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Background  Amylose content (AC) is a critical factor for the quality of rice. It is determined by the biosynthesis gene  Waxy  ( Wx ) and a variety of quantitative trait loci (QTLs). Although many QTLs have been reported to affect rice AC, few of them have been investigated under varying growth conditions, especially various temperatures, which are known to greatly influence the AC.    Results  We analyzed the AC at different temperatures and planting seasons in a set of chromosome segment substitution lines (CSSLs) which were derived from a cross between the  indica  variety 9311 and the  japonica  variety Nipponbare carrying the same  Wx   b   allele. A joint analysis detected a single locus,  qSAC3 , with a high logarithm of odds (LOD) score in four different conditions. The  qSAC3  from  indica  9311 ( qSAC3   ind  ) substantially increased the AC in  japonica  Nipponbare under all tested growth conditions. Furthermore, introducing the  qSAC3   ind   into the soft rice variety Nangeng9108 with  Wx   mq  , a mutant allele of  Wx   b  , also moderately increased its AC and improved its appearance quality significantly by reducing the chalkiness of the polished rice.    Conclusions  Our results indicate that the  qSAC3   ind   could increase the AC of  japonica  rice in different environments as well as in the background of different  Wx  alleles and that  qSAC3  is a valuable locus for fine-tuning the rice AC and ameliorating the dull endosperm in rice varieties with the  Wx   mq   allele.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1860-5) contains supplementary material, which is available to authorized users.

The qSAC3 locus from indica rice effectively increases amylose content under a variety of conditions