Uso Sinérgico de Biotecnologías, Selección Genómica y Tecnologías de Reproducción Asistida en Programas de Cría de Animales de Producción

Alison Van Eenennaam, Ph.D. Cooperative Extension Specialist Animal and Genomics Department of Animal Science University of , Davis, USA

Email: [email protected] Twitter: @BioBeef Blog: http://biobeef.faculty.ucdavis.edu Website:http://animalscience.ucdavis.edu/animalbiotech Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Criadores de animales han hecho importantes avances genéticos basados únicamente en selección fenotípica

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education El peso de pollos de carne de 8 semanas ha aumentado de 0.81 kg a 3.14 kg entre 1957 y el 2001 . Aproximadamente 80% de este incremento es el resultado de selección genética

Havenstein, G., et al. (2003). Growth, livability, and feed conversion of 1957 versus 2001 broilers when fed representative 1957 and 2001 broiler diets. Poultry Science 82, 1500-1508. Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Y si no # de animales hubiéramos usados para consumo en el mejorado 2009 genéticamente nuestros animales de producción? 1.3 billones de cerdos 2.6 billones de patos 52 billones de pollos • 59 millones de toneladas de huevos. • 90 millones de toneladas de carne

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Producción total 2014 Cantidad Otras en USA en 2014 necesitada para necesidades 1950 Soybeans 3,927,090,000 BU 82,591,000 180,971,889 ~ 98 million Acres Acres Acres (235,562,540,000 lb) (106,849,370,802 kg) (33,423,392 ha) (73,236,725 ha)

(~40 million ha)

Corn 14,215,532,000 BU 83,136,000 372,134,346 ~ 289 million Acres Acres Acres (796,069,979,000 lb) (361,091,268,460 kg) (33,643,946 ha) (150,597,427 ha) (~120 million ha) Dairy cattle 206,046,000,000 lbs 9,257,166 head 38,774,181 head ~ 30 million head milk

(93,460,893,469 kg)

Broilers 51,373,100,000 lbs 8,544,100,000 16,679,545,455 ~ 8 billion head meat head head + an additional 81.5 billion lbs (23,302,446,000 kg) feed due to less efficient FCR

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education La tasa de ganancia genetica depende de los 4 componentes de la ecuación del criador

ΔG = Intensidad de selección X

Exactitud de selección X

(√Variación genética en la población/

intervalo generacional )

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Convenio en Biodiversidad Genética : “Biotecnologías y cualquier aplicación de tecnologías que use sistemas biológicos, organismos vivos, o derivados para hacer o modificar productos o procesos para usos específicos.”

Genetics/breeding Nutrition Health

Artificial insemination Feed additives: Amino acids, Molecular diagnostics enzymes & probiotics Progesterone monitoring Prebiotics Recombinant vaccines Estrus synchronization Silage additives (enzymes and Conventional vaccines microbial inoculants) Invito fertilization and Ionophores Sterile insect technique embryo transfer (SIT) Cryopreservation Molecular Single cell proteins Bioinformatics markers; genomic selection Semen and embryo sexing Recombinant somatotropins Molecular markers; genomic Solid state fermentation of selection lignocellulosics GREEN = Potential for generating impact Cloning Molecular gut microbiology (time frame <10 years) Genetic Engineering/ Genome editing Uruguay 10/10/2016 Animal Genomics and Biotechnology Education 1944: 25.6 million animals; total annual milk production of 53.1 billion kg. 1997: 9.2 million animals; total annual milk production of 84.2 billion kg.

Cerca de la mitad de este 369% aumento en eficiencia de producción es atribuible a mejoramiento genético gracias a la inseminación artificial

A I

VandeHaar, M.J. and St-Pierre, N. (2006). Major Advances in Nutrition: Relevance to the Sustainability of the Dairy Industry. Journal of Dairy Science 89, 1280-1291. Uruguay 10/10/2016 Animal Genomics and Biotechnology Education La inseminación artificial fue inicialmente un tema controversial

“In the initial stages of attempting to develop AI there were several obstacles. The general public was against research that had anything to do with sex. Associated with this was the fear that AI would lead to abnormalities. Finally, it was difficult to secure funds to support research because influential cattle breeders opposed AI, believing that this would destroy their bull market.”

