Presentation at the 2009 ADSA meeting on techniques for visualizing data from genomic evaluations.

1. John B. ColeJohn B. Cole
Animal Improvement Programs Laboratory
Agricultural Research Service, USDA
Beltsville, MD 20705-2350
john.cole@ars.usda.gov
Visualization of Results from
Genomic Predictions

2. ADSA, July 2009 (2) Cole
Introduction
• Genomic evaluation produces lots
of numbers
• Holsteins: 38K SNP × 31 traits
• Data are difficult to compare
• Levels of detail are obscured
• Results cannot easily be tabulated

3. ADSA, July 2009 (3) Cole
Visualization
• “Graphical methods can retain the
information in the data.” ― Deming
• Complements numerical techniques
• Tukey (1977), Tufte (1983, 1990, 1997,
2006) , Cleveland (1985, 1993)
• Some work by animal breeders
• Huang and Shanks (1995), Kachman (2004),
VanRaden and Tooker (2007), Schlesser et
al. (2009)

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Marker Effects ― Small Multiples

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Marker Effects ― Detail

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Marker Effects ― NCBI Mashup

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Net Merit by Chromosome
Freddie (1HO08784)Freddie (1HO08784) - highest Net Merit bull- highest Net Merit bull

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Chromosomal EBV Sparklines

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Text with Chromosomal EBV Sparklines
“For example, cows with
positive CEBV for
chromosomes 13, 14, 16, 17,
19, or 20 might be selected
for breeding to the bull O-Bee
Manfred Justice-ET
(7HO6417; Figure 5).”
(Cole et al. 2009. J. Dairy Sci. 92(6):2931―2946.)

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Text with Genetic Trend Figure
“The incidence of
SB increased from
11.2% in 1980 to
12.0% in 2004 for
heifers, and
decreased from
5.8% in 1980 to
5.6% in 2005 for
multiparous
cows.”
(Cole et al. 2007. J. Dairy Sci. 90(5):2480―2488.)

11. ADSA, July 2009 (11) Cole
Text with Genetic Trend Sparklines
“The incidence of SB increased
from 11.16% in 1980
to 11.08% in 2005 for heifers,
and decreased from 5.29% in
1980 to 4.83% in 2005
for multiparous cows.”
(Cole et al. 2007. J. Dairy Sci. 90(5):2480―2488.)

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Location of Autosomal Recessives

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Genotype Parents and Grandparents
Manfred
O-Man
Jezebel
O-Style
Teamster
Deva
Dima

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Expected Relationship Matrix1
PGS PGD MGS MGD Sire Dam Bull
Manfred 1.0 .0 .0 .0 .5 .0 .25
Jezebel .0 1.0 .0 .0 .5 .0 .25
Teamster .0 .0 1.0 . 0 .0 .5 .25
Dima .0 .0 .0 1.0 .0 .5 .25
O-Man .5 .5 .0 .0 1.0 .0 .5
Deva .0 .0 .5 .5 .0 1.0 .5
O-Style .25 .25 .25 .25 .5 .5 1.0
1
Calculated assuming that all grandparents are unrelated
1HO9167 O-Style1HO9167 O-Style

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Pedigree Relationship Matrix
PGS PGD MGS MGD Sire Dam Bull
Manfred 1.053 .090 .090 .105 .571 .098 .334
Jezebel .090 1.037 .051 .099 .563 .075 .319
Teamster .090 .051 1.035 .120 .071 .578 .324
Dima .105 .099 .120 1.042 .102 .581 .342
O-Man .571 .563 .071 .102 1.04
5
.086 .566
Deva .098 .075 .578 .581 .086 1.060 .573
O-Style .334 .319 .324 .342 .566 .573 1.043
1HO9167 O-Style1HO9167 O-Style

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Genomic Relationship Matrix
PGS PGD MGS MGD Sire Dam Bull
Manfred 1.201 .058 .050 .093 .609 .054 .344
Jezebel .058 1.131 .008 .135 .618 .079 .357
Teamster .050 .008 1.110 .100 .014 .613 .292
Dima .093 .135 .100 1.139 .131 .610 .401
O-Man .609 .618 .014 .131 1.16
6
.080 .626
Deva .054 .079 .613 .610 .080 1.148 .613
O-Style .344 .357 .292 .401 .626 .613 1.157
1HO9167 O-Style1HO9167 O-Style

17. ADSA, July 2009 (17) Cole
Difference (Genomic – Pedigree)
PGS PGD MGS MGD Sire Dam Bull
Manfred .149 -.032 -.040 -.012 .038 -.043 .010
Jezebel -.032 .095 -.043 .036 .055 .004 .038
Teamster -.040 -.043 .075 -.021 -.057 .035 -.032
Dima -.012 .036 -.021 .097 .029 .029 .059
O-Man .038 .055 -.057 .029 .121 -.006 .060
Deva -.043 .004 .035 .029 -.006 .087 .040
O-Style .010 .038 -.032 .059 .060 .040 .114
1HO9167 O-Style1HO9167 O-Style

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Pseudocolor Plots ― O-Style

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Pseudocolor Plot ― Simulated Pedigree

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Pseudocolor Plot ― Interbreed Relationships

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Closing Thoughts
• Substance over style
• The goal is greater insight
• Better tools are needed
• Scripting is essential
• Color is still difficult
• Print versus electronic publication
• We need to share ideas
• Not all ideas will be good ones

22. ADSA, July 2009 (22) Cole
Acknowledgments
• Genotyping and DNA extraction:
• BFGL, U. Missouri, U. Alberta, GeneSeek,
Genetics & IVF Institute, Genetic Visions,
and Illumina
• Computing:
• AIPL staff (Leigh Walton, Jay Megonigal)
• Funding:
• NRI grants 2006-35205-16888 and 2006-
35205-16701
• Agriculture Research Service
• Holstein, Jersey and Brown Swiss breed
associations
• Cooperative Dairy DNA Repository (CDDR)

23. ADSA, July 2009 (23) Cole
CDDR Contributors
• National Association of Animal Breeders
(Columbia, MO)
• ABS Global (DeForest, WI)
• Accelerated Genetics (Baraboo, WI)
• Alta (Balzac, AB, Canada)
• Genex (Shawano, WI)
• New Generation Genetics (Fort Atkinson,
WI)
• Select Sires (Plain City, OH)
• Semex Alliance (Guelph, ON, Canada)
• Taurus-Service (Mehoopany, PA)