Fetching SNPs: A Dog Genotyping Laboratory for Undergraduate Biology

Author(s):

Keith Hultman and Eve Mellgren

Overview:
This multi-week lab project is designed to increase comprehension of the core concept of genetic variation, and give undergraduate students experience with applying their knowledge of genetic variation using derived Cleaved Amplified Sequence (dCAPS) genotyping on DNA isolated from dogs. Students collect buccal samples of canine DNA, extract genomic DNA, and use PCR followed by restriction digests to determine which SNP alleles are present in each dog. They then analyze the genotype information to answer proposed forensic scenarios and test student-generated hypotheses involving the association of SNP markers with several dog traits. The lab can be used in a sophomore level genetics class where students are just being introduced to the concepts of genetic variation and genotype detection and have very little experience using molecular techniques. It can also be adapted for upper-level laboratories with the inclusion of primer design of additional dCAPS markers.
Genetics Concept(s) Addressed:

Transmission/patterns of inheritance: How can one deduce information about genes, alleles, and gene functions from analysis of genetic crosses and patterns of inheritance?

Genetic variation: How do different types of mutations affect genes and the corresponding mRNAs and proteins?

Evolution and Population Genetics: What are the processes that can affect the frequency of genotypes and phenotypes in a population over time?

Genetics of Model Organisms: How do the results of molecular genetic studies in model organisms help us understand aspects of human genetics and genetic diseases?
Core Competencies Addressed:

Students should be able to implement observational strategies to formulate a question.

Students should be able to generate testable hypotheses.

Students should be able to design an experiment using appropriate controls and appropriate sample sizes.

Students should be able to gather and evaluate experimental evidence, including qualitative and quantitative data.

Students should be able to effectively explain genetics concepts to different audiences.

Students should be able to identify and critique scientific issues relating to society or ethics.

Audience:

Intermediate undergraduate (advanced undergraduate option); biology/genetics majors
Activity Type:

Laboratory Exercise
Activity Length:

3 or 4 three-hour lab periods

Keywords:

Genetic Variation, SNP, Genotyping, dCAPS, Dog, Genetic Markers, Population Genetics, Ancestry, Forensic Applications

Citation:

Hultman, Keith and Mellgren, Eve (2014). Fetching SNPs: A Dog Genotyping Laboratory for Undergraduate Biology. Genetics Society of America Peer-Reviewed Education Portal (GSA PREP): 2014.001; doi: 10.1534/gsaprep.2014.001

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Resource Justification and Instructor Guide

Inclusive List of Instrumentation and Reagents

Student Laboratory Manual(PDF, Word)

Supplementary Materials:

Sample Collection Handout(PDF, Word)

dCAPS Genotyping Slides (Pre-Lab Discussion)