Presentation is loading. Please wait.

Presentation is loading. Please wait.

John B. Cole, Ph.D. Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD, USA The U.S. genetic.

Published byAshley Fowler Modified over 9 years ago

Similar presentations

Presentation on theme: "John B. Cole, Ph.D. Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD, USA The U.S. genetic."— Presentation transcript:

1 John B. Cole, Ph.D. Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD, USA john.cole@ars.usda.gov The U.S. genetic evaluation system

2 Department of Animal Sciences, University of Sassari, 23 May 2012 (2) U.S. dairy population and milk yield

3 Department of Animal Sciences, University of Sassari, 23 May 2012 (3) U.S. DHI dairy statistics (2011) l 9.1 million U.S. cows l ~75% bred AI l 47% milk recorded through Dairy Herd Information (DHI) w 4.4 million cows − 86% Holstein − 8% crossbred − 5% Jersey − <1% Ayrshire, Brown Swiss, Guernsey, Milking Shorthorn, Red & White w 20,000 herds w 220 cows/herd w 10,300 kg/cow

4 Department of Animal Sciences, University of Sassari, 23 May 2012 (4) Dairy genetic evaluation program AIPL CDCB AIPL Animal Improvement Programs Lab., USDA CDCBCouncil on Dairy Cattle Breeding DHIDairy Herd Information (milk recording organizations) NAABNational Association of Animal Breeders (AI) PDCAPurebred Dairy Cattle Association (breed registries) NAAB PDCA DHI Universities

5 Department of Animal Sciences, University of Sassari, 23 May 2012 (5) Traditional data flow AIPL AI organization AI organization Milk testing laboratory DHI herd Dairy records processing center Breed association Breed association registered pedigree data lactation records registered pedigree data registered pedigree data milk samples bull status genetic evaluations genetic evaluations grade pedigree data, genetic evaluations test-day data management reports test-day data, pedigree data, breeding data component percentage somatic cell score

6 Department of Animal Sciences, University of Sassari, 23 May 2012 (6) Genetic evaluation advances YearAdvanceGain, % 1862USDA established 1895USDA begins collecting dairy records 1926Daughter-dam comparison100 1962Herdmate comparison50 1973Records in progress10 1974Modified contemporary comparison5 1977Protein evaluated4 1989Animal model4 1994Net merit, productive life, and somatic cell score50 2008Genomic selection>50

7 Department of Animal Sciences, University of Sassari, 23 May 2012 (7) Animal model l 1989 – present l Introduced by George Wiggans and Paul VanRaden l Advantages w Information from all relatives w Adjustment for genetic merit of mates w Uniform procedures for males and females w Best prediction (BLUP) w Crossbreds included (2007)

8 Department of Animal Sciences, University of Sassari, 23 May 2012 (8) Dairy cattle traits evaluated by USDA YearTraitYearTrait 1926Milk & fat yields2000Calving ease 1 1978Conformation (type)2003Daughter pregnancy rate 1978Protein yield2006Stillbirth rate 1994Productive life2006Bull conception rate 2 1994Somatic cell score (mastitis) 2009Cow and heifer conception rates 1 Sire calving ease evaluated by Iowa State University (1978–99) 2 Estimated relative conception rate evaluated by DRMS@Raleigh (1986–2005)

9 Department of Animal Sciences, University of Sassari, 23 May 2012 (9) Evaluation methods for traits l Animal model (linear) w Yield (milk, fat, protein) w Type (Ayrshire, Brown Swiss, Guernsey, Jersey) w Productive life w Somatic cell score w Daughter pregnancy rate Heritability 8.6% 3.6% 3.0% 6.5% l Sire – maternal grandsire model (threshold) w Service sire calving ease w Daughter calving ease w Service sire stillbirth rate w Daughter stillbirth rate 25 – 40% 7 – 54% 8.5% 12% 4%

10 Department of Animal Sciences, University of Sassari, 23 May 2012 (10) Type traits l Stature l Strength l Body depth l Dairy form l Rump angle l Thurl width l Rear legs (side) l Rear legs (rear) l Foot angle l Feet and legs score l Fore udder attachment l Rear udder height l Rear udder width l Udder cleft l Udder depth l Front teat placement l Rear teat placement l Teat length

11 Department of Animal Sciences, University of Sassari, 23 May 2012 (11) Genetic trend – Holstein milk Phenotypic base = 11,828 kg Cows Sires 79 kg/yr

12 Department of Animal Sciences, University of Sassari, 23 May 2012 (12) Genetic trend – Holstein fat Phenotypic base = 432 kg Sires Cows 2.7 kg/yr

13 Department of Animal Sciences, University of Sassari, 23 May 2012 (13) Genetic trend – Holstein protein Phenotypic base = 356 kg Sires Cows 2.6 kg/yr

