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Show-Me-Select Board Approves Genomic Testing Requirement for Natural Service Sires

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All bulls purchased after February 1st, 2019 for use as natural service sires in the Show-Me-Select Replacement Heifer Program™ must be DNA tested to have genomic-enhanced EPDs. All bulls used as natural service sires after February 1st, 2020 must have genomic-enhanced EPDs, regardless of when they were purchased. Seedstock producers classifying bulls as Show-Me-Select qualified in sale books must have genomic-enhanced EPDs on those lots.
Bulls purchased prior to February 1st, 2019 will be grandfathered into the program, as is the common practice with all natural service sires. However, this grandfather grace period will end February 1st, 2020. At that time for a bull to qualify for use in the program, it must have genomic-enhanced EPDs.

Why the change? The Show-Me-Select Replacement Heifer Program has the goal of producing premium heifers that perform predictably as 2 year olds. The program has a history of requiring Show-Me-Select producers to go beyond typical cattle production pr…

BIF 2019: Bovine Respiratory Disease (BRD) Research at US-MARC

Larry Kuehn and Tara McDaneld
U.S. Meat Animal Research Center

Bovine Respiratory Disease may be hard to diagnosis. Have to keep in mind that prey animals, like ruminants, have evolved to hide being sick.

What are the BRDC pathogens?
Bacteria

Mannheimia HaemolyticaPasteurella multocidaMycoplasma bovisOthers
Virus

Parainfluencza-3Infectious Bovine RhinotracheitisBovine Viral DiarrheaBovine Respiratory Syncytial VirusBovine Coronnavirus (implications relatively recent)

Viruses typically aren't severe on their own, but they are often the gateway for bacteria infections to start.

Difficulty of BRDC treatment records as phenotypes
Disease incidence measured as 0 or 1
Subclinicals/shedders analyzed as healthy

How do we overcome these difficulties?
Large sample sizes are needed. USDA MARC is not using a subset of USMARC Germplasm Evaluation Program. MARC is also working to improve the quality of diagnoses/necropsy. They are also looking for indicator traits. They are collecting nasal samples …

BIF 2019: The use of 'Big Data' in a modern swine breeding program now and in the future

Jeremy Howard
Smithfield Premium Genetics 

Smithfield Premium Genetics is the nucleus that provides sows (over 1 million) for Smithfield and the sires of the terminal market pigs. At Smithfield, they mate a Landrace to a Large White to produce the commercial F1 sow. These sows are then breed to a Duroc. The terminal pig then has maximal heterosis (maternal heterosis and direct heterosis). SPG uses single sire semen of Durocs to mate to commerical farms in Missouri and North Carolina. They collect 60,000 carcass data points per year.
On the maternal side, it is had to get stayability data because generations are turned over so quickly. They use commercial test herds to collect this data on sows.
Howard said that genomic information on purebred animals prior to selection allows them to better predict performance in a commercial setting. This genomic data also allows them to figure out if problematic meat is produced at a company owned farm or an outside source.

Big data is driven by volu…

BIF 2019:The Latest Agri-Tech Emerging in the Australian Grazing Industries

Mark Trotter
Central Queensland University

His research is outcome, not technology driven. It is not finding shiny new tools and asking how can I use it. Rather, it is looking at problems in the industry and finding solutions, including technology, to help it.

Northern Australia is much more similar to central America that it is to the United States. Southern Australia is similar to the southern US.

There are several tools for stocking rate management, but there is a need to get good tools into these systems. There is now high spatial and temporal satellite data  that is now basically available for free. There are emerging radar satellite systems.

There's a lot of hype around "smart tags" and other agtech, but what's the actual need and value? There are three key bits of information producers would love to have from a sensor system:

LocationBehaviorHealth
Producers see lots of applications for smart tags.

Location
We went from big backpacks on cattle to neck collars whi…

BIF 2019: The Next Generation of Genetic Tools

John Genho
Neogen GeneSeek

Why do we use a crossbreeding system? To gain the advantage of heterosis, the cross outperforming the parent average. Retained heterosis is the amount of this advantage that is maintained after multiple generations of mating crossbreed animals (not mating the purebred parents).

Dominance, over dominance, and epistasis likely all contribute to heterosis.

In general, traits with higher heritabilities have lower heterosis and traits with low heritability have higher heterosis.

Why don't commercial producers use crossbreeding? The average herd size is 40 head and 9% of herds have >100 head. It is harder to implement a crossbreeding program in a smaller herd.

Researchers in Canada have developed genomic indicators of retained heterosis. They use the genomic data to infer the breed proportion of the animals. They can then square these breed proportions, add them up, and subtract from zero to estimate the retained heterosis. Another approach is to count the n…

BIF 2019: Developing DNA Tests for Improved Fertility and Reduced Embryonic Loss in US Cattle Breeds

Jeremy Taylor
University of Missouri

Taylor is going to cover several things:

GGP-F250ImputationHaplotype diversityEmbryonic Lethals

The GGP-F250 is a very unique assay compared to other SNP panels. All of the other available assays (SNP panels) use common variants. The GGP-F250 has many rare variants, most of which are located in genes or other functional elements.

Why is rare variation important? Most of the variation in mammalian genomes, including the genomes of cattle, contain rare variation. Most of the DNA differences between different individuals are rare variants. We can't tag this rare variation with the common variants included in most SNP panels. To accurately measure genetic differences (and predict EPDs), we have to account for rare variation.

Imputation is the process of:
1. Sorting DNA variants onto each chromosome (phasing)
2. Filling in missing genotypes

We can impute from 50,000 SNPs to 700,000 SNPs to 15 million variants. But, we can't do this accurately for …

BIF 2019: Update on Gene Editing

Alison Van Eenennaam
UC-Davis

United States beef cattle inventory has decreased since the 1970s. However, over that same time period, we have produced more beef. This means we are more efficiently producing more beef per cow. This is very different compared to other countries such as Brazil and India.

We have seen inflection points in the genetic progress of beef production as various technologies have been adopted? Will gene editing be that next inflection point?

Gene editing technologies are simply scissors that cut DNA. There are various types, such as Zinc Finger Nucleases, TALENS, and CRISPR/Cas9. CRISPR has become very popular recently because it uses a guide RNA to make the cut at a specific location. CRISPR can make site-specific variants (mutations) as the cell repairs the double stranded breaks. CRISPR can also be used to insert new sequence from a different animal, species, or kingdom.

There are 13 papers that describe edits for 12 different traits in cattle.

Gene editing fo…

BIF 2019: Producer Experience with Sex-Sorted Semen

Brent Mason
Mason-Knox Ranch

Mason-Knox Ranch develops heifers to market bred heifers. They like to purchase the heifer calves back from their customers. They also like to breed heifers to producer heifer calves, because we know that heifer calves are lighter compared to bull calves. Mason also sees an opportunity to quick change a cow herd by using sex sorted semen.

Mason said, "Those who know me, know I'm a nervous nelly." The first time they did split time AI, Mason looked at all of the heifers in the hold pen and was nervous. Dave Patterson told him to eat dinner. Mason ate dinner, came back, and still very few heifers in heat. Patterson said, "Just let them be." Next morning, lots of heifers were in heat.

Mason also sees opportunity for sexed-semen in seedstock. Think about breeding that cow who always produces a great bull, to male select semen.

"There is a difference between burlap and satin," Mason quoted a friend. Mason believes in using quali…