12/11/2015
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Stepping ForwardDecember 9 & 10 | Dairy Summit 2015 | Baraboo, Wis.
Application of Genomic Selection on Your Dairy
P. C. Hoffman
Vita Plus Corp, Madison, WI
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19000 21000 23000 25000 27000 29000 31000 33000 35000 37000 39000
% o
f 1s
t L
acta
tion
Cow
s
305 d Milk Yield, lbs
1st Lactation Milk Production (30,000 lb herd)Bred AI 50 + years
Genetic variance of milk production is increasing not decreasing!
12/11/2015
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Stepping ForwardDecember 9 & 10 | Dairy Summit 2015 | Baraboo, Wis.
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29000
31000
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35000
37000
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% of 1st Lactation Cows
305 d Milk Yield, lbs
What causes the variance?
Parent Average +
Mendelian Sampling Effect
Environment/Management
Genetic variance of milk production is worth more $$ today!
How do we find more of the variance ?
12/11/2015
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Stepping ForwardDecember 9 & 10 | Dairy Summit 2015 | Baraboo, Wis.
Single Nucleotide Polymorphism
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SNP
SNP
Courtesy of George Wiggans, USDA‐AIPL
Stepping ForwardDecember 9 & 10 | Dairy Summit 2015 | Baraboo, Wis.
Estimating SNP Effects on Production
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-50
-30
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30
50
70
90
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PT
A f
or
Pro
tein
Yie
ld
Number of Copies of the ND-SNP Allele
Slope of the line indicates the estimated SNP effect, which is the change in PTA protein per extra copy of a given SNP allele
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Genomics- Commercial Testing ABCs
Reg. #
USD
A AIN
Vacc. #
Oth
er
6751 982000133517324 x US4071556 F HO 11/21/2010 7H7853 355HE8261
6754 982000133517327 x US4071540 F HO 11/28/2010 200H3218 35SHE8183
6758 982000133517331 x US4071529 F HO 11/30/2010 200H6004 35SHE7962
6759 982000133517332 x US4071533 F HO 11/30/2010 7H10489 35SHE7938
6764 982000133517337 x US4071521 F HO 12/6/2010 14H4929 35SHE7999
6766 982000133517339 x US4071517 F HO 12/8/2010 11H9703 35SLS7488
6768 982000133517341 x US4071525 F HO 12/9/2010 7H9030 35SHE5165
6770 982000133517343 x US4071550 F HO 12/12/2010 29H13245 35SHE5981
6771 982000133517344 x US4071513 F HO 12/12/2010 14H4929 840003003932331
6775 982000133517348 x US4071554 F HO 12/15/2010 29H13245 35TDN0336
6857 98200013351430 x US4071536 F HO 4/12/2011 29H13245 35SHE5128
Hand Entry
Dairy Comp 305 (Cut and Paste)
On‐farm ID (Herd
Management #)
Sire
Registration #
Birth Date
(yyyy/mm/d
d) or Birth
YearSex
Sample
Collector
Barcode
Official ID (Registration
#, USDA AIN, Calfhood
Vaccination #)
Breed
(HO/JE/
BS)
Dam Registration # or
USDA AIN
Fill out the Form- Done by bar code to Dairy Comp- Improper Parent/Sire/Dam/Breed ID = 10-15 % Normal
12/11/2015
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Genomic Lab Results* Samples Due 1st of Month
* Lab Turnaround = 30-40 days
GPTA Milk +1114 +141 -1041 +490Average = 176 GPTA Milk
• Genomic Results GPTA Milk (4 Heifer Example)
12/11/2015
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11 Presentation Title – 00/00/12 (Optional)
University of Wisconsin(Marshfield, Arlington, UW Dairy Cattle Center)
Data AnalysisMarch 2015
12 Presentation Title – 00/00/12 (Optional)
Sire of ConceptionBull # Herd
PregnantMilk PTA
NM$ PTA
DPR PTA
Rel.
GOLD CHIP (7H10920) 46 -151 139 0.7 95
TABBER (29H14258) 44 519 307 0.6 91
ARMITAGE (29H14961) 44 656 395 3.8 94
YANCE (7H9925) 44 1427 433 1 91
ALTAMETEOR (11H10661) 44 1233 475 1.4 96
•The strategy to using genomic-proven bulls is to use a group, spreading semen usage over more bulls.
•This strategy will minimize the impact of PTAs changing for any one sire due to the lower reliability.
•UW is primarily using daughter-proven bulls•~20% of conceptions are to genomic-proven bulls
12/11/2015
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13 Presentation Title – 00/00/12 (Optional)
305ME Production=28847+3.8*GPTA MilkCorrelation=0.45
Herd Response to Genetic Selection
Observed 3.8lbs/GPTA MilkExpected 2lbs/GPTA Milk
Genomics management is just trying to find the top and the bottom. A dairy can’t cullall their heifers!
12/11/2015
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EffectiveUseofGenomicsinSireSelectionandReplacementHeiferManagement
Dr.KentA.WeigelDepartmentofDairyScience
UniversityofWisconsin– Madison
ResultsfromtheUW‐MadisonHerd
27,498
29,247
29,67329,864
26,780
27,864
30,050
31,581
24000
25000
26000
27000
28000
29000
30000
31000
32000
Bottom 25% Bottom 25‐50% Top 25‐50% Top 25%
Sorted by Sire's Current PTA Milk
Sorted by Genomic PTA Milk as a Yearling Heifer
First Lactation 305‐Day M
E Milk Yield (lb)
Quartile Ranking
Average first lactation ME 305‐day milk yield for 411 Holstein cows in the AllensteinDairy Herd at UW‐Madison, according to quartile for genomic PTA milk at 12 months of age and quartile for sire’s current PTA for milk yield.