14 Department of Animal Sciences, University of Sassari, 23 May 2012 (14) Genetic trend – Holstein productive life Phenotypic base = 27.2 mo Sires Cows 0.2 mo/yr

15 Department of Animal Sciences, University of Sassari, 23 May 2012 (15) Genetic trend – Holstein somatic cell score Sires Cows  0.02/yr Phenotypic base = 3.0

16 Department of Animal Sciences, University of Sassari, 23 May 2012 (16) Genetic trend – Holstein daughter pregnancy rate Phenotypic base = 22.6% Sires Cows  0.1%/yr

17 Department of Animal Sciences, University of Sassari, 23 May 2012 (17) Genetic trend – Holstein calving ease Daughter Service-sire phenotypic base = 7.9% Daughter phenotypic base = 7.5% Service sire  0.18%/yr  0.01%/yr

18 Department of Animal Sciences, University of Sassari, 23 May 2012 (18) Genetic trend – Holstein stillbirth rate Service sire Daughter Service-sire phenotypic base = 8.1% Daughter phenotypic base = 7.3%  0.04%/yr  0.10%/yr

19 Department of Animal Sciences, University of Sassari, 23 May 2012 (19) Trait Relative value (%) Net merit Cheese merit Fluid merit Milk (lb)0–1519 Fat (lb)191320 Protein (lb)16250 Productive life (PL, mo)221522 Somatic cell score (SCS, log 2 )–10–9–5 Udder composite (UC)757 Feet/legs composite (FLC)434 Body size composite (BSC)–6–4–6 Daughter pregnancy rate (DPR, %)11812 Calving ability (CA$, $)535 Genetic-economic indices (2010)

20 Department of Animal Sciences, University of Sassari, 23 May 2012 (20) Trait Relative emphasis on traits in index (%) PD$ 1971 MFP$ 1976 CY$ 1984 NM$ 1994 NM$ 2000 NM$ 2003 NM$ 2006 NM$ 2010 Milk5227–265000 Fat4846452521222319 Protein…27534336332316 PL………2014111722 SCS………–6–9 –10 UDC…………7767 FLC…………4434 BDC…………–4–3–4–6 DPR……………7911 SCE……………–2…… DCE……………–2…… CA$………………65 Index changes

21 Department of Animal Sciences, University of Sassari, 23 May 2012 (21) Traditional evaluation summary l Evaluation procedures have improved l Fitness traits have been added l Effective selection has produced substantial annual genetic improvement l Indexes enable selection for overall economic merit l Fertility evaluations prevent continued decline l USDA serves the dairy industry with reliable evaluations and research to improve procedures

22 Department of Animal Sciences, University of Sassari, 23 May 2012 (22) Genomic evaluation system l Provides timely evaluations of young bulls for purchasing decisions l Increases accuracy of evaluations of bull dams l Assists in selection of service sires, particularly for low-reliability traits l High demand for semen from genomically evaluated 2-year-old bulls

23 Department of Animal Sciences, University of Sassari, 23 May 2012 (23) Genomic data flow DHI herd DNA laboratory AI organization, breed association DNA samples genotypes genomic evaluations nominations, pedigree data genotype quality reports genomic evaluations DNA samples genotypes DNA samples AIPL

24 Department of Animal Sciences, University of Sassari, 23 May 2012 (24) Illumina genotyping arrays l BovineSNP50 w 54,001 SNPs (version 1) w 54,609 SNPs (version 2) w 45,187 SNPs used in evaluation l BovineHD w 777,962 SNPs w Only BovineSNP50 SNPs used w >1,700 SNPs in database l BovineLD w 6,909 SNPs w Allows for additional SNPs BovineSNP50 v2 BovineLD BovineHD

25 Department of Animal Sciences, University of Sassari, 23 May 2012 (25) Genotyped bulls

26 Department of Animal Sciences, University of Sassari, 23 May 2012 (26) Genotyped Holsteins Date SNP Estimation* Young animals** All animals BullsCows BullsHeifers 04-10 9,770 7,41516,007 8,630 41,822 08-1010,430 9,37218,65211,021 49,475 12-1011,29312,82521,16118,336 63,615 04-1112,15211,22425,20236,545 85,123 08-1116,51914,38029,09052,053112,042 09-1116,81214,41530,18556,559117,971 10-1116,83214,57331,86561,045124,315 11-1116,83414,71632,97565,330129,855 12-1117,28817,23633,86168,051136,436 01-1217,68117,41835,40474,072144,575 02-1217,71017,67936,59780,845152,831 *Traditional evaluation **No traditional evaluation