Foote, R.H. 2002. The history of artificial insemination: Selected notes and notables. J. Anim. Sci., 80 (E. Suppl.) (2002), pp. E22–E32

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Uso de recursos y desechos en la industria lechera en USA en el 2007 comparada con la de 1944

GHG = Greenhouse gas

1/3

Capper, JL and DE Bauman, 2013. The Role of Productivity in Improving the Environmental Sustainability of Ruminant Production Systems. Annual Review of Animal Biosciences. 1 pp. 9.1–9.21

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Que es un marcador genetico?

A DNA sequence variation that has been associated with a given trait in one or more populations

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Queremos usar marcadores genéticos (SNPs), pedigríes e información de producción para seleccionar los mejores animales

Animal Biotechnology and Genomics Uruguay 10/10/2016 Education Tecnologías genotípicas de alto rendimiento permitieron el desarrollo de “SNP chips” (marcadores) de alta densidad

The sequencing of the bovine genome allowed for the development of a 50,000 SNP chip, then the 800,000 SNP chip; and now whole genome sequence (3 billion)!

Uruguay 10/10/2016 Podemos usar estos SNP CHIPS para selección “genética”?

TRAINING POPULATION 1,000s animals Training = estimate the value of every chromosome – Phenotypes fragment contributing – Genotypes variation in a population with phenotypic observations

Prediction = the results of training can then be used to develop prediction equations to predict the merit of new animals (e.g. young bulls)

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Registros en bases de datos de lecherias en USA

 Pedigree records 71,974,045  Animal genotypes 1,035,590

 Lactation records (since 1960) 132,629,200

 Daily yield records (since 1990) 641,864,015

 Reproduction event records 179,559,035

 Calving difficulty scores 29,528,607

 Stillbirth scores 19,567,198

Data from George Wiggins, USDA ARS (7/2015) Animal Genomics and Biotechnology Education 1200000 45000 40000 Low-Young 35000 30000 25000 1000000 20000 Low-Old 15000 10000 5000

50-Young 0 New Genotypes per Month per Genotypes New

800000 Jul-14

Oct-10 Apr-13 Oct-15

Jan-12 Jun-12

Mar-11 Mar-16

Feb-14

Aug-11 Nov-12 Sep-13 Dec-14

May-10 May-15 F-50-Old

600000 M-50-Old

400000 Genotipos

200000

0

Oct-09 Oct-10 Oct-11 Oct-12 Oct-13 Oct-14 Oct-15

Jun-12 Jun-09 Jun-10 Jun-11 Jun-13 Jun-14 Jun-15

Feb-10 Feb-11 Feb-12 Feb-13 Feb-14 Feb-15 Feb-16

Slide courtesy Curt Van Tassell May 24, 2016 Prediccion del valor de cruce en toros lecheros Graphic kindly provided by Gonzalo Rincon

Young sire Young sire Young sire Parent Average Progeny Test Genomic Selection

x x x

Birth 5 years; $50,000 cost Birth; << $50,000 cost

AS AD AS AD AS AD

Mendelian Sampling ? Mendelian Sampling Mendelian Sampling

Accuracy 0.20 Accuracy 0.90 Accuracy 0.80

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Seleccion genetica puede doblar la tasa de ganancia genetica

Rate of genetic gain ΔG

ΔG = (im rm +if rf)/ (Lm + Lf) genetic standard deviation/year

= (2*0.9 + 0)/ (6+2) = 0.225 s.d./year (progeny test)

= (2*0.8 + 0.8*0.8)/ (2+2) = 0.56 (genomic selection)

i = intensity of selection r = accuracy of selection L = generation interval

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education La tasa de ganancia genética en toros comerciales Holando se ha duplicado

600 Average gain: 500 $87.49/year

400

($) 300 Average gain: 200 $47.95/year 100 Average gain:

net merit merit net 0 -100 $19.42/year -200

-300 Average 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 Year entered AI Data from George Wiggins, USDA ARS (7/2015) La selección genómica puede ayudar criadores a identificar animales con valores de producción superiores desde que son jóvenes

