BIF 2018: GeneSeek Genomics Symposium

Stewart Bauck
Neogen Vice President of Agrigenomics

This is the 50th aniversary of the BIF Symposium. Fifteen years ago at BIF, the sequencing of Dominette for the first cattle genome sequence was announced.
GeneSeek now has laboratories all over the world. They have worked with customers and collaborators to develop over 50 custom assays (DNA tests).

There are 3 pillars of GeneSeek's success:

  • High quality data
  • Fast Turn-Around Time
  • Fair Pricing

Dr. Mitch Abrahamsen
Executive Vice President, Chief Scientific Officer
Recombinetics
Precision Breeding for Animal Health and Productivity:
What does it take to deploy technology in the market place?

Recombinetics has 3 product lines. Two are focused on applications of gene-editing to human medicine. 
The agriculture product is called Acceligen. Acceligen uses gene editing to move DNA variants from one breed to a different breed. 
Recombinetics has 22 patents. 
To date, all genetic progress is the result of traditional animal breeding programs.
  • Mate best animals together
  • Select the best progeny based on data available
  • Repeat
Gene editing allows us to focus on animal welfare traits and to make rapid and intentional progress. "We don't have to wait on random chance," Abrahamsen said. 

Gene editing is a complementary tool to use in addition to traditional and genomic selection.

What are the drivers for innovation in Animal Agriculture?
  • Consumer Expectations
  • Interest in how food is raised 
  • Animal Welfare
  • Environment impact
  • Evolving regulations for animal production
We are in the Green Revolution 2.0 in Animal Agriculture:
  • Accelerated productivity
  • Sustainable 
  • Global food security

This is done through big data, genetic improvement by genome prediction, and genetic improvement by gene editing.
Recombinetics Acceligen is focused on health and welfare traits.
They have produced 
1. Naturally hornless (polled)
2. Naturally-cool (slick mutatation)
3. Naturally-casturated

Have to influence with science and passion. Just science information will not be enough.
Acceligen will have macro-traits that they share with all of their collaborators and customers. Later down the road they will also have micro-traits that are specific to certain scenarios, will be proprietary, and provide a competitive advantage.

Semex and Recombinetics have announced a partnership to focus on animal welfare traits.

Acceligen's position is to regulate the product not process at USDA. Currently, this happens by the FDA regulating the process. 

Gene-editing using natural processes to introduce existing mutations into breeds. For example, introducing existing Angus polled mutation into elite horned Holsteins.

"We need to take steps that are really paradigm shifts," Abrahamsen said. "At some point we have to start doing things differently."

Matt Barten
Embruon, LLC

With intact embryos from embryo transfer, we see pregnancy rates around 65%. With biopsied embryos, pregnancy rates are around 50%. 
However, the biopsies are small and have very little DNA. GeneSeek has to amplify this DNA. This is like taking a bushel of corn and copying it to two semi trailer loads of corn.
This allows us to select which embryos we transfer and which we never use. We can choose to only implant embryos for those that will become desirable animals.
See more about Embruon at these blog posts:


Dr. J.R. Tait
GeneSeek
Biology, the random sampling of genes and chromosomes, leads to variability produced by a good bull. GeneSeek is working with commercial customers to identify appropriate tools to make decisions about which animals to select.
There is significant variation even between cattle that are closely related. From a set of full siblings (same mother and father), one calf can be in the bottom 10% and another calf can be in the top 10%.
Production systems on commercial operations often doesn't allow for BIF adjustments.
  • We don't know the age of the calf
  • We don't know the age of the dam
  • We may not match the calf to the dam
  • The cow may not have an ID
  • Calf weights may not be taken in the right age window
In other words, commercial producers don't have management practices like a seedstock producer. However, DNA testing can provide genetic predictions for commercial producers without the difficulties of acting like a seedstock producer.

Neogen has a product called Igenity Beef.
Angus, Red Angus, Hereford, SImmental, Gelbvieh and Limousin were used in the development of these products. 
Igenity Silver has 6 traits plus parentage.
Igenity Gold has 13 traits plus parentage.
Often these results are reported on an online dashboard. Customers can also create a custom index. 
50 to 70 years ago dairy selection emphasis was all on milk production. Does this mean fertility didn't change... No, fertility got worse over this time period. We have to practice multiple trait select and we need to select on all the important traits.

Igenity has launched an Igenity Production Index. This index assumes the producer is keeping their own replacements and marketing cattle on a grid. They are also going to soon release a maternal index and a terminal index.

The Igenity Production Index focuses on certain production traits. But, we see favorable genetic trends for a suite of traits.  

Igenity Beef are the multi/crossbreed products (Igenity Gold and Igenity Silver).
They also have breed specific panels including:
  • Igenity Angus
  • Igenity Gelbvieh
  • Red Navigator
  • Igenity Brangus
  • Igenity Santa Gertrudis
  • Igenity Beefmaster

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