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2015
John B. Cole
Animal Genomics and Improvement Laboratory
Agricultural Research Service, USDA
Beltsville, MD
john.cole@...
CRV, Arnhem, The Netherlands, 14 April 2015 (2) Cole
U.S. DHI dairy statistics (2011)
l 9.1 million U.S. cows
l ~75% bred ...
CRV, Arnhem, The Netherlands, 14 April 2015 (3) Cole
Genomic data flow
DNA samples
genotypes
Dairy Herd Improvement
(DHI) ...
CRV, Arnhem, The Netherlands, 14 April 2015 (4) Cole
Genotypes are abundant
0
100000
200000
300000
400000
500000
600000
70...
CRV, Arnhem, The Netherlands, 14 April 2015 (5) Cole
Sources of DNA for genotyping
Source Samples (no.) Samples (%)
Blood ...
CRV, Arnhem, The Netherlands, 14 April 2015 (6) Cole
SNP count for different chips
Chip SNP (no.) Chip SNP (no.)
50K 54,00...
CRV, Arnhem, The Netherlands, 14 April 2015 (7) Cole
2014 genotypes by chip SNP density
Chip SNP
density Female Male
All
a...
CRV, Arnhem, The Netherlands, 14 April 2015 (8) Cole
2014 genotypes by breed and sex
Breed Female Male
All
animals
Female:...
CRV, Arnhem, The Netherlands, 14 April 2015 (9) Cole
Genotypes by age (last 12 months)
0
5,000
10,000
15,000
20,000
25,000...
CRV, Arnhem, The Netherlands, 14 April 2015 (10) Cole
Growth in bull predictor population
Breed Jan. 2015 12-mo gain
Ayrsh...
CRV, Arnhem, The Netherlands, 14 April 2015 (11) Cole
Growth in US predictor population
Bulls Cows1,2
Breed Jan. 2015
12-m...
CRV, Arnhem, The Netherlands, 14 April 2015 (12) Cole
Trait Bias*
Reliability
(%)
Reliability
gain (%
points)
Milk (kg) −8...
CRV, Arnhem, The Netherlands, 14 April 2015 (13) Cole
Reliability gains
Reliability (%) Ayrshire
Brown
Swiss Jersey Holste...
CRV, Arnhem, The Netherlands, 14 April 2015 (14) Cole
0
20
40
60
80
100
120
140
2007 2008 2009 2010 2011 2012 2013
Parenta...
CRV, Arnhem, The Netherlands, 14 April 2015 (15) Cole
Active AI bulls that were genomic bulls
0
10
20
30
40
50
60
70
80
20...
CRV, Arnhem, The Netherlands, 14 April 2015 (16) Cole
Marketed Holstein bulls
Year
entered
AI
Traditional
progeny-
tested
...
CRV, Arnhem, The Netherlands, 14 April 2015 (17) Cole
Genetic merit of marketed Holstein bulls
-100
0
100
200
300
400
500
...
CRV, Arnhem, The Netherlands, 14 April 2015 (18) Cole
Stability of genomic evaluations
l 642 Holstein bulls
w Dec. 2012 NM...
CRV, Arnhem, The Netherlands, 14 April 2015 (19) Cole
% genotyped mates of top young bulls
0
10
20
30
40
50
60
70
80
90
10...
CRV, Arnhem, The Netherlands, 14 April 2015 (20) Cole
Haplotypes affecting fertility
l Rapid discovery of new recessive de...
CRV, Arnhem, The Netherlands, 14 April 2015 (21) Cole
Name
BTA
chromo-
some
Location*
(Mbp)
Carrier
frequency
(%) Earliest...
CRV, Arnhem, The Netherlands, 14 April 2015 (22) Cole
Recessive
Haplo-
type
BTA
chromo-
some
Tested
animals
(no.)
Concord-...
CRV, Arnhem, The Netherlands, 14 April 2015 (23) Cole
Weekly evaluations
l Released to nominators, breed
associations, and...
