An Introduction to Genomics Melvin Tooker Animal Improvement

An Introduction to Genomics Melvin Tooker Animal Improvement Programs Laboratory USDA Agricultural Research Service, Beltsville, MD, USA Melvin. Tooker@ars. usda. gov 2009 2007

Genomic Goals Ø Ø Ø Predict young bulls and cows more accurately Compare actual DNA inherited Use exact relationship matrix G instead of expected values in A Ø Trace chromosome segments Ø Locate genes with large effects India Emerging Markets Conference, May 2009 (2) Melvin Tooker 2009

Short history Ø Ø Ø Illumina Bovine. SNP 50™ Bead. Chip developed Accuracy of genomic information assessed by using 2004 evaluations of bulls born before 2000 to predict 2009 evaluations of young bulls Unofficial genomic evaluations of bull calves provided to industry beginning in April 2008 Ø Jersey results released in October 2008 Ø Over 23, 000 animals genotyped through Mar. 2009 India Emerging Markets Conference, May 2009 (3) Melvin Tooker 2009

Source of genomic evaluations Ø DNA extracted from blood, hair, or semen Ø ~40, 000 genetic markers (SNPs) evaluated Ø Ø For each SNP, difference in PTA estimated between animals with 1 allele compared to the other allele Genomic data contribute ~11 daughter equivalents to reliability India Emerging Markets Conference, May 2009 (4) Melvin Tooker 2009

How Related are Relatives? Ø Example: Full sibs • • Ø are expected to share 50% of their DNA on average may actually share 45% or 55% of their DNA because each inherits a different mixture of chromosome segments from the two parents. Combine genotype and pedigree data to determine exact fractions India Emerging Markets Conference, May 2009 (5) Melvin Tooker 2009

Genomic Relationships Ø Measures of genetic similarity • • • A = Expected % genes identical by descent from pedigree (Wright, 1922) G = Actual % of DNA shared (using genotype data) T = % genes shared that affect a given trait (using genotype and phenotype) India Emerging Markets Conference, May 2009 (6) Melvin Tooker 2009

Markers vs QTLs Ø Models contain markers, not QTLs • • Ø M is markers inherited minus freq M M’ / ∑ p(1 -p) = G List all QTL affecting a trait • • Q is alleles inherited minus freq q contains effects of alleles u = Q q , var(q) = Vq var(u) = E(u u’) = Q Vq Q’ = T India Emerging Markets Conference, May 2009 (7) Melvin Tooker 2009

QTL Relationship Matrix (T) Ø Three bulls have +50 PTA protein. Ø Do they have the same genes? • • Extremely unlikely. Bull A could have 10 positive genes. Bull B could have 10 positive genes, but on different chromosomes. Bull C could have 20 positive and 10 negative genes. India Emerging Markets Conference, May 2009 (8) Melvin Tooker 2009

Genes in Common at One Locus w = gene from sire of sire x = gene from dam of sire y = gene from sire of dam z = gene from dam of dam If Full Sib 1 inherits: w, y If Full Sib 2 w, z inherits: x, y x, z w, y 2 1 1 0 India Emerging Markets Conference, May 2009 (9) w, z 1 2 0 1 x, y 1 0 2 1 x, z 0 1 1 2 Melvin Tooker 2009

Unrelated Individuals? Ø Ø Ø No known common ancestors Many unknown common ancestors born before the known pedigree Relationships in base • • • 0 ± x. x% due to earlier ancestors Called linkage disequilibrium (LD) Poor terminology, genes may not be physically linked India Emerging Markets Conference, May 2009 (10) Melvin Tooker 2009

Traditional Pedigree Sire of Sire Dam of Sire Animal Sire of Dam Dam of Dam India Emerging Markets Conference, May 2009 (11) Melvin Tooker 2009

Genomic Pedigree India Emerging Markets Conference, May 2009 (12) Melvin Tooker 2009

Example of a SNP haplotype SNP SNP Chr 1 caacgtat … atccgcat … tctaggat … Chr 2 caacggat … atccgaat … tctcggat … Haplotype 1 tca Haplotype 2 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. India Emerging Markets Conference, May 2009 (13) Melvin Tooker 2009