27 Department of Animal Sciences, University of Sassari, 23 May 2012 (27) Calculation of genomic evaluations l Deregressed values derived from traditional evaluations of predictor animals l Random allele substitution effects estimated for 45,187 SNP (Bayes A) l A polygenic effect accounts for genetic variation not explained by SNP l Selection index combines genomic and traditional information not included in genomic l Applied to yield, fitness, calving, and type traits

28 Department of Animal Sciences, University of Sassari, 23 May 2012 (28) Genomic evaluation results

29 Department of Animal Sciences, University of Sassari, 23 May 2012 (29) Holstein prediction accuracy Trait a Bias b bREL (%)REL gain (%) Milk (kg)−64.30.9267.128.6 Fat (kg)−2.70.9169.831.3 Protein (kg) 0.70.8561.523.0 Fat (%) 0.01.0086.548.0 Protein (%) 0.00.9079.040.4 PL (months)−1.80.9853.021.8 SCS 0.00.8861.227.0 DPR (%) 0.00.9251.221.7 Sire CE 0.80.7331.010.4 Daughter CE−1.10.8138.419.9 Sire SB 1.50.9221.8 3.7 Daughter SB− 0.20.8330.313.2 a PL=productive life, CE = calving ease and SB = stillbirth. b 2011 deregressed value – 2007 genomic evaluation.

30 Department of Animal Sciences, University of Sassari, 23 May 2012 (30) Reliabilities for young Holsteins* *Animals with no traditional PTA in April 2011 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 404550556065707580 Reliability for PTA protein (%) Number of animals 3K genotypes 50K genotypes

31 Department of Animal Sciences, University of Sassari, 23 May 2012 (31) Parents selected Dam inseminated Embryo transferred to recipient Bull born Semen collected (1 yr old) Daughters born (9 mo later) Daughters calve (2 yr later) Bull receives progeny test (5 yr old) Life cycle of bull Genomic test

32 Department of Animal Sciences, University of Sassari, 23 May 2012 (32) Benefits of genomics l Determine value of bull at birth l Increase accuracy of selection l Reduce generation interval l Increase selection intensity l Increase rate of genetic gain

33 Department of Animal Sciences, University of Sassari, 23 May 2012 (33) Genomic evaluation summary l Extraordinarily rapid implementation of genomic evaluations l Chips provide genotypes of high accuracy l Comprehensive checking insures quality of genotypes stored l Young-bull acquisition and marketing now based on genomic evaluations l Genotyping of many females because of lower cost low-density chips

Download ppt "John B. Cole, Ph.D. Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD, USA The U.S. genetic."

Similar presentations

Importance of Genetic Evaluation for Structure in the US Dairy Industry October 10, 2012 Sam Comstock, Ph.D.

Importance of Genetic Evaluation for Structure in the US Dairy Industry October 10, 2012 Sam Comstock, Ph.D.
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
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 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD USDA Dairy Goat.

2003 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD USDA Dairy Goat.
George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD 2008 Genetic trends.

George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD 2008 Genetic trends.
George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Select Sires’

George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Select Sires’
G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2009 G.R. WiggansCroatian.

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2009 G.R. WiggansCroatian.
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);
But who will be the next GREAT one?. USA Bull Proofs * Bulls are ranked based upon their DAUGHTER’S (progeny) production and physical characteristics.

But who will be the next GREAT one?. USA Bull Proofs * Bulls are ranked based upon their DAUGHTER’S (progeny) production and physical characteristics.
2007 Jana L. Hutchison Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350, USA

2007 Jana L. Hutchison Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD , USA
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,
WiggansARS Big Data Workshop – July 16, 2015 (1) George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville,

WiggansARS Big Data Workshop – July 16, 2015 (1) George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville,
December 2014 Proof Changes

December 2014 Proof Changes
WiggansANSC UMD(1) 2013 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350, USA

WiggansANSC UMD(1) 2013 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD , USA
2014 John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD Genetic improvement.

2014 John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD Genetic improvement.
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.
Wiggans, 2013SRUC Imputation (1) Dr. George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350,

Wiggans, 2013SRUC Imputation (1) Dr. George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD ,
 PTA mobility was highly correlated with udder composite.  PTA mobility showed a moderate, positive correlation with production, productive life, and.

 PTA mobility was highly correlated with udder composite.  PTA mobility showed a moderate, positive correlation with production, productive life, and.
Norway (1) 2005 Status of Dairy Cattle Breeding in the United States Dr. H. Duane Norman Animal Improvement Programs Laboratory Agricultural Research Service,

Norway (1) 2005 Status of Dairy Cattle Breeding in the United States Dr. H. Duane Norman Animal Improvement Programs Laboratory Agricultural Research Service,

Similar presentations

Ads by Google