Presentation is loading. Please wait.

Presentation is loading. Please wait.

Paul VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2014 Paul VanRaden Advancing.

Published byRaymond McCormick Modified over 8 years ago

Similar presentations

Presentation on theme: "Paul VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2014 Paul VanRaden Advancing."— Presentation transcript:

1 Paul VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD paul.vanraden@ars.usda.gov 2014 Paul VanRaden Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ, Feb 19, 2014 (1) Impact of Genomics on Genetic Improvement

2 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (2) Progress from previous workshops l Previous progress w 1995 workshop - PL w 2003 workshop - DPR l Progress requires w Organized trait definition, collection w Large database and genetic evaluation w Extension, education l Future progress will require increased cooperation DPR Trend

3 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (3) NM$ trend measured by historical indexes 659 617 537 2012

4 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (4) Expected and realized NM$ progress l Actual progress $80 / year vs. $90 in theory l Female selection has largest genomic benefit w Shorter generation interval and higher REL w Embryo transfer now more valuable l Male selection has reduced age and REL w 3% of sons in AI had young sires in 2008 compared to 81% in 2012, >90% in theory

5 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (5) Embryo transfer calves, by year

6 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (6) Genetic choices l Before genomics: w Proven bulls with daughter records (PTA) w Young bulls with parent average (PA) l After genomics: w Young animals with DNA test (GPTA) w Reliability of GPTA ~70% compared to PA ~35% and PTA ~85% for Holstein NM$

7 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (7) Young bulls: 2013 NM$ vs. 2010 PA

8 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (8) Proven bulls: 2013 vs. 2010 NM$

9 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (9) Young bulls: 2013 vs. 2010 NM$

10 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (10) Top Proven Bulls from April 2010 Net MeritDaughters 20132010PA 201020132010 Freddie747827496834673 O-Man6147242719896258474 Planet6686543232629969 Super61461543911796104 Man O Man5956093583982105 Mano65060254113780 McCormack53359548410766135 Alta Ross4165923978275103 Top 8 Avg605652414

11 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (11) Top Young Bulls from April 2010 Net MeritDaughters 20132010PA 201020132010 Observer65484855214040 Robust7658215223100 Twist7538174913310 Edward5937895321560 Erdman8037785292980 Networth6947715661110 Bookem6917615756390 Mauser6757594641930 Top 8 Avg704793529

12 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (12) Proven bull: Reliability across time

13 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (13) Young bull: Reliability across time Revised calculation

14 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (14) Example PTA changes (Observer) Daugh-ProteinSCS ReleasetersDYDTradPTAGPTAPAGPTA Aug ’120--47462.70 Dec ’1210524945 2.70 Apr ’13218605952472.76 Aug ’13800434442462.84 Dec ’131,40447 43462.87

15 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (15) Genomic reliability by breed Breed ReliabilityAYBSJE 1 HO Genomic REL (%)37546170 PA REL (%)2830 Difference+9+24+31+40 Bulls in reference6805,7674,20724,547 Animals genotyped1,7889,01659,923469,960 Exchange partnersCANInterbull, CAN CAN, DNKCAN, ITA, GBR 1 Jersey statistics include 2% REL gain from 1,068 DNK bulls added in January

16 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (16) Genomic reliability by trait for HO Trait ReliabilityYieldSCSPLDPR Genomic REL (%)76726968 PA REL (%)38343029 Difference+38+39 TypeStatureUd DepDCE Genomic REL (%)7577 60 PA REL (%)353938 Difference+40+38+39+22

17 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (17) Previous and future biases l Previous biases have been reduced: w Polygenic effect added (2010), cow adjustments (2010), DGV weight reduced (2012, 2013), PL correlations reduced (2012) l Future biases will need to be reduced: w Genomic pre-selection of progeny or mates w Early daughters not from random sampling

18 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (18) % genotyped mates of top young bulls Net Merit (Aug 2013 ) Percentage of mates genotyped Supersire Numero Uno S S I Robust Topaz Garrold Mogul

19 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (19) TraitMeanSDMinMax NM$89033 Protein0001 Prod Life.1.0.5 Dtr Preg Rate.1.0.3 SCS-.01.01-.03.00 Final Score.02.03-.01.10 Udder Depth.03.04-.01.13 Future bias from young bull mates

