Progenitor-derivative relationships of Hordeum polyploids (Poaceae, Triticeae) inferred from sequences of TOPO6, a nuclear low-copy gene region

Abstract

Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (4×, 6×) of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii) possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (4×, 6×) was identified as allopolyploid throughout most of its distribution area. The use of a proof-reading DNA polymerase in PCR reduced the proportion of chimerical sequences in polyploids in comparison to Taq polymerase.

Figure 1. Phylogenetic tree derived from TOPO6 sequences of the diploid Hordeum taxa and eight outgroup species calculated with Bayesian inference.

Posterior probability values of the clades are indicated along the branches. Bold letters depict genome denominations following Blattner (2009). After the species name and individual number the different copies found per individual are indicated (A–C) in case of cloned sequences.

Figure 2. Phylogenetic tree derived from cloned TOPO6 sequences from diploid and polyploid Hordeum taxa and eight outgroup species calculated with Bayesian inference.

Posterior probability values of the clades are indicated along the branches. Clades containing diploid and polyploid-derived sequences are indicated to the right. Genome denominations are given in bold type.

Figure 3. Scheme summarizing phylogenetic relationships of species and cytotypes in the genus Hordeum based on TOPO6.

Diploid taxa were drawn directly at the tree, while tetra- and hexaploids were connected by lines to their inferred parental taxa. Dashed lines indicate uncertainties and double lines depict an autopolyploid origin. Colors refer to the ploidy level of the taxa (tetraploid blue lines, hexaploid green lines).