Abstract: The nucleotide sequences of the hotspot region in the chloroplast genomes were determined in Ae. speltoides and Ae. ovata, and compared with the corresponding sequences in T. aestivum, Ae. crassa 4× and Ae. squarrosa. The total number of nucleotides between a stop codon of rbcL gene and a HindIII site in cemA gene were 2 808 and 2 810 bp in Ae. speltoides and Ae. ovata. Compared with the Ae. crassa 4x, a 791 bp deletion in both of Ae. speltoides and T. aestivum, and a 793 bp deletion in Ae. ovata were identified, respectively. The deleted segment in Ae. ovata is 2 base (TT) longer than that of T. aestivum and Ae. speltoides. This result suggests that the deletion in Ae. ovata occurred independently with that of T. aestivum and Ae. Speltoides. The size and position of a large deletion in Ae. speltoides is identical to that of T. aestivum, this strongly supports the previous conclusion that Ae. speltoides is a donor species of a chloroplast genome to common wheat. In addition to the large segment deletions, a total of 7 insertion/deletion and 15 substitution mutations were observed in the hotspot region. The results indicate that the sequence analysis of the hotspot region is a very powerful tool to investigate genetic variations of chloroplast genome in Triticum and Aegilops.

Key words: T. aestivum, Aegilops, Chloroplast DNA, Hotspot region, Length variation