ΔG = intensity of selection X

accuracy of selection X

(√genetic variance in population /

generation interval)

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Secuenciación masiva ha sido integrada a la industria lechera • High use of AI • Only one breed • Clear selection goal (total net merit) • Large number of high accuracy A.I. sires for training • Extensive, uniform collection of data on traits • Central evaluation (AIPL) receiving genotypes • Obvious way to increase rate of genetic gain • AI companies funding the genotyping because they get a clear cost savings in terms of young sire program Uruguay 10/10/2016 Animal Biotechnology and Genomics Education

Kasinathan, P. et al. 2015. Acceleration of genetic gain in cattle by reduction of generation interval. Sci. Rep. 5, 8674; DOI:10.1038/srep08674

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Animal Biotechnology and Genomics Education Approximate genetic AN: Angus GV: Gelbvieh BM: Beefmaster LM: Limousin distance between BN: Brangus MA: Maine Anjou breeds using data from BR: Brahman RA: Red Angus the 2,000 Bull Project. BU: Braunvieh SA: Salers Larry Keuhn, USDA MARC CA: Chiangus SG: Santa Gertrudis http://www.nbcec.org/topics/ CH: Charolais SH: Shorthorn BeefBreeds.pdf HH: Hereford SM: Simmental HL: Line 1 HH

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education La tasa de ganancia genética (ΔG) depende de los 4 componentes de la ecuación del criador

ΔG = intensity of selection X

accuracy of selection X

(√genetic variance in population /

generation interval)

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Aplicaciones de la ingeniería genética en agricultura engineering

Van Eenennaam, A.L. 2015. Animal Biotechnology: scientific, regulatory and public acceptance issues associated with cloned and genetically engineered animals. Chapter 26 in Molecular and Quantitative Animal H. Khatib (ed.) Wily-Blackwell

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education EnviropigTM (Heces con bajo fosforo)

Nature Biotechnology 10:176 – 181. 1992 Nature Biotechnology 19, 741–745 . 2001

“reduces fecal phosphorus output by up to 75%”

www.uoguelph.ca/enviropig Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Vacas resistentes a la mastitis (inflamacion de la glandula mamaria )

Nature Biotechnology 23:445-451. 2005

www.ars.usda.gov Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Cerdos Omega-3 (Cerdos clonados después de haber sido modificados genéticamente)

Nature Biotechnology 24:435-436. 2006

University of Missouri/Massachusetts General Hospital and Harvard Medical School

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Pollos GE que no transmiten la gripe aviar Breakthrough could prevent future bird flu epidemics

Science 331:223-226. 2011 www.roslin.ed.ac.uk/public-interest/gm-chickens Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Bill & Melinda Gates Foundation y National Science Foundation invirtieron $2 millones para desarrollar ganado resistente a trypanosomiasis ApoL1 GE

• Trypanosomiasis is a disease caused by blood parasites of the genus Trypanosoma and transmitted in Africa by tsetse flies (Glossina spp). More than 30 tsetse fly species and subspecies infest an area of 8.7 million

http://www.genomics.liv.ac.uk/tryps/Key_Papers/PuttingSleepingSicknessToBed.pdf Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Aplicaciones de animales transgenicos en agricultura Species Transgene Origin Effect/Goal Cattle Lysozyme Human Milk composition PrP Knockout Animal health α−,κ-Casein Bovine Milk composition Omega-3 Nematode Milk composition Lysostaphin Bacterial Mastitis resistance Chicken alv6 envelope glycoprotein Viral Disease resistance short hairpin RNA Viral Disease resistance LacZ Bacterial Animal Health Carp Growth Hormone Piscine Growth rate Lactorferrin Human Disease resistance Catfish Cercopin B Insect Disease resistance Goat Lysozyme Human-Bovine Animal Health Monosat. fat. acid Rat-Bovine Mastitis resistance Lactoferrin Human Prophylactic treatment Human beta-defensin 3 Human Milk composition Pig Phytase E. Coli-Mouse Feed uptake Growth hormone Human-Porcine Growth rate cSKI Chicken Muscle development Lysozyme Human Piglet survival Unsat. fat. acid Spinach Meat composition Omega-3 Nematode Meat composition α-lactalbumin Bovine Piglet survival Mx1 Murine influenza resistance Salmon Growth hormone Piscine Growth rate Lysozyme Piscine Animal health wflAFP-6 Piscine Cold tolerance Sheep IGF-1 Ovine Wool growth CsK Bacterial Wool growth Visna resistance Viral Disease resistance PrP knockout Animal health Silkworm eGFP, DsRed, or mKO Cnidarian Silk color A2S814 Arachnid Silk strength Trout Follistatin Piscine Muscle development

