Happy Bulls, Happy Cows, Haplotypes Melvin Tooker and Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA [email protected] 200 200 79 What is a Haplotype? A group of alleles on a single chromosome that are closely linked usually inherited as a unit. Council on Dairy Cattle Breeding, April 2010 (2) Melvin Tooker Chromosome to Nucleotide sequence Council on Dairy Cattle Breeding, April 2010 (3)
Melvin Tooker Example of a SNP haplotype SNP SNP SNP Chr1 caacgtat atccgcat tctaggat Chr2 caacggat atccgaat tctcggat Haplotype A tca Haplotype B gac
Haplotype is a set of single nucleotide polymorphisms (SNPs) associated on a single chromosome. Identification of a few alleles of a haplotype block can identify other polymorphic sites in the region. Council on Dairy Cattle Breeding, April 2010 (4) Melvin Tooker Example Bull: O-Style Council on Dairy Cattle Breeding, April 2010 (5) Melvin Tooker Genotyped Ancestors of OStyle T B Elevat Elevation Bova Cubby Magnet Chief Valiant Elevation
Chief Manfred Valiant Tesk ggdam Rocket P Iv Star Bell Mars Tony Ivanhoe O Man P Iv Star Bell Elton Heilo Bell Chief
Glendell Needle Glendell Jezebel Rotate Melwood ggdam Council on Dairy Cattle Breeding, April 2010 (6) P Combn Chief Mark Bova Melvin Tooker Genotyped Ancestors of OStyle Elevation Starbuck
Majesty Aerostar Rudolph Citation Mattador Valiant Cavalier Teamster Ned Boy Chairman Mascot ggdam Tradition Leadman Mark Elevation
Deva Starbuck Chief Prelude Mtoto Chairman Blackstar Mark Valiant Dima Royalty Comotion ggdam Council on Dairy Cattle Breeding, April 2010 (7) Bell
Ned Boy Mascot Cleitus Melvin Tooker O-Style Haplotypes chromosome 15 Council on Dairy Cattle Breeding, April 2010 (8) Melvin Tooker Find Haplotypes AB coding Genotypes: Oman BB,AA,AA,AB,AA,AB,AB,AA,AA,AB Ostyle BB,AA,AA,AB,AB,AA,AA,AA,AA,AB Haplotypes:
OStyle (pat) B A OStyle (mat) B A A A Council on Dairy Cattle Breeding, April 2010 (9) _ _ A B A A A A A A A A
Melvin Tooker _ _ Find Haplotypes 0,1,2 coding Genotypes: codes 0 = BB, 1 = AB or BA, 2 = AA Oman 0 2 2 1 2 1 1 2 2 1 Ostyle 0 2 2 1 1 2 2 2 2 1 Haplotypes: codes 0 = B , 1 = unknown, 2 = A OStyle (pat) OStyle (mat) 0 2 2 1 2 2 2 2 2 1 0 2 2 1 0 2 2 2 2 1 Council on Dairy Cattle Breeding, April 2010 (10)
Most frequent haplotype in first segment of chromosome 15 for Holsteins had 4,316 copies = 41,822 * 2 * .0516 Council on Dairy Cattle Breeding, April 2010 (11) Melvin Tooker Imputed Dams If progeny and sire both genotyped First progeny inherits 1 of dams 2 haplotypes Second progeny has 50:50 chance to get same or other haplotype Haplotypes known with 1, 2, 3, etc. progeny are ~50%, 75%, 87%, etc. Council on Dairy Cattle Breeding, April 2010 (12)
Melvin Tooker Applications of Haplotyping Imputation of non-genotyped parents Fill in missing SNPs on genotyped animals by looking at relatives Imputation of different size SNP chip sets: 3K to 50K Council on Dairy Cattle Breeding, April 2010 (13) Melvin Tooker
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