What s new in beef cattle genetics

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1 What s new in beef cattle genetics Alison Van Eenennaam, Ph.D. Animal Genomics and Biotechnology Cooperative Extension Specialist Department of Animal Science University of California, Davis, CA U.S.A. Ph: (530) Twitter:@BioBeef alvaneenennaam@ucdavis.edu

2 Animal breeders have made remarkable genetic progress based solely on phenotype-based selection

3 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:

4 Breeding Objective A breeding objective need not be economic. For example, in many companion animal species it is tempting to believe that the breeding objective must be the maintenance of a ridiculous appearance and congenital abnormalities! (John Gibson, UNE)

5 Historically not all cattle breeding objectives have been economic Photo taken in 1949 at Red Bluff Bull Sale, CA. Kindly provided by Cathy Maas from Crowe Hereford Ranch, Millville, CA.

6 1953. Grand Champion Angus Female, International, Grand Champion Steer, International, weighing 1025 lbs "Coblepond New Yorker" weighed 2529 lbs and measured 65 inches tall at 35 mos. (Frame 10) when he was Denver Champion Grand Champion Bull, National Polled Hereford Show (frame 10). Images from Harlan Ritchie s historical review of type

7 US Cattle Inventory Stocks Down ( 000 Head; blue, left) vs. Production Up ( 000 Tonnes; red, right)

8 2016 Global Beef Production Numbers Cattle numbers ( 000 Head; blue, left) vs. Beef production ( 000 Tonnes; red, right)

9 EPD expected progeny difference use information from pedigree and perfomance r EPD is an estimate of the genetic merit of future progeny of an individual based on the animals pedigree, its own performance, and the performance of its progeny

10 Many breeds have indexes which combine EPDs according to economics TERMINAL MATERNAL $B, $F, $G (Angus) $W, $EN (Angus) TI (Simmental) API (Simmental) CHB$ (Hereford) BMI$, BII$, CEZ$ (Hereford) MTI (Limousin) HerdBuilder (Red Angus) EPI and FPI (Gelbvieh) $Cow (Gelbvieh) Charolais $M (Beefmaster) GridMaster (Red Angus) $T (Beefmaster) $Profit (Topline-Leachman Bulls)

11 Website: ebeef.org YouTube: ebeef Twitter ebeef was developed as part of USDA NIFA grants # # #

12 ebeef.org

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15 Simple (qualitative) traits Genotype = phenotype Gender (male, female) Coat color Certain genetic diseases Double muscling Horns

16 What is a Genetic Marker? A DNA sequence variation that has been associated with a given trait in one or more populations

17 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

18 Recessive genetic conditions currently being monitored by U.S. breed associations.

19 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 Biotechnology and Genomics Education

20 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. Animal Biotechnology and Genomics Education

21 Early extension education about dwarfism explaining carriers and inheritance Image from Special Collections University Libraries, Virginia Tech:

22 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%)

23 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%) Results from a typicalproducer meeting Animal Biotechnology and Genomics Education

24 Recent case where the CA (Contractural Arachnodactyly) test also known as Fawn Calf Syndrome did not prove to be predicitive in Gelbvieh Animal Biotechnology and Genomics Education

25 2 Complex (quantitative) traits Genetics Environment Phenotype

26 SIMPLE TRAITS (Qualitative) e.g. Polled, Genetic conditions COMPLEX TRAITS (Quantitative) e.g. Marbling, Feed Efficiency GENETICS 100 % GENETICS ENVIRONMENT

27 Tests for quantitative traits before SNPs Meat Tenderness Quality Grade (Marbling) Beef Cattle Feed Efficiency Meat Yield Disease Resistance

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29 DNA TEST FOR MARBLING EXPLAINS 15% of GENETIC VARIATION IN THE TRAIT DNA TEST OTHER GENES 85% Heritability h 2 ~.37 37% GENETICS 63% ENVIRONMENT EPD estimates all genes

30 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

31 High-throughput genotyping technology enabled the development of high density SNP chips 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! Animal Biotechnology and Genomics Education

32 We want to use DNA markers (SNPs) in addition to pedigree and performance information to help select the best animals Animal Biotechnology and Genomics Education

33 Need to integrate DNA information into National Cattle Evaluation (NCE) 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).

