Can Biotechnology Bring Home the Bacon? - Without Netflix Clip - Dr. Alison Van Eenennaam, University of California, Davis, from the 2017 North American PRRS/National Swine Improvement Federation Joint Meeting, December 1‐3, 2017, Chicago, Illinois, USA. More presentations at http://www.swinecast.com/2017-north-american-prrs-nsif-joint-meeting

1. Animal Genomics and Biotechnology Education
Can Biotechnology Bring Home
the Bacon?
Alison Van Eenennaam
Cooperative Extension Specialist
Animal Biotechnology and Genomics
Department of Animal Science
University of California, Davis, USA
Email: alvaneenennaam@ucdavis.edu
Twitter: @BioBeef Blog: http://biobeef.faculty.ucdavis.edu/
http://animalscience.ucdavis.edu/animalbiotech

2. Fish (wild & cultured) is the largest source of animal protein – pigs are second

3. 0
100
200
300
400
500
600
1980 1990 2002 2015 2030 2050
Totalconsumption(milliont)
Developing - meat
Developed - meat
Developing - milk
Developed - milk
Past and projected trends in consumption of meat and milk in developing and
developed countries
(Thornton, P.K. 2010 Livestock production: recent trends, future prospects. Philosophical Transactions of the Royal Society B: Biological Sciences 365:2853-2867).

4. If I wanted to select for more efficient pig
• Increase litter size
• Increase the number of litters per year
• Increase the amount of lean meat (pork/bacon) per pig
• Decrease the amount of time needed to get to market weight
• Improve the efficiency of feed digestion (feed conversion ratio)
• Decrease the feed needed to produce a finished pig (increase growth rate)

5. U.S. Domestic Pork Production Per Sow, 1930 - 2015
Tokach et al 2016 (Performance enhancing technologies in swine production, Animal Frontiers, doi:10.2527/af.2016-0039)
4,200 lb
800 lb

6. Tokach et al 2016 (Performance enhancing technologies in swine production, Animal Frontiers, doi:10.2527/af.2016-0039)
20151980
Trait 1980 2015
Feed conversion (feed/gain) 3.2 2.6
Lean meat/carcass (lb) <80 >118
Pigs marketed/sow/year 9.2 22
Pork produced; lb/sow/year 1770 4200

7. If not for pig genetic improvement in last 35 years…
• Market pigs require 4% < feed today to produce a 17% heavier carcass than 35 yr ago
• Of the 41 lb increase in live weight, 93% of the increase is lean muscle provided by
each carcass, with today’s pigs producing > 118 lb of lean meat per animal.
• This has allowed for a 28% increase in pork production with only a 10% increase in the
annual number of animals harvested over the same time period.
• Combining increases in sow productivity & market weight, the average U.S. pig farms
are producing > 4,200 lb of live weight /sow/year compared with ~1770 lb in 1980.
• Without these genetic improvements, it would take another 9 million
sows (approximately 15 million in total) compared with today’s 6
million sows to achieve current level of US pork production.
1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000

8. If I wanted to select for more efficient pig
• Increase litter size
• Increase the number of litters per year
• Increase the amount of lean meat (pork/bacon) per pig
• Decrease the amount of time needed to get to market weight
• Improve the efficiency of feed digestion (feed conversion ratio)
• Decrease feed needed to produce a finished pig (increase growth rate)
• Decrease the undigested nutrients coming out the back end in manure
• Improve the health profile of pig products for human consumption

9. EnviropigTM (Low-phosphorus manure)
“reduces fecal phosphorus
output by up to 75%”
Nature Biotechnology 2001
www.uoguelph.ca/enviropig
↓Phosphorus in
manure by 75%

10. Omega-3 Pigs
(Pigs cloned after genetically engineering cell)
“reduces fecal phosphorus
output by up to 75%”
Nature Biotechnology 24:435-436. 2006
University of Missouri/Massachusetts General Hospital and Harvard Medical School Meat with ↑ n-3 fatty acids

12. Snout
Cloven hoof
Litter bearing
Curly tail
What
makes
a pig
a pig?
Single stomach
Beady eyes

13. $60 million budget

14. Mandatory, premarket regulation of
genetically engineered (GE) animals by FDA
The Food and Drug Administration’s Center for Veterinary Medicine (CVM)
evaluates GE animals under the new animal drug provisions of the Federal Food
Drug and Cosmetic Act (FFDCA). The act defines drugs as “articles (other than
food) intended to affect the structure or any function of the body of man or other
animals.” The rDNA construct in the resulting GE animal is thus a regulated article
that meets the drug definition; the GE animal itself is not a drug.
The FDA defines “genetically engineered (GE) animals” as those animals modified
by rDNA techniques, including the entire lineage of animals that contain the
modification, and regulates based on the use of rDNA techniques. All GE animals
are captured under these provisions, regardless of their intended use.
Thus although the review is product based, the process used to produce the
genetic change that results in the product (e.g. rDNA versus traditional
breeding) has implications for triggering regulatory oversight