2,366 lb
4,801 lb
12/11/2015
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ResultsfromtheUW‐MadisonHerd
116.5
124.9
104.9
113.1
125.9
114.9113.6
104.9
90
95
100
105
110
115
120
125
130
Bottom 25% Bottom 25‐50% Top 25‐50% Top 25%
Sorted by Sire's Current PTA DPR
Sorted by Genomic PTA DPR as a Yearling Heifer
Quartile Ranking
First Lactation Days Open
Average days open in first lactation for 240 Holstein cows in the Allenstein Dairy Herd at UW‐Madison, according to quartile for genomic PTA for daughter pregnancy rate at 12 months of age and quartile for sire’s current PTA for daughter pregnancy rate.
3.4 d21.0 d
ResultsfromtheUW‐MadisonHerd
2.202.14
2.22
1.65
2.38
2.162.10
1.56
1.25
1.50
1.75
2.00
2.25
2.50
Bottom 25% Bottom 25‐50% Top 25‐50% Top 25%
Sorted by Sire's Current PTA SCS
Sorted by Genomic PTA SCS as a Yearling Heifer
Quartile Ranking
First Lactation log SCC
Average log somatic cell count in first lactation for 216 Holstein cows in the Allenstein Dairy Herd at UW‐Madison, according to quartile for genomic PTA for somatic cell score at 12 months of age and quartile for sire’s current PTA for somatic cell score.
0.820.55
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ResultsfromtheaCommercialHerd
Genomic PTA computed in August 2013 was compared with actual first lactation production, fertility, and udder health
All Holstein cows that had first calving after August 2013 were included in the analysis
ResultsfromaCommercialHerd
Quartile Ranking
First Lactation 305‐Day M
E Milk Yield
Average standardized 305‐day ME milk yield in first lactation for 407 Holstein cows in the herd, according to quartile for genomic PTA for milk yield prior to first calving.
27,341
30,331 30,218
32,402
29,314
29,868
30,296
30,779
26000
27000
28000
29000
30000
31000
32000
33000
34000
Bottom 25% Bottom 25‐50% Top 25‐50% Top 25%
Genomic PTA as a Yearling Heifer
Current Sire PTA
1,465 lb
5,061 lb
MILK
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ResultsfromaCommercialHerd
Quartile Ranking
First Lactation 305‐Day M
E Fat Yield
Average standardized 305‐day ME fat yield in first lactation for 407 Holstein cows in the herd, according to quartile for genomic PTA for fat yield prior to first calving.
1,286
1,332
1,380
1,391
1,311
1,343 1,345
1,385
1260
1280
1300
1320
1340
1360
1380
1400
1420
Bottom 25% Bottom 25‐50% Top 25‐50% Top 25%
Genomic PTA as a Yearling Heifer
Current Sire PTA
74 lb
105 lb
FAT
ResultsfromaCommercialHerd
Quartile Ranking
First Lactation 305‐Day M
E Protein Yield
Average standardized 305‐day ME protein yield in first lactation for 407 Holstein cows in the herd, according to quartile for genomic PTA for protein yield prior to first calving.
922
972
996
1,015
933
982
989
999
900
920
940
960
980
1000
1020
1040
Bottom 25% Bottom 25‐50% Top 25‐50% Top 25%
Genomic PTA as a Yearling Heifer
Current Sire PTA
66 lb
93 lb
PROTEIN
12/11/2015
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ResultsfromaCommercialHerd
Quartile Ranking
First Lactation Days Open
Average days open in first lactation for 192 Holstein cows in the herd, according to quartile for genomic PTA for daughter pregnancy rate prior to first calving.
143
120
117
112
146
112
109
125
100
110
120
130
140
150
160
Bottom 25% Bottom 25‐50% Top 25‐50% Top 25%
Genomic PTA as a Yearling Heifer
Current Sire PTA
21 d
31 d
DAYS OPEN
ResultsfromaCommercialHerd
Quartile Ranking
First Lactation Somatic Cell Score
Average somatic cell score in first lactation for 407 Holstein cows in the herd, according to quartile for genomic PTA for somatic cell score prior to first calving.
2.48
2.03
1.97
1.92
2.19 2.19
2.10
1.93
1.70
1.80
1.90
2.00
2.10
2.20
2.30
2.40
2.50
2.60
Bottom 25% Bottom 25‐50% Top 25‐50% Top 25%
Genomic PTA as a Yearling Heifer
Current Sire PTA
SOMATIC CELL SCORE
0.26
0.56
12/11/2015
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Stepping ForwardDecember 9 & 10 | Dairy Summit 2015 | Baraboo, Wis.
Take Home Messages
To increase genetic progress and revenue, genomics requires a protocol for sire selection, sexed semen, genomic testing, health status, early culling, etc.
There is no perfect “one size fits all” protocol
The appropriate protocol for a given herd will depend on genetic level, facilities, expansion plans, feed costs, cash flow, and other factors
Genomic information is not research data. It is an enhancement of genetic probabilities
Like other new management tools (rBST, BMR, GMO) genomics has its share of detractors