Origins of domestication and polyploidy in oca (Oxalis tuberosa: Oxalidaceae): nrDNA ITS data

Abstract

As part of a study aimed at elucidating the origins of the octoploid tuber crop "oca," Oxalis tuberosa, DNA sequences of the internal trancribed spacer of nuclear ribosomal DNA (nrDNA ITS) were determined for oca and several wild Oxalis species, mostly from Bolivia. Phylogenetic analysis of these data supports a group of these species as being close relatives of oca, in agreement with morphology and cytology, but at odds with traditional infrageneric taxonomy. Variation in ITS sequences within this group is quite low (0-7 substitutions in the entire ITS region), contrasting with the highly divergent (unalignable in some cases) sequences within the genus overall. Some groups of morphologically differentiated species were found to have identical sequences, notably a group that includes oca, wild populations of Oxalis that bear small tubers, and several other clearly distinct species. The presence of a second, minor sequence type in at least some oca accessions suggests a possible contribution from a second genome donor, also from within this same species group. ITS data lack sufficient variation to elucidate the origins of oca precisely, but have identified a pool of candidate species and so can be used as a tool to screen yet unsampled species for possible progenitors.

Characterization of the nuclear ribosomal DNA unit in Oxalis tuberosa Oxalidacea and related species

“…In this context, previous studies of rDNA using the ITS support the O. tuberosa alliance hypothesis (Tosto and Hopp, 1996;Emshwiller and Doyle, 1998). The naturalness of the group has been also supported by other studies based on the chloroplast-expressed glutamine synthetase (Emshwiller and Doyle, 1999;Emshwiller and Doyle, 2002) and AFLPs (Tosto and Hopp, 2000).…”

Chloroplast-Expressed Glutamine Synthetase (ncpGS): Potential Utility for Phylogenetic Studies with an Example from Oxalis (Oxalidaceae)

“…1) were used to amplify a region of ncpGS using template genomic DNA from eight Oxalis species selected from among those sampled previously for ITS (Emshwiller and Doyle, 1998a; see Table 1 of that study for collection data of these specimens and an explanation of nomenclatural problems with two of the taxa sampled here). Amplification reactions contained the following final concentrations: 20 mM Tris-HCl, 50 mM KCl, 3 mM MgCl 2 , and 0.5 U Taq polymerase (all from Gibco BRL); 250 µM each dNTP (Promega); and 0.6 µM each of primers GScp687f and GScp994r; to which 1 µl of each template genomic DNA solution was added.…”

“…Comparison of single most parsimonious trees identified by phylogenetic analyses of sequences of ncpGS and ITS of eight Oxalis species. (The segregate genus Xanthoxalis may be polyphyletic and is considered here to be part of Oxalis; see Emshwiller and Doyle, 1998a, for a discussion of nomenclature.) Open hashmarks indicate substitutional changes, striped hashmarks indicate the homoplasious character, black hashmarks indicate indels (see text for treatment of gap characters in the respective analyses).…”

“…Arrows point to the clades that are in conflict between these two gene trees. Letters a, b, and c on the ITS tree indicate particular substitution characters as discussed in the text and in Emshwiller and Doyle, 1998a. changes to 0.909 when either ''duplicate'' sequence is removed (the inclusion of identical sequences in a matrix increases RI). The reanalysis of ITS data using only the eight plants sampled for ncpGS resulted in a single most parsimonious tree that is free of homoplasy (CI and RI of 1.00).…”

“…EMSHWILLER AND DOYLE that were used in the main analyses of our previous study (Emshwiller and Doyle, 1998a), but including only the sequences of the eight taxa sampled here for ncpGS. For the ITS searches, gaps were treated as missing data and subsequently mapped onto the trees.…”