15. Timeline of AquAdvantage
regulatory process
Year Event
1989 • Founder AquAdvantage fish produced in Canada
1995 • FDA review of AquAdvantage salmon begins (INAD)
2001 • First regulatory study submitted by Aqua Bounty Technologies to U.S. FDA for a New
Animal Drug Applications (NADA)
2009 • FDA guidance on how GE animals will be regulated
• Final AquAdvantage regulatory study submitted to FDA
26yearsfromdiscoverytoapproval?
Van Eenennaam 1/15/2017
Does it work?
Is it safe?
Is it durable?
What is its phenotype?
What is its genotype?
rDNA description

16. Fast growing salmon
The founder female was generated in 1989 – 21 years ago
Nature Biotechnology 10:176 – 181. 1992
University of Toronto/Memorial University of Newfoundland, Canada

18. Timeline of AquAdvantage regulatory process
Year Event
1989 • Founder AquAdvantage fish produced in Canada
1995 • FDA review of AquAdvantage salmon begins (INAD)
2001 • First regulatory study submitted by Aqua Bounty Technologies to U.S. FDA for a New Animal Drug
Applications (NADA)
2009 • FDA guidance on how GE animals will be regulated
• Final AquAdvantage regulatory study submitted to FDA
2010 • FDA VMAC meeting on AquAdvantage salmon (9/20/10)
2015 • November 19th, 2015 Approval (~$70 million to bring the AquAdvantage® salmon through the
regulatory approval process)
2016 • January: US FDA issues a ban on the import and sale of GE salmon until FDA “publishes final
labeling guidelines for informing consumers of such content”. The ban was the result of language
Alaska Sen. Lisa Murkowski introduced into the 2016 fiscal budget, or omnibus, bill. It
also authorizes “an independent scientific review” of the effects of GE salmon on wild salmon
stocks and for human consumption.”
• March: a coalition of environmental organizations sues US FDA over approval of GE salmon
approval
• May: Canadian Approval of AquAdvantage for sale in Canada
• December: FDA bills AquaBounty for $113,000 “Animal Drug” User Fee for their “approved”
animal drug product despite continued FDA ban on the import and commercial sale of
AquAdvantage® fillets
26yearsfromdiscoverytoapproval?

19. Meganuclease
Zinc finger
TALENs
CRISPR/Cas9
Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotech 2014;32:347-355.
Genome editing may or may not introduce
rDNA and it may or may not be transgenic

20. Gene Edited Polled Calves
Carlson DF, Lancto CA, Zang B, Kim E-S, Walton M, et al. 2016. Production of hornless dairy
cattle from genome-edited cell lines. Nat Biotech 34: 479-81
Naturally-occurring bovine allele at polled locus

21. https://www.youtube.com/watch?v=-Qks_LMmodw

22. Celtic allele (PC) corresponding to a duplication of 212 bp
(chromosome 1 position 1705834–1706045) in place of a 10-bp
sequence = horned (1706051–1706060) at POLLED
TALENs introgress
Pc Polled allele
bovine fibroblast
Cell line
Somatic Cell
Nuclear Transfer
(SCNT) cloning
Embryo transfer2 bull calves
10 bp
212 bp
Born April 2015
POLLED
GENE

23. 5 bull calves and 1 heifer calf were born in September, 2017
- They are all hornless (polled)

24. Will breeders be
able to use gene
editing or will it
go the way of
GMOs ……

27. January 18th, 2017 FDA draft guidance considers
all gene edited animals whose genomes have
been “altered intentionally” to be drugs
http://www.fda.gov/downloads/AnimalVeterinary/GuidanceComplianceEnforcement/GuidanceforIndustry/UCM113903.pdf
Image by Aleksandra Domanović and Spencer Lowell

28. Draft FDA regulations consider all
animals whose genomes have been
altered intentionally as drugs
In the past, FDA has used the term “genetically engineered” to refer to animals containing
recombinant DNA constructs (rDNA) intended to alter the structure or function of the body of the
animal.
The new guidance uses the phrase “animals whose genomes have been altered intentionally”
– REMOVING THE rDNA trigger for regulation
The presence of ANY “intentionally altered genomic DNA” produced using “modern molecular
technologies” in an animal should trigger mandatory, premarket animal drug evaluation,
irrespective of product risk or novelty of the genomic alteration.
The Guidance includes nucleotide insertions, substitutions, or deletions; however, it clarifies
selective breeding and random mutagenesis followed by phenotypic selection are not included as
triggers.
In general, each specific genomic alteration is considered to be a separate new animal drug
subject to new animal drug approval requirements.
http://www.fda.gov/downloads/AnimalVeterinary/GuidanceComplianceEnforcement/GuidanceforIndustry/UCM113903.pdf

29. Animals were 20X sequenced to look for off target mutations and none were found - only the intended edit (where
the polled allele replaced the horned allele) mapped to within 10 bp of any of the identified degenerate targets
supporting the high specificity of TALENs for this locus. Carlson et al. 2016 Nat Biotech 34: 479-81
Are Gene Edited Horn-less calves a drug?
Naturally-occurring bovine allele at Polled locus
What is the “new animal drug” in this case?
I am not a
drug