CRV, Arnhem, The Netherlands, 14 April 2015 (24) Cole
SNP used for genomic evaluations
l 60,671 SNP used after culling on
...
CRV, Arnhem, The Netherlands, 14 April 2015 (25) Cole
Some novel phenotypes studied recently
● Claw health (Van der Linde ...
CRV, Arnhem, The Netherlands, 14 April 2015 (26) Cole
Evaluation methods for traits
l Animal model (linear)
w Yield (milk,...
CRV, Arnhem, The Netherlands, 14 April 2015 (27) Cole
-2.0
0.0
2.0
4.0
6.0
8.0
1960 1970 1980 1990 2000 2010
Breedingvalue...
CRV, Arnhem, The Netherlands, 14 April 2015 (28) Cole
6.0
7.0
8.0
9.0
10.0
11.0
1980 1985 1990 1995 2000 2005 2010
PTA
(%d...
CRV, Arnhem, The Netherlands, 14 April 2015 (29) Cole
What do US dairy farmers want?
 National workshop in Tempe, AZ in
F...
CRV, Arnhem, The Netherlands, 14 April 2015 (30) Cole
What can farmers do with novel traits?
 Put them into a selection i...
CRV, Arnhem, The Netherlands, 14 April 2015 (31) Cole
What can DRPCs do with novel traits?
 Short-term – Benchmarking too...
CRV, Arnhem, The Netherlands, 14 April 2015 (32) Cole
International challenges
 National datasets are siloed
 Recording ...
CRV, Arnhem, The Netherlands, 14 April 2015 (33) Cole
Conclusions
Genomic research is ongoing
Detect causative genetic var...
CRV, Arnhem, The Netherlands, 14 April 2015 (34) Cole
Questions?
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Crv 2015 jbc

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The national genetic evaluation program
for dairy cattle in the United States is described. Topics include an historical overview of traits and statistical methodology, the structure of the contemporary dairy genetics industry, and the implementation of genomic selection.

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Crv 2015 jbc

  1. 1. 2015 John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD john.cole@ars.usda.gov Genomic improvement programs for US dairy cattle
  2. 2. CRV, Arnhem, The Netherlands, 14 April 2015 (2) Cole 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
  3. 3. CRV, Arnhem, The Netherlands, 14 April 2015 (3) Cole Genomic data flow DNA samples genotypes Dairy Herd Improvement (DHI) producer Council on Dairy Cattle Breeding (CDCB) DNA laboratory AI organization, breed association
  4. 4. CRV, Arnhem, The Netherlands, 14 April 2015 (4) Cole Genotypes are abundant 0 100000 200000 300000 400000 500000 600000 700000 800000 NumberofGenotypes Run Date Imputed, Young Imputed, Old <50k, Young, Female <50k, Young, Male <50k, Old, Female <50k, Old, Male 50k, Young, Female 50k, Young, Male 50k, Old, Female 50k, Old, Male
  5. 5. CRV, Arnhem, The Netherlands, 14 April 2015 (5) Cole Sources of DNA for genotyping Source Samples (no.) Samples (%) Blood 10,727 4 Hair 113,455 39 Nasal swab 2,954 1 Semen 3,432 1 Tissue 149,301 51 Unknown 12,301 4
  6. 6. CRV, Arnhem, The Netherlands, 14 April 2015 (6) Cole SNP count for different chips Chip SNP (no.) Chip SNP (no.) 50K 54,001 GP2 19,809 50K v2 54,609 ZLD 11,410 3K 2,900 ZMD 56,955 HD 777,962 ELD 9,072 Affy 648,875 LD2 6,912 LD 6,909 GP3 26,151 GGP 8,762 ZL2 17,557 GHD 77,068 ZM2 60,914
  7. 7. CRV, Arnhem, The Netherlands, 14 April 2015 (7) Cole 2014 genotypes by chip SNP density Chip SNP density Female Male All animals Low 239,071 29,631 268,702 Medium 9,098 14,202 23,300 High 140 28 168 All 248,309 43,861 292,170
