Genomic Composition of the Artificial Hybrid ×Trititrigia cziczinii (Hordeeae, Poaceae) and Related Taxa According to Molecular Phylogenetic Data

×<i>Trititrigia cziczinii</i> Tzvelev is a promising crop developed through distant hybridization between <i>Elytrigia intermedia</i> (Host) Nevski (=<i>Thinopyrum intermedium</i> (Host) Barkworth & D.R. Dewey) and <i>Triticum aestivum</i> L., followed by backcrossing with wheat. This study elucidates the genomic composition of this hybrid and its parental taxa using molecular phylogenetic analysis of nuclear (ITS, ETS) and chloroplast (<i>trn</i>K-<i>rps</i>16, <i>ndh</i>F) DNA markers, complemented by Next-Generation Sequencing (NGS) of the 18S-ITS1-5.8S rDNA region. Results from Sanger sequencing revealed that the primary nuclear ribosomal DNA (rDNA) of the hybrid originates from <i>Triticum aestivum</i>; a finding strongly supported by both Bayesian inference and Maximum Likelihood analyses. Chloroplast DNA data unequivocally indicate maternal inheritance from <i>T. aestivum</i>. In contrast, ETS sequence analysis showed phylogenetic affinity to <i>Elytrigia intermedia</i>, suggesting complex genomic reorganization or chimeric sequence formation in the hybrid. NGS data corroborate the dominance of <i>T. aestivum</i>-like ribotypes in the hybrid's rDNA pool, with only a minor fraction identical to the main ribotype of <i>E. intermedia</i>. Genetic structure analysis further revealed geographic heterogeneity in the genomic composition of <i>E. intermedia</i> populations. The predominance of the wheat genome in ×<i>T. cziczinii</i> is likely a consequence of stabilizing backcrosses and illustrates a case of rDNA elimination from one parental genome during hybridization. This research underscores the complex genomic dynamics in artificial hybrids and the utility of multi-marker phylogenetic approaches for clarifying their origins.