UPIC

UPIC optimizes selection of SSR/STR marker combinations to maximize discriminatory power for DNA fingerprinting and genotyping experiments.

Key Features:

• Marker Combination Optimization: Evaluates unique patterns of SSR/STR alleles across sample subsets to identify marker combinations that maximize discrimination with minimal marker count.
• Exhaustive Combination Evaluation: Computationally evaluates all possible combinations of markers to identify those that provide maximum discriminatory power.
• Resource Efficiency: Enables selection of small informative marker subsets and demonstrates that as few as three markers may suffice to distinguish 12 genotypes.
• Comparative Efficiency: Shows that four markers can provide nearly equivalent information to six markers (23 vs. 25 patterns), complementing polymorphism-information content (PIC) metrics.
• Comprehensive Analysis Tools: Provides Perl scripts to calculate percentage of heterozygous loci and three distinct PIC values tailored to fertilization types and allele frequencies.

Scientific Applications:

• DNA fingerprinting and genotyping: Optimization of SSR marker panels for discriminating individual genotypes in fingerprinting and genotyping studies.
• Population genetics: Selection of informative SSR markers for analyses of genetic variation and allele frequency distributions.
• Conservation biology: Identification and differentiation of genotypes for conservation management and genetic monitoring.
• Breeding programs: Design of cost-effective genotyping schemes for cultivar identification and breeding selection.

Methodology:

UPIC begins with screening SSR markers on a subset of samples and uses Perl scripts to evaluate all possible marker combinations, identify those with maximal discriminatory power and minimal marker use, and compute percentage heterozygous loci and three PIC values tailored to fertilization types and allele frequencies.