Computational protocol: ISSR Marker Based Population Genetic Study of Melocanna baccifera (Roxb.) Kurz: A Commercially Important Bamboo of Manipur, North-East India

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[…] Distinct, reproducible, well resolved fragments were scored as present (1) or absent (0) for each ISSR reaction and were displayed as part of a binary matrix. The data matrices obtained were analyzed using POPGENE version 1.31 []. Genetic parameters such as percentage of polymorphic band(s) (PPB), observed number of alleles (Na), the effective number of alleles (Ne), Nei's genetic diversity (H), Shannon's information index (I), total genetic diversity (Ht), genetic diversity within population (Hs), Nei's genetic differentiation index among populations (Gst), and gene flow estimates between populations (Nm) were determined with POPGENE version 1.31 []. Genetic divergence between populations of the bamboo species was also investigated using Nie's unbiased genetic distances and genetic identities []. A study on the correlation (Mantel test) between genetic and geographic distance between the bamboo populations was done using TEPGA version 1.3 with 999 permutations []. An analysis of molecular variance (AMOVA) was performed to estimate the variance components and their significance levels of genetic variation within and among populations using GenALEx version 6.5 []. The unbiased genetic distance was utilized for the construction of a dendrogram using UPGMA (Unweighted Pair Group Arithmetic Mean Method) in POPGENE program version 1.31. In addition, Nei's genetic distance matrix was used to construct Neighbor-Joining dendrogram for the 93 individuals belonging to 7 different populations of M. baccifera using Mega 5.10 []. Principal coordinate analysis (PCoA) was performed using GenALEx version 6.5 [] to determine relative genetic distance between individuals and to check the consistency of population genetic differentiation as defined by cluster analysis. The Bayesian model base clustering method of STRUCTURE software version 2.2 was employed to evaluate the genetic population structure and detect the gene pools contributing to bamboo germplasm collection []. Ancestry model with admixture and correlated allele frequency model were used to determine the posterior probability of the data and a burn in period of 10,000 was set followed by 10,000 Markov Chain Monte Carlo (MCMC) replications. The number of K was set from 1 to 8 with 10 independent runs for every K value. The results of the STRUCTURE outfile were utilized to determine the optimum K value following the simulation method of Evanno et al. [] employing software STRUCTURE HARVESTER []. […]

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