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Waxy wheat offers unique benefits in food processing, including improving the smoothness and performance of the product. However, waxy wheat is not yet commercially available. The protein characteristics, including the protein content, subunit distribution, secondary structure, chemical interactions, and microstructure of the gluten, were explored to realize the full potential of waxy wheat. The results showed that the noodles prepared from waxy wheat had a gentle and glutinous texture compared with GY2018 and YM13. Partial-waxy and waxy wheat had a lower gluten index and glutenin macropolymer (GMP) content than GY2018, indicating a reduced gluten strength. Confocal laser scanning microscopy (CLSM) images showed that the starch granules were not securely attached to the partial-waxy and waxy wheat protein matrix. In addition, the waxy protein chains appeared more elongated and they weakened the protein network. In particular, HMW-GS subunit 2 + 12 may be the essential cause of the weak dough from SKN1. Compared with GY2018 and YM13, SKN1 had the highest number of free sulfhydryl groups. Rather than ionic bonds, hydrophobic interactions increased the gluten network in GY2018, YM13, and SKN1. The weak molecular forces in the gluten will result in a soft noodle texture.

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