Genome analyses reveal the hybrid origin of the staple crop white Guinea yam ( <i>Dioscorea rotundata</i> )

Abstract

White Guinea yam (<i>Dioscorea rotundata</i>) 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 <i>Dioscorea</i> species using an improved reference genome sequence of <i>D. rotundata</i> In contrast to a previous study suggesting that <i>D. rotundata</i> originated from a subgroup of <i>Dioscorea praehensilis</i>, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species <i>D. praehensilis</i> and the savannah-adapted species <i>Dioscorea abyssinica</i> We identified a greater genomic contribution from <i>D. abyssinica</i> in the sex chromosome of Guinea yam and extensive introgression around the <i>SWEETIE</i> 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.