The formation process of starch in the grain is influenced by both genetic characteristics and environmental factors, which can affect starch quality. Waxy wheat Yangnuo1 (YN1) and non-waxy wheat Yangmai15 (YM15) were subjected to heat stress at the early, medium, and late grain-filling stages using artificial intelligence temperature control. Heat stress increased the short-chain content of amylopectin in both cultivars and decreased their amylose contents. The effect of heat stress on the wheat amylopectin structure was most pronounced 16–20 days after anthesis (DAA). The crystallinity and enthalpy of starch decreased, as did the swelling potential, solubility, and transmittance, but the retrogradation degree showed an opposite trend after heat stress. Compared with YM15, YN1 exhibited superior physical and chemical properties as well as anti-aging properties of starch and consequently had greater thermal stability under heat stress due to its higher degree of branching. The most sensitive stage to heat stress for yield was 6–10 DAA, which resulted in significant decreases in grain number and 1000-grain weight, followed by 16–20 DAA, which resulted in a significant decrease only in 1000-grain weight. Our study indicated that heat stress during the early stage of grain filling resulted in a decrease in both grain weight and yield, whereas during the middle stage of grain filling, it led to a decline in starch quality, especially in non-waxy wheat.
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