Computational protocol: Global Wild Annual Lens Collection: A Potential Resource for Lentil Genetic Base Broadening and Yield Enhancement

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Protocol publication

[…] The entire set of Lens species was used for developing a core collection using “PowerCore” ( software developed at the Rural Development Administration (RDA), South Korea . Separate sets were developed using both quantitative and qualitative data in combination as well as in isolation. “PowerCore” creates subsets representing all alleles or observation classes, with the least allelic redundancy, and ensures a highly reproducible list of entries. The Shannon Diversity Index was used to compare the representativeness of the entire holding and the accessions selected as core entries. [...] Diversity analysis was conducted using both qualitative and quantitative phenotypic data of complete set of 405 accessions as well as of the core set developed from it. Genetic relationships among accessions were determined by means of Dice’s coefficient in case of qualitative data. Phenotypic relationships based on quantitative data were determined from the Euclidean distances. Trees were constructed using hierarchical clustering method by means of Jaccard’s coefficient with UPGMA mode with the DARwin 5.0 software , . […]

Pipeline specifications

Software tools PowerCore, DARwin
Applications Phylogenetics, WGS analysis
Organisms Lens culinaris, Meleagris gallopavo