Choosing Plants for PCR AnalysisChoosing Plants for PCR Analysis

Measuring Gene HomologyMeasuring Gene Homology

• We would like to study the diversity of We would like to study the diversity of GAPC and GAPC-2 genes in various plant GAPC and GAPC-2 genes in various plant speciesspecies

• To assess the relatedness of plant To assess the relatedness of plant species, we can look for similarities in species, we can look for similarities in gene sequencesgene sequences

• The sequences of the GAPC and GAPC-2 The sequences of the GAPC and GAPC-2 genes in genes in ArabidopsisArabidopsis can be used to find can be used to find plants with similarities and differences to plants with similarities and differences to studystudy

Using a BLAST search toUsing a BLAST search to locate similar sequences locate similar sequences

• Go to Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi

• Select “nucleotide blast”Select “nucleotide blast”

• Add the sequence for either GAPC or GAPC-2 Add the sequence for either GAPC or GAPC-2 to the box at the top of the page (will be to the box at the top of the page (will be posted in a Word doc to be copied and posted in a Word doc to be copied and pasted) 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

BLAST BLAST ResultsResults

Max (Bit) Score indicates the

overall quality of the alignment

“Identities” will show how many

nucleotides match exactly

Select the record of interestSelect the record of interest

Species nameSpecies name soybeanssoybeans

Included in the Introduction and Included in the Introduction and Hypothesis Submission on 1-14Hypothesis Submission on 1-14

• Propose three plant species for possible Propose three plant species for possible PCR analysisPCR analysis

• Indicate whether the gene for GAPC or Indicate whether the gene for GAPC or GAPC-2 was used to find related sequencesGAPC-2 was used to find related sequences

• Provide scientific name, common name, bit Provide scientific name, common name, bit score and identities score and identities

• Be sure that the plants are available in the Be sure that the plants are available in the Southern California area and can be Southern California area and can be recognized and collectedrecognized and collected

Sample Table for Proposing Plant Species Sample Table for Proposing Plant Species

Scientific Name

Common Name

Bit Score Identities

Gene: ____________________ (GAPC or GAPC-1)

Bio-Rad List of Suggested SpeciesBio-Rad List of Suggested Species

Dr. Colavito’s Suggestions Based Dr. Colavito’s Suggestions Based on Prior SMC Experienceson Prior SMC Experiences

• DNA isolation works better from DNA isolation works better from thinthin leaves leaves than from other plant partsthan from other plant parts

• Plants available on campus include: Plants available on campus include: sage (3 varieties), lemon grass, sugar cane, sage (3 varieties), lemon grass, sugar cane, marjorammarjoram

• Plants obtained from home/market: Plants obtained from home/market: brussels sprouts, cabbage, mint, oregano, brussels sprouts, cabbage, mint, oregano, parsley, schefflera, spinach, thymeparsley, schefflera, spinach, thyme