Bovine Genomics 101 The Technology and its Applications

Bovine Genomics 101 - The Technology and its Applications Gerrit Kistemaker Chief Geneticist, Canadian Dairy Network (CDN) Many slides were created by Brian Van Doormaal CDN General Manager and Holstein Canada CEO

Genetic Evaluations in Canada § Production: Ø Yields of Milk, Fat and Protein Ø Fat and Protein deviations Ø Somatic Cell Score Ø Lactation Persistency Ø Each trait analyzed separately for lactations 1, 2 and 3 and then combined into an overall value § Conformation (29 traits) § Functional: Ø Herd Life, Milking Speed, Milking Temperament, Calving Ability (CA) and Daughter Calving Ability (DCA) Ø Daughter Fertility (DF), Semen Fertility

What is Genomics? § Genetics: ØThe science of genes, heredity and variation in living organisms § Study of the hereditary transmission of traits expressed by individuals § Genomics: ØDiscipline in genetics concerning the study of genomes of organisms § DNA sequencing § DNA is unique for each individual/animal § Can be used for genetic improvement

Genome

DNA Sequencing & SNPs SNP (“snip”) = Single Nucleotide Polymorphism Difference in a Single base pair Many SNPs have no effect on cell function

SNP panels § Thousands of SNPs are combined into Genotyping Chips: Ø Bovine. SNP 50 § 54, 609 SNPs Ø Bovine. LD (replaces 3 k SNP chip) § 6, 909 SNPs – Imputed to 50 k Ø Bovine. HD § 777, 962 SNPs

DNA Genotyping § The genotyping process identifies if the animal carries 0, 1 or 2 copies of a specific allele for each SNP § 0 and 2 = homozygous § 1 = heterozygous

Implementation History § Genotyping in North America since 2008 Ø Started with 50 K panel Ø 3 K in September 2010, replaced with LD panel Ø Agreement to share all USA and Canadian genotypes Ø Adding Italy and UK genotypes in 2011 § Official genomic evaluations launched: Ø August 2009 for Holstein Ø April 2010 for Jersey Ø August 2011 for Brown Swiss § Progeny proven Ayrshires all HD genotyped

Genotyping Activity in North America Currently over 128, 000 genotyped Holsteins in NA >1, 700 new 50 K/mo >3, 500 new 3 K/mo

Genotyped Females - October 2011 Breed HO JE Group 50 K 3 K Total % of Total Heifers 16, 153 37, 330 53, 483 71. 3% Cows 13, 177 8, 347 21, 524 28. 7% Total: 29, 330 45, 677 75, 007 Percentage: 39. 1% 60. 9% Heifers 339 5, 783 6, 122 59. 3% Cows 889 3, 310 4, 199 40. 7% Total: 1, 228 9, 093 10, 321 Percentage: 11. 9% 88. 1%

Genotyped Holstein Young Candidate Bulls Year of Birth 2005* 2006* 2007* 2008 2009 2010 2011 (inc. ) Number Genotyped 2, 188 2, 325 3, 168 5, 036 7, 357 11, 606 6, 990 * includes some bulls that are now progeny proven

Genomic Evaluation Services in Canada § Genotyping services are provided by Holstein Canada for all dairy breeds § All genotypes sent by labs to USDA for centralized quality assurance § All Genotypes are forwarded by USDA to CDN monthly § Genotypes are used to improve the accuracy of existing breeding values.

Gain in Reliability - Holstein, August 2011 Sub-Group 50 K Young Bulls and Heifers (Born 2008 -2011) Younger Cows in 1 st or 2 nd Lactation (50 K) Foreign Cows with MACE in Canada 1 st Crop Proven Sires in Canada Foreign Sires with MACE in Canada Average Reliability (%) Traditional Genomics Gain 37 66 29 54 71 17 43 69 26 86 90 4 70 81 11

Genomics 101 § Use genotypes to improve the accuracy of breeding values § Allows much more accurate selection of young animals Ø Improves genetic gain by improving selection of young bulls. § Can reduce rearing cost and/or increase genetic progress by selecting female replacement at a much younger age

Genomics 102 Other uses for genotypes § Individual verification Ø Used by IA studs to verify that the bull calf they bought is the one they received. § Parentage testing Ø Will most likely become the standard § Pedigree discovery Ø Use the animals genotype and match it against the complete database of genotypes to find its parents and/or grand parents § Traceability

Haplotypes affecting fertility Research at USDA § 5 haplotypes (groups of SNP markers that are usually inherited together) that affect fertility. § 3 in Holstein § 1 each in Jersey and Brown Swiss § No homozygous animals have been genotyped and associated with lower fertility: Ø Failed conception, or Ø Embryonic loss