34 Information sources for EPDs DNA just one source of data for GE-EPD r r Accuracy (r) correlation between test result and actual genetic merit

35 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 Animal Biotechnology and Genomics Education

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37 Genomics in National Cattle Evaluation (NCE) Currently several breeds are using genomic information in their national cattle evaluation programs Angus - Hereford Red Angus - Gelbvieh Limousin - Charolais Simmental - Santa Gertrudis Beefmaster - Brangus Other breeds are trying to incorporate genomic information Virtually only National Cattle Evaluation traits only traits with enough data

38 Angus: Current implementation size 7.7M birth weights 8.4M weaning weights 4.1M post-weaning gain records 1.5M heifer calving ease scores 112K carcass records 1.8M ultrasound records 19K individual intake records 237K docility scores 57K heifer pregnancy observations 199K mature cow weights Slide courtesy of Steve Miller 5/9/2017

39 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.

40 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 are at least 75% Angus. PredicGEN ($19.50) is a test marketed by Zoetis as a heifer selection tool for straight-bred or crossbred British/Continental animals The Igenity Beef Profile ($29) marketed by Neogen as DNA profiles for crossbred and purebred cattle. Predictions for weaning weight, yearling weight and hot carcass weight for a total of 16 traits scored on a 1 10 scale, plus two new selection indexes. The Igenity profile was designed and validated for crossbred or straightbred cattle with backgrounds of Angus, Red Angus, Simmental, Hereford, Limousin and Gelbvieh There aren t yet any independent, peer-reviewed papers documenting the field performance of these tests for commercial cattle.

41 The economics needs to be carefully considered heifers tested with a genetic test = 100 x $20 = $2000 This was used to cull the bottom 30 based on marbling score Then bred to top Angus sires Got higher average marbling score in offspring IS MARBLING WHAT REPLACEMENT HEIFERS SHOULD BE SELECTED UPON?

42 When making selection decisions to improve fertility which group of cattle should selection focus upon? 1. Bulls 2. Cows 3. Heifers

43 Genetic composition of the herd: 87% of genetic composition of calf crop is determined by the sires used over the last 3 generations Maternal great-grand sires (12.5%) Maternal grand sires (25%) Sires (50%) Image adapted from More Beef from Breeding workshop (2007). Meat and Livestock (MLA), Australia

44 Time line for beef breeding Bull purchase/selection Image adapted from More Beef from Breeding Workshop (2007). Meat and Livestock (MLA), Australia Progeny born Progeny slaughtered Female progeny used for breeding

45 Testing of commercial cattle I doubt $29 is cost effective for choosing heifers. For that, simple parentage might be as helpful as anything. I still contend that sire selection is the most critical. The only time genotypes are really valuable on commercial animals is if the data transfers throughout the system

46 Some questions to ask when getting started with DNA testing What do you want to test? Parentage and paternity testing Single Gene Tests SNP Chip Tests Purebred Crossbred are the tests accurate in my breed mix? PredicGEN Igenity Beef Profile What kind of sample do you need to submit? Which company do you want to use for testing? How much do genetic tests cost? What do you do with the results? Cost effective?

47 Take Homes DNA testing can be used it identify parentage, genetic defects, and to improve the accuracy of breed EPDs Tests have not been shown to work well in predicting genetic merit of crossbreds Economics of testing commercial cattle needs to be carefully considered will depend on a number of factors return greater on males than females

48 Website: ebeef.org YouTube: ebeef Twitter ebeef was developed as part of USDA NIFA grants # # #

49 NBCEC 2018 Brownbagger Webinar Series Available at ebeef YouTube Channel Recent Changes to Genetic Evaluations Novel Trait Development Encouraging Data Collection and Correct Breed Utilization Decision Support Tools 2019 Beef Improvement Federation Annual Meeting Invite Billings, South Dakota Jun 18, Jun 21, 2019

50 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 , , and