ebeef was developed as part of USDA NIFA grants # # # Animal Genomics and Biotechnology Education

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1 Use of genetic marker information in beef cattle selection, Ph.D. Animal Genomics and Biotechnology Cooperative Extension Specialist Outline Department of Animal Science University of California, Davis, CA U.S.A. Ph: (530) ebeef Background to genetic markers Simple traits and parentage How can genomics help accelerate genetic progress? Why genomics helps the dairy industry Why genomics is harder in the beef industry Current products on the market for beef ebeef.org Website: ebeef.org YouTube: ebeef Twitter ebeef was developed as part of USDA NIFA grants # # #

2 The genome age PARENTAGE TESTING What is a Genetic Marker? A DNA sequence variation that has been associated with a given trait in one or more populations We want to use DNA markers (SNPs) in addition to pedigree and performance information to help select the best animals Simple (qualitative) traits Genotype = phenotype Gender (male, female) Coat color Certain genetic diseases Double muscling Horns 2

3 There are a large number of genetic disorders in cattle occurring in a variety of breeds. Images from an article by David S. Buchanan, NDSU Many of these genetic disorders are the result of intentional selection for a given trait and line breeding An early '50's advertisement that superimposed a measuring stick in the picture of this bull who was nick-named "Short Snorter." Based upon his height and age, he was less than a frame score 1. Image from Animal breeders have made remarkable genetic progress by selecting on appearance alone but this has often come along with some genetic disorders associated with the selected trait Genetic Defects in Dogs Every one of the 50 most popular pedigree-dog breeds has at least one aspect of its physical conformation that predisposes it to a disorder. The association of some of these conditions with official breed standards make conformational extremes an area which needs to be addressed to safeguard the welfare of pedigreed dogs in the future. Asher et al. (2009) Inherited defects in pedigree dogs. Part 1. Disorders related to breed standards. The Veterinary Journal. 182: Van Eenennaam 1/16/2015 Animal Genomics and Biotechnology Education Animal Biotechnology and Genomics Education Van Eenennaam 1/16/2015 Historically not all beef cattle breeding objectives have been economic A 1956 survey of Hereford breeders in the USA identified 50,000 dwarfproducing animals in 47 states. Through detailed pedigree analysis and test crosses, the American Hereford Association, in concert with breeders and scientists, virtually eliminated the problem from the breed. Because carrier status was difficult to prove and required expensive progeny testing, some entire breeding lines were eliminated. Photo taken in 1949 at Red Bluff Bull Sale, CA. Kindly provided by Cathy Maas from Crowe Hereford Ranch, Millville, CA. Animal Biotechnology and Genomics GenomicsEducation Education 3

4 Early extension education about dwarfism explaining carriers and inheritance Grand Champion Angus Female, International, Grand Champion Steer, International, weighing 1025 lbs "Coblepond New Yorker" 1988 Grand Champion Bull, National weighed 2529 lbs and measured 65 Polled Hereford Show (frame 10). inches tall at 35 mos. (Frame 10) Images from Harlan Ritchie s historical review of type when he was Denver Champion. If you breed a carrier cow (Aa) to a free bull (AA), what is the chance that the resulting offspring will be affected (aa)? 3. 0 ¼ (25%) ½ (50%) 4. ⅔ (66%) If you breed a carrier cow (Aa) to a free bull (AA), what is the chance that the resulting offspring will be affected (aa)? ¼ (25%) 3. ½ (50%) 4. ⅔ (66%) 5. ¾ (75%) 6. 1 (100%) ¾ (75%) 1 (100%) Image from Special Collections University Libraries, Virginia Tech: Results from a typicalproducer meeting pages/73798/how-to-getstarted-with-dna-testing 4

5 SIMPLE TRAITS (Qualitative) e.g. Polled Genetic conditions 100 % GENETICS COMPLEX TRAITS (Quantitative) e.g. Marbling GENETICS ENVIRONMENT Tests for quantitative traits before SNPs Meat Tenderness Quality Grade (Marbling) Beef Cattle Feed Efficiency Meat Yield Disease Resistance DNA TEST FOR MARBLING EXPLAINS 15% of GENETIC VARIATION IN THE TRAIT DNA TEST OTHER GENES 85% 37% GENETICS EPD estimates all genes 63% ENVIRONMENT What is wrong with having only a few markers for quantitative traits? A few markers are not sufficient to account for much (>20%) of the additive genetic variation so little obvious relationship between phenotype and DNA-test results and little genetic progress likely to result from markerassisted selection (MAS) Need to have lots of markers to explain more of the genetic variation 5

6 High-throughput genotyping technology enabled the development of high density SNP chips We can use these SNP CHIPS for genomic selection? The sequencing of the bovine genome allowed for the development of a 50,000 SNP chip 50,000 DNA markers evenly spaced throughout the genome TRAINING POPULATION Training = estimate the value of every chromosome fragment contributing variation in a population with phenotypic observations 1,000s animals Phenotypes Genotypes Prediction = the results of training can then be used to develop prediction equations to predict the merit of new animals (e.g. young bulls) Dairy industry ideally suited to increasing rate of genetic gain (G/ year) using genomic selection Mostly one breed High use of AI Clear selection goal ($ 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 decrease age of selection in sires AI companies funding the genotyping because they get a clear cost savings in terms of young sire program Breeding value prediction in kindly provided Dairy Sires Graphic by Gonzalo Rincon Young sire Parent Average Young sire Progeny Test x x Birth AS AD x 5 years; $50,000 cost AS AD Mendelian Sampling? Mendelian Sampling 0.20 Accuracy Young sire Genomic Selection 0.90 Accuracy Birth; << $50,000 cost AS AD Mendelian Sampling 0.80 Accuracy The Beef Cattle Industry Wiggans, 2013 Little use of AI Relatively few high accuracy sires for training Multiple competing selection goals cow/calf, feedlot, processor little data sharing between sectors Few/no records on many economically-relevant traits Many breeds, some small with limited resources Crossbreeding is important No centralized national cattle evaluation Not clear who should pay for testing breeders? Breed associations? public funds? 6

