Computational protocol: Traditional agroecosystems as conservatories and incubators of cultivated plant varietal diversity: the case of fig (Ficus carica L.) in Morocco

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[…] For each SSR locus, alleles were detected and identified by locus name and allele size in bp. Genetic distances between fig genotypes were estimated according to the Jaccard similarity coefficient and UPGMA algorithm using a program developed by J. Brzustowski http://www.biology.ualberta.ca/jbrzusto/cluster.php. The corresponding phenogram was drawn based on the software Treeview 6.1. Discriminating power, D, was calculated for each SSR locus as Dj = ∑pi [(Npi-1)/N-1)] [] where pi was the frequency of the i-th molecular pattern revealed by locus j, and N was the number of genotypes. We used the Dj values to compute the exact probabilities of getting at least one pair of genotypes differing only at 0, 1, 2, 3, 4, 5 and 6 loci.The number of alleles per locus (A), observed heterozygosity (HO), expected heterozygosity (HE) and Wright's fixation index (F = 1- HO/HE) were computed using the software Genetix 4.5 []. Genetic diversity was compared among geographic zones using parameters corrected for sample size []. Genetic differentiation between populations was assessed using FST values and the software Genepop 3.1 []. The significance of population differentiation was estimated using exact tests [].To assess genetic isolation by distance, spatial genetic structure was investigated using a spatial autocorrelation method. Genetic relationships between all pairs of genotypes were regressed on the linear and the logarithmic geographical distance using the software SPAGeDi []. The kinship coefficient of Loiselle et al. [], robust against the presence of low frequency alleles, was used. Significance of the regression coefficients was assessed through 10,000 permutations. […]

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