On the genome constitution and evolution of intermediate wheatgrass (Thinopyrum intermedium: Poaceae, Triticeae)

Abstract

Background: The wheat tribe Triticeae (Poaceae) is a diverse group of grasses representing a textbook example of reticulate evolution. Apart from globally important grain crops, there are also wild grasses which are of great practical value. Allohexaploid intermediate wheatgrass, Thinopyrum intermedium (2n = 6x = 42), possesses many desirable agronomic traits that make it an invaluable source of genetic material useful in wheat improvement. Although the identification of its genomic components has been the object of considerable investigation, the complete genomic constitution and its potential variability are still being unravelled. To identify the genomic constitution of this allohexaploid, four accessions of intermediate wheatgrass from its native area were analysed by sequencing of chloroplast trnL-F and partial nuclear GBSSI, and genomic in situ hybridization.

Results: The results confirmed the allopolyploid origin of Thinopyrum intermedium and revealed new aspects in its genomic composition. Genomic heterogeneity suggests a more complex origin of the species than would be expected if it originated through allohexaploidy alone. While Pseudoroegneria is the most probable maternal parent of the accessions analysed, nuclear GBSSI sequences suggested the contribution of distinct lineages corresponding to the following present-day genera: Pseudoroegneria, Dasypyrum, Taeniatherum, Aegilops and Thinopyrum. Two subgenomes of the hexaploid have most probably been contributed by Pseudoroegneria and Dasypyrum, but the identity of the third subgenome remains unresolved satisfactorily. Possibly it is of hybridogenous origin, with contributions from Thinopyrum and Aegilops. Surprising diversity of GBSSI copies corresponding to a Dasypyrum-like progenitor indicates either multiple contributions from different sources close to Dasypyrum and maintenance of divergent copies or the presence of divergent paralogs, or a combination of both. Taeniatherum-like GBSSI copies are most probably pseudogenic, and the mode of their acquisition by Th. intermedium remains unclear.

Conclusions: Hybridization has played a key role in the evolution of the Triticeae. Transfer of genetic material via extensive interspecific hybridization and/or introgression could have enriched the species' gene pools significantly. We have shown that the genomic heterogeneity of intermediate wheatgrass is higher than has been previously assumed, which is of particular concern to wheat breeders, who frequently use it as a source of desirable traits in wheat improvement.

Figure 1

Bayesian phylogenetic tree based on the chloroplast trnL-F region. Thinopyrum intermedium sequences are in bold. Branches found in both Bayesian and maximum parsimony (MP) 85% majority-rule consensus trees are indicated in bold lines. Numbers above and below branches are Bayesian posterior probabilities and bootstrap values for MP, respectively. For GenBank accession numbers, see Methods and Table 1.

Figure 2

Bayesian phylogenetic tree based on the GBSSI sequences. Branches found in both Bayesian and maximum parsimony (MP) 85% majority-rule consensus trees are indicated by bold lines. Thinopyrum intermedium sequences are in bold. Clone designations refer to individual plants analysed (numerical identifiers) and individual clones of each plant (letters). After each clone identifier, the number of identical clones and the total number of clones sequenced for that accession is given in parentheses, see also Table 2. The numbers above and below branches are Bayesian posterior probabilities and bootstrap values for MP, respectively.

Figure 3

Molecular cytogenetic analysis of Thinopyrum intermedium. Molecular cytogenetic analysis of accessions Thinopyrum intermedium-2 (a, c and d) and Thinopyrum intermedium-3 (b). (a, b) Fluorescent signals of total DNA of Pseudoroegneria spicata labeled with digoxigenin (red pseudocolor), total genomic DNA of Taeniatherum caput-medusae labeled with biotin (green pseudocolor) and total genomic DNA of Dasypyrum villosum (blue pseudocolor) labeled with digoxigenin after washing and reprobing of the slide. Each of these three probes produced dispersed signal over 14 chromosomes, presumably representing individual subgenomes. (c, d) Fluorescent signals of total genomic DNA of P. spicata labeled with digoxigenin (red pseudocolor) and total genomic DNA of D. villosum labeled with biotin (blue pseudocolor), and, after washing and reprobing, total genomic DNA of Aegilops tauschii (c) labeled with biotin (green pseudocolor) and total genomic DNA of Thinopyrum elongatum (d) labeled with digoxigenin (green pseudocolor). Note the overlapping signal of T. caput-medusae, Th. elongatum, and Ae. tauschii on one subgenome.