Download - Cow Adjustment and Genomic Database Update
T. A. Cooper and G.R. WiggansAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA Beltsville, MD
Council on Dairy Cattle Breeding meeting April 2010 (1)
Cow Adjustmentand
Genomic Database Update
Council on Dairy Cattle Breeding meeting April 2010 (2)
Cow Adjustment
Council on Dairy Cattle Breeding meeting April 2010 (3)
Gains in Reliability as of 2008
Council on Dairy Cattle Breeding meeting April 2010 (4)
DGV vs Traditional PTA (Bulls)
DGV – based on allele effects of all genotyped animalsTraditional PTA – no genomics
-500
0
500
1000
1500
2000
-155 276 588 794 962 1104 1252 1403 1578 1867
PA Milk (pounds)
Milk
(p
ou
nd
s)
Bull DGV Bull Traditional PTA
Council on Dairy Cattle Breeding meeting April 2010 (5)
DGV vs Traditional PTA (Cows)
DGV – based on allele effects of all genotyped animalsTraditional PTA – no genomics
-1000
-500
0
500
1000
1500
2000
2500
-715 284 576 793 960 1104 1253 1414 1592 1936
PA Milk (pounds)
Mil
k (p
ou
nd
s)
Cow DGV Cow Traditional PTA
-1000
-500
0
500
1000
1500
2000
2500
-715 284 576 793 960 1104 1253 1414 1592 1936
PA Milk (pounds)
Mil
k (p
ou
nd
s)
Cow DGV Cow Traditional PTA Adjusted Traditional PTA
Council on Dairy Cattle Breeding meeting April 2010 (6)
high PTA values were causing the genomic predictions to suffer in accuracy
added information from genotyped cows was not increasing reliability
Why reduce cow bias through adjustment?
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Which animals were adjusted?
All genotyped and imputed cows
All genotyped animals including bulls, were affected by the adjustment made to the maternal portion of the parent average
Brown Swiss adjustments were not implemented due to low numbers of genotyped cows
Council on Dairy Cattle Breeding meeting April 2010 (8)
How was the adjustment made?
0
500
1000
1500
2000
2500
0.4 0.6 1.0 2.5Daughter Equivalent (progeny)
Std
. D
ev o
f D
ere
g M
.S.
(Milk)
CowBull
-400
-200
0
200
400
600
800
1000
2000 2001 2002 2003 2004 2005 2006 2007
Birth year
Milk (
lbs.)
Cow
Bull
Cow SD Adj
Variance Adjustment
Mean Adjustment
Council on Dairy Cattle Breeding meeting April 2010 (9)
How was the adjustment made?
Deregressed Mendelian Sampling (MS) =
(PTA-PA) / f(REL)
Adj. MS = .84*MS - 784
Adj. PTA = f(REL)*(Adj. MS+ PAn) + (1- f(REL)*PAn)
f(REL) = weight in PTA from own records and progeny
Council on Dairy Cattle Breeding meeting April 2010 (10)
Effects of Cow Adjustment (Holstein)
Bias Regression Gain REL
No Yes Diff No Yes Diff No Yes Diff
Milk (lb) -75.3 -27.9 47.4 .93 .90 -.03 29.5 32.5
3.0
Fat (lb) -5.7 -2.9 2.8 .98 .97 -.01 34.0 37.1
3.1
Protein (lb)
-0.2 0.8 1.0 .90 .97 .07 25.0 27.1
2.1
Fat (%) 0.0 0.0 0.0 .97 .99 .02 49.8 52.4
2.6
Protein (%)
0.0 0.0 0.0 .87 .88 .01 38.8 41.5
2.7
Council on Dairy Cattle Breeding meeting April 2010 (11)
Effects of Cow Adjustment (Jersey)
Bias Regression Gain REL
No Yes Diff No Yes Diff No Yes Diff
Milk (lb) -44.0 81.5 125.5 .99 .99 .00 10.8 19.6 8.8
Fat (lb) -7.3 7.9 15.2 .78 .84 .06 9.4 18.2 8.8
Protein (lb) 1.7 4.3 2.6 .86 .90 .04 4.1 12.7 8.6
Fat (%) 0.0 0.0 0.0 .90 .95 .05 29.9 37.6 7.7
Protein (%) 0.0 0.0 0.0 .87 .93 .06 24.8 34.2 9.4
Council on Dairy Cattle Breeding meeting April 2010 (12)
Example (Cow Milk PTA 1934 381)
0
500
1000
1500
2000
2500
Progeny 1 Jan PA April PA Progeny2
Mil
k (
po
un
ds
)
Council on Dairy Cattle Breeding meeting April 2010 (13)
The future
Investigate solutions to the problem of not being able to compare genotyped and non-genotyped cows
− Reduce heritability− Add dam-herd interaction− Varying heritability by herd− Other
With 3K chip, adjustments may need to vary by sub-population
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Genomic Database
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Genotyped Holstein by run
Run Date
Old* Young**
TotalMale Female Male Femal
e
0904 7600 2711 9690 1943 21944
0906 7883 3049 11459 2974 25365
0908 8512 3728 12137 3670 28047
0910 8568 3965 13288 4797 30618
1001 8974 4348 14061 6031 33414
1002 9378 5086 15328 7620 37412
10041005Imputed
97709958
73007940
(1955)
