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

What is Genomics?  Genetics:  The science of genes, heredity and variation in living organisms  Study of the hereditary transmission of traits expressed by individuals  Genomics:  Discipline 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:  BovineSNP50  54,609 SNPs  BovineLD (replaces 3k SNP chip)  6,909 SNPs –Imputed to 50k  BovineHD  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  Started with 50K panel  3K in September 2010, replaced with LD panel  Agreement to share all USA and Canadian genotypes  Adding Italy and UK genotypes in 2011  Official genomic evaluations launched:  August 2009 for Holstein  April 2010 for Jersey  August 2011 for Brown Swiss  Progeny proven Ayrshires all HD genotyped

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

Genotyped Females - October BreedGroup50K3KTotal% of Total HOHeifers16,15337,33053, % Cows13,1778,34721, % Total:29,33045,67775,007 Percentage:39.1%60.9% JEHeifers3395,7836, % Cows8893,3104, % Total:1,2289,09310,321 Percentage:11.9%88.1%

Genotyped Holstein Young Candidate Bulls * 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

Genomics 101  Use genotypes to improve the accuracy of breeding values  Allows much more accurate selection of young animals  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  Used by IA studs to verify that the bull calf they bought is the one they received.  Parentage testing  Will most likely become the standard  Pedigree discovery  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:  Failed conception, or  Embryonic loss