Impact van Genomics in de VS Albert Reurink (Accelerated

11/6/2014
Impact van Genomics in de VS
Albert Reurink (Accelerated Genetics)
met dank aan Kent Weigel
genetic advisor NAAB,
Prof University Wisconsin, Madison
Structuur fokwaarde schatting US
Gebruik genomics
Effect op structuur fokprogramma’s
Nieuwe mogelijkheden
Internationale kansen
25th NAAB Technical Conference
25th NAAB Technical Conference
Council on Dairy Cattle Breeding
Council on Dairy Cattle Breeding
(CDCB)
Structure
National Association of Animal
Breeders (NAAB)
Dairy Record Processing
Centers
Added to CDCB in 2012
Certified Semen Services
A.I. Stations
DRMS
National Dairy Herd
Information
Association (NDHIA)
Ag Source
AgriTech
Purebred Dairy Cattle Association
Holstein Ayrshire Jersey
Quality Certification Services
25th NAAB Technical Conference
Provo
Guernsey
Milking Shorthorn Brown Swiss R&W Holstein
25th NAAB Technical Conference
U.S. Federal Government
Council on Dairy Cattle Breeding
12 voting Board Members and up to 2 non-voting Allied Industry
Advisory Board Members
November 11, 2012
United States Department of
Agriculture (USDA)
Agriculture Research Service (ARS)
NAAB
DRPs
DRPCs
PDCA
(3)
(3)
(3)
(3)
Allied
Industry
(2)
Nonvoting
Animal Improvement
Programs Laboratory (AIPL)
Bovine Functional Genomic
Laboratory (BFGL)
Animal Genomics and Improvement Laboratory (AGIL 2014)
Animal Improvement Program (AIP within AGIL)
25th NAAB Technical Conference
25th NAAB Technical Conference
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11/6/2014
Waarom
OVEREENKOMST
• March 2013, CDCB 5 jaar afspraak met US overheid
onderzoeks afdeling
• Voor Genomics fokwaardeschattingen meer service nodig en
• CDCB bekostigt en levert service aan de berekening en
distributie van fokwaarden richting de verschillende
gebruikers groepen
• Genomics hebben meer phenotype data nodig, niet minder
• AIP binnen AGIL voert onderzoek uit en levert nieuwe en
up todate statistische algoritmes
grotere investeringen in reken capaciteit
• Lange termijn financiele en personeels continuiteit
• Database op USDA niveau (open/onafhankelijk)
25th NAAB Technical Conference
Round-Oak Rag Apple Elevation
(part of chromosome 1)
Cooperative Dairy DNA Repository
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202021211222120222002121210121210201100111222121101
National Genetic Evaluation Program
USJersey
Open karakter
• Iedereen kan een genomic fokwaarde ontvangen tegen
een redelijke ‘participatie prijs’
Rate
code
Kind of participation Female
fee $
Initial male
fee $
AI Service
male fee $
1
Total program
0
20
800
2
member
2
30
800
3
Non-member
5
200
800
4
Canada
8
200
800
5
Approved partners
10
20
800
6
All others
10
200
1600
25th NAAB Technical Conference
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11/6/2014
Pre-Genomics Progeny Testing in the USA
Animal genotypes in the CDCB Cooperator
Database Jan 2009 through Sept. 2014
No. Bulls Tested in 2006
Ayrshire
6
Brown Swiss
27
Guernsey
14
Holstein
1,329
Jersey
136
Milking Shorthorn
3
Breed
AY
BS
HO
JE
Total
%
Female
Male
Total
2,174
1,283
3,457
2,652
14,876 17,528
485,019 108,290 593,309
67,308
12,414 79,722
557,153 136,863 694,016
80.28
19.72
Percent
0.50
2.53
85.49
11.49
25th NAAB Technical Conference
Genomic PTA (GPTA) for a Young Calf
Reference Population of Older
Animals
+
10120001120222
….
Gain in Reliability due to Genomics
Estimated SNP Effects
=
 We are essentially “buying reliability” early in life, instead
of waiting for phenotypes to be measured
Calf with Genotype
(and corrected or discovered parentage)
Gain in Reliability due to Genomics
Trait
Final score
Stature
Dairy form
Rump angle
Rump width
Feed and legs
Fore udder attachment
Rear udder height
Udder depth
Udder cleft
Front teat placement
Teat length
Bias*
0.1
−0.2
−0.2
0.0
−0.2
0.2
−0.2
−0.1
−0.3
−0.2
−0.2
−0.1
Reliability
(%)
58.8
68.5
71.8
70.2
65.0
44.0
70.4
59.4
75.3
62.1
69.9
66.7
Reliability
gain (%)
22.7
30.6
34.5
34.7
28.1
12.8
33.1
22.2
37.7
25.1
32.6
29.4
Overall Adoption of Genomic Testing
 2013 deregressed PTA vs. 2009 genomic PTA for US Holstein bulls
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Industry Use of Genomic Young Sires
Flow of Genomic Information
Dairy Herd Improvement
(DHI) producer
Holstein
AI organization,
breed association
DNA laboratory
Jersey
% Breedings to
Genotyped Bulls
< 4 Years of Age
% Breedings to Ungenotyped Bulls
< 4 years of age
2007
0
28
2014
30-70
0
2007
0
25
2014
30-70
0
Council on Dairy Cattle
Breeding (CDCB)
Cole, 2014
Average Merit of Holstein AI Bulls
Hutchison, Cole, and Bickhart, 2013
Dynamiek van de KI fokpogramma’s is veranderd
Elite vrouwelijke dieren worden duur verkocht
Cole, 2014
Impact on Generation Interval for Males
Bull A is
born and is
selected
based on
his EBV.
