1. Choosing Plants for PCR Analysis

2. Measuring Gene Homology We would like to study the diversity of GAPC and GAPC-2 genes in various plant speciesWe would like to study the diversity of GAPC and GAPC-2 genes in various plant species To assess the relatedness of plant species, we can look for similarities in gene sequencesTo assess the relatedness of plant species, we can look for similarities in gene sequences The sequences of the GAPC and GAPC-2 genes in Arabidopsis can be used to find plants with similarities and differences to studyThe sequences of the GAPC and GAPC-2 genes in Arabidopsis can be used to find plants with similarities and differences to study

3. Using a BLAST search to locate similar sequences Go to http://blast.ncbi.nlm.nih.gov/Blast.cgiGo to http://blast.ncbi.nlm.nih.gov/Blast.cgihttp://blast.ncbi.nlm.nih.gov/Blast.cgi Select “nucleotide blast”Select “nucleotide blast” Add the sequence for either GAPC or GAPC-2 to the box at the top of the page (will be posted in a Word doc to be copied and pasted)Add the sequence for either GAPC or GAPC-2 to the box at the top of the page (will be posted in a Word doc to be copied and pasted) For Database, select “Nucleotide Collection”For Database, select “Nucleotide Collection” Optimize for “Somewhat Similar Sequences”Optimize for “Somewhat Similar Sequences” Select the blue “BLAST” button at the bottomSelect the blue “BLAST” button at the bottom

4. BLAST Results Max (Bit) Score indicates the overall quality of the alignment “Identities” will show how many nucleotides match exactly

5. Select the record of interest Species name  soybeans

6. Included in the Introduction and Hypothesis Submission on 1-14 Propose three plant species for possible PCR analysisPropose three plant species for possible PCR analysis Indicate whether the gene for GAPC or GAPC-2 was used to find related sequencesIndicate whether the gene for GAPC or GAPC-2 was used to find related sequences Provide scientific name, common name, bit score and identitiesProvide scientific name, common name, bit score and identities Be sure that the plants are available in the Southern California area and can be recognized and collectedBe sure that the plants are available in the Southern California area and can be recognized and collected

7. Sample Table for Proposing Plant Species Scientific Name Common Name Bit ScoreIdentities Gene: ____________________ (GAPC or GAPC-1)

8. Bio-Rad List of Suggested Species

9. Dr. Colavito’s Suggestions Based on Prior SMC Experiences DNA isolation works better from thin leaves than from other plant partsDNA isolation works better from thin leaves than from other plant parts Plants available on campus include: sage (3 varieties), lemon grass, sugar cane, marjoramPlants available on campus include: sage (3 varieties), lemon grass, sugar cane, marjoram Plants obtained from home/market: brussels sprouts, cabbage, mint, oregano, parsley, schefflera, spinach, thymePlants obtained from home/market: brussels sprouts, cabbage, mint, oregano, parsley, schefflera, spinach, thyme