20 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (20) Economics of fertility defect HH1 l Pawnee Farm Arlinda Chief (born 1962) w Contributed 14% of global Holstein genes w $25 billion value of increased milk yield w $0.4 billion cost of HH1 mid-term abortions l How many more fertility defects are there? w ~0.2 / animal estimated from inbreeding depression (VanRaden and Miller, 2006 JDS)

21 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (21) Haplotype tests, then lab tests FrequencyLab tests 1 GenotypesJH1HH1JH1HH1 Normal76.597.29,867113,792 Carrier21.32.42,7502,793 Homozygous0.0 00 No call2.10.4276464 Total100.0 12,893117,049 1 Data from the Geneseek Genomic Profiler (GGP) and GGP-HD for causative mutations (JH1 = CWC15 and HH1 = APAF1)

22 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (22) Jay Lush, 1948 (The Genetics of Populations) l “The rapid rate at which genes have been found in each species, whenever people started to study it genetically, and the fact that in most of these species the rate of finding new genes actually seemed to increase with continued study until so many genes were known that interest in keeping stocks of each new one waned.” (p. 32)

23 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (23) Discovery of missing ancestors Ancestor Discovered (if genotyped) SireMGSMGGS Breed% Correct * % Correct Holstein1009792 Jersey10095 Brown Swiss1009785 * % Correct = Top ranked candidate ancestor matches the true ancestor. In 2013, >50,000 missing or incorrect sires were discovered and reported to breeders

24 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (24) Haplotype pedigree Chromosome 15, O-Style

25 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (25) What’s the best cow we can make? A “Supercow” constructed from the best haplotypes in the Holstein population would have an EBV(NM$) of $7515

26 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (26) After the cow is perfected l Beyond genomics could be transgenics w Create traits not yet available in nature w Add or subtract genes as needed or desired w Produce higher value milk, create polled l Preserving genetic variation is a key to adapting to different definitions of perfection

27 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (27) Conclusions l Recent progress is much faster, but emphasis has shifted to different traits l Genomic predictions are more accurate for populations with more reference bulls l Statistical adjustments have reduced upward biases, but new biases may soon occur l Young animals with improved reliability and high merit can greatly speed genetic progress

28 Paul VanRaden 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond, Phoenix, AZ Feb 19, 2014 (28) l Jan Wright, Mel Tooker, Tabatha Cooper, John Cole, Dan Null, and Jana Hutchison assisted with computation and graphics l Members of the Council on Dairy Cattle Breeding (CDCB) provided data Acknowledgments

Download ppt "Paul VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2014 Paul VanRaden Advancing."

Similar presentations

2002 Paul M. VanRaden and Ashley H. Sanders Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD

2002 Paul M. VanRaden and Ashley H. Sanders Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD
Genomic evaluation of Ayrshire dairy cattle and new haplotypes affecting fertility and stillbirth in Holstein, Brown Swiss and Ayrshire breeds T.A. Cooper*,

Genomic evaluation of Ayrshire dairy cattle and new haplotypes affecting fertility and stillbirth in Holstein, Brown Swiss and Ayrshire breeds T.A. Cooper*,
2007 Paul VanRaden and Jeff O’Connell Animal Improvement Programs Lab, Beltsville, MD U MD College of Medicine, Baltimore, MD

2007 Paul VanRaden and Jeff O’Connell Animal Improvement Programs Lab, Beltsville, MD U MD College of Medicine, Baltimore, MD
2007 Paul VanRaden, George Wiggans, Jeff O’Connell, John Cole, Animal Improvement Programs Laboratory Tad Sonstegard, and Curt Van Tassell Bovine Functional.

2007 Paul VanRaden, George Wiggans, Jeff O’Connell, John Cole, Animal Improvement Programs Laboratory Tad Sonstegard, and Curt Van Tassell Bovine Functional.
Wiggans, 2013RL meeting, Aug. 15 (1) Dr. George R. Wiggans, Acting Research Leader Bldg. 005, Room 306, BARC-West 301-504-8334 (main office); 301-504-8092.