Traditional AI breeding program
(before genomics)
0 yr
Progeny
of Bull A
are born
Generation
Interval =
63 mo
1 yr 3 mo
2 yr
4 yr
4 yr 6 mo
Progeny
of Bull A
calve
Sons of
Bull B
are born
Sons of
Bull A are
born
Grandsons of
Bull B
born
.
5 yr 3 mo
Milk Production
data from
progeny of Bull
B are available
to calculate his
EBV
0 yr
1 yr
Bull B
reaches
sexual
maturity
and is used
as a sire of
sons
1 yr 9 mo
Generation
Interval =
21 mo
2 yr 9 mo
Sons of Bull
B reach
sexual
maturity and
are used as
sires of sons
3 yr 6 mo
Great
grandsons of
Bull B
are born
.
.
Aggressive AI breeding program
(after genomics)
Impact on Generation Interval
.
Bull A is
progeny
tested.
Bull B is
born and
selected
based on
GEBV.
Milk production
data from progeny
of Bull A are
available to
calculate his EBV.
Bull A is used as
sire of sons.
4 yr 6 mo
5y 3 mo
Grand-sons
of Bull B
reach sexual
maturity and
are used as
sire of sons
Schefers and Weigel, 2012
Van Tassell, 2013
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11/6/2014
Effecten voor de KI fokprogramma’s
Nieuwe commerciele dynamiek fokprogramma’s
 Naar jonge stieren meer vraag, maar ze produceren lager aantal rietjes
per jaar
 Eerste sperma van elite jonge stieren verkocht voor erg hoge
 Traditionele groeps huisvesting voor wachtstieren verandert in complete
individuele huisvesting
prijzen: 500 – 1000 dollar
 Nog steeds grote vraag voor oudere stieren, met dochter fokwaarden
 Silver, Supershot, 1stClass, and Ocean PP as examples
 (voor) selectie van grote aantallen stieren bij fokkers
 95% van jonge stieren stammen af van jonge stieren (zonder dochters)
 Nieuwe balance in samenwerking tussen fokkers en fokprogramma’s
 Beloning for KI programma en fokker
 Fokkers zien investeerders geld komen met eis voor Rendement
 Ki programma’s investeren in vrouwelijke dieren, met dynamiek voor
omvang, risico en vooruitgang, binnen financiele randvoorwaarden.
 Continue genetica uitwisseling tussen fokprogramma’s
 ET, IVF etc, versnellen kansen voor het verkorten van generatie interval
Number of Genotyped Jerseys
Adoption of Low-Density Genotyping
Genotype Imputation
Aoccdrnig to rscheearch at Cmabrigde Uinervtisy, it
deosn't mttaer in waht oredr the ltteers in a wrod are,
the olny iprmoetnt tihng is taht the frist and lsat ltteer
be at the rghit pclae. The rset can be a toatl mses and
you can sitll raed it wouthit a porbelm. Tihs is bcuseae
the huamn mnid deos not raed ervey lteter by istlef, but
the wrod as a wlohe.
1000
900
800
700
600
500
400
300
200
100
0
3K
 Your brain does this after learning a language
50K
 Imputation algorithms do this with 99% accuracy after
Chip Type
Males
learning what haplotypes exist in cows and bulls of the same
breed that have been tested with a more expensive chip
Females
Tracking Inheritance using SNPs
Results from the UW-Madison Herd
Cole, 2013
Hoffman, Fjarlie, Vanderwerff, and Weigel, 2013
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11/6/2014
Strategies for Genotyping Females
Strategies for Genotyping Females
 Test the whole herd
 Test the whole herd
 Test potentially elite animals for marketing
 Test potentially elite animals for marketing
 Test potentially inferior animals for culling
 Test potentially inferior animals for culling
 Test animals that are “on the bubble”
 Test animals that are “on the bubble”
Genomic Stier advies programma
Selection for New Traits (feed efficiency)
2008 (using progeny testing)
2013 (using genomics)
Cost of measuring phenotype =
$200 per cow
Cost of measuring phenotype =
$200 per cow
Progeny test population = 1,500
bulls x 100 daughters per bull =
150,000 cows per year
Cost of genomic testing = $100
per animal (less with imputation)
Total cost = $30 million per year
$20,000 per progeny tested bull
Reference population = 20,000
cows + 2,000 new cows per year
Selection candidates = 5,000
young bulls per year
Total cost = $1.37 million per year
 Based on 1,017 genotyped Jerseys born from 2005-2009
Selection for New Traits (feed efficiency)
$275 per genome tested bull
Internationale samenwerking
Wetenschappelijk, politiek en commercieel debat over de
internationale uitwisseling van SNP’s of Genomic Mace
SNP uitwisseling geven een meer nauwkeurige schatting van de
benodigde ‘outliers’ in de deelnemende populaties
SNP uitwisseling zal genetische vooruitgang versnellen
US welcomes snip exchange as next level international
cooperation
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11/6/2014
Samenvatting
Deelname in genomic selectie in de VS is uitgebreid en de informatie is publiek
THANK YOU!
Structuur fokwaardeschatting is open en transparant
Conituniteit van gegevensverzameling in de praktijk nog meer relevant
Fokprogramma’s zijn qua structuur en dynamiek verandert
Kansen voor vrouwelijke selectie binnen bedrijven, genomic paringsadvies en
meer kansen voor nieuwe kenmerken
Uitdaging en grote kans voor grote global database via uitwisseling van snips
voor internationale fokwaardeschatting.
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