Detecting a Transposon Tag in Arabidopsis

Overview & Concepts

This lab - produced by the DNA Learning Center and available at http://www.greenomes.org/ - allows students to investigate a gene in Arabidopsis to analyze the molecular relationship between genotyes and phenotypes.  It also helps them understand the use of transposable elements to mutagenize and tag genes as well as the role of homeotic genes in plant and animal development.  Some of the lab techniques utilized in this lab include DNA extraction and purification, PCR, and gel electrophoresis.

Grade Level: 

Concepts Covered: 

Genetics, DNA sequence, gel electrophoresis, DNA extraction and purification, PCR

Prior Knowledge Required: 

Students should have an understanding of genetics and DNA.   They should also be introduced to the concept of transposon mutagenesis stemming from Barbara McClintock’s work with maize.  Student should be familiar with the process of gel electrophoresis and PCR as well as the basic anatomy of flowering plants.

Activity Notes

Days to Teach: 

1-2 Weeks

Materials: 

This activity was produced by the DNA Learning Center and is available online at http://www.greenomes.org/.Please see page 18 of “Detecting a Transposon Tag in Arabidopsis” by DNA Learning Center, Cold Spring Harbor Laboratory for a list of all reagents, supplies, and equipment needed. Pages 1-11 served as my student handout for this lesson.

Teaching Tips / Activity Overview: 

  1. 3-4 weeks before you want to isolate the DNA from Arabidopsis, plant the seeds, water them, and allow them to grow.  Follow the directions on page 4 of “Detecting a Transposon Tag in Arabidopsis" for specific planting instructions.
  2. When you are ready to start the lab have students read the introduction to the activity on pg. 1-2 of “Detecting a Transposon Tag in Arabidopsis.”  Discuss any questions the students have and share with them the general time frame you plan to follow for the next few days including a listing of the major lab techniques that will be used (gel electrophoresis, DNA extraction and purification, PCR).  There is a nice lab flow chart to share with students on page 3 of “Detecting a Transposon Tag in Arabidopsis.”
  3. Explain that the major concepts to be learned are the relationship between genotype and phenotype, the use of transposable elements to mutagenize and tag genes, and the role of homeotic genes in plants and animal development.
  4. Have students pair up for the lab exercises and hand out pg. 4-11 of “Detecting a Transposon Tag in Arabidopsis.”  (If supplies are limited it would also work to have students work in groups of 4.)  Assign students to review the methods and analysis sections of the lab on pg 4-10. 
  5. The pacing at which you complete the lab will vary based on the amount of time you have your students in class.  There is an activity time table I found helpful to reference on pg. 19 of “Detecting a Transposon Tag in Arabidopsis.”  I think this activity would work best in classes on block schedule or if you have double lab periods with students on alternating days. The traditional 40ish minute class periods would most likely be too short to accomplish most of the PCR and gel electrophoresis procedures unless the teacher completes many of the procedures for the students before or after the students are in class.
  6. There is also a bioinformatics portion of “Detecting a Transposon Tag in Arabidopsis" which starts on pg. 12.

Assessment: 

  • Formative assessment: I would suggest using red, yellow, and green triangle "traffic cards" at student lab stations so that students can effectively communicate their level of confidence while completing the lab so the teacher will know which groups they need to focus their attention on. 
  • For a summative assessment, I would require students to submit a photo of their gel on a piece of paper with all bands labeled with their identification and size.  On the paper with their gel photo students would have to answer the following question: Why is a second primer set CLF1/Ds used to identify the insertion allele, rather than SLF1/CLF2?  (This question was taken from pg. 11 of “Detecting a Transposon Tag in Arabidopsis.”

Extensions: 

  • There is  a bioinformatics portion of “Detecting a Transposon Tag in Arabidopsis" on pg. 12-17.

Resources: 

  • DNA Learning Center: The Greenomes site is a laboratory- and Internet-based curriculum to keep students current with modern plant research. It includes a set of laboratories illustrating key concepts of gene analysis in plants, including the relationship between phenotype and molecular genotype, genetic modification of plants and detection of transgenes in foods, and linkage and bioinformatics methods for gene mapping.  “Detecting a Transposon Tag in Arabidopsis" can be found of the DNA Learning Center site: http://www.greenomes.org/
  • ABRC: Arabidopsis Biological Resource Center: The ABRC site is full of information on ordering Arabidopsis seed stock, how to pland and handle seeds, and has a link to a bank of educational resources that use Arabidopsis (see below).  http://abrc.osu.edu/
  • Arabidopsis Educational Resources, ABRC Educational Website: This site contains lots of different modules for high school classroom and laboratory projects along with the resources needed for their completion.  It has lots of helpful and entertaining animations, pictures, and videos.  http://abrcoutreach.osu.edu/

Acknowledgements: 

The activity was produced by the DNA Learning Center and is available at http://www.greenomes.org/. These teacher notes and resources, produced by Melissa Barr, adapted from DNA Learning Center, Cold Spring Harbor Laboratory, 2005, outline how a teacher could use the resource in a classroom.

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