Computational protocol: Diversity and population structure of red rice germplasm in Bangladesh

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Protocol publication

[…] The band-size for each of the markers was scored using the AlphaEaseFC 4.0 software. Using PowerMarker version 3.25 [], summary statistics included the following: the number of alleles, the major allele size and its frequency, gene diversity, and the polymorphism information content (PIC) value. For the unrooted phylogenic tree, the genetic distance was calculated using MEGA 6 based on Nei’s unbiased pairwise [, ]. Binary form for allele frequency was prepared using PowerMarker software and used for dendrogram construction by NTSYS-pc software []. The unweighted pair grouping method using arithmetic average (UPGMA) was used to determine a similarity matrix following the Dice coefficient with the SAHN subprogram.Population STRUCTURE for germplasm was determined using STRUCTURE, (version 2.3.4) [, ]. The number of clusters (K) investigated, in this study, ranged from one to fifteen, with five replications for analysis of each K value. The model following admixture and correlated allele frequency with a 5,000 burn period and a run length of 50,000 were used for conducting model-based structure analysis. Output of analysis was collected using the STRUCTURE harvester [] and identified 4 as the best K value based on the LnP(D) and Evanno’s ΔK []. Principal components analysis (PCA) analysis was conducted also using the STRUCTURE software. In order to summarize the major patterns of variation within the multi-locus dataset, an analysis of molecular variance (AMOVA) using GenAlEx V6.5 [] was also performed. […]

Pipeline specifications

Software tools PowerMarker, MEGA, Structure Harvester, GenAlEx
Applications Phylogenetics, Population genetic analysis
Organisms Oryza longistaminata, Oryza sativa