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Polyphenol oxidase (PPO) activity and yellow pigment content (YPC) are two important quality traits determining the color of wheat end-products. Synthetic hexaploid wheat (SHW) has been largely synthesized and widely used in wheat breeding. In this study, we investigated PPO activity and YPC of 118 accessions consist of Aegilops tauschii , Triticum turgidum , Triticum aestivum and synthetic hexaploid wheat. Irrespective of PPO activity or YPC, T. aestivum tended to a lower value and a more concentrated range. As for PPO activity, synthetic hexaploid wheat showed a large number of genetic variation comparable to T. turgidum . Each T. turgidum – SHW – Ae. tauschii combination represents an independent wheat hexaploidization process. By comparing 29 synthetic hexaploid wheats with their corresponding parents (maternal, T. turgidum , BBA u A u ; paternal, Ae. tauschii , DD), our report highlighted different performances for PPO activity and YPC during wheat hexaploidization processes: the PPO activity of SHW can be higher, lower than both parents, or in the middle; in contrast, all the combinations showed a relative stable YPC trend. Besides, take these two traits we tested as an example, from an evolutionary perspective, the uniqueness of traits and their potential functions on polyploidy adaption or stress responses were also discussed. [ABSTRACT FROM AUTHOR]