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Oxytenanthera abyssinica (A. Rich.) Munro; lowland bamboo (Poaceae, Bambusinea) in Ethiopia: Genetic diversity, population structure and gene flow analysis

Citation

Oumer, Oumer Abdie (2021), Oxytenanthera abyssinica (A. Rich.) Munro; lowland bamboo (Poaceae, Bambusinea) in Ethiopia: Genetic diversity, population structure and gene flow analysis, Dryad, Dataset, https://doi.org/10.5061/dryad.b5mkkwh8z

Abstract

As one of the most important non-timber forest resources, a potential alternative to wood and wood product and fastest-growing plant in the world (91 cm (35 in) per day), bamboo is a member of the grass family (Poaceae) and constitutes a single subfamily Bambusoideae. 67% of total area of bamboo in Africa and 7% of world total is contributed by Ethiopia giving more than 1.44 million hectares. Silica gel dried young fresh leaves from 130 individuals of O. abyssinica were collected for DNA extraction and PCR amplification. Each of the PCR amplified ISSR fragments using 19 ISSR primers were used to study band pattern and heterozigosity, level of polymorphism, calculating marker efficiency, Nei`s (H) and Shannon (I) genetic diversity, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA) and admixture results. High genetic variation at species level was observed with the percentage of the polymorphic loci (PPL) = 84.48%. The H, I, observed number of alleles (Na) and effective number of alleles (Ne) at species level was 0.2702, 0.4061, 1.8448, and 1.4744, respectively, showing a relatively high level of genetic diversity. However, the genetic differentiation at the population level was relatively low. AMOVA using grouped populations revealed that, most of the diversity was distributed within the populations (61.05%) with FST = 0.38949, FSC = 0.10486 and FCT = 0.31797. Cluster analysis grouped the populations into sharply distinct clusters, which could be attributed to cross pollination nature of the plant and long lived to the area. STRUCTURE analyses for all population and excluding Gambella population gives different result K = 2 and K = 11. Using these markers, we find strong evidence linking geographic origin of diversity and samples from Gambella Region found different from others and might tell the availability of additional bamboo species in the country.

Methods

Silica gel dried young fresh leaves from 130 individuals representing 13 naturally grown populations of O. abyssinica were collected for DNA extraction and PCR amplification. Each of the PCR amplified ISSR fragments using best 19 ISSR primers out of 38 primers were scored manually. According to the weight of the DNA ladder, the same weight bands were marked as a line. The bands that were clearly visible and repeatable on the electrophoresis map were marked as "1", the absence of a band at the same site was marked as "0" and "?" for the ambiguous bands that were not clearly shown were scored as a missing data. Intensity variations among fragments having approximately the same molecular size were not considered although in some cases intensity differences of the bands were observed.  A binary data matrix was compiled with individuals in the column and the ISSR markers in the row for each primer set and vice-versa according to the requirements of the software’s. Each amplified fragments was named by the code of the primers across the row and/or column followed by the Arabic numbers starting from the fragment having high molecular weight to the fragments with low molecular weight. Both the total number of bands amplified by each primer and the number of polymorphic bands were calculated. On the basis of the recorded band profiles, different software’s were employed for the analysis of the data. used to study band pattern and heterozigosity, level of polymorphism, calculating marker efficiency, Nei`s (H) and Shannon (I) genetic diversity, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA) and admixture results.

Funding

International Fund for Agricultural Development, Award: 2000000529/2000000979

Carnegie Corporation of New York, Award: RU/2016/Carnegie/DFS/007