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Background  It is becoming clear that ozone affects not only grain yield but also grain quality in rice. However, the biochemical mechanisms responsible for ozone-induced changes in appearance quality or components are poorly understood. We analyzed appearance quality and starch composition in the rice cultivars “Koshihikari” ( japonica ) and “Kasalath” ( indica ) grown under elