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Background  Hexaploid triticale could be either synthesized by crossing tetraploid wheat with rye, or developed by crossing hexaploid wheat with a hexaploid triticale or an octoploid triticale.    Methodology/Principal Findings  Here two hexaploid triticales with great morphologic divergence derived from common wheat cultivar M8003 ( Triticum aestivum  L.) × Austrian rye ( Secale cereale  L.) were reported, exhibiting high resistance for powdery mildew and stripe rust and potential for wheat improvement. Sequential fluorescence  in situ  hybridization (FISH) and genomic  in situ  hybridization (GISH) karyotyping revealed that D-genome chromosomes were completely eliminated and the whole A-genome, B-genome and R-genome chromosomes were retained in both lines. Furthermore, plentiful alterations of wheat chromosomes including 5A and 7B were detected in both triticales and additionally altered 5B, 7A chromosome and restructured chromosome 2A was assayed in N9116H and N9116M, respectively, even after selfing for several decades. Besides, meiotic asynchrony was displayed and a variety of storage protein variations were assayed, especially in the HMW/LMW-GS region and secalins region in both triticales.    Conclusion  This study confirms that whole D-genome chromosomes could be preferentially eliminated in the hybrid of common wheat × rye, “genome shock” was accompanying the allopolyploidization of nascent triticales, and great morphologic divergence might result from the genetic variations. Moreover, new hexaploid triticale lines contributing potential resistance resources for wheat improvement were produced.

Spontaneous and Divergent Hexaploid Triticales Derived from Common Wheat × Rye by Complete Elimination of D-Genome Chromosomes