Happy Bulls Happy Cows Haplotypes Melvin Tooker and
Happy Bulls, Happy Cows, Haplotypes Melvin Tooker and Paul Van. Raden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA Melvin. Tooker@ars. usda. gov 2009 2007
What is a Haplotype? Ø 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 Chr 1 caacgtat … atccgcat … tctaggat … Chr 2 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 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 Comb’n 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, AB, AA, AB Ostyle BB, AA, AB, 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 _ _ Melvin Tooker
Find Haplotypes – 0, 1, 2 coding Genotypes: codes 0 = BB, 1 = AB or BA, 2 = AA Oman 0 2 2 1 1 2 2 1 Ostyle 0 2 2 1 1 2 2 1 Haplotypes: codes 0 = B , 1 = unknown, 2 = A OStyle (pat) OStyle (mat) 0 2 2 1 2 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% 02222020020020202000020020200002202222220 02202022000200220222000022002002000002002222000022020022202200200022020220000222200202220 02202022200202202020000202220000202002 0222202022020200220000020222202000002020220002022 022020022202200200022020220000222200202220 02200222202022022020022200000002022220002220 022002220022022002020020220200020202002020 02222020200000022020220020220200020202002020 0220022200202000222000020220000020202220 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 Ø If progeny and sire both genotyped • • • First progeny inherits 1 of dam’s 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 Ø Ø Ø Imputation of non-genotyped parents Fill in missing SNPs on genotyped animals by looking at relatives Imputation of different size SNP chip sets: 3 K to 50 K Council on Dairy Cattle Breeding, April 2010 (13) Melvin Tooker
- Slides: 13