1. Geneomics and Database Mining and Genetic Mapping
DNA make RNA makes Protein and proteins do things…

2. Sequence databases change how we “do” biology

3. Mapping requires: The ability to measure traits Differences that segregate in populations Statistical and computational techniques to build maps in conventional and unconventional populations

4. What techniques can we use to measure genetic differences and similarities?
RFLPs showing co-dominant inheritance in an F2

5. PCR-based CAPs, SNPs, SSRs…….
Markers showing expected 7:1 segregation in an inbred backcross populations (BC2S5)

6. AFLPs showing dominant inheritance.

7. How to “mine” sequence data for:
Genetic markers
SSRs, SNPs, Conserved motifes
How to analyze sequence data using distributed resources
Identification of ORFs
Identification of probable gene function
more….

8. Saturated maps and targeted marker hunts
Many crops and model species have saturated genetic maps
Marker data can be accessed through specialized web sites (e.g. SGN for tomato
map position
trait data (cross specific)
Sequence of selected RFLPs

9. Detection of SNPs “in silico”
Align
BLAST two sequences ClustalX

10. Finding signal through the noise
False positive
The rate of
PM < error
True SNP

11. Sequence data opens up possibilities of designing markers in silico from conserved regions (e.g. resistance gene analogs).

12. New applications: Proteomics – from protein to gene

13. 2-DE of low stringency fractions (soluble protein)
Inoculated Un-inoculated 2353

14. 2-DE of high stringency fractions (membrane bound)

15. From protein to gene O

16. From protein to gene
From peptide fragments or amino acid sequence to DNA sequence is software driven.
Example:
Expert Protein Analysis System proteomics server of the Swiss Institute of Bioinformatics
Protein Prospector UCSF Mass Spectrometry Facility

17. Before we use markers in the lab for a mapping exercise……
Introduction to public data-bases
Basic DNA sequence manipulation (FASTA format, Sequence utilities, ORF finder, BLAST)
Peptide Sequence searching
Exercise (first hand experience)