Choosing Plants for PCR Analysis
Measuring Gene Homology
• We 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 sequences
• The sequences of the GAPC and GAPC-2
genes in Arabidopsis can be used to find
plants with similarities and differences to
study
Using a BLAST search to
locate similar sequences
• Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi
• 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)
• For Database, select “Nucleotide Collection”
• Optimize for “Somewhat Similar Sequences”
• Select the blue “BLAST” button at the bottom
BLAST
Results
Max (Bit) Score
indicates the
overall quality of
the alignment
“Identities” will
show how many
nucleotides match
exactly
Select the record of interest
Species name
 soybeans
Included in the Introduction and
Hypothesis Submission on 1-14
• Propose three plant species for possible
PCR analysis
• Indicate whether the gene for GAPC or
GAPC-2 was used to find related sequences
• Provide 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 collected
Sample Table for Proposing Plant Species
Gene: ____________________
(GAPC or GAPC-1)
Scientific
Name
Common
Name
Bit Score
Identities
Bio-Rad List of Suggested Species
Dr. Colavito’s Suggestions Based
on Prior SMC Experiences
• DNA isolation works better from thin leaves
than from other plant parts
• Plants 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, thyme