SNP Pedigree atagatcg ctgtagcgatcg ctgtagcttagg agatctagatcg agggcgcgcagt ctgtctagatcg cgatctagatcg atgtcgcgcagt cggtagatcagt agagatcgatct atgtcgctcacg atggcgcgaacg ctatcgctcagg India Emerging Markets Conference, May 2009 (14) Melvin Tooker 2009

Haplotype Pedigree atagatcg ctgtagcgatcg ctgtagcttagg agatctagatcg agggcgcgcagt ctgtctagatcg cgatctagatcg atgtcgcgcagt cggtagatcagt agagatcgatct atgtcgctcacg atggcgcgaacg ctatcgctcagg India Emerging Markets Conference, May 2009 (15) Melvin Tooker 2009

Translate Haplotype to Genotype ctgtagcgatcg agatctagatcg 11120200 India Emerging Markets Conference, May 2009 (16) Melvin Tooker 2009

Genotype Pedigree Count number of second allele 121101011110 11120200 101121101111 122221121111 101101111102 011111012011 121120011010 0 = homozygous for first allele (alphabetically) 1 = heterozygous 2 = homozygous for second allele (alphabetically) India Emerging Markets Conference, May 2009 (17) Melvin Tooker 2009

Genotype Data for Elevation Chromosome 1 10001112200200121110111121111001121100020122002220111 1202101200211122110021112001111001011011010220011002201101 12002011010202221211221020100111000112202212221120120 201002022020000211000112020112211102201111000021220200 0221012020002211220111012100111211102112110020102100022000 2201000201100002202211210112111012222001211212220020020202012221100222222200221211112100211112001101120 0202220001112011010211121211102022100211201211001111102111 2110211122000101101110202200221110102011121111011202102102 121101102212200121101202201100222002110001110021 1021101110002220020221212110002220102002222121221121112002 0110202001222222112212021211210110012110110200220002001002 000111101100121102121211120101012120221010101111102112 211111121211121011012001111102111101111122012121101022 202021211222120222002121210201100111222121101 India Emerging Markets Conference, May 2009 (18) Melvin Tooker 2009

Genotype Data from Inbred Bull Chromosome 24 of Megastar 1021222101021021011102110112112110022020002020220 000022002022220220200002002022222200002022220000022020000200200000022220000002022002000222020222220002 2022222000020022020222020002200002202220000002200 2020002222002002020222222220200020220220222202022000222022002220000022020000200200200222220 0022220202002220200000022222020200002002002222000 2022022220002222022002222020200022022022220022000200 220200000220222000022000222202002222000220020020202 202000222002220220220000022022002002002022000222202 200222002022020022220000020220002020200022000002 2022200202220200022002002000200220222220022022000020000202202002000022200200222000022 02200200220220202020002220200022020020220220000 20202000020202000222222000200220222200000202200202 02202202020002002202200 India Emerging Markets Conference, May 2009 (19) Melvin Tooker 2009

Genotype Parents and Grandparents Manfred O-Man Jezebel O-Style Teamster Deva Dima India Emerging Markets Conference, May 2009 (20) Melvin Tooker 2009

Expected Relationship Matrix 1 1 HO 9167 O-Style PGS PGD MGS MGD Sire Dam Bull Manfred 1. 0 . 0 . 5 . 0 . 25 Jezebel . 0 1. 0 . 0 . 5 . 0 . 25 Teamster . 0 1. 0 . 0 . 5 . 25 Dima . 0 . 0 1. 0 . 5 . 25 O-Man . 5 . 0 1. 0 . 5 Deva . 0 . 5 . 0 1. 0 . 5 . 25 . 5 1. 0 O-Style 1 Calculated assuming that all grandparents are unrelated India Emerging Markets Conference, May 2009 (21) Melvin Tooker 2009

Pedigree Relationship Matrix 1 HO 9167 O-Style PGS PGD MGS MGD Sire Dam Bull Manfred 1. 053 . 090 . 105 . 571 . 098 . 334 Jezebel . 090 1. 037 . 051 . 099 . 563 . 075 . 319 Teamster . 090 . 051 1. 035 . 120 . 071 . 578 . 324 Dima . 105 . 099 . 120 1. 042 . 102 . 581 . 342 O-Man . 571 . 563 . 071 . 102 1. 045 . 086 . 566 Deva . 098 . 075 . 578 . 581 . 086 1. 060 . 573 O-Style . 334 . 319 . 324 . 342 . 566 . 573 1. 043 India Emerging Markets Conference, May 2009 (22) Melvin Tooker 2009

