Origin and phylogeny of Guinea yams as revealed by RFLP analysis of chloroplast DNA and nuclear ribosomal DNA.

The origin and phylogeny of the Guinea yams, consisting of the white yam (Dioscorea rotundata Poir.) and the yellow yam (D. cayenensis Lamk.), has been investigated. Fourteen cultivars of Guinea yams were sampled with 12 accessions from seven wild yam species. A total of 26 accessions were surveyed for restriction fragment length polymorphisms (RFLP) in chloroplast DNA (cpDNA) and nuclear ribosomal DNA (rDNA) using seven restriction endonucleases and various heterologous probes. Chloroplast DNA probes covering 80% of the total chloroplast genome revealed nine restriction site changes and one length mutation among the cpDNAs of Guinea yams and their wild relatives. The estimated numbers of nucleotide substitutions per site (d) among these cpDNAs were very low (0.0005-0.0027), indicating a rather recent divergence of this group. On the basis of these ten mutations, five chloroplast genome types (A-E) were recognized. It was revealed that two cultivated species (D. rotundata and D. cayenensis) display the same chloroplast genome type, type A, as the three wild species D. praehensilis, D. liebrechtsiana and D. abyssinica. Chloroplast genome types B, C, D and E were found in D. minutiflora, D. burkilliana, D. smilacifolia and D. togoensis, respectively. Maximum parsimony analysis produced a hypothetical phylogeny of three primary lineages among cpDNAs of Guinea yams and their relatives: the genome type A lineage, the genome type B lineage and one lineage including genome types C, D and E.Using rDNA clones of rice and taro as probes, we detected ribosomal DNA variation, presumably at the intergenic spacer region, in Guinea yams and their wild relatives. The survey of rDNA together with that of cpDNA indicates that D. rotundata (white yam) was domesticated from either D. abyssinica, D. liebrechtsiana or D. praehensilis or their hybrid, and that D. cayenensis (yellow yam) is derived from hybridization between a male plant of either D. burkilliana, D. minutiflora or D. smilacifolia and a female plant of either D. rotundata, D. abyssinica, D. liebrechtsiana or D. praehensilis. We propose that the previous nomenclature of white yam should be retained, D. rotundata Poir. nomen nudum, and that yellow yam should be treated as a variety of D. rotundata, denoted as D. rotundata var. x 'cayenensis'.