Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data

Clonal propagation enables favourable crop genotypes to be rapidly
selected and multiplied. However, the absence of sexual propagation can
lead to low genetic diversity and accumulation of deleterious mutations,
which may eventually render crops less resilient to pathogens or
environmental change. To better understand this trade-off, we characterise
the domestication and contemporary genetic diversity of Enset (Ensete
ventricosum), an indigenous African relative of bananas (Musa) and
principal starch staple for 20 million Ethiopians. Wild enset is strictly
sexually outcrossing, but in cultivation is propagated clonally and
associated with diversification and specialisation into hundreds of named
landraces. We applied tGBS sequencing to generate genome-wide genotypes
for 192 accessions from across enset’s cultivated distribution, and
surveyed 1340 farmers on enset agronomic traits. Overall, reduced
heterozygosity in the domesticated lineage was consistent with a
domestication bottleneck that retained 37% of wild diversity. However, an
excess of putatively deleterious missense mutations at low frequency
present as heterozygotes suggested accumulation of mutational load in
clonal domesticated lineages. Our evidence indicates that the major
domesticated lineages initially arose through historic sexual
recombination associated with a domestication bottleneck, followed by
amplification of favourable genotypes through an extended period of clonal
propagation. Among domesticated lineages we found significant phylogenetic
signal for multiple farmer-identified food, nutrition and disease
resistance traits and little evidence of contemporary recombination.
Development of future-climate adapted genotypes may require crop breeding,
but outcrossing risks exposing deleterious alleles as homozygotes. This
trade-off may partly explain the ubiquity and persistence of clonal
propagation over recent centuries of comparative climate stability.