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The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development

Authors
  • Biswas, Manosh Kumar1
  • Darbar, Jaypal N.1
  • Borrell, James S.2
  • Bagchi, Mita1
  • Biswas, Dhiman3
  • Nuraga, Gizachew Woldesenbet1, 4
  • Demissew, Sebsebe4
  • Wilkin, Paul2
  • Schwarzacher, Trude1, 5
  • Heslop-Harrison, J. S.1, 5
  • 1 University of Leicester, Leicester, LE1 7RH, UK , Leicester (United Kingdom)
  • 2 Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK , Kew, Richmond (United Kingdom)
  • 3 Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India , Kolkata (India)
  • 4 Addis Ababa University, Addis Ababa, Ethiopia , Addis Ababa (Ethiopia)
  • 5 Chinese Academy of Sciences, Guangzhou, People’s Republic of China , Guangzhou (China)
Type
Published Article
Journal
Scientific Reports
Publisher
Springer Nature
Publication Date
Sep 17, 2020
Volume
10
Issue
1
Identifiers
DOI: 10.1038/s41598-020-71984-x
Source
Springer Nature
License
Green

Abstract

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/[email protected] (or https://enset.aau.edu.et/index.html, downloadable from Figshare).

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