Location: Plant Genetic Resources
Title: AlleleCoder: a PERL script for coding codominant polymorphism data for PCA analysis Authors
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.