Genomics Beyond EBVs John B Cole Animal Improvement

Genomics Beyond EBVs John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705 -2350 john. cole@ars. usda. gov

Whole-genome selection (2008) • Use many markers to track inheritance of chromosomal segments • Estimate the impact of each segment on each trait • Combine estimates with traditional evaluations to produce genomic evaluations (GPTA) • Select animals shortly after birth using GPTA • Very successful worldwide 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (2) Cole

Traditional data flow somatic cell score component percentage Milk testing laboratory health and fitness data Dairy records processing center On-farm computers milk samples y da ta da t- s te t en r DHI herd pe reg di iste gr r ee ed da ta rts o ep m e ag an m ev gen alu et at ic te io pe st-d ns br dig ay ee re da di e d ta ng a , da ta, ta registered pedigree data lactation records AIPL Breed association a, d a t e a r t d ns te da e s e i r atio g ree g e i u r ig ed val d p e e p de tic a gr ene g bull status genetic evaluations 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (3) AI organization Cole

Genomic data flow DHI herd DN A sa m pl es es pl m sa ic A m ns no tio DN ge lua a ev DNA samples DNA laboratory AI organization, breed association pe rts ty po no re s ge y t i pe al ty qu eno g n pe om di ina gr t i g ev en ee d ons al om at , ua a tio ic ns genotypes AIPL 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (4) Cole

Illumina genotyping arrays • Bovine. SNP 50 v 2 • 54, 001 SNPs (version 1) • 54, 609 SNPs (version 2) • 45, 187 SNPs used in evaluation Bovine. HD Bovine. LD • Bovine. HD • 777, 962 SNPs • Only Bovine. SNP 50 SNPs used • >1, 700 SNPs in database • Bovine. LD • 6, 909 SNPs • Allows for additional SNPs 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (5) Cole

Reliabilities for young Holsteins* Number of animals 9000 50 K genotypes 8000 3 K genotypes 7000 6000 5000 4000 3000 2000 1000 0 40 45 50 55 60 65 70 75 80 Reliability for PTA protein (%) *Animals with no traditional PTA in April 2011 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (6) Cole

Genotyped Holsteins Date 04 -10 08 -10 12 -10 04 -11 08 -11 09 -11 10 -11 11 -11 12 -11 01 -12 02 -12 SNP Estimation* Bulls Cows 9, 770 7, 415 10, 430 9, 372 11, 293 12, 825 12, 152 11, 224 16, 519 14, 380 16, 812 14, 415 16, 832 14, 573 16, 834 14, 716 17, 288 17, 236 17, 681 17, 418 17, 710 17, 679 *Traditional evaluation Young animals** Bulls Heifers 16, 007 8, 630 18, 652 11, 021 21, 161 18, 336 25, 202 36, 545 29, 090 52, 053 30, 185 56, 559 31, 865 61, 045 32, 975 65, 330 33, 861 68, 051 35, 404 74, 072 36, 597 80, 845 All animals 41, 822 49, 475 63, 615 85, 123 112, 042 117, 971 124, 315 129, 855 136, 436 144, 575 152, 831 **No traditional evaluation 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (7) Cole

Imputation • Identify haplotypes in population using many markers • Track haplotypes with fewer markers • e. g. , use 5 SNP to track 25 SNP • 5 SNP: 22020 • 25 SNP: 20220200200202200 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (8) Cole

Phenotypes • Animal model (linear) • • • l Yield (milk, fat, protein) Type (Ayrshire, Brown Swiss, Guernsey, Jersey) Productive life Somatic cell score Daughter pregnancy rate Sire – maternal grandsire model (threshold) w Service sire calving ease w Daughter calving ease w Service sire stillbirth rate w Daughter stillbirth rate 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (9) Heritability 25 – 40% 7 – 54% 8. 5% 12% 4% 8. 6% 3. 0% 6. 5% Cole

What can we do beyond EBVs? • Quantitative Genetics • Validate theoretical predictions • Understand genetic variation • Functional Biology • Fine-map recessives • Relate phenotypes to genotypes • Identify important genes in complex systems 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (10) Cole

Predicted selection limits Trait Breed DPR BS HO JE Milk BS HO JE NM$ BS HO JE Lower 20 40 19 14, 193 24, 883 16, 133 3, 857 7, 515 4, 678 Upper Largest DGV 53 8 139 8 53 5 34, 023 4, 544 77, 923 7, 996 40, 249 5, 620 9, 140 1, 102 23, 588 2, 528 11, 517 1, 556 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (11) Cole

What’s the best cow we can make? Cole and Van. Raden, 2011 (J. Anim. Breed. Genet. 128: 448 -455) A “supercow” constructed from the best haplotypes in the Holstein population would have an EBV(NM$) of $7, 515 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (12) Cole

Genotype parents and grandparents Manfred O-Man Jezebel O-Style Teamster Deva Dima 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (13) Cole

Pedigree relationship matrix 1 HO 9167 O-Style PGS PGD MGS MGD Sire Dam Bull 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 Manfred 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (14) Cole

Genomic relationship matrix 1 HO 9167 O-Style PGS PGD MGS MGD Sire Dam Bull 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 Manfred 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (15) Cole

