritable genetic variation.

 We do have EPDs for feed intake and fertility, but they are not as pervasive as other (weight and carcass) traits.

Continued phenotypic data collection and recording is critically needed. But, the breed associations have to do something with the data. Otherwise, progressive seedstock producers will look outside breed associations for genetic evaluations. This will not be a great outcome for commercial cattle producers.

Nine breeds are already incorporating genomic information into EPD, with many other breeds right on the cusp of releasing genomic-enhanced EPDs.

As genotyping becomes more common and more animals are genotyped, many of the current limitations are eliminated. But, there is continued room for statistical approaches to be refined.

 Genotyping entir…