Development of a core set from a large rice collection using a modified heuristic algorithm to retain maximum diversity.

A new heuristic approach was undertaken for the establishment of a core set for the diversity research of rice. As a result, 107 entries were selected from the 10 368 characterized accessions. The core set derived using this new approach provided a good representation of the characterized accessions present in the entire collection. No significant differences for the mean, range, standard deviation and coefficient of variation of each trait were observed between the core and existing collections. We also compared the diversity of core sets established using this Heuristic Core Collection (HCC) approach with those of core sets established using the conventional clustering methods. This modified heuristic algorithm can also be used to select genotype data with allelic richness and reduced redundancy, and to facilitate management and use of large collections of plant genetic resources in a more efficient way.

PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets.

MOTIVATION: Core sets are necessary to ensure that access to useful alleles or characteristics retained in genebanks is guaranteed. We have successfully developed a computational tool named 'PowerCore' that aims to support the development of core sets by reducing the redundancy of useful alleles and thus enhancing their richness. RESULTS: The program, using a new approach completely different from any other previous methodologies, selects entries of core sets by the advanced M (maximization) strategy implemented through a modified heuristic algorithm. The developed core set has been validated to retain all characteristics for qualitative traits and all classes for quantitative ones. PowerCore effectively selected the accessions with higher diversity representing the entire coverage of variables and gave a 100% reproducible list of entries whenever repeated. AVAILABILITY: PowerCore software uses the .NET Framework Version 1.1 environment which is freely available for the MS Windows platform. The files can be downloaded from http://genebank.rda.go.kr/powercore/. The distribution of the package includes executable programs, sample data and a user manual.