Population Genomics of Yams: Evolution and Domestication of Dioscorea Species

Abstract

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.

Association mapping of plant sex and cross-compatibility related traits in white Guinea yam (Dioscorea rotundata Poir.) clones

“…Based on the allele variant segregation analyses, sex in D. rotundata was controlled by the female parent since more than 90% of female clones were heterozygous for sex markers while the male population was 92–100% homozygous. Using a different method (GWAS) and different plant materials, this study confirmed the female heterogametic sex determination (ZZ/ZW) system proposed for D. rotundata yam [ 7 , 11 , 17 ]. In such a system, ZW determines female sex phenotype and ZZ the male sex phenotype.…”

“…Flowering in D. rotundata is characterized by a female heterogametic sex determination system (ZZ/ZW), and maleness is the default phenotype [ 7 ]. Hence, monoecy could be expressed as the failure of the W allele to feminize a subset of flowers [ 7 , 11 ]. The ZW individuals can potentially change sex over time and across locations, indicating that the Z-suppressing function can be affected by the environment.…”

“…Previous attempts at introducing marker-assisted selection for sex detection identified a female-specific marker (sp16) and a male-specific marker (sp1) on the pseudo-chromosome 11, a 17 Mb long chromosome estimated from a diploid female genotype TDr96_F1 reference genome [ 7 ]. Based on previous reports, the prediction accuracy of these markers is not always perfect since sex determination in D. rotundata is a multi-genic trait [ 8 , 11 , 12 ]. In addition, the phenotypic sex switch across environments is another indication that sex expression in white yam is multi-genic and still under evolution [ 15 ].…”

Exploring the Bush yam (Dioscorea praehensilis Benth) as a Source of Agronomic and Quality Trait Genes in White Guinea yam (Dioscorea rotundata Poir) Breeding

“…This was partly explained by the vegetative propagation (planting tubers) used for yam cultivation since its domestication. This clonal propagation gradually reduced the genetic diversity and led to the vulnerability to plant diseases and the difficulty of purging deleterious mutations from the germplasms [13]. Broadening the genetic base of existing yam (Dioscorea spp.)…”

“…The genus Dioscorea consists of ~600 yam species, of which eight are grown in West Africa, where D. cayenensis and D. rotundata are native and predominant species [16,17]. These two native species emerged from the domestication of wild yams, mainly, D. praehensilis, D. burkilliana, and D. abyssinica [13,18,19]. These wild yam species which are related to the cultivated species, therefore, constitute a vast reservoir of genetic resources that can be exploited to improve the white Guinea yam.…”