1600216594
87329772
4180444264
* Animals with traditional evaluation** Animals with no traditional evaluation
Council on Dairy Cattle Breeding meeting April 2010 (16)
Genotyped Jersey by run
Run Date
Old* Young**
TotalMale Female Male Femal
e
1002 1977 479 1172 197 3825
10041005Imputed
20722079
637702
(150)
12501368
202231
41614320
* Animals with traditional evaluation** Animals with no traditional evaluation
Council on Dairy Cattle Breeding meeting April 2010 (17)
Genotyped Brown Swiss by run
Run Date
Old* Young**
TotalMale Female Male Femal
e
1002 1168 54 179 15 1416
10041005Imputed
11851188
98114(63)
188199
3134
15021535
* Animals with traditional evaluation** Animals with no traditional evaluation
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Genotype Processing
2,000 New Genotypes a month
Four labs
− GeneSeek
− Genetic Visions
− DNA LandMarks
− GIVF
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All animals should be nominated by the time sample reaches lab
Goal: Parents and Grandparents on every genotyped animal
Minimum: Valid ID
Genotype Processing: Nomination
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Genotypes must pass 62 edits to be added to the database
Most common reasons a genotype fails
− Low call rate
− Parent / Progeny conflict
− Possible split embryo / twin
− Wrong gender
− Breed Check
− Switched samples
Genotype Processing: Edits
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Continuous Updates
Pedigree changes update genotype usability daily
Harmonization with breed association important to maintain usability
Blanking a genotyped dam will make the genotype unusable
No automatic receipt of foreign pedigree updates
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Low call rate
80% on X chromosome
90% on autosomal chromosomes (43,382)
Labs generally do not send genotypes with low call rates
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Parent Progeny Conflict
Sire / Dam conflict
> 200 SNP conflicts
Sire / dam proposed if genotyped
Sire conflict - young animals from mixed flush
Sire conflicts represent $50,000 genotype cost
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Split embryo / Identical twin / Clone <1000 SNP differences considered
identical
98% similar, accounts for genotyping errors
Stored in clone table if valid
Animals registered as ETS or ETN (automatic)
Otherwise verification must come from requester
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Wrong Gender
> 50 heterozygous SNP on X (not male)
< 50 heterozygous SNP on X (not female)
Homozygous X female
Common ancestor (source of X)
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Source of X
Jeff
Erin
Elegant
BW Marshall
Tanya
Sam
12144058
BellwoodMara
PatronMary
MarkSue
Patron
14860763
Council on Dairy Cattle Breeding meeting April 2010 (27)
Breed Check
622 SNP
Nearly monomorphic in 1 breed and have fewer than 30% of animals homozygous for that allele in another breed
An error when a higher number of conflicts for the reported breed than for another breed
> 10 SNP conflicts reported to requester, but remains usable
Higher conflicts for foreign animals
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Switched Samples
Sample pair with reversed parents
Switched at the lab
Switched at the farm
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Conflicts to Requester
Genotype conflicts reported to the requester immediately
Genotype remains stored in AIPL database as an unusable genotype until conflict is resolved
2-3 days to fix conflicts before cutoff
Once a month all conflicts remaining in the system are sent to requesters
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Issues Reported to Lab for QC
SNP that have call rate <90%
SNP that have high parent-progeny conflicts
SNP that deviate from HW equilibrium
Labs have the opportunity to re-cluster genotypes
Council on Dairy Cattle Breeding meeting April 2010 (31)
Closing Thoughts
Currently 477 animals with failed or conflicted genotypes
Big increase in volume when 3K becomes available
Edits will remain with different thresholds for 3K data