1. Genotyping module

2. Genetic analyzer 3730xl

4. Capillary electrophoresis

5. Capillary electrophoresis

6. Capillary electrophoresis

7. Capillary electrophoresis

8. Capillary electrophoresis

9. Example of genotyping PCR
Sample 1: Homozygous for SSR; alleles are the same size, one band on a gel e.g. 120/120
Sample 2: Heterozygous for SSR; alleles are not the same size, 2 bands on gel e.g. 120/126
Biological significance??

11. Gene Mapper Software
GeneMapper is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems.
Applications: amplified fragment length polymorphism (AFLP), loss of heterozygosity (LOH), microsatellite, and SNP genotyping.

12. Capillary electrophoresis

13. Creating a customized project
KIT
Cassava SSR
PANEL
Co-load group 1
MARKERS
M1 (PET)/ M2 (VIC)/ M3 (6-FAM)/ M4 (NED)

14. Failed PCR

15. Non-specific PCR

16. Primer dimers

17. Pull ups

18. A+/A- hybrid

19. Stuttering

20. 1 marker + Liz 500

21. 1 marker

22. 1 marker- 4 alleles

23. Configuring panels
Defn Panel: A set of markers that can be loaded together
Considerations:
Load markers of different size lengths
Distinguish different markers from those with overlapping size ranges by using dye labels
Use more PCR prdt labeled with dyes of low emission intensity than dyes of high emission intensity.
6-FAM (blue), VIC (green) > NED (black) > PET (red) > LIZ (orange)(highest to lowest)
Liz 500 is the size standard; range: bp, 16 single- strand labeled fragments (35, 50, 75, 100, 139, 150, 160, 200, 250, 300, 340, 350, 400, 450, 490, & 500 bases).

24. Co loading strategy

25. Co loading strategy

26. Co loading strategy