30. Use of gene editing to introduce a
naturally-occurring polled allele into
Holstein cattle versus selective breeding
Attribute Polled Holstein
through gene
editing
Polled Holstein
through
introgression
Phenotype: No horns YES YES
Mutation uniquely detectable NO – polled allele NO – polled allele
Food safety concerns
associated with phenotype
NO NO
# generations taken to achieve
polled >15/16 Holstein
ONE
(FAST)
MANY
(SLOW)
Linkage drag? NO YES
Improved animal welfare YES YES
Regulated? Yes because of human
intention???
NO
Likely to happen Not if takes years and
costs millions of dollars
NO

31. Does it really make sense to regulate polled
dairy calves differently to polled beef calves?
Carroll D, Van Eenennaam AL, Taylor JF, Seger J, Voytas DF. 2016. Regulate genome-edited
products, not genome editing itself. Nat Biotech 34: 477-9

32. Gene editing regulations must be considered in the
context of natural “gene editing” also known as de
novo mutations (dnm)
 In one recent analysis of whole-genome sequence data from 234
taurine cattle representing three breeds, >28 million variants were
observed, comprising insertions, deletions and single-nucleotide
variants
 On average every new animal will have around 65 de novo mutations
of which approximately 5 will be small insertion-deletions and the
remaining 60 will be single nucleotide substitutions
Chad Harland, Carole Charlier, Latifa Karim, Nadine Cambisano, Manon Deckers, Myriam Mni, Erik Mullaart, WouterCoppieters, Mic
hel Georges. 2017. Frequency of mosaicism points towards mutation-prone early cleavage cell divisions.
doi: https://doi.org/10.1101/079863. https://www.biorxiv.org/content/early/2017/06/29/079863
Carroll D, Van Eenennaam AL, Taylor JF, Seger J, Voytas DF. 2016. Regulate genome-edited
products, not genome editing itself. Nat Biotech 34: 477-9

33. Draft FDA regulations consider all animals
whose genomes have been altered
intentionally as drugs
In the past, FDA has used the term “genetically engineered” to refer to animals containing
recombinant DNA constructs intended to alter the structure or function of the body of the animal. The
new guidance uses the phrase “animals whose genomes have been altered intentionally”.
http://biobeef.faculty.ucdavis.edu/2017/01/22/fda-seeks-public-comments-on-regulation-of-genetically-altered-animals/

34. https://www.pinterest.com/pin/475552041874709302/
Mr. Chow from The Hangover

35. Scientific Community
Biotech Companies
Public
Regulators

36. • Increase litter size
• Increase the number of litters per year
• Increase the amount of lean meat (pork/bacon) per pig
• Decrease the amount of time needed to get to market weight
• Improve the efficiency of feed digestion (feed conversion ratio)
• Decrease the feed needed to produce a finished pig (increase growth rate)
• Decrease the undigested nutrients coming out the back end in manure
• Improve the health profile of pig products for human consumption
• Select for pigs that do not get sick (improve the health of the pig)
• Reduce the amount of fat and improve piglet survival
If I wanted to select for more efficient pig

37. Disease-Resistant Pigs
Nature Biotechnology 2015
University of Missouri Resistant to PRRS virus

38. Disease-Resistant Pigs
Roslin Institute Resistant to African Swine Fever
https://www.theguardian.com/science/2015/jun/23/could-these-piglets-become-britains-first-commercially-viable-gm-animals
Scientific Reports 2016

39. Disease-Resistant Pigs
PLOS Pathogens 2017
Roslin Institute Resistant to PRRS virus

40. Low-fat pigs & improved survival PNAS 2017
Chinese Academy of Sciences
Low-fat and ↑survivability

41. We need to call out policy not based on science – or else risk
losing access to innovation in agricultural breeding
BAD REGULATIONS
It is up to the you to defend
agricultural breeding,
innovation, and the need for
science-based policy

42. • Regulatory processes should be proportional to risk and consistent across products that have
equivalent levels of risk. Regulations based on how products are made are inconsistent with
science-based risk assessment unless there is something inherently risky about the process that
was used to make them, as compared to existing methods
• GE animal regulatory burdens are disproportionately high and are associated with unaccountable
delay and considerable uncertainty. These regulatory burdens are not justified by scientific
evidence or experience
• Currently regulatory language is not science-based – human intention is not associated with risk,
and regulating every SNP as a drug ignores the very real plasticity of genomes which are
constantly undergoing spontaneous de novo mutations (aka genetic variation and evolution)
• Given the importance of enabling safe innovation in breeding, there is an urgent need to ensure a
science-based, risk-driven regulatory framework for the use of gene editing in agricultural
breeding programs.
Summary

43. https://www.youtube.com/watch?v=C0MBl0BANHg

44. Thanks for inviting me!
My laboratory receives public funding support from the
National Institute of Food and Agriculture and the
Biotechnology Risk Assessment Grant (BRAG) program,
U.S. Department of Agriculture, under award numbers
2011-68004-30367, 2013-68004-20364, 2015-67015-
23316, 2015-33522-24106 and 2017-33522-27097 .
Animal Genomics and Biotechnology Education