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

Kiflu Gebramicael Tesfamicael,Timothy J March,Endale Gebre,Diane E Mather,Beata Sznajder,Carlos Marcelino Rodríguez López

doi:10.1038/s41438-020-00409-7

Kiflu Gebramicael Tesfamicael, Timothy J March + Show 4 more

Open Access

https://doi.org/10.1038/s41438-020-00409-7

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Abstract

Enset (Ensete ventricosum (Welw.) Cheesman) is a drought tolerant, vegetatively propagated crop that was domesticated in Ethiopia. It is a staple food for more than 20 million people in Ethiopia. Despite its current importance and immense potential, enset is among the most genetically understudied and underexploited food crops. We collected 230 enset wild and cultivated accessions across the main enset producing regions in Ethiopia and applied amplified fragment length polymorphism (AFLP) and genotype by sequencing (GBS) analyses to these accessions. Wild and cultivated accessions were clearly separated from each other, with 89 genes found to harbour SNPs that separated wild from cultivated accessions. Among these, 17 genes are thought to be involved in flower initiation and seed development. Among cultivated accessions, differentiation was mostly associated with geographical location and with proximity to wild populations. Our results indicate that vegetative propagation of elite clones has favoured capacity for vegetative growth at the expense of capacity for sexual reproduction. This is consistent with previous reports that cultivated enset tends to produce non-viable seeds and flowers less frequently than wild enset.

Highlights

Plant domestication and breeding can alter and shrink genetic diversity[1]
SNP discovery and analysis genotype by sequencing (GBS) of 149 (125 cultivated and 24 wild) enset accessions generated a total of 569,324,179 reads with 74 bp length and 50% of GC content
Genomic regions under selection pressure The genome scan approach (LOSITAN-based Fst-outlier detection method) implemented in this study identified 158 (2.56%) SNPs, whose frequency was significantly different between cultivated and wild enset populations, which are dispersed throughout the 11 chromosomes of the wild banana reference genome (Fig. 4)

Summary

Introduction

Plant domestication and breeding can alter and shrink genetic diversity[1]. This entails a shift from sexual to vegetative propagation[2]. Enset (Ensete ventricosum (Welw.) Cheesman) is a hapaxanth diploid (2n = 18) plant that belongs to the Musaceae family[3]. Enset propagates by seed[4]. The native distribution of wild enset encompasses the eastern coast Africa, from South Africa to Ethiopia, and extends west into the Congo[5]. In Ethiopia, which is considered to be the centre of origin of E. ventricosum, wild enset grows mainly along

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