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/EnMom@base.html (or https://enset.aau.edu.et/index.html, downloadable from Figshare).
Highlights
Several thousand landraces with high genetic diversity have been reported in banana[9] worldwide
Including Hawassa University, Wolkite University, Southern Agricultural Research Institute (SARI)[12,13] and Ethiopian Biodiversity Institute (EBI)[14].Unlike triploid banana, the diploid enset is able to produce plants from the seeds of its non-edible fruits, most enset grown on farms is not permitted to flower and is propagated clonally
Genetic diversity and population structure studies are required for enset in Ethiopia for germplasm management, identifying landraces or cultivars, collection-management, and determining phylogenetic relationships
Summary
Several thousand landraces with high genetic diversity have been reported in banana[9] worldwide. With the knowledge gap about enset genetics, distribution and diversity, several studies have been conducted to estimate genetic diversity and define relationships among the limited enset germplasm stocks Most of these studies use DNA markers including Random Amplified Polymorphic DNA (RAPD)[16], Inter-Simple Sequence Repeats (ISSR)[11], and Amplified Fragment Length Polymorphism (AFLP)[17], some of these marker techniques are high-cost, show limited reproducibility, or identify only dominant alleles (from a heterozygous crop without systematic inbreeding). Development of large numbers of microsatellite markers—thousands to tens of thousands—from genomic DNA sequences is possible Their applications include genetic diversity surveys[21,22,23,24,25], population structure analysis26,27, genotyping[28,29,30], association mapping[31,32,33,34,35], linkage mapping[36,37] and plant breeding. Large microsatellite databases have been developed for many crop p lants[41,42]
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