  8. 8. CRV, Arnhem, The Netherlands, 14 April 2015 (8) Cole 2014 genotypes by breed and sex Breed Female Male All animals Female: male Ayrshire 1,485 209 1,694 88:12 Brown Swiss 944 8,641 9,585 10:90 Guernsey 1,777 333 2,110 84:16 Holstein 212,765 30,883 243,648 87:13 Jersey 31,323 3,793 35,116 89:11 Milking Shorthorn 2 1 3 67:33 Normande 0 1 0 0:100 Crossbred 13 0 13 100:0 All 248,309 43,861 292,170 85:15
  9. 9. CRV, Arnhem, The Netherlands, 14 April 2015 (9) Cole Genotypes by age (last 12 months) 0 5,000 10,000 15,000 20,000 25,000 30,000 35,000 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24-… 36-… 48-… 60 Frequency(no) Age (mo) Holstein male Holstein female Jersey male Jersey female 
  10. 10. CRV, Arnhem, The Netherlands, 14 April 2015 (10) Cole Growth in bull predictor population Breed Jan. 2015 12-mo gain Ayrshire 711 29 Brown Swiss 6,112 336 Holstein 26,759 2,174 Jersey 4,448 245
  11. 11. CRV, Arnhem, The Netherlands, 14 April 2015 (11) Cole Growth in US predictor population Bulls Cows1,2 Breed Jan. 2015 12-mo gain Jan. 2015 12-mo gain Ayrshire 711 29 69 40 Brown Swiss 6,112 336 1,138 350 Holstein 26,759 2,174 109,714 51,950 Jersey 4,448 245 26,012 10,601 1Predictor cows must have domestic records. 2Counts include 3k genotypes, which are not included in the predictor population.
  12. 12. CRV, Arnhem, The Netherlands, 14 April 2015 (12) Cole Trait Bias* Reliability (%) Reliability gain (% points) Milk (kg) −80.3 69.2 30.3 Fat (kg) −1.4 68.4 29.5 Protein (kg) −0.9 60.9 22.6 Fat (%) 0.0 93.7 54.8 Protein (%) 0.0 86.3 48.0 Productive life (mo) −0.7 73.7 41.6 Somatic cell score 0.0 64.9 29.3 Daughter pregnancy rate (%) 0.2 53.5 20.9 Sire calving ease 0.6 45.8 19.6 Daughter calving ease −1.8 44.2 22.4 Sire stillbirth rate 0.2 28.2 5.9 Daughter stillbirth rate 0.1 37.6 17.9 Holstein prediction accuracy *2013 deregressed value – 2009 genomic evaluation
  13. 13. CRV, Arnhem, The Netherlands, 14 April 2015 (13) Cole Reliability gains Reliability (%) Ayrshire Brown Swiss Jersey Holstein Genomic 37 54 61 70 Parent average 28 30 30 30 Gain 9 24 31 40 Reference bulls 680 5,767 4,207 24,547 Animals genotyped 1,788 9,016 59,923 469,960 Exchange partners Canada Canada, Interbull Canada, Denmark Canada, Italy, UK Source: VanRaden, Advancing Dairy Cattle Genetics: Genomics and Beyond presentation, Feb. 2014
  14. 14. CRV, Arnhem, The Netherlands, 14 April 2015 (14) Cole 0 20 40 60 80 100 120 140 2007 2008 2009 2010 2011 2012 2013 Parentage(mo) Bull birth year Sire Dam Parent ages of marketed Holstein bulls
  15. 15. CRV, Arnhem, The Netherlands, 14 April 2015 (15) Cole Active AI bulls that were genomic bulls 0 10 20 30 40 50 60 70 80 2005 2006 2007 2208 2009 2010 PercentagewithGstatus Bull birth year
  16. 16. CRV, Arnhem, The Netherlands, 14 April 2015 (16) Cole Marketed Holstein bulls Year entered AI Traditional progeny- tested Genomic marketed All bulls 2008 1,768 170 1,938 2009 1,474 346 1,820 2010 1,388 393 1,781 2011 1,254 648 1,902 2012 1,239 706 1,945 2013 907 747 1,654 2014 661 792 1,453
