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Amylose content controlled by Wx determines rice grain quality, which is easily affected by high temperature. Wxa and Wxb are the two typical Wx alleles in rice, however, their effects on quality formation in response to high temperature under the backgrounds of indica rice and japonica rice have not been systematically compared. In this study, the near-isogenic lines (NILs) of Wxa and Wxb with japonica rice 2661 and indica rice 3611 backgrounds were treated by high temperature during the grain-filling stages. High temperature accelerated the grain ripening process, decreased the thousand-kernel weight, and increased the chalkiness degree of all rice samples. However, these traits of Wx NILs with 3611 background were more susceptible to high temperature than those with 2661 background. Furthermore, high-temperature treatment decreased the amylose contents (AC) and starch viscosities but increased the gelatinization temperature of all the Wx NILs. The 3611-Wxa was atypical Wxa-type rice, whose AC was more sensitive to high temperature. The AC result was consistent with quantitative analysis of GBSSI by Western blot. In addition, the effects of Wx genotype and genetic background on rice physicochemical quality (such as the gel consistencies, starch crystallinity, and the morphological structure of starch grains) in response to high temperature were systematically analyzed. These results have important guiding significance for rice-quality improvement under high-temperature climate. [ABSTRACT FROM AUTHOR]