Computational protocol: Using genetic diversity information to establish core collections of Stylosanthes capitata and Stylosanthes macrocephala

Similar protocols

Protocol publication

[…] Allele frequencies, observed and expected heterozygosities (HO and HE) and Roger’s genetic distance modified by were calculated using the Tools for Population Genetic Analysis (TFPGA) software (). Population structure was inferred using STRUCTURE 2.0 software (), and the accessions were assigned to groups based on their genotypes. STRUCTURE uses model-based clustering in which a Bayesian approach identifies clusters based on their fit to Hardy-Weinberg and linkage equilibria.The optimum number of populations (K) was selected after ten independent runs with a burn-in period of 300,000 and 400,000 replications using a model that does not allow for admixture or correlated allele frequencies. The procedure described by was used to estimate the most probable number of distinct genetic groups (K) in each germplasm collection. Nei’s GST among the groups defined by the STRUCTURE analysis was calculated using the software FSTAT ().Genetic relationships among the accessions based on the genotypic data and Roger’s genetic distance were estimated using a Neighbor-Joining method in DARwin 5.0 software ().Finally, by using the software COREFINDER () we assembled a core collection that should represent 100% of the genetic diversity present within the entire collection. […]

Pipeline specifications

Software tools TFPGA, DARwin
Applications Phylogenetics, Population genetic analysis
Organisms Magnusiomyces capitatus