Computational protocol: Assessment of the Genetic Diversity Among Potato Cultivars from Different Geographical Areas Using the Genomic and EST Microsatellites

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Protocol publication

[…] Reproducible and clear bands were scored as binary characters (i.e., their presence () or absence (0)). The PowerMarker software Ver. 3.25 () was used to estimate the number of alleles per locus, observed heterozygosity (Ho), gene diversity (expected heterozygosity, He), and the polymorphism information content (PIC). The power of discrimination was calculated using the formula: PD = 1-Σgi2, where gi is the frequency of the ith genotype (). Dissimilarity matrices (1000 bootstraps) were calculated for the single data based on presence/absence of the alleles using the Jaccard coefficient, and the cluster analysis was performed using unweighted paired group method with arithmetic average (UPGMA) as implemented in DARwin 5 software (). Genetic relationships among genotypes were further analyzed by the principal component analysis (PCA) of a similarity matrix according to the extracted Eigen vectors in NTSYSpc version 2.02i. POPGENE 1.32 software () was used to calculate the effective number of alleles per locus (Ne), expected heterozygosity (He), Shannon’s Information index (I), and the gene flow (Nm). The program STRUCTURE 2.3.3 was applied to classify individuals into their origin and identification of the genetic relationship as well as ancestral source populations of the potato’s genotypes (29; available at http://pritch.bsd.uchicago.edu/structure.html) by two independent runs of K = 1-2 using the admixture model with 10,000 repetitions of MCMC. […]

Pipeline specifications

Software tools PowerMarker, NTSYSpc, POPGENE
Application Population genetic analysis
Organisms Solanum tuberosum
Diseases Genetic Diseases, Inborn