North American Cooperation in Genomic Prediction

1
North American Cooperation in Genomic Prediction
2
Sequencing and Genotyping

• Cattle genome sequenced in 2004
• 30 chromosome pairs (including X,Y)
• 3 billion letters from each parent
• Illumina BovineSNP50 BeadChip
• 58,000 genetic markers in 2007
• 38,416 used in genomic predictions
• Current cost lt 250 per animal

3
History of Genomic Cooperation

• 1992 USDA request for CAN, USA AI companies to
  join Dairy Bull DNA Repository maintained at U.
  Illinois
• CIAQ (Brian Van Doormaal) provided 1110 straws
  from 110 bulls
• 1999 Cooperative Dairy DNA Repository maintained
  at Beltsville, MD
• Semex and Alta contributed semen for all progeny
  tested bulls

4
CDDR Contributors

• National Association of Animal Breeders (NAAB,
  Columbia, MO)
• ABS Global (DeForest, WI)
• Accelerated Genetics (Baraboo, WI)
• Alta (Balzac, AB)
• Genex (Shawano, WI)
• New Generation Genetics (Fort Atkinson, WI)
• Select Sires (Plain City, OH)
• Semex Alliance (Guelph, ON)
• Taurus-Service (Mehoopany, PA)

5
Genotype Data for Elevation
Chromosome 1
10001112200200121110111121111011110011211000201220
02220111 12021012002111221100211120011110010110110
10220011002201101 12002011010202221211221020100111
00011220221222112021120120 20100202202000021100011
20201122111211102201111000021220200 02210120200022
11220111012100111211102112110020102100022000 22010
00201100002202211022112101121110122220012112122200
200 0200202020122211002222222002212111121002111120
011011101120 0202220001112011010211121211102022100
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011211012022011002220021002110001110021 1021101110
002220020221212110002220102002222121221121112002 0
11020200122222211221202121121011001211011020022000
2001002 000111101100121102121211120101012120221010
1011111021102112 211111121211121011012001111102111
1011111220121012121101022 202021211222120222002121
210121210201100111222121101
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Genotype Data from Inbred BullChromosome 24 of
Megastar
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022220202 2202020202200022002220220022200000220200
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222202200222202020002202202222002220022000200 2202
00000220022022200002200002200022220200222200022002
0020202 202000222000222002220220220000022022002002
0020220002000222202 200222002022020022220222000002
0220002020020202000220022000002 202220020222020002
2002000200022002002000200220222220022022000 200002
00020000202200202202002000022200002220020002002220
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7
Close Inbreeding (F14.7) Double Grandson of
Aerostar
Aerostar
Megastar
Aerostar
Chromosome 24
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Holstein Experimental Design

• Compute genomic evaluations and parent averages
  from 2003 data
• 3576 older Holstein bulls born 1952-1998
• Compare ability to predict daughter deviations in
  2008 data
• 1759 younger bulls born 1999-2002
• Test results for 27 traits 5 yield, 5 health, 16
  conformation, and Net Merit

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Genotyped Holsteins (n6005)As of April 2008
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Jersey and Brown Swiss

• Jersey experimental design
• Data from 579 bulls born before 1999 and 204 cows
  with data before 2003
• Predict 352 bulls born during or after 1999
• Brown Swiss experimental design
• Data from 225 bulls born before 1999
• Predict 118 bulls born during or after 1999

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Genomic Methods

• Direct genomic evaluation
• Evaluate genotyped animals by summing effects of
  38,416 genetic markers (SNPs)
• Combined genomic evaluation
• Include phenotypes of nongenotyped ancestors by
  selection index
• Transferred genomic evaluation
• Propagate info from genotyped animals to
  nongenotyped relatives (not done yet)

12
Significance Tests for Net Merit
13
Marker Effects for Net Merit
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Major Gene on Chromosome 18Net Merit, Productive
Life, Calving Ease, Stature, Strength, Rump Width
15
Marker Effects for Milk
16
Marker Effects for Final Score
17
Reliability Gain by Breed
Trait HO JE BS
Net merit 23 14 3
Milk 23 6 0
Fat 33 10 5
Protein 22 3 1
Fat 43 31 10
Protein 34 22 5

18
Reliability Gain by Breed
Trait HO JE BS
Productive life 18 8 2
Somatic cell score 21 3 16
Dtr pregnancy rate 16 3 -
Final score 18 4 -
Udder depth 35 11 3
Foot angle 14 8 -
Stature 26 8 3
19
Reliability Gains for Proven Bulls

• Proven bulls included in test had
• gt10 daughters in August 2003
• gt10 increase in reliability by 2008
• Numbers of bulls in test ranged from 104 to 735
  across traits
• Predicted the change in evaluation
• Significant increase in R2 (P lt .001) for 26 of
  27 traits

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Net Merit by Chromosome for O ManTop bull for
Net Merit
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SNPs on X Chromosome

• Each animal has two evaluations
• Expected genetic merit of daughters
• Expected genetic merit of sons
• Difference is sum of effects on X
• SD .1 sG, smaller than expected
• Correlation with sire