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Choosing Plants for PCR Analysis: Exploring Gene Homology in Diverse Species

This guide focuses on studying gene diversity of GAPC and GAPC-2 genes across various plant species. Through sequence similarities, we assess relatedness between plants, utilizing Arabidopsis sequences as a reference. Using the BLAST search tool, we identify similar nucleotide sequences to select relevant species for PCR analysis. Our project proposes three species available in Southern California, considering factors such as gene type, scientific names, and PCR suitability based on prior experiences. Effective sampling strategies are also discussed, emphasizing the importance of leaf selection for DNA isolation.

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Choosing Plants for PCR Analysis: Exploring Gene Homology in Diverse Species

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  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 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

  3. 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

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

  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 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

  7. Sample Table for Proposing Plant Species 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 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

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