Multiple origins of U genome in two UM genome tetraploid Aegilops species, Ae. columnaris and Ae. triaristata, revealed based on the polymorphism of a genome-specific PCR fragment.

To elucidate the evolutionary mode of the formation of species via polyploidization, we conducted phylogenetic analysis of the U genome of the UM genome tetraploid Aegilops species, Ae. columnaris and Ae. triaristata. Using the genome-specific PCR primer set U31, we investigated the variation of the U genome of 48 accessions each of Ae. columnaris and Ae. triaristata and 72 accessions of their diploid ancestor Ae. umbellulata. As a result, three alleles were distinguishable by amplified length and CAPS polymorphisms, namely, allele I = normal size with an MspI site, allele II = normal size without an MspI site, and allele III = shorter size caused by a 123bp deletion. All three alleles were detected both in diploid and tetraploid accessions. Sequence comparison indicated the inheritance of alleles I and III from the diploid to the tetraploids, suggesting multiple origins of the U genome of the tetraploids. Regarding allele II, however, the sequence comparison indicated that parallel mutations at the MspI site produced allele II several times. The phylogenetic tree based on the sequences of the U31 region demonstrated the presence of a third lineage of the U genome from Ae. umbellulata to Ae. columnaris. Consequently, we concluded that the U genome had at least three origins in Ae. columnaris, and at least two, probably more, in Ae. triaristata.