The aim of the presented study is a genetic characterization of the hexaploid wheat (Triticum aestivum L.) by PCR-based haplotype analysis of the fourth intron of Wknox1d and of the fifth-to-sixth-exon region of Wknox1b of 20 hexaploid wheat samples. PCR-based haplotype analysis of the fourth intron of Wknox1d and of the fifth-to-sixth exon region of Wknox1b of all 20 hexaploid wheat samples was carried out.

Fifth-to-Sixth Exon Region of Wknox1b PCR-based haplotype analysis of the fifth-to-sixth exon region of Wknox1b showed that the 157-bp MITE inserted band (588 bp) is present in T. turgidum subsp. durum cv. ‘Langdon’, CS, ‘Red Doly’. This band is absent in tetraploid T. turgidum subsp. carthlicum, T. aestivum L. subsp. carthlicoides, T. aestivum subsp. macha (M1–M13). In the fourth intron of Wknox1d in common wheat, a 122-bp MITE insertion has been reported.

The MITE containing band (411 bp) was missing in all tetraploid wheat accessions and was observed in all subspecies of common wheat. In the case of subsp. macha (11 samples) the 453 bp band was observed. PCR-based haplotype analysis of the fourth intron of Wknox1d and the fifth-to-sixth-exon region of Wknox1b provides an opportunity to make an assumption that hexaploid wheats T. aestivum subsp. macha var. palaeocolchicum and var. letshckumicum differ from other macha samples by the absence of a 42 bp insertion in the fourth intron of Wknox1d.

One possible explanation for this observation would be that two Aegilops tauschii Coss. (A) and (B) participated in the formation of hexaploids through the D genome: Ae. tauschii (A) - macha (1–5, 7, 8, 10–12), and Ae. tauschii (B) - macha M6, M9, T. aestivum subsp. aestivum cv. ‘Chinese Spring’ and cv. ‘Red Doly’.