1. DSEC October 2009

2. Percent correctly called genotypes, linkages, and paternity by breed and group.

3. Haplotype probability with 100 markers per chromosome

4. Haplotype probability with 12 markers per chromosome

5. Gains from tracing true or estimated parent haplotypes using 12 markers per chromosome as compared to genotyping progeny for 1000 markers per chromosome.

6. Benefits 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

7. Regressions and squared correlations (x100) using August 2006 data to predict August 2009, and observed reliability gains as compared to November 2004 cutoff.
Parent Avg
Genomic prediction
REL Gain
Trait
REL R2
Bias
Regression
Nov 2004
Aug 2006
Net merit 35 14 27
-25
.81 59 21 23
Milk 39 18 41
-54
.89 70 32
Fat 16 42 -4
.91 75 36
Protein 19 -1
.86 67 20 28
Fat % 62
.00
.96 92 47 54
Protein % 58 80 37 PL 33 31
-1.0
1.08 66
SCS 15 30
-.01
.80 61 25
DPR
-.1
1.07 53

8. Lower and Higher Density Chips
384 marker low-cost assay
96 parentage 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

9. Best Chromosome 1 Co-Op Boliver Lisha

10. Best Chromosome 2 Kellercrest Earnit Hank

11. Best Chromosome 3 Wesselcrest Sidney Aric

13. Best Chromosomes 1-30 Genomics Extraordinaire, +3148 Net Merit $

14. Embryo 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