Bovine Genomics 101 - The Technology and its Applications Gerrit Kistemaker Chief Geneticist,...
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Transcript of Bovine Genomics 101 - The Technology and its Applications Gerrit Kistemaker Chief Geneticist,...
Bovine Genomics 101 - The Technology and its
Applications
Gerrit KistemakerChief 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 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
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* 3,168
2008 5,036
2009 7,357
2010 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