  17. 17. CRV, Arnhem, The Netherlands, 14 April 2015 (17) Cole Genetic merit of marketed Holstein bulls -100 0 100 200 300 400 500 600 700 800 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 Averagenetmerit($) Year entered AI Average gain: $19.77/year Average gain: $52.00/year Average gain: $85.60/year
  18. 18. CRV, Arnhem, The Netherlands, 14 April 2015 (18) Cole Stability of genomic evaluations l 642 Holstein bulls w Dec. 2012 NM$ compared with Dec. 2014 NM$ w First traditional evaluation in Aug. 2014 w 50 daughters by Dec. 2014 l Top 100 bulls in 2012 w Average rank change of 9.6 w Maximum drop of 119 w Maximum rise of 56 l All 642 bulls w Correlation of 0.94 between 2012 and 2014 w Regression of 0.92
  19. 19. CRV, Arnhem, The Netherlands, 14 April 2015 (19) Cole % genotyped mates of top young bulls 0 10 20 30 40 50 60 70 80 90 100 700 725 750 775 800 825 850 875 900 925 Maurice Elvis ISYAltatrust Fernand Net Merit (Aug 2013) Percentageofmatesgenotyped Supersire Numero Uno S S I Robust Topaz Garrold Mogul
  20. 20. CRV, Arnhem, The Netherlands, 14 April 2015 (20) Cole Haplotypes affecting fertility l Rapid discovery of new recessive defects w Large numbers of genotyped animals w Affordable DNA sequencing l Determination of haplotype location w Significant number of homozygous animals expected, but none observed w Narrow suspect region with fine mapping w Use sequence data to find causative mutation
  21. 21. CRV, Arnhem, The Netherlands, 14 April 2015 (21) Cole Name BTA chromo- some Location* (Mbp) Carrier frequency (%) Earliest known ancestor HH1 5 63.2* 3.8 Pawnee Farm Arlinda Chief HH2 1 94.9 – 96.6 3.3 Willowholme Mark Anthony HH3 8 95.4* 5.9 Glendell Arlinda Chief, Gray View Skyliner HH4 1 1.3* 0.7 Besne Buck HH5 9 92.4– 93.9 4.4 Thornlea Texal Supreme JH1 15 15.7* 24.2 Observer Chocolate Soldier JH2 26 8.8– 9.4 2.6 Liberators Basilius BH1 7 42.8 – 47.0 13.3 West Lawn Stretch Improver BH2 19 10.6 – 11.7 15.6 Rancho Rustic My Design AH1 17 65.9* 26.0 Selwood Betty’s Commander Haplotypes affecting fertility *Causative mutation known
  22. 22. CRV, Arnhem, The Netherlands, 14 April 2015 (22) Cole Recessive Haplo- type BTA chromo- some Tested animals (no.) Concord- ance (%) New carriers (no.) Brachyspina HH0 21 ? ? ? BLAD HHB 1* 11,782 99.9 314 CVM HHC 3* 13,226 — 2,716 DUMPS HHD 1* 3,242 100.0 3 Mule foot HHM 15* 87 97.7 120 Polled HHP 1 345 — 2,050 Red coat color HHR 18* 4,137 — 5,927 SDM BHD 11* 108 94.4 108 SMA BHM 24* 568 98.1 111 Weaver BHW 4 163 96.3 32 Haplotypes tracking known recessives *Causative mutation known
  23. 23. CRV, Arnhem, The Netherlands, 14 April 2015 (23) Cole Weekly evaluations l Released to nominators, breed associations, and dairy records processing centers at 8 am each Tuesday l Calculations restricted to genotypes that first became usable during the previous week l Computing time minimized by not calculating reliability or inbreeding
  24. 24. CRV, Arnhem, The Netherlands, 14 April 2015 (24) Cole SNP used for genomic evaluations l 60,671 SNP used after culling on w MAF w Parent-progeny conflicts w Percentage heterozygous (departure from HWE) l SNP for HH1, BLAD, DUMPS, CVM, polled, red, and mulefoot included w JH1 included for Jerseys l Some SNP eliminated because incorrect location haplotype non-inheritance
