Yu Sugihara, Kwabena Darkwa, Hiroki Yaegashi, Satoshi Natsume, Motoki Shimizu, Akira Abe, Akiko Hirabuchi, Kazue Ito, Kaori Oikawa, Muluneh Tamiru-Oli, Atsushi Ohta, Ryo Matsumoto, Paterne Agre, David De Koeyer, Babil Pachakkil, Shinsuke Yamanaka, Satoru Muranaka, Hiroko Takagi, Ben White, Robert Asiedu, Hideki Innan, Asrat Asfaw, Patrick Adebola, and Ryohei Terauchi

PNAS December 15, 2020 117 (50) 31987-31992

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.

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.

See: https://www.pnas.org/content/117/50/31987

Figure 1: Genetic diversity and phylogenomics of Guinea yam and its wild relatives. (A) Ancestry proportions of each Guinea yam accession with 6,124,093 SNPs. TDr96_F1 is the sample used as the reference genome. (B) PCA result of the 336 Guinea yam accessions. (C) NJ tree of four African yam lineages reconstructed using D. alata as an outgroup based on 463,293 SNPs. The numbers indicate bootstrap values after 100 replications. The sequences of D. rotundata in the previous study (10) were included in the tree. (D) Evolutionary relationship of three African wild yam lineages (D. abyssinica, Western D. praehensilis, and Cameroonian D. praehensilis) as inferred by ∂a∂i (15) using 17,532 SNPs. N, M, and T represent the relative population size from N_anc, migration rate, and divergence time, respectively.