Download Understanding the role of markers in locating genes: Flowering Time

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
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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?
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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.
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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.
Field observation of
switchgrass varieties
and accession survey
Lab techniques:
Leaf tissue collection,
DNA extraction, PCR &
gel electrophoresis
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Marker analysis
using t-test & JGI
site
Development of
switchgrass genetics
lesson plan
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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
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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.
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Learning objectives
Science and
Disciplinary Core
Cross-cutting
Engineering Practices
Ideas
Concepts
Developing and Using LS1: From
Patterns
Models
Molecules to
Organisms:
Scale, Proportion and
Analyzing and
Structures and
Quantity
Interpreting Data
Processes
Systems and System
Using Mathematics LS3: Heredity:
Models
and Computational Inheritance
Thinking
and Variation of
Structure and Function
Traits
Science is a Human
Endeavor*
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Switchgrass seed planting
Lesson flow
Scaffolded
modeling
activities
Quantitative
Traits (QTs)
Quantitative
Trait Locus (QTL)
and Markers
QTL Marker
Analysis
(identification of
significant
markers using
student t-test)
DNA gel
electrophoresis
Inheritance of
QTs
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Mapping the
marker and
determination
of possible
associated
quantitative
trait
(via JGI website)
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.
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Assessment
Formative Assessment
QT, marker and QTL modeling activities:
1. Using an example, describe how quantitative traits are
different from classic Mendelian (qualitative) traits.
2. Explain the significance of molecular markers to QTLs.
Switchgrass DNA gel electrophoresis:
1. Describe how gel electrophoresis (GE) illustrates the unique
characteristics between lowland and upland switchgrass
varieties.
2. 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:
1. How do we figure out what markers are linked to QTLs that
are associated with flowering time?
2. Describe how this analysis can be applied to biomedical
science or other scientific fields.
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Summative Assessment
Mini-poster
lab report
(using the guideline
provided to the students)
Switchgrass genetics
test
(addressing the standards,
particularly the Science
Practices)
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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)
1. With your dominant hand, write a word.
2. Next, write the same word below what you just wrote, but this time, hold
your pen with both hands.
3. Repeat Step 2, but this time, hold one pen with both your hands and those
of your partner.
4. Compare the three writings. Do they all look the same? List down other
factors that may have affected your handwriting.
5. Compare the different parts of the model to our concept of quantitative
traits. How are they similar? Complete the table below.
6. What are some of the limitations of this model? List them in Table 1.
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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_22169964. Go to the Phytozome 11 site and
perform a marker analysis.
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Remaining Concerns
• Availability of materials and equipment
• Time constraints
• Scaffolding process to successfully unpack this complex
lesson
• Rubrics
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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
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Questions?
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