Computational protocol: Assessment of Genetic Diversity of Sweet Potato in Puerto Rico

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Protocol publication

[…] The scored data for the 23 SSR markers were converted into a weight matrix in Microsoft Excel and further converted into text using TextPad ver. 6.2.2 (Helios Software Solutions, Longridge, England). The GenoDive program was used to determine the genetic diversity estimators [i.e. observed and total heterozygosity (HO and HT, respectively), and inbreeding coefficient (Gis)] and allele frequencies. Since in a hexaploid is not possible to determine the actual genotype of an individual based on molecular markers, GenoDive program uses a maximum likelihood method to correct for the unknown dosage of alleles. Briefly, for every incomplete genotype information of an individual, all possible underlying genotypes are considered, new alleles frequencies for this particular locus are determined, and the genotype that end in producing the most likelihood allele frequencies is selected. Thus, this algorithm was employed for every SSR locus in our study. From the weight data, a binary matrix was constructed based on presence and absence of alleles (1, 0) . The matrix was used to determine the PIC value of SSRs and Euclidean genetic distances among accessions as implemented in PowerMarker V3.25 program . The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster method was employed with the Euclidean genetic distances as implemented in PowerMarker V3.25 program. The dendrogram was visualized using the international Tree of Life (iTOL) program , . The population structure group was estimated using the Bayesian cluster analysis as implemented in the Structure 2.3.3 software . The admixtures model with correlated allele frequencies was implemented, with 50,000 burn-in period length and 150,000 MCMC interactions including 3 independent runs for each k set from 1 to 12. Subsequently, the number of groups was determined based on deltaK (ΔK) as implemented in Structure Harvester software , . Lastly, independent runs from the actual number of groups were integrated by CLUMPP version 1.1.2 . The analysis of molecular variance (AMOVA), employing the number of groups previously identified and the binary matrix, was performed using GeneAlEx 6.5 . […]

Pipeline specifications

Software tools Genodive, PowerMarker, iTOL, Structure Harvester, CLUMPP
Applications Phylogenetics, Population genetic analysis
Organisms Ipomoea batatas, Homo sapiens