Molecular Characterization and Systematics of Korarima [Aframomum Corrorima (Braun) P.C.M. Jansen] from Ethiopia
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Date
2017-05-30
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Addis Ababa University
Abstract
Molecular Characterization and Systematics of Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] from Ethiopia
Dagmawit Chombe (PhD candidate)
Addis Ababa University, 2017
Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] is a perennial aromatic herb plant species native to Ethiopia. Morphologically it is classified in the genus Aframomum and family Zingebraceae. It is widely grown in Southwestern part for its fine flavor as a spice in various Ethiopian traditional dishes. A few molecular studies have been performed on this species and no molecular evidence for its taxonomy is present up to date. This study was conducted (1) to determine the magnitude of genetic diversity in cultivated korarima using inter simple sequence repeats, (2) to characterize the population genetic structure and relationships between cultivated and wild korarima using microsatellites, (3) to compare genetic diversity of cultivated korrarima for inter simple sequence repeats and microsatellites markers; and (4) to investigate the phylogenetic relationships in the genus Aframomum including A. corrarima based upon DNA sequences from plastid regions and the internal transcribed spacer region of nuclear ribosomal DNA. High levels of genetic diversity were detected in cultivated A. corrarima (Percentage of polymorphic band = 97.67 %, Gene Diversity = 0.35, Shannon information index = 0.52) when analyzed using seven inter simple sequence repeats. Analysis of molecular variance showed that 27.47% of the variation is attributed to the variation among population and 72.53% to the variation within population. The Fst (0.28) value showed a significant (p < 0.0001) genetic differentiation among populations. This was supported by the high coefficient of gene differentiation (Gst = 0.32) and low gene flow (Nm = 1.08) estimated. A neighbor-joining dendrogram, two and three dimentional PCoA clusters did not reveal clear pattern of clustering of populations based on their respective collection sites which may be because of human-mediated genetic material transfer between different localities. A total of 195 individuals representing 63 wild and 132 cultivated korarima were analyzed using newely developed eleven polymorphic microsatellite markers. Sequencing of these microsatellite regions of A. corrorima showed that most of the loci possess dinucleotide repetitive sequences. A total of 53 alleles were observed across all loci and individuals, with 32 different alleles being detected in cultivated korarima populations and 49 alleles in the wild korarima populations. Higher genetic variation was found in wild korarima than in the cultivated counterpart. Analysis of molecular variance and pair wise fixation index showed low divergence between cultivated and wild korarima populations also supported by neighbor-joining dendrogram and STRUCTURE analyses which failed to group cultivated and wild populations into two distinct clusters. The close genetic proximity between cultivated and wild korarima could be explained by historical and contemporary gene flow between the two gene pools. Comparison between inter simple sequence repeat and microsatellite markers were made in analyzing the genetic diversity of 129 korarima landraces. Ten Simple Sequence Repeats (SSR) and 7 Inter Simple Sequence Repeats (ISSR) markers were used separately. The percentage of polymorphic loci and the average Shannon diversity index among population were higher for SSR as compared to ISSR markers. These results indicated that SSRs revealed more genetic diversity than ISSR markers, although both ISSR and SSR methods provided useful genetic information. Higher variation was found within groups in the AMOVA analysis for both markers (104.30 % and 72.53 % for SSR and ISSR, respectively). Cluster analysis of ISSR and SSR using unweighted pair group method with arithmetic mean classified all the populations into two clusters, although SSR and ISSR markers led to dendrograms with different topologies. Thirtynine different taxa of Aframomum maintained in the gene bank plus six new genotypes of A. corrarima from Ethiopia were analyzed to investigate the phylogenetic relationships in the genus Aframomum. DNA sequence from chloroplast (trnL-trn-F) and nuclear ribosomal DNA (ITS) regions were used. The two molecular datasets and the combined data of the evolutionary relationships of the genus Aframomum resulted in generally congruent and compatible trees. However, disagreement was seen from combination of the three taxa of the genus Alpinia with the in-groups in trnL-trn-F region analysis. This showed the relatedness of the species within the two genera. The maximum parsimony analysis based on ITS and combined data strongly supported the monophyly of Aframomum. In addition the phylogenetic analysis suggested that A. corrorima is sister to the rest of the members of Aframomum. The present study revealed relatively higher level of genetic diversity in population of A. corrorima from southwestern part of Ethiopia using both inter simple sequence repeat and microsatellite markers. These findings should be taken into account when conservation action management policy for the species and site identification for in situ and ex situ conservation strategies are developed. Mizan Teferi II population in the ISSR analysis showed the highest genetic diversity. On the other hand Mizan-Teferi_ C2 and Masha_C2 displayed the highest genetic diversity in the ISSR analysis. Therefore, these populations should be considered as the key site in designing conservation strategies for this crop.
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Keywords
Aframomum Corrorima, Conservation, Cpdna, Gene Flow, Genetic Diversity, Genetic Structure, ISSR, ITS, Korarima, Molecular Phylogeny, Ssrs