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Applications of SNP Technology

Applications of SNP Technology. Mahdi Saatchi Department of Animal Science, Iowa State University. . Applications:. QTL Mapping LD Mapping (Association Mapping) Genomic Selection. QTL Mapping:. M. Q. Quantitative Trait Loci (QTL): polygenes affecting complex trait. M. Q. M. Q.

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Applications of SNP Technology

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  1. Applications of SNP Technology Mahdi Saatchi Department of Animal Science, Iowa State University.

  2. Applications: • QTL Mapping • LD Mapping (Association Mapping) • Genomic Selection

  3. QTL Mapping: M Q • Quantitative Trait Loci (QTL): polygenes affecting complex trait M Q M Q m q m q m q

  4. Some concepts: • Phenotypic variance. • Genetic and environmental variances. • Heritability.

  5. QTL Mapping: • Needs to special experimental designs which: 1- control starting genetic variance 2- reduce the environmental variance 3- increase the number of meiosis as desired Most designs starts with two inbred parents.

  6. QTL Mapping: Experimental Designs

  7. QTL Mapping: Interval Mapping

  8. Q Q Q Q Q Q Q M M M M M M M q q q q q m m m m m q q q q q Q m m m m m m q q Q Q Q Q Q M M M M M M M LD Mapping (Association Mapping): • Linkage disequilibrium (LD) is the nonrandom association of alleles.

  9. Factors affecting LD mapping: • The heritability of trait • The number of genes affecting trait • The penetrance and expressivity of the QTL • The extend and uniformity of LD • Population stratification

  10. Population-based Case-Control: • Marker frequencies are determined in a sample of affected individuals (the “cases”) and compared with marker frequencies in sample of unaffected (the “controls”). • Observed and expected frequencies can be contrasted by a chi-square analysis.

  11. Population-based Case-Control:

  12. Genome Wide Association Study (GWAS): • It became feasible to scan entire genomes for association with disease or phenotypes.

  13. Genome Wide Association Study (GWAS):

  14. Genomic Selection:

  15. MAS limitations: • Not capturing all genetic variance of a complex trait with few number of markers.

  16. Genomic Selection:

  17. Genomic Selection:

  18. Genomic Selection:

  19. Genomic selection in animals:

  20. Genomic selection in plants:

  21. Genomic Selection Problems: • Large p Small N problem.

  22. Genomic Selection Problems: • Incomplete LD between marker and QTL. • DNA chips with more than 700000 SNPs are now available (NGS data also coming!). • Why from 50k to 700k? • Do you think that it could help? • How about using tag SNPs?

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