1 Understanding the role of markers in locating genes:Flowering Time in Switchgrass (Panicum virgatum L.) Cherrie Anne Maner Fond du Lac School Fond du Lac, WI GLBRC RET Program, Summer 2016

2 2 Overarching Question How are the advancements in genetics used in improving bioenergy crops? INQUIRY ACTIVITY Research question: How do we figure out what markers are linked to QTLs that are associated with flowering time?

3 3 Research background The switchgrass research that is done by USDA-ARS is a meld of traditional plant breeding and modern genomic techniques. Using marker-assisted breeding of upland and lowland cultivars, their aim is to produce a progeny that is winter hardy and has a delayed flowering time. This is key to a successful propagation of switchgrass in colder regions while increasing biomass yield, which is crucial for an efficient cellulosic biofuel production.

4 4 Research background With the mentorship of Dr. M Casler and collaboration with Dr. CE Tornqvist, I developed an AP curriculum material that not only introduces genetic analysis to my students but also providing them the opportunity to experience real-life science. Lab techniques: Leaf tissue collection, DNA extraction, PCR & gel electrophoresis Marker analysis using t-test & JGI site Field observation of switchgrass varieties and accession survey Development of switchgrass genetics lesson plan

5 Learning objectives Students will…5 Learning objectives Students will… Develop models to understand the complexity of quantitative traits and markers, including how these markers are inherited. Run DNA gel electrophoresis to visualize the inheritance of these markers in switchgrass progeny. Perform a statistical analysis (t-test) to identify the significant markers from a set of known markers. Identify possible quantitative trait that the DNA markers are associated with. Use this data to evaluate the significance of DNA markers in studying traits for the improvement of bioenergy crops

6 6 Learning objectives HS-LS1-1. Construct an explanation based on evidence how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells. HS-LS3-1. Ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring. HS-LS3-2. Make and defend a claim based on evidence that inheritable genetic variations may result from: (1) new genetic combinations through meiosis, (2) viable errors occurring during replication, and/or (3) mutations caused by environmental factors. HS-LS3-3. Apply concepts of statistics and probability to explain the variation and distribution of expressed traits in a population.

7 Science and Engineering Practices Disciplinary Core Ideas7 Learning objectives Science and Engineering Practices Disciplinary Core Ideas Cross-cutting Concepts Developing and Using Models Analyzing and Interpreting Data Using Mathematics and Computational Thinking LS1: From Molecules to Organisms: Structures and Processes LS3: Heredity: Inheritance and Variation of Traits Patterns Scale, Proportion and Quantity Systems and System Models Structure and Function Science is a Human Endeavor*

8 Lesson flow Scaffolded modeling activities8 Lesson flow QTL Marker Analysis (identification of significant markers using student t-test) Mapping the marker and determination of possible associated quantitative trait (via JGI website) Scaffolded modeling activities Quantitative Traits (QTs) Quantitative Trait Locus (QTL) and Markers Inheritance of QTs DNA gel electrophoresis Switchgrass seed planting

9 Key activity: Genetic Linkage Analysis9 Key activity: Genetic Linkage Analysis Statistical analysis using student t-test The task of the students is to perform a two-tailed student t-test on each of the markers in a given data set to determine which biomarker is significantly linked with the gene or QTL associated with flowering time. It will provide the students the opportunity to use real-life data from an actual research on plant breeding and simulate techniques in genomic data analysis. Marker analysis using JGI Phytozome 11 website Once they have identified the significant marker, students will now try to locate that marker along the specified chromosome. They will determine the possible quantitative trait this marker is associated with using the JGI (Joint Genomics Institute) Phytozome 11 website. This provides the students an opportunity to explore and formulate questions based on the information from this database website.

10 Switchgrass genetics test10 Assessment Formative Assessment Summative Assessment Mini-poster lab report (using the guideline provided to the students) Switchgrass genetics test (addressing the standards, particularly the Science Practices) QT, marker and QTL modeling activities: Using an example, describe how quantitative traits are different from classic Mendelian (qualitative) traits. Explain the significance of molecular markers to QTLs. Switchgrass DNA gel electrophoresis: Describe how gel electrophoresis (GE) illustrates the unique characteristics between lowland and upland switchgrass varieties. Describe an application of GE to other branches of science. Marker Inheritance Modeling: Use your understanding of crossing over in meiosis, explain how biomarkers and QTLs are inherited. Guided Inquiry: How do we figure out what markers are linked to QTLs that are associated with flowering time? Describe how this analysis can be applied to biomedical science or other scientific fields.

11 Let’s try it out! Part 2. Background: Modeling of quantitative traits11 Let’s try it out! Part 2. Background: Modeling of quantitative traits Goal → to visualize quantitative traits using analogy maps and models. Materials: sheet of paper, pen or pencil (any color) With your dominant hand, write a word. Next, write the same word below what you just wrote, but this time, hold your pen with both hands. Repeat Step 2, but this time, hold one pen with both your hands and those of your partner. Compare the three writings. Do they all look the same? List down other factors that may have affected your handwriting. Compare the different parts of the model to our concept of quantitative traits. How are they similar? Complete the table below. What are some of the limitations of this model? List them in Table 1.

12 12 Let’s try it out! Part 5. Marker analysis using JGI Phytozome 11 website Goal → to locate that marker along the specified chromosome and determine the possible quantitative trait this marker is associated with using the JGI (Joint Genomics Institute) Phytozome 11 website. Task → Assume that the significant marker you have identified is c2a_ Go to the Phytozome 11 site and perform a marker analysis.

13 Remaining Concerns Availability of materials and equipment13 Remaining Concerns Availability of materials and equipment Time constraints Scaffolding process to successfully unpack this complex lesson Rubrics

14 14 Acknowledgements The development of this lesson would not have been possible without the help and support of the following: Dr. Michael Casler, the Switchgrass Yoda (UW-Madison and USDA-ARS) Dr. Carl-Erik Tornqvist, Lord of the QTL analysis (GLBRC, UW-Madison and USDA-ARS) John Raasch, lab technician extraordinaire (USDA-ARS) Joe Halinar, field technician (USDA-ARS) Great Lakes Bioenergy Research Center (GLBRC): Leith Nye for all the valuable feedback and suggestions; Dr. John Greenler, Dr. Joyce Parker and Megan Collins for the support Fellow RETs: Dr. Leon Walls and Lisa Sorlie for the valuable feedback and brainstorming

15 15 Questions?