Difference (Genomic – Pedigree) 1 HO 9167 O-Style PGS PGD MGS MGD Sire Dam Bull . 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 . 060 . 040 . 114 Manfred O-Man Deva O-Style 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (16) Cole

Bull–MGS relationships Van Tassell (personal communication) 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (17) Cole

Should we really care about inbreeding? Cole and Van. Raden, 2011 (J. Anim. Breed. Genet. 128: 448 -455) Bank semen and embryos to preserve genetic diversity and select the best haplotypes. Chromosomal EBV will reflect the value of marker diversity. 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (18) Cole

O-Style haplotypes (chromosome 15) 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (19) Cole

Recessive defect discovery 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (20) Cole

Dystocia complex • Markers on chromosome 18 have large effects on several traits: • Dystocia and stillbirth: Sire and daughter calving ease and sire stillbirth • Conformation: rump width, stature, strength, and body depth • Efficiency: longevity and net merit • Large calves contribute to reduced lifetimes and decreased profitability 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (21) Cole

Marker effects for dystocia complex ARS-BFGL-NGS-109285 Cole et al. , 2009 (J. Dairy Sci. 92: 2931– 2946) 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (22) Cole

Correlations in dystocia complex 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (23) Cole

Biology of the dystocia complex • The key marker is ARS-BFGL-NGS 109285 at 57, 125, 868 Mb on BTA 18 • Located in a cluster of CD 33 -related Siglec genes • Many Siglecs involved in leptin signaling • Recent results indicate effects on gestation length and calf birth weight 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (24) Cole

One SNP isn’t the whole story! AIPL (http: //aipl. arsusda. gov/Report_Data/Marker_Effects/marker_effects. cfm? Breed=HO&Trait=Sire_Calv_Ease) 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (25) Cole

What do we do next? • Markers with large effects don’t explain that much variation • What about groups of SNP? • Individual markers may not have significant effects • Groups of markers may collectively have significant effects 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (26) Cole

We have divergent populations Cole et al. , 2005 (J. Dairy Sci. 88(4): 1529– 1539) 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (27) Cole

Gene set enrichment analysis-SNP Gene pathways (G) GWAS results SNP ranked by significance (L) Includes all SNP, S, that are included in L Score increases for each Li in S Score increase is proportional to SNP test statistic Permutation test and FDR SNP in pathway genes (S) The more SNP in S that appear near the top of L, the higher the Enrichment Score Nominal p-value corrected for multiple testing Pathways with moderate effects Holden et al. , 2008 (Bioinformatics 89: 1669 -1683. doi: 10. 2527/jas. 2010 -3681) 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (28) Cole

We hope to identify regulatory networks Candidate genes and pathways that affect age at puberty common to both breeds Fortes et al. , 2011 (J. Animal Sci. 89: 1669 -1683. doi: 10. 2527/jas. 2010 -3681) 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (29) Cole

Challenges in pathway analysis • This is a new procedure for our lab • There are many steps involving lots of data sources • Positive results can be challenging to explain • Negative results are not necessarily definitive 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (30) Cole

Unresolved issues in genomic research • Genotypes from universities and research organizations • More widespread sharing of genotypes across countries • Genotypes needed to predict SNP effects for future chips • Annotation of the bovine genome • http: //www. innatedb. com/ • Intellectual property concerns 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (31) Cole

Conclusions • We need more data • Genotypes AND phenotypes • Big p, small n • More complex methodology • We are all systems biologists now • Can genomics be used on the farm? • Mate selection • Identify animals susceptible to disease • Pedigree discovery 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (32) Cole

i. BMAC Consortium Implementation Team • Illumina (industry) • AIPL • • • Marylinn Munson Cindy Lawley Diane Lince Lu. Ann Glaser Christian Haudenschild • • Curt Van Tassell Lakshmi Matukumalli Steve Schroeder Tad Sonstegard • Beltsville (USDA-ARS) • Univ Missouri (Land-Grant) • • • Paul Van. Raden George Wiggans John Cole Leigh Walton Duane Norman • • • Marcos de Silva Tad Sonstegard Curt Van Tassell • Kent Weigel • BFGL • University of Wisconsin Funding • USDA/NRI/CSREES • • • 2006 -35616 -16697 2006 -35205 -16888 2006 -35205 -16701 2008 -35205 -04687 2009 -65205 -05635 • USDA/ARS • • • 1265 -31000 -081 D 1265 -31000 -090 D 5438 -31000 -073 D • Stewart Bauck • • Accelerated Genetics ABS Global Alta Genetics CRI/Genex Select Sires Semex Alliance Taurus Service • Merial • • • Jerry Taylor Bob Schnabel Stephanie Mc. Kay • University of Maryland • NAAB School of Medicine • Gordon Doak • Steve Moore • Partners • • Tim Smith Mark Allan • Univ Alberta (University) • Clay Center, NE (USDA-ARS) • Jeff O’Connell • • Gene. Seek DNA Landmarks Expression Analysis Genetic Visions 2 nd International Workshop on Genomics Applied to Livestock, Araçatuba, Brasil, February 27, 2012 (33) Cole 33