Bovine Genomic Improvements Realized from the Application of SNP Chips. Matthew McClure, PhD

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1 Bovine Genomic Improvements Realized from the Application of SNP Chips Matthew McClure, PhD National Institute of Animal Science Symposium. Suwon, South Korea September 6 th, 2013

2 Select the Best

3 Select the Best

4 Genomic Selection Commercial Chips Irish Cattle Breeding Federation, 2013

5

6 Genomic Selection Dairy Beef Genetic Disease Causative mutation Haplotypes Identification Parentage identification Breeding stock selection Breed identification Future Disease resistance Irish Cattle Breeding Federation, 2013

7 Genomic Improvements Visual Selection Breeding Values Genomic Selection

8 Lifecycle of dairy bull Parents Selected Dam Inseminated ~60% reliability ~$300 Bull Born Genomic Test Semen collected (1yr) Daughters Born (9 m later) Daughters have calves (2yr later) ~80% reliability ~$50,000 Bull Receives Progeny Test (5 yrs)

9 Does Genomics Work USA Dairy Vanraden et al. 2008, J. Dairy Science

10 Does Genomics Work Irish Beef Index uro Stars uro Index 5 Stars 87 4 stars 63 3 stars 50 2 stars 36 1 star 10 Diff 154 Weanling Wt Value kg Finisher CWt Value Age kg , , , , , Retailer HVC VHVC Value kg kg , , , , , /Cow difference between unengaged and fully engaged herds in Cattle Breeding Activities Worth 100m/annum at an Irish industry level.

11 Genomic Improvements 1) Genomic Selection 2) Genetic Diseases

12 Mendelian Diseases Illumina BovineHDSNP Illumina BovineSNP50 Genome Sequence Draft assemble Affymetrix 15K Genome-wide linkage maps From Nicholas (2012) in Bovine Genomics (ed. J Womack). Wiley-Blackwell, Ames, Iowa (in pr Irih Cattle Breeding Federation, 2013

13 Irish Cattle Breeding Federation, 2013

14 Mapping to Diagnostic 5 Mb 0.5 Mb 153 SNP NRCAM PNPLA8 CTTNBP2 41 SNP 1 Haplotype

15 Rectovaginal Constriction Identified in USA Jersey s 1970 s Progeny identified carriers Mapped with SNP ~3 months Irish Cattle Breeding Federation, 2013

16 Haplotype Diseases Irish Cattle Breeding Federation, 2013

17 Manage Genetic Improvement with Disease Risk O-BEE MANFRED JUSTICE-ET (O Man)

18 Identification Parent Verification <1990 s Present Future

19 Microsatellite Imputation Breed SNP SNP+MS Abondance Angus Aubrac Ayshire Bazadaise Beefmaster Belmont Red 40 Belgian Blue Blonde D'Aquitain Brahman Brangus Braunvieh Bretonne Pie Noire Brown Swiss Brune Des Alpes Charolais Chiangus 19 0 Crossbred Devon Dexter Fresian Gasconne Gelbvieh 44 0 Gir Guernsey Hereford Holstein Jersey Kerry 1 0 Limousin Longhorn Maine Anjou Montbeliarde Murray Grey 22 N'Dama 24 0 Nelore Normande Parthenaise Pie Rouge Des Plaines Piedmontese Red Angus Red Pie (italial) 2 0 Romagnola Rouge Flamande Salers Santa Gertrudis 99 0 Sheko 18 0 Shorthorn Simmental Swedish Red 12 9 Tarentaise Tropical Composite 336 Vosgienne Watusi TOTAL

20 Microsatellite Imputation BM1824 Imputated Allele Haplotype Brown Swiss Guernesy Holstein Jersey Overall BABBAABBAAAABBBAABABABBBABBBAAAB BAABAABBAAAABBBAABABABBBABBBAAAB BBBBAABBAAAABBBAABABABBBABBBAAAB BABBAABBAAAABBBAABABABBBAABBBBAB BABBAABBAAAABBBAABABABBBABBBAABA BAABBAABBAAABBBAABABABABABBBAAAB BAABABABBAAABBAABAABABBBABAAAABA BAABABABBAAABBAABAABABBBABBBAAAB AABBAABBBAAABBAABAABABBBABBBAAAB AAAABAAABBABBAAABAABABABABAAAAAB AAAABAAABBABBAAABAABABABABAAAABA AAAABAAABBABBAAABAABABABABAAAAAA BAABBAABBBABBBAABBABABABABABAAAA AAAABAAABBABBAAABAABABABABABAAAA BABBAABBAABAABBBBBBABAAABABBBBAB BAAABABBAABAABBBBBBABAAABABBBBAB BAABAABBAABAABBBBBBABAAABABBBBAB _188 AABBAABBAABAABBBBBBABAAABABBBBAB AAAABABBAABAABBBBBBABAAABABBBBAB _ _ _190 BM /180

21 Irish Parent Verification Process Report Generated Certificate Issued Herdbook Rules Applied Failed Verified Verified Verified Wrong Sire Verify Result No Sire MS Failed Verified Imputed MS ICBF Database Weatherbys Hair Roots

22 Identification Parent Verification Replacement Selection

23 Choose the Best Replacement?

24 Now we know which heifer is best The best has a PTA NM$ of +868 and a REL of 73%. PLANET has 3,783 genotyped daughters which one do you want in your herd? The worst has a PTA NM$ of +48 and a REL of 68%. John Cole, USDA-ARS-AIPL

25 Genetic Merit for NM$ 46 Holstein Heifers with Genetic Net Merit 600 If we cull the lowest 10 Average of the remaining ones is +$99.2 higher John Cole, USDA-ARS-AIPL

26 Identification Parent Verification Replacement Selection National Disease Surveillance

27 National Genetic Disease Overview Citrullinaemina <1% DUMPs 0% CVM-4% Branchspina-2% Curly Calf 0% Mulefoot <1% Osteopetrosis <1%

28 Identification Parent Verification Replacement Selection National Disease Surveillance Breed Composition

29 Breed ID?

30 PCA analysis of 45 breeds

31 Breed ID

32 Disease Resistance Mendelian Infectious

33 Health?

34 Number of bulls TB sire prevalence Prevalence Ian Richardson

35 Thank You BFGL (USDA-ARS) Curt Van Tassell Tad Sonstegard Heather Huson Larry Shade George Liu Derek Bickhart Steve Schroeder Alicia Beavers Euisoo Kim Lakshmi Matukumalli AIPL (USDA-ARS) Paul VanRaden Dan Null John Cole George Wiggans Tabatha Cooper Univ. of Missouri Jeremy Taylor Robert Schnabel Stephanie McKay Jae Woo Kim Jared Decker Megan Rolf Tasia Taxis Sarah Gregg Rich Chapple Yao Ping Weaver-Italian Brown Swiss Paolo Ajmone Licia Colli Enrico Santus Industry / Breed Associations Sally Northcutt (Angus Assoc) Cari Wolfe (Jersey Assoc) Holstein Assoc Brown Swiss Assoc Cofactor Genomics Jon Armstrong Jarret Glasscock Illumina Cindy Lawley Microsatellite Bovine HapMap Breed Associations Sue Denise Alison Van Eneenaam Cecilila Penedo John Keele Mike Coffey Marie-Yvonne Boshcher Donagh Berry Andrew Cromie Fernando Garcia Milla Albuquerqu Luciana Regitano

36 Questions