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United States Department of Agriculture

Agricultural Research Service

Research Project: CONSERVATION AND CHARACTERIZATION OF GERMPLASM OF SELECTED VEGETABLE CROPS

Location: Plant Genetic Resources

Title: AlleleCoder: a PERL script for coding codominant polymorphism data for PCA analysis

Authors
item Baldo, Angela
item Francis, David -
item Caramante, Martina -
item Robertson, Larry
item Labate, Joanne

Submitted to: Plant Genetic Resources: Characterization and Utilization
Publication Type: Review Article
Publication Acceptance Date: June 29, 2011
Publication Date: July 22, 2011
Citation: Baldo, A.M., Francis, D., Caramante, M., Robertson, L.D., Labate, J.A. 2011. AlleleCoder: a PERL script for coding codominant polymorphism data for PCA analysis. Plant Genetic Resources: Characterization and Utilization. 10: 1-3.

Technical Abstract: A useful biological interpretation of diploid heterozygotes is in terms of the dose of the common allele (0, 1 or 2 copies). We have developed a PERL script that converts FASTA files into coded spreadsheets suitable for Principal Component Analysis (PCA). In combination with R and R Commander, two- and three-dimensional plots can be generated for visualizing genetic relationships. Such plots are useful for characterizing plant genetic resources. This method nicely illustrated the spectrum of genetic diversity in tomato landraces and varieties categorized according to human-mediated dispersal.

Last Modified: 4/18/2014