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Enset (Enseteventricosum (Welw.) Cheesman) is a multipurpose, drought-tolerant and a key food security crop, which is the staple food for peoples in the South and Southwestern parts of Ethiopia. Despite its importance, enset is an orphan crop as regards genetic research and breeding. In this study, we characterized genetic diversity, population structure and selection signatures in 226 cultivated and 10 wild enset accessions collected from diverse enset growing regions of Ethiopia using 3505 high-quality SNP markers obtained from ddRAD-sequences. The population structure and cluster analyses clearly distinguished between cultivated and wild enset. AMOVA revealed much higher levels of genetic variation within populations and regions (91.2 and 92.4%, respectively) than between populations and regions (8.8 and 7.6%, respectively). This shows that the region of origin and environmental heterogeneity have little influence on the genetic variation. However, the genetic differentiation between regions was moderate to large (FST = 0.06–0.17). The genetic structure of enset was mainly shaped by eco-geographic factors, mode of propagation and cultivation status. Six genes potentially involved in sexual reproduction and flowering signalling, which are key processes underlying domestication and adaptation, were under positive selection demonstrating that sexual reproduction plays an important role in shaping enset diversity. A lot of unexplored diversity is available for improving enset in Ethiopia, with patterns of diversity consistent with divergent selection on adaptive traits. This diversity also shows potential for introducing enset as a more food secure crop for the food insecure regions in the dry north of Ethiopia.

Background: Enset (Ensete ventricosum (Welw.) Cheesman) is a staple food for more than 20 million Ethiopians and only cultivated in the native indigenous farming systems of Ethiopia. In contrast to other cultivated species in the Musaceae family, enset has been relatively little studied at the molecular level. Application of advanced molecular genetic techniques requires rapid extraction of DNA of high quality and quantity. Fresh, lyophilized tissues, as well as tissues stored in liquid nitrogen are mainly preferred to avoid DNA degradation, thus most of the DNA extraction protocols recommend these types of tissues as starting material. However, such sample processing techniques are difficult to utilize in many developing countries and at collection sites of many endemic plant species, underutilized or orphan crop species like enset. These situations necessitate the development of alternative protocols for leaf preservation and optimized methods for isolating high-quality DNA from dried or preserved leaf samples. Results: In this study, three different leaf preservation and two DNA extraction methods were compared. Fresh young leaf tissue was preserved using the minor modified saturated NaCl-CTAB solution, silica gel or 96% ethanol at ambient temperature for more than 35 days. Subsequently, DNA was extracted using either the DNeasy Plant Mini Kit or the CTAB method. As compared to silica gel and 96% ethanol, the minor modified saturated NaCl-CTAB solution preserved the quality, quantity, and integrity of enset genomic DNA. This method consistently produced genomic DNA of high-quality and quantity at affordable cost. The DNeasy Plant Mini Kit method was found to be more efficient than the standard CTAB method, being faster and producing genomic DNA of higher quality. Conclusions: Using saturated NaCl-CTAB solution is an accessible, efficient, scalable, and inexpensive way to preserve enset leaves during collection and transportation. The preservation protocol was validated for leaf tissues of all cultivated and wild enset, and Entada landraces. Genomic DNA of high quality and quantity was obtained from preserved enset leaves, which can be used for further downstream applications including PCR and sequencing.