Development of SSR markers and genetic diversity analysis in enset (Ensete ventricosum (Welw.) Cheesman), an orphan food security crop from Southern Ethiopia

Abstract

BackgroundEnset (Ensete ventricosum (Welw.) Cheesman; Musaceae) is a multipurpose drought-tolerant food security crop with high conservation and improvement concern in Ethiopia, where it supplements the human calorie requirements of around 20 million people. The crop also has an enormous potential in other regions of Sub-Saharan Africa, where it is known only as a wild plant. Despite its potential, genetic and genomic studies supporting breeding programs and conservation efforts are very limited. Molecular methods would substantially improve current conventional approaches. Here we report the development of the first set of SSR markers from enset, their cross-transferability to Musa spp., and their application in genetic diversity, relationship and structure assessments in wild and cultivated enset germplasm.ResultsSSR markers specific to E. ventricosum were developed through pyrosequencing of an enriched genomic library. Primer pairs were designed for 217 microsatellites with a repeat size > 20 bp from 900 candidates. Primers were validated in parallel by in silico and in vitro PCR approaches. A total of 67 primer pairs successfully amplified specific loci and 59 showed polymorphism. A subset of 34 polymorphic SSR markers were used to study 70 both wild and cultivated enset accessions. A large number of alleles were detected along with a moderate to high level of genetic diversity. AMOVA revealed that intra-population allelic variations contributed more to genetic diversity than inter-population variations. UPGMA based phylogenetic analysis and Discriminant Analysis of Principal Components show that wild enset is clearly separated from cultivated enset and is more closely related to the out-group Musa spp. No cluster pattern associated with the geographical regions, where this crop is grown, was observed for enset landraces. Our results reaffirm the long tradition of extensive seed-sucker exchange between enset cultivating communities in Southern Ethiopia.ConclusionThe first set of genomic SSR markers were developed in enset. A large proportion of these markers were polymorphic and some were also transferable to related species of the genus Musa. This study demonstrated the usefulness of the markers in assessing genetic diversity and structure in enset germplasm, and provides potentially useful information for developing conservation and breeding strategies in enset.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0250-8) contains supplementary material, which is available to authorized users.

Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset

“…The results presented here indicate that cultivated and wild enset accessions exhibit similar gene diversity and polymorphic information content (PIC) (Table 4). This is similar to what has been reported based on SSR marker analysis of enset genetic diversity (Gerura et al , 2019), but differs from what has been reported by Olango et al (2015), which reported that higher gene diversity in cultivated enset population (0.59) than wild enset population (0.40), but similar hetrozygosity for cultivated and wild enset populatons (0.5). The genetic diversity for both cultivated and wild enset reported in the current study (Table 4) is lower than previous enset genetic diversity studies conducted using SSR makers (Getachew et al , 2014; Olango et al, 2015 ; Gerura et al , 2019).…”

“…The high heterozygosity of cultivated enset might be due to vegetative propagation maintaining heterozygosity across clonal generations. In addition, the wild enset habitat has been sharply declining in Ethiopia because of population growth and deforestation (Birmeta et al, 2004; Olango et al, 2015). This reduction in effective population size might have contributed to the observed lower heterozygosity due to the increase of chances of inbreeding in wild enset populations.…”

“…The native distribution of wild enset encompasses the eastern coast Africa, from South Africa to Ethiopia, and extends west into the Congo (Borrell et al, 2019). In Ethiopia, which is considered to be the centre of origin of E. ventricosum , wild enset grows mainly along riversides and deep forest, extending into cultivated land and gardens in some regions (Olango et al , 2015; Eshetae et al , 2019).…”

“…Genetic analysis of intraspecific variation in enset has mainly relied upon data for ‘anonymous’ molecular markers, such as amplified fragment length polymorphisms (AFLP) (Tsegaye & Struik, 2002), random amplified polymorphic DNA (RAPD) (Birmeta et al, 2004), inter simple sequence repeats (ISSR) (Tobiaw & Bekele, 2013) and microsatellites (simple sequence repeat (SSR) polymorphisms (Getachew et al , 2014; Olango et al , 2015; Gerura et al , 2019). Given that enset is vegetatively propagated, genetic divergence among cultivars may be minimal (McKey et al, 2010) and could be difficult to detect using these marker types.…”

Biodiversity in Ethiopian linseed (Linum usitatissimum L.): molecular characterization of landraces and some wild species

“…Cheesm.) (Olango et al 2015); tef (Eragrostis tef (Zucc.)) Trotter (Bedane et al 2015;Ayalew et al 2015); coffee (Tadele et al 2014); sesame (Gebremichael and Parzies 2011); and barley (Muhe and Assefa 2011) have many landraces shown to have high genetic diversity in Ethiopia.…”