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

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.

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

“…8a ). The few intra-chromosome differences observed could represent bona fide rearrangements between species or, possibly, imperfections in the D. rotundata v2 assembly 21 that could have arisen from the reliance on linkage mapping to order and orient D. rotundata scaffolds, especially in recombination-poor pericentromeric regions of the genome. Under the assumption that D. rotundata chromosomes are in 1:1 correspondence with D. alata chromosomes, we can provisionally assign four large but unmapped D. rotundata scaffolds to chromosomes ( Fig.…”

“…Here we describe a chromosome-scale reference genome for D. alata and a dense 10k marker consensus genetic linkage map from five populations involving seven distinct parental genotypes. Comparison of the D. alata reference genome with the recently sequenced genomes of the distantly related D. rotundata 21 and D. zingiberensis 22 reveals substantial conservation of chromosome structure between D. alata and D. rotundata but considerable rearrangement relative to more deeply divergent D. zingiberensis lineage. Analysis of the D. alata genome supports the existence of ancient polyploidy events shared across Dioscoreales, and reveals chromosome rearrangements after the most recent pan-Dioscoreales genome duplication.…”

Diversity of white Guinea yam (Dioscorea rotundataPoir.) cultivars from Benin as revealed by agro-morphological traits and SNP markers

“…Plants of a yam clone in a farmer's field are genetically homogenous with negligible recombination rates, as farmers select their planting material from tubers and not from botanical seed. However, the molecular evidence on ennobled cultivars showed that the tubers collected by farmers from wild environments are often a mixture of wild (D. abyssinica and D. praehensilis) and interspecific hybrid (D. rotundata × wild species) yams (Scarcelli et al, 2006(Scarcelli et al, , 2017Sugihara et al, 2020). This could partly explain the origin of the genetic admixture identified among the Beninese white Guinea yam accessions.…”

The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing

“…Most species in the genus Dioscorea (Dioscoreaceae) are dioecious [ 125 ] and have XY sex chromosomes [ 81 , 126 , 127 ], suggesting dioecy may have evolved ~80 million years ago (MYA) [ 128 ]. In D. alata a recent genetic map uncovered a ~10 Mb male-specific region of the Y (MSY) [ 81 ].…”