7 Technology developers had a rocky start in the beef industry Need to integrate DNA information into National Cattle Evaluation (NCE) Information sources for EPDs DNA just one source of data for GE-EPD Information from DNA tests only has value in selection when incorporated with all other available forms of performance information for economically important traits in National Cattle Evaluation (NCE), and when communicated in the form of an EPD with a corresponding BIF accuracy. (Tess, 2008). r r Accuracy (r) correlation between test result and actual genetic merit AN: Angus GV: Gelbvieh BM: Beefmaster LM: Limousin BN: Brangus MA: Maine Anjou BR: Brahman RA: Red Angus BU: Braunvieh SA: Salers CA: Chiangus SG: Santa Gertrudis CH: Charolais SH: Shorthorn HH: Hereford SM: Simmental HL: Line 1 HH Approximate genetic distance between breeds using data from the 2,000 Bull Project. Larry Keuhn, USDA MARC BeefBreeds.pdf No. Genomic- Genotype Genetic New traits in development Animals enhanced provider evaluation genotyped EPDs? provider AGI 1 Angus >250,000 Y GeneSeek Feed intake EPD has been implemented, feet and leg phenotypes being collected, PAP score (indicator of brisket Zoetis disease), adaptability-heat stress/fescue tolerance ABRI 2 Brahman 400 Y (for GeneSeek Plan to roll out GE-EPDs for all traits in current evaluation by mid to late 2016 tenderness) Zoetis LGS 3 Brangus 4,316 Y GeneSeek Fertility and end product indexes, stayability, docility, feet and leg scoring system Zoetis Beef Master 400 Target 2016 LGS Plan to deploy maternal and terminal indexes in Spring 2016 Developed static terminal index Charolais 2136 Y GeneSeek AGI Revamping Stayability definition to require a calf be born Gelbvieh Y GeneSeek IGS 4 every year (more indicative of actual reproductive performance). Carcass weight EPD, heifer calving rate, sustained cow Hereford >20,000 Y GeneSeek ABRI fertility, feed intake, docility Feed intake/efficiency, maternal data: breeding, udder Limousin 5660 Y GeneSeek IGS score, body condition scoring and mature weights Maine-Anjou ~1000 Not yet IGS Red Angus Y IGS GeneSeek Feet and leg scoring genomic data incorporated into threshold traits, feed intake, and environmental stress Zoetis Santa 3,320 Y GeneSeek LGS Tenderness EPDs have been implemented, have developed two indexes for growth and carcass. Introducing 3 new Gertrudis EPDs, Heifer Pregnancy, Breed Back, and Scrotal Circumference Angus 940 Target 2016 IGS Multibreed: Stayability and Heifer Pregnancy Simmental 25,296 Y GeneSeek IGS [1] Angus Gene,cs Inc. h1p:// [2] Agricultural Business Research Ins,tute h1ps://abri.une.edu.au [3] Livestock Gene,c Services, LLC [4] Interna,onal Gene,c Solu,ons h1p:// 7

8 How much do genetic tests cost? ~ $13-20 for parentage testing ~$20-$30 per animal for a single mutation test for a disease or trait $75-90 for the high-density SNP chips for genomic-enhanced EPDs. $45-50 for the low-density imputation chips. Breed associations work to include that genomic information to provide genomic-enhanced EPDs (GE-EPD) that have improved accuracy due to the inclusion of the genomic information in the EPD calculations. If multiple tests can be performed on a single DNA sample or a large volume of samples is tested then the cost per test is reduced. Additional costs can include the cost of DNA cards, sample collection, sample storage and shipping and sample processing, again depending on sample type, test and application. There are several tests that are being marketed for use on commercial cattle that are not directly part of a breed association genetic evaluation program. GeneMax Advantage ($39) and GeneMax Focus ($17). Distributed by Angus Genetics Inc. (AGI) and marketed by Zoetis for cattle that at least 75% Angus. Igenity has Angus Gold ($40) and Angus Silver ($25) PredicGEN ($19.50) is a test marketed by Zoetis as a heifer selection tool for straight-bred or crossbred British/Continental animals Igenity Gold ($40) and Silver ($25) tests are being marketed by Neogen as DNA profiles for crossbred and purebred cattle. A single prediction equation is used for each trait to give the score or molecular breeding value, irrespective of the breed makeup of the animal being tested. The six main datasets used to form the training data set for this test were from six breed associations: Angus, Hereford, Gelbvieh, Limousin, Red Angus, and Simmental. There aren t yet any independent, peer-reviewed papers documenting the field performance of these tests for commercial cattle. What do you do with the results? Parentage and mutation test results often need to be reported to specific breed associations for registration purposes. This is also true for SNP results for breeds that use them for genetic evaluation. Results of disease, trait and coat color mutation tests can be used to manage breeding decisions to avoid undesirable phenotypes in offspring. DNA testing can be used for a variety of purposes such as aiding in selection and breeding choices, sorting into management groups, pedigree verification and even marketing. The value of DNA testing to an individual operation depends on a number of factors. This includes the breed(s) and number of animals that will be tested, what the information will be used for, and often the availability of other performance records, pedigrees and EPDs. Thanks for grant support from USDA # # # # # QUESTIONS Thanks for inviting me, Ph.D. Cooperative Extension Specialist Animal Biotechnology and Genomics Department of Animal Science University of California, Davis, USA alvaneenennaam@ucdavis.edu Twitter:@Biobeef 8