Abstract
White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding.
Highlights
White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa
In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannahadapted species Dioscorea abyssinica
Our results suggest that diploid D. rotundata was most likely derived from homoploid hybridization between D. abyssinica and D. praehensilis
Summary
Using the SNP information, we constructed a rooted neighborjoining (NJ) tree [14] based on 308 Guinea yam accessions sequenced in the present study (excluding cluster 1 triploid accessions), as well as 80 D. rotundata, 29 D. abyssinica, 21 Western D. praehensilis, and 18 Cameroonian D. praehensilis accessions that were sequenced in a previous study [10] using two accessions of Asian species D. alata as an outgroup (Fig. 1C). To elucidate the evolutionary relationships of the three wild Dioscorea species that are closely related to D. rotundata—D. abyssinica (designated as A), Western D. praehensilis (P), and Cameroonian D. praehensilis (C)—we performed diffusion approximations for demographic inference (∂a∂i) analysis [15], which allows for estimation of demographic parameters based on an unfolded site frequency spectrum. D. abyssinica D. rotundata (in Scarcelli et al 2019) D. rotundata (in this study)
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