Genomic Prediction Results

Genomic Prediction Results

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)

Melvin Tooker Most Frequent Haplotypes 5.16% 4.37% 4.36% 3.67% 3.66% 3.65% 3.51% 3.42% 3.24% 3.22% 022222222020020022002020200020000200202000022022222202220 022020220202200020022022200002200200200000200222200002202 022020022202200200022020220000220202200002200222200202220 022020222020222002022022202020000202220000200002020002002 022222222020222022020200220000020222202000002020220002022 022020022202200200022020220000220202200002200222200202220 022002222020222022022020220200222002200000002022220002220 022002222002220022022020220020200202202000202020020002020 022222222020200000022020220020200202202000202020020002020 022002222002220022002020002220000202200000202022020202220

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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