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DSEC October 2009

This article discusses the benefits of using haplotyping and genotyping in animal breeding, including gains in reliability, improved prediction of traits, and faster generation turnover. It also explores the prospects of lower and higher density chips and the potential of embryo selection using genotyped embryos.

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DSEC October 2009

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  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 12markers 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.

  8. Lower 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

  9. Best Chromosome 1 Co-Op Boliver Lisha

  10. Best Chromosome 2 Kellercrest Earnit Hank

  11. Best Chromosome 3 Wesselcrest Sidney Aric

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

  13. 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

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