DNA Fingerprinting
PBG/MCB 620
Sept. 24 to Oct. 15, 2012
Instructors:
Dr. Alfonso Cuesta-Marcos
245 Crop Science Bldg. ph: 737-5088 alfonso.cuesta-marcos@oregonstate.edu
The objective of this module is to introduce DNA fingerprinting methodology. The student will be introduced to DNA fingerprinting platforms, the analysis of fingerprinting data, and the pertinent software. Upon completion of this module, the student will be able to generate, analyze, and interpret DNA fingerprinting information.
Sept. 29 to Oct. 13
Lecture Topics
1.
DNA Fingerprinting
Reading:
Weising, et al. (2005), Chapter 6 – Applications of DNA fingerprinting in Plant Sciences
2.
DNA Polymorphism a.
Principles b.
Applications
Reading:
Weising, et al. (2005), Chapter 1 – Repetitive DNA: An Important Source of Variation in
Eukaryotic Genomes
3.
Common Marker Systems a.
Advantages b.
Disadvantages
Reading:
Weising, et al. (2005), Chapter 2 – Detecting Variation by Molecular Markers
4.
New Generation of Whole-Genome Genotyping Platforms
Reading:
Weising, et al. (2005), Chapter 9 – Future Prospects: SNiPs and Chips for DNA and RNA
Profiling
Syvänen, A.-C. (2005). Toward genome-wide SNP genotyping. Nature Genetics 37: S5 -
S10.
Fan, J.-B., M. S. Chee, et al. (2006). Highly parallel genomic assays. Nature Reviews
Genetics 7(8): 632-644.

5.
Marker Utility and Informativeness
Reading:
Weising, et al. (2005), Chapter 8 – Which Marker for What Purpose: A Comparison
Powell, W., M. Morgante, et al. (1996). The comparison of RFLP, RAPD, AFLP and
SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2(3): 225-
238.
Jones, C. J., K. J. Edwards, et al. (1997). Reproducibility testing of RAPD, AFLP and
SSR markers in plants by a network of European laboratories. Molecular Breeding
3(5): 381-390.
6.
Multivariate Analysis of DNA genotypes a.
Genetic similarity measures b.
Principal components analysis c.
Cluster analysis d.
Population Structure
Reading:
Weising, et al. (2005), Chapter 5 – Evaluation of Molecular Marker Data
Mohammadi, S. A. and B. M. Prasanna (2003). Analysis of Genetic Diversity in Crop
Plants--Salient Statistical Tools and Considerations. Crop Science 43(4): 1235-1248.
Reif, J. C., A. E. Melchinger, et al. (2005). Genetical and Mathematical Properties of
Similarity and Dissimilarity Coefficients Applied in Plant Breeding and Seed Bank
Management. Crop Science 45(1): 1-7.
Homework
Students will be given datasets and a homework problem that has to be completed before the hands-on exercise period.
Hands-on Exercise
Students will meet in the Crop Science Bldg. computer lab (CS150) where they will be introduced to the following software for the analysis of DNA fingerprinting data:
POWERMARKER ( http://statgen.ncsu.edu/powermarker/ )- A user-friendly comprehensive set of programs for genetic marker data and population genetic data analyses.
MEGA ( http://www.megasoftware.net/ ) - An integrated tool for automatic and manual sequence alignment, phylogenetic tree construction, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
STRUCTURE ( http://pritch.bsd.uchicago.edu/software.html
) – A tool to use model-based
(Bayesian) clustering using multilocus genotype data to infer population structure and assign individuals to populations.
TASSEL ( http://www2.maizegenetics.net/index.php?page=bioinformatics/tassel/index.html
) - A software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.

Students will be given datasets for analysis and problem questions that need to be completed before the end of this module.
Grading:
Grading for this module will be based on completion of a) a homework problem; b) a hands-on exercise project; and c) class participation. a. Homework problem – 35% of grade b. Hands-on project – 45% of grade c. Participation – 20% of grade
Books for Reference:
B. Flury. 1988. Common principal components and related multivariate models. Wiley, New
York, NY.
Call No. QA278.5 .F58 1988
B. S. Everitt et al. 2001.Cluster Analysis. New York, Oxford University Press.
Call No. QA278 .E9 2001
D.M. Hillis et al. Molecular systematics. Sinauer Associates, Sunderland, MA.
Call No. QH83 .M665 1996
B.-H. Liu. 1998. Statistical Genomics: Linkage, Mapping and QTL analysis. CRC Press LLC,
Boca Raton, FL.
Call No. QH438.4.S73 L55 1998
S.D.J. Pena et al. 1993. DNA fingerprinting : State of the Science. Birkhäuser Verlag, Boston,
MA.
Call No. RA1057.55 .D637 1993
K. Weising, et al. 2005. DNA Fingerprinting in Plants : Principles, Methods, and Applications.
Taylor & Francis Group, Boca Raton, FL.
Call No. QK981.45 .D54 2005
B.S. Weir. 1990. Genetic data analysis. Sinauer Associates, Sunderland, MA.
Call No. QH438.4.S73 W5 1990
B.S. Weir. 1996. Genetic data analysis II: Methods for discrete population genetic data. Sinauer
Associates, Sunderland, MA.
Call No. QH438.4.S73 W5 1996
K. Weising, et al. 1995. DNA fingerprinting in plants and fungi. CRC Press, Boca Raton, FL.
Call No. QK981.45 .D54 1995