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Salmones de crecimiento rápido The founder female was generated in 1989 – 24 years ago

Nature Biotechnology 10:176 – 181. 1992

University of Toronto/Memorial University of Newfoundland, Canada

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Que son los Salmon AquAdvantage?

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Peces que alcanzan el peso adulto a los 16 o 18 meses en vez de a los 30

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Salmones de crecimiento rápido genéticamente editados ( Primero producido en 1989)

AquAdvantage salmon: Transgenic and conventional sibling at the same age Approved by FDA on November 19, 2015 Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Cronología del proceso regulatorio para la aprobación de AquAdvantage

Year Event

25+ 25+ years from discovery to application? 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 • FDA approval of first GE animal pharmaceutical • Final AquAdvantage regulatory study submitted to FDA 2010 • FDA VMAC meeting on AquAdvantage salmon (9/20/10) 2011 • Political efforts to defund FDA, ban fish, delay approval 2012 • FDA released “FONSI” finding of environmental assessment 2015 • November 19th, 2015 Approval • AquaBounty Total R&D investment ~ $85 million to develop and bring the AquAdvantage salmon through regulatory • Can’t legally sell the fish until FDA develops labeling guidance

• Lawsuit against FDA by environmental activist groups

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Mejoramiento genético (permanente, acumulativo) como solución para enfermedades en remplazo del uso de antibióticos/ químicos

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education Holtkamp et al. 2016. Gene- edited pigs are protected from porcine reproductive and respiratory syndrome virus (PRRSV). Nature Biotechnology. 34: 20–22.

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Animales resistentes a enfermedad conlleva al bienestar animal y a la salud humana

Van Eenennaam, A.L. and A.E. Young. 2015. Animal agriculture and the importance of agnostic governance of biotechnology. Agriculture and Food Security 4:21 Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Y si pudiéramos (genéticamente) descornar terneros de alto rendimento?

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Terneros sin cuernos genéticamente editados Naturally-occurring bovine allele at polled locus

Tan et al. 2013. Efficient nonmeiotic allele introgression in livestock using custom endonucleases. PNAS 110: 16526-31; and Carlson DF et al. 2016. Production of hornless dairy cattle from genome-edited cell lines. Nat Biotech 34: 479-81. Uruguay 10/10/2016 Animal Genomics and Biotechnology Education

Tener una regulación diferente para terneros sin cuernos lecheros o de carne, tiene sentido?

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 rdcu.be/hUVn .

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Los programas de mejoramiento animal potenciados por la biotecnologia tienen el potencial de mejorar las metas de sustentabilidad incluyendo el bienestar animal, la eficiencia de produccion y el impacto ambiental

• Naturally polled Holsteins • Disease resistant animals • Sex selection for ♀ in dairy and egg industries

Animal Biotechnology and Genomics Education Resumen

• Breeding programs increasingly utilize a combination of advanced reproductive technologies and genomic tools to accelerate the rate of genetic gain by manipulating components of the breeder’s equation.

• There are a number of that involve the use of in vitro processes, and many result in genetic modifications that are indistinguishable from the naturally-occurring variation that is the driver of both traditional breeding programs and evolution.

• A number of useful traits including disease resistance and animal welfare traits have been successfully introduced into various livestock species using both genetic engineering and gene editing techniques.

• Ultimately these biotechnologies complement the genetic improvement that can be accomplished using traditional selection techniques and, if judged acceptable, offer an opportunity to synergistically accelerate genetic improvement in food animal species.

Uruguay 10/10/2016 Animal Biotechnology and Genomics Education Gracias por la invitacion!

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 and 2015-33522-24106.

Uruguay 10/10/2016 Animal Genomics and Biotechnology Education