Visualization of results from genomic predictions
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Visualization of Results from Genomic Predictions. 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. Visualization.

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Visualization of Results from Genomic Predictions

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Visualization of results from genomic predictions

Visualization of Results from Genomic Predictions


Introduction

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


Visualization

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)


Marker effects small multiples

Marker Effects ― Small Multiples


Marker effects detail

Marker Effects ― Detail


Marker effects ncbi mashup

Marker Effects ― NCBI Mashup


Net merit by chromosome

Net Merit by Chromosome

Freddie (1HO08784) - highest Net Merit bull


Chromosomal ebv sparklines

Chromosomal EBV Sparklines


Text with chromosomal ebv sparklines

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.)


Text with genetic trend figure

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.)


Text with genetic trend sparklines

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.)


Location of autosomal recessives

Location of Autosomal Recessives


Genotype parents and grandparents

Genotype Parents and Grandparents


Expected relationship matrix 1

Expected Relationship Matrix1

1HO9167 O-Style

1Calculated assuming that all grandparents are unrelated


Pedigree relationship matrix

Pedigree Relationship Matrix

1HO9167 O-Style


Genomic relationship matrix

Genomic Relationship Matrix

1HO9167 O-Style


Difference genomic pedigree

Difference (Genomic – Pedigree)

1HO9167 O-Style


Pseudocolor plots o style

Pseudocolor Plots ― O-Style


Pseudocolor plot simulated pedigree

Pseudocolor Plot ― Simulated Pedigree


Pseudocolor plot interbreed relationships

Pseudocolor Plot ― Interbreed Relationships


Closing thoughts

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


Acknowledgments

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)


Cddr contributors

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)


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