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Significance Guinea yam is an important staple tuber crop in West Africa, where it contributes to the sustenance and sociocultural lives of millions of people. Understanding the genetic diversity of Guinea yam and its relationships with wild relatives is important for improving this important crop using genomic information. A recent genomics study proposed that Guinea yam originated from a wild relative, the rainforest species Dioscorea praehensilis . Our results based on sequencing of 336 Guinea yam accessions do not support this notion; rather, our results indicate a hybrid origin of Dioscorea rotundata from crosses between the savannah species Dioscorea abyssinica and D. praehensilis.

Yam is a collective name of tuber crops belonging to the genus Dioscorea. Yam is important not only as a staple food crop but also as an integral component of society and culture of the millions of people who depend on it. However, due to its regional importance, yam has long been regarded as an “orphan crop” lacking a due global attention. Although this perception is changing with recent advances in genomics technologies, domestication processes of most yam species are still ambiguous. This is mainly due to the complicated evolutionary history of Dioscorea species caused by frequent hybridization and polyploidization, which is possibly caused by dioecy that imposed obligate outcrossing to the species of Dioscorea. In this chapter, we provide an overview of the evolution of Dioscorea and address the domestication of yam from population genomics perspectives by focusing on the processes of hybridization and polyploidization. A review is given to the recent population genomics studies on the hybrid origin of D. rotundata in West and Central Africa, the global dispersion of D. alata through human migrations, and the whole-genome duplication of the South America species of D. trifida. In the end, we give a summary of current understanding of sex-determination system in Dioscorea.

Significance Guinea yam is an important staple tuber crop in West Africa, where it contributes to the sustenance and sociocultural lives of millions of people. Understanding the genetic diversity of Guinea yam and its relationships with wild relatives is important for improving this important crop using genomic information. A recent genomics study proposed that Guinea yam originated from a wild relative, the rainforest species Dioscorea praehensilis. Our results based on sequencing of 336 Guinea yam accessions do not support this notion; rather, our results indicate a hybrid origin of Dioscorea rotundata from crosses between the savannah species Dioscorea abyssinica and D. praehensilis., 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.