Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
Royal Botanic Gardens, Kew, Richmond, TW9 3AE, Surrey, UK.
Sci Rep. 2020 Sep 17;10(1):15312. doi: 10.1038/s41598-020-71984-x.
Ensete ventricosum (Musaceae, enset) is an Ethiopian food security crop. To realize the potential of enset for rural livelihoods, further knowledge of enset diversity, genetics and genomics is required to support breeding programs and conservation. This study was conducted to explore the enset genome to develop molecular markers, genomics resources, and characterize enset landraces while giving insight into the organization of the genome. We identified 233 microsatellites (simple sequence repeats, SSRs) per Mbp in the enset genome, representing 0.28% of the genome. Mono- and di-nucleotide repeats motifs were found in a higher proportion than other classes of SSR-motifs. In total, 154,586 non-redundant enset microsatellite markers (EMM) were identified and 40 selected for primer development. Marker validation by PCR and low-cost agarose gel electrophoresis revealed that 92.5% were polymorphic, showing a high PIC (Polymorphism Information Content; 0.87) and expected heterozygosity (He = 0.79-0.82). In silico analysis of genomes of closely related species showed 46.86% of the markers were transferable among enset species and 1.90% were transferable to Musa. The SSRs are robust (with basic PCR methods and agarose gel electrophoresis), informative, and applicable in measuring enset diversity, genotyping, selection and potentially breeding. Enset SSRs are available in a web-based database at https://enset-project.org/EnMom@base.html (or https://enset.aau.edu.et/index.html , downloadable from Figshare).
芭蕉芋（芭蕉科，芭蕉芋）是埃塞俄比亚的一种粮食安全作物。为了实现芭蕉芋在农村生计中的潜力，需要进一步了解芭蕉芋的多样性、遗传学和基因组学，以支持其育种计划和保护。本研究旨在探索芭蕉芋的基因组，开发分子标记、基因组资源，并对芭蕉芋地方品种进行特征分析，同时深入了解基因组的组织。我们在芭蕉芋基因组中鉴定出了每兆碱基 233 个微卫星（简单序列重复，SSR），占基因组的 0.28%。单核苷酸和二核苷酸重复基序的比例高于其他 SSR 基序类。总共鉴定出了 154586 个非冗余芭蕉芋微卫星标记（EMM），并从中选择了 40 个用于引物开发。通过 PCR 和低成本琼脂糖凝胶电泳进行的标记验证显示，92.5%的标记具有多态性，表现出较高的 PIC（多态性信息含量；0.87）和预期杂合度（He=0.79-0.82）。对近缘物种基因组的分析表明，46.86%的标记可在芭蕉芋物种间转移，1.90%的标记可转移到 Musa 中。这些 SSR 标记具有稳健性（采用基本的 PCR 方法和琼脂糖凝胶电泳）、信息丰富性，可用于衡量芭蕉芋的多样性、基因分型、选择，甚至可能用于育种。芭蕉芋 SSR 标记可在基于网络的数据库 https://enset-project.org/EnMom@base.html（或 https://enset.aau.edu.et/index.html ，可从 Figshare 下载）中获取。