Wiggans, 2013RL meeting, Aug. 15 (1) Dr. George R. Wiggans, Acting Research Leader Bldg. 005, Room 306, BARC-West (main office);
2007 Paul VanRaden 1, Curt Van Tassell 2, George Wiggans 1, Tad Sonstegard 2, Jeff O’Connell 1, Bob Schnabel 3, Jerry Taylor 3, and Flavio Schenkel 4,

2007 Paul VanRaden 1, Curt Van Tassell 2, George Wiggans 1, Tad Sonstegard 2, Jeff O’Connell 1, Bob Schnabel 3, Jerry Taylor 3, and Flavio Schenkel 4,
2007 Paul VanRaden 1, George Wiggans 1, Curt Van Tassell 2, Tad Sonstegard 2, Jeff O’Connell 1, Bob Schnabel 3, Jerry Taylor 3, and Flavio Schenkel 4,

2007 Paul VanRaden 1, George Wiggans 1, Curt Van Tassell 2, Tad Sonstegard 2, Jeff O’Connell 1, Bob Schnabel 3, Jerry Taylor 3, and Flavio Schenkel 4,
Changes in the use of young bulls K. M. Olson* 1, J. L. Hutchison 2, P. M. VanRaden 2, and H. D. Norman 2 1 National Association of Animal Breeders, Columbia,

Changes in the use of young bulls K. M. Olson* 1, J. L. Hutchison 2, P. M. VanRaden 2, and H. D. Norman 2 1 National Association of Animal Breeders, Columbia,
Impacts of inclusion of foreign data in genomic evaluation of dairy cattle K. M. Olson 1, P. M. VanRaden 2, D. J. Null 2, and M. E. Tooker 2 1 National.

Impacts of inclusion of foreign data in genomic evaluation of dairy cattle K. M. Olson 1, P. M. VanRaden 2, D. J. Null 2, and M. E. Tooker 2 1 National.
2007 Paul VanRaden Animal Improvement Programs Lab, Beltsville, MD 2011 Avoiding bias from genomic pre- selection in converting.

2007 Paul VanRaden Animal Improvement Programs Lab, Beltsville, MD 2011 Avoiding bias from genomic pre- selection in converting.
George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD National Association.

George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD National Association.
2007 Paul VanRaden, Curt Van Tassell, George Wiggans, Tad Sonstegard, and Jeff O’Connell Animal Improvement Programs Laboratory and Bovine Functional Genomics.

2007 Paul VanRaden, Curt Van Tassell, George Wiggans, Tad Sonstegard, and Jeff O’Connell Animal Improvement Programs Laboratory and Bovine Functional Genomics.
John B. Cole* and Paul M. VanRaden Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350

John B. Cole* and Paul M. VanRaden Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD
2003 G.R. Wiggans,* P.M. VanRaden, and J.L. Edwards Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD

2003 G.R. Wiggans,* P.M. VanRaden, and J.L. Edwards Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD
2007 Paul VanRaden, George Wiggans, Jeff O’Connell, John Cole, Animal Improvement Programs Laboratory Tad Sonstegard, and Curt Van Tassell Bovine Functional.

2007 Paul VanRaden, George Wiggans, Jeff O’Connell, John Cole, Animal Improvement Programs Laboratory Tad Sonstegard, and Curt Van Tassell Bovine Functional.
John B. Cole 1, Daniel J. Null *1, Chuanyu Sun 2, and Paul M. VanRaden 1 1 Animal Genomics and Improvement 2 Sexing Technologies Laboratory Navasota, TX.

John B. Cole 1, Daniel J. Null *1, Chuanyu Sun 2, and Paul M. VanRaden 1 1 Animal Genomics and Improvement 2 Sexing Technologies Laboratory Navasota, TX.
John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350, USA The use and.

John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD , USA The use and.
2007 Paul VanRaden, Mel Tooker, Jan Wright, Chuanyu Sun, and Jana Hutchison Animal Improvement Programs Lab, Beltsville, MD National Association of Animal.

2007 Paul VanRaden, Mel Tooker, Jan Wright, Chuanyu Sun, and Jana Hutchison Animal Improvement Programs Lab, Beltsville, MD National Association of Animal.
2007 Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2009 Mixing Different SNP Densities Mixing Different.

2007 Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2009 Mixing Different SNP Densities Mixing Different.
2007 Paul VanRaden, George Wiggans, Jeff O’Connell, John Cole, Animal Improvement Programs Laboratory Tad Sonstegard, and Curt Van Tassell Bovine Functional.

2007 Paul VanRaden, George Wiggans, Jeff O’Connell, John Cole, Animal Improvement Programs Laboratory Tad Sonstegard, and Curt Van Tassell Bovine Functional.

Similar presentations

Ads by Google