  25. 25. CRV, Arnhem, The Netherlands, 14 April 2015 (25) Cole Some novel phenotypes studied recently ● Claw health (Van der Linde et al., 2010) ● Dairy cattle health (Parker Gaddis et al., 2013) ● Embryonic development (Cochran et al., 2013) ● Immune response (Thompson-Crispi et al., 2013) ● Methane production (de Haas et al., 2011) ● Milk fatty acid composition (Soyeurt et al., 2011) ● Persistency of lactation (Cole et al., 2009) ● Rectal temperature (Dikmen et al., 2013) ● Residual feed intake (Connor et al., 2013)
  26. 26. CRV, Arnhem, The Netherlands, 14 April 2015 (26) Cole Evaluation methods for traits l Animal model (linear) w Yield (milk, fat, protein) w Type (AY, BS, GU, JE) w Productive life w Somatic cell score w Daughter pregnancy rate w Heifer conception rate w Cow conception rate l Sire–maternal grandsire model (threshold) w Service sire calving ease w Daughter calving ease w Service sire stillbirth rate w Daughter stillbirth rate Heritability 8.6% 3.6% 3.0% 6.5% 25 – 40% 7 – 54% 8.5% 12% 4% 1% 1.6%
  27. 27. CRV, Arnhem, The Netherlands, 14 April 2015 (27) Cole -2.0 0.0 2.0 4.0 6.0 8.0 1960 1970 1980 1990 2000 2010 Breedingvalue(%) Birth year Holstein daughter pregnancy rate (%) Phenotypic base = 22.6% Sires Cows
  28. 28. CRV, Arnhem, The Netherlands, 14 April 2015 (28) Cole 6.0 7.0 8.0 9.0 10.0 11.0 1980 1985 1990 1995 2000 2005 2010 PTA (%difficultbirthsinheifers) Birth year Holstein calving ease (%) Daughte r Service-sire phenotypic base = 7.9% Daughter phenotypic base = 7.5% Service sire 0.01%/yr
  29. 29. CRV, Arnhem, The Netherlands, 14 April 2015 (29) Cole What do US dairy farmers want?  National workshop in Tempe, AZ in February  Producers, industry, academia, and government  Farmers want new tools  Additional traits (novel phenotypes)  Better management tools  Foot health and feed efficiency were of greatest interest
  30. 30. CRV, Arnhem, The Netherlands, 14 April 2015 (30) Cole What can farmers do with novel traits?  Put them into a selection index  Correlated traits are helpful  Apply selection for a long time  There are no shortcuts  Collect phenotypes on many daughters  Repeated records of limited value  Genomics can increase accuracy
  31. 31. CRV, Arnhem, The Netherlands, 14 April 2015 (31) Cole What can DRPCs do with novel traits?  Short-term – Benchmarking tools for herd management  Medium-term – Custom indices for herd management  Additional types of data will be helpful  Long-term – Genetic evaluations  Lots of data needed, which will take time
  32. 32. CRV, Arnhem, The Netherlands, 14 April 2015 (32) Cole International challenges  National datasets are siloed  Recording standards differ between countries  ICAR standards help here  Farmers are concerned about the security of their data  Many populations are small  Low accuracies  Small markets
  33. 33. CRV, Arnhem, The Netherlands, 14 April 2015 (33) Cole Conclusions Genomic research is ongoing Detect causative genetic variants Find more haplotypes affecting fertility Improve accuracy through more SNPs, more predictor animals, and more traits Genetic trend is favorable for some important, low-heritability traits More traits are desirable Data availability remains a challenge for new phenotypes
  34. 34. CRV, Arnhem, The Netherlands, 14 April 2015 (34) Cole Questions?

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