Biswas_PHHEnseteMicrosatelliteSSRLandscape2020-Scientific_Reports.pdf (2.75 MB)
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The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development

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journal contribution
posted on 13.10.2021, 09:50 by Manosh Kumar Biswas, Jaypal N Darbar, James S Borrell, Mita Bagchi, Dhiman Biswas, Gizachew Woldesenbet Nuraga, Sebsebe Demissew, Paul Wilkin, Trude Schwarzacher, J S Pat Heslop-Harrison
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).

Funding

GCRF Foundation Awards for Global Agricultural and Food Systems Research, entitled, ‘Modelling and genomics resources to enhance exploitation of the sustainable and diverse Ethiopian starch crop enset and support livelihoods’ [Grant No. BB/P02307X/1].

History

Citation

Sci Rep 10, 15312 (2020). https://doi.org/10.1038/s41598-020-71984-x

Author affiliation

Department of Genetics and Genome Biology

Version

VoR (Version of Record)

Published in

Scientific Reports

Volume

10

Issue

1

Publisher

Springer Nature

issn

2045-2322

eissn

2045-2322

Copyright date

2020

Available date

13/10/2021

Spatial coverage

England

Language

English