dsec october 2009
DESCRIPTION
DSEC October 2009. Percent correctly called genotypes, linkages, and paternity by breed and group. Haplotype probability with 100 markers per chromosome. Haplotype probability with 12 markers per chromosome. - PowerPoint PPT PresentationTRANSCRIPT
2007
Paul VanRaden Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA
2009
DSEC October 2009DSEC October 2009
DSEC, October 2009 (2) Paul VanRaden200
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Percent correctly called genotypes, linkages, and Percent correctly called genotypes, linkages, and paternity by breed and group.paternity by breed and group.
Correct Calls (%) Breed Number Group Genotype Linkage Paternity Holstein 1,361 Imputed 94.5 88.0 94.5 5,369 Proven 99.9 95.3 96.5 11,646 Young 99.8 96.8 97.7 Jersey 145 Imputed 95.2 87.7 92.1 1,361 Proven 99.6 93.1 94.4 706 Young 99.8 93.9 95.2 Brown Swiss 48 Imputed 95.5 88.4 92.2 506 Proven 99.9 93.6 94.6 207 Young 99.9 93.0 94.5 Example 8 Imputed 98.7 99.9 50.0 117 Proven 99.9 96.9 97.3 185 Young 99.8 96.4 96.8
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Haplotype probability with 100 Haplotype probability with 100 markers per chromosomemarkers per chromosome
0
0.5
1
1 129 257 385 513 641 769 897 1025
SNP Number
Pat
ern
al P
rob
abili
ty
Dense SNPs
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Haplotype probability with 12Haplotype probability with 12markers per chromosomemarkers per chromosome
0
0.5
1
1 129 257 385 513 641 769 897 1025
SNP Number
Pat
ern
al P
rob
abili
ty Dense SNPs
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Gains from tracing true or estimated parent haplotypes Gains from tracing true or estimated parent haplotypes using 12 markers per chromosome as compared to using 12 markers per chromosome as compared to
genotyping progeny for 1000 markers per chromosome.genotyping progeny for 1000 markers per chromosome.
Squared correlations * 100 12 markers
Breed
Corr(low, high density
GEBV) Parent
average True
haplotypes Estimated haplotypes
1000 markers
Percent of Gain
Holstein .91 21 77 76 88 82 Jersey .92 22 80 80 90 85 Brown Swiss .88 43 73 73 96 58 Example .92 23 52 52 60 83
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Benefits of HaplotypingBenefits of Haplotyping
Gains in reliability above PA with haplotyping and 384 markers:• 80% of the 50K gains if genotypes of both
parents are available • Nearly as good for all traits and breeds
Without haplotyping:• 30-40% of gain for Net Merit• Less for other traits and breeds
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Regressions and squared correlations (x100) using Regressions and squared correlations (x100) using August 2006 data to predict August 2009, and observed August 2006 data to predict August 2009, and observed reliability gains as compared to November 2004 cutoff.reliability gains as compared to November 2004 cutoff.
Parent Avg Genomic prediction REL Gain
Trait REL R2 R2 Bias Regression RELNov 2004
Aug 2006
Net merit 35 14 27 -25 .81 59 21 23
Milk 39 18 41 -54 .89 70 23 32
Fat 39 16 42 -4 .91 75 27 36
Protein 39 19 39 -1 .86 67 20 28
Fat % 39 23 62 .00 .96 92 47 54
Protein % 39 28 58 .00 .86 80 37 41
PL 33 16 31 -1.0 1.08 66 32 33
SCS 35 15 30 -.01 .80 61 21 25
DPR 33 18 27 -.1 1.07 53 25 20
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Lower and Higher Density ChipsLower and Higher Density Chips
384 marker low-cost assay• 96 parentage + 288 selected for Net Merit $• Available in fall 2009
600,000 marker chip• Expected to be available in 2010
3 billion full sequence of individual• Blackstar (most related to HO breed)• Already done by USDA Bovine Functional
Genomics Lab
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Best Chromosome 1 Best Chromosome 1 Co-Op Boliver LishaCo-Op Boliver Lisha
-40
0
40
80
120
160
X 2 4 6 8 10 12 14 16 18 20 22 24 26 28
Chromosome
Net
Mer
it $
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Best Chromosome 2 Best Chromosome 2 Kellercrest Earnit HankKellercrest Earnit Hank
-40
0
40
80
120
160
X 2 4 6 8 10 12 14 16 18 20 22 24 26 28
Chromosome
Net
Mer
it $
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Best Chromosome 3 Best Chromosome 3 Wesselcrest Sidney AricWesselcrest Sidney Aric
-40
0
40
80
120
160
X 2 4 6 8 10 12 14 16 18 20 22 24 26 28
Chromosome
Net
Mer
it $
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Boliver
-40
-20
0
20
40
60
80
100
Lisha
-40
-20
0
20
40
60
80
100
120
140
160
Hank
-60
-40
-20
0
20
40
60
80
100
120
140
160
Aric
-60
-40
-20
0
20
40
60
80
100
120
140
160
Cactus
-40
-20
0
20
40
60
80
100
120
Walkman
-60
-40
-20
0
20
40
60
80
100
120
Snow
-60
-40
-20
0
20
40
60
80
100
120
140
Ringo
-60
-40
-20
0
20
40
60
80
100
120
140
Taffy
-60
-40
-20
0
20
40
60
80
100
120
140
Merit
-60
-40
-20
0
20
40
60
80
100
120
Elegant
-60
-40
-20
0
20
40
60
80
100
120
140
Lon
-60
-40
-20
0
20
40
60
80
100
120
140
Planet
-40
-20
0
20
40
60
80
100
120
Wizard
-60
-40
-20
0
20
40
60
80
100
120
Moses
-40
-20
0
20
40
60
80
100
120
140
160
Diddley
-40
-20
0
20
40
60
80
100
120
140
Bram
-60
-40
-20
0
20
40
60
80
100
120
Tuple
-40
-20
0
20
40
60
80
100
Classic
-60
-40
-20
0
20
40
60
80
100
120
Skyler
-40
-20
0
20
40
60
80
100
120
140
Calypso
-150
-100
-50
0
50
100
150
Gaston
-40
-20
0
20
40
60
80
100
Cri
-60
-40
-20
0
20
40
60
80
100
Howie
-60
-40
-20
0
20
40
60
80
100
120
Impressive
-100
-50
0
50
100
150
Luther
-60
-40
-20
0
20
40
60
80
100
120
Mic
-40
-20
0
20
40
60
80
100
120
Blade
-40
-30
-20
-10
0
10
20
30
40
50
60
70
Tabbon
-100
-80
-60
-40
-20
0
20
40
60
80
100
Sherry
-40
-20
0
20
40
60
80
100
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Best Chromosomes 1-30Best Chromosomes 1-30Genomics Extraordinaire, +3148 Net Merit $Genomics Extraordinaire, +3148 Net Merit $
-40
0
40
80
120
160
X 2 4 6 8 10 12 14 16 18 20 22 24 26 28
Chromosome
Net
Mer
it $
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Embryo SelectionEmbryo Selection
In vitro embryos from heifers before puberty• Further reduce generation interval
Frozen, genotyped embryo market• Cost of genotyping < cost of ET• Could replace AI if accuracy high
Very rapid generation turnover• Velogenetics not yet feasible