Bovine Genomics 101 - The Technology and its

Applications

Gerrit KistemakerChief Geneticist, Canadian Dairy Network (CDN)

Many slides were created by Brian Van DoormaalCDN General Manager and Holstein Canada CEO

Genetic Evaluations in Canada

Production:Yields of Milk, Fat and ProteinFat and Protein deviationsSomatic Cell ScoreLactation PersistencyEach 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 2008Started with 50K panel3K in September 2010, replaced with LD panelAgreement to share all USA and Canadian genotypesAdding Italy and UK genotypes in 2011

Official genomic evaluations launched:August 2009 for HolsteinApril 2010 for JerseyAugust 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 2011 -

Breed Group 50K 3K Total % of Total

HO 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%

JE 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 Number Genotyped

2005* 2,188 2006* 2,325 2007* 3,1682008 5,0362009 7,3572010 11,606

2011 (inc.) 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-GroupAverage Reliability (%)

Traditional Genomics Gain

50K Young Bulls and Heifers (Born 2008-2011) 37 66 29

Younger Cows in 1st or 2nd Lactation (50K) 54 71 17

Foreign Cows with MACE in Canada 43 69 26

1st Crop Proven Sires in Canada 86 90 4

Foreign Sires with MACE in Canada 70 81 11

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 102Other 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 fertilityResearch 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