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

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).

The genotypic and genetic diversity of enset (Ensete ventricosum) landraces used in traditional medicine is similar to the diversity found in starchy landraces

“…Twenty one enset SSRs primer-pairs (14 from Olango et al [26], and 7 from Biswas et al [28], were initially screened for good ampli cation, polymorphism and speci city to their target loci using 15 samples. This led to the selection of 15 primer-pairs to genotype the landraces (Table 2).…”

A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops

“…Simple sequence repeats are identified in ESTs (Expressed Sequence Tag) [22,23] and genomic sequences in species from fungi to vascular plants [3,7,[24][25][26][27]. However, the occurrence and frequency of SSRs in plant pre-microRNAs (miRNAs) has not been investigated.…”

Inheritance of Qualitative Morphological Traits and Variation of Quantitative Agronomic Traits of Enset (Ensete Ventricosum (Welw.) Cheesman) Clones Obtained From Wolaita Zone, Southern Ethiopia

“…Genetic diversity study on available genotypes either from molecular and phenotypic data may help to understand the extent of the variation in the species (Biswas, et al, 2020). The source of variation in enset crop lacks to pin point either due to cross pollination (recombination) or entirely due to ancestors' inherent genetic makeup.…”