Genomic Relationship Matrix 1 HO 9167 O-Style PGS PGD MGS MGD Sire Dam Bull Manfred 1. 201 . 058 . 050 . 093 . 609 . 054 . 344 Jezebel . 058 1. 131 . 008 . 135 . 618 . 079 . 357 Teamster . 050 . 008 1. 110 . 100 . 014 . 613 . 292 Dima . 093 . 135 . 100 1. 139 . 131 . 610 . 401 O-Man . 609 . 618 . 014 . 131 1. 166 . 080 . 626 Deva . 054 . 079 . 613 . 610 . 080 1. 148 . 613 O-Style . 344 . 357 . 292 . 401 . 626 . 613 1. 157 India Emerging Markets Conference, May 2009 (23) Melvin Tooker 2009

Difference (Genomic – Pedigree) 1 HO 9167 O-Style PGS PGD MGS MGD Sire Dam Bull Manfred . 149 -. 032 -. 040 -. 012 . 038 -. 043 . 010 Jezebel -. 032 . 095 -. 043 . 036 . 055 . 004 . 038 Teamster -. 040 -. 043 . 075 -. 021 -. 057 . 035 -. 032 Dima -. 012 . 036 -. 021 . 097 . 029 . 059 . 038 . 055 -. 057 . 029 . 121 -. 006 . 060 -. 043 . 004 . 035 . 029 -. 006 . 087 . 040 . 010 . 038 -. 032 . 059 . 040 . 114 O-Man Deva O-Style India Emerging Markets Conference, May 2009 (24) . 060 Melvin Tooker 2009

Conclusions Ø Relationships can be defined as: • • • Ø Ø Ø A = expected genes in common G = actual DNA in common T = QTL alleles in common for a trait Full sibs share 50% ± 3. 5% of DNA. “Unrelated” animals share more or fewer unknown ancestors than average. Reliability can increase if genomic (G) replace traditional (A) relationships India Emerging Markets Conference, May 2009 (25) Melvin Tooker 2009

Where are the Major Genes? India Emerging Markets Conference, May 2009 (26) Melvin Tooker 2009

Distribution of Marker Effects (Net Merit) India Emerging Markets Conference, May 2009 (27) Melvin Tooker 2009

Distribution of Marker Effects (DPR) India Emerging Markets Conference, May 2009 (28) Melvin Tooker 2009

Marker Effects on Website India Emerging Markets Conference, May 2009 (29) Melvin Tooker 2009

Marker Effects on Website India Emerging Markets Conference, May 2009 (30) Melvin Tooker 2009

Marker Effects on Website India Emerging Markets Conference, May 2009 (31) Melvin Tooker 2009

Positive or Negative Traits India Emerging Markets Conference, May 2009 (32) Melvin Tooker 2009

From whom did the bad allele come? Round Oak Rag Apple Elevation (7 HO 00058) India Emerging Markets Conference, May 2009 (33) Melvin Tooker 2009

Net Merit by Chromosome Freddie (1 HO 08784) - highest Net Merit bull India Emerging Markets Conference, May 2009 (34) Melvin Tooker 2009

Net Merit by Chromosome O Man (7 HO 06417) – Sire of Freddie India Emerging Markets Conference, May 2009 (35) Melvin Tooker 2009

Net Merit by Chromosome Die-Hard (29 HO 08538) - maternal grandsire India Emerging Markets Conference, May 2009 (36) Melvin Tooker 2009

New Chromosomal PTA Query India Emerging Markets Conference, May 2009 (37) Melvin Tooker 2009

Chromosomal PTA Query Example India Emerging Markets Conference, May 2009 (38) Melvin Tooker 2009

Acknowledgments Ø Genotyping and DNA extraction: • Ø Computing: • Ø USDA Bovine Functional Genomics Lab, U. Missouri, U. Alberta, Gene. Seek, Genetics & IVF Institute, Genetic Visions, and Illumina AIPL staff (Mel Tooker, Leigh Walton, Jay Megonigal) Funding: • National Research Initiative grants – • • • 2006 -35205 -16888, 2006 -35205 -16701 Agriculture Research Service Holstein, Jersey & Brown Swiss breed associations Contributors to Cooperative Dairy DNA Repository (CDDR) India Emerging Markets Conference, May 2009 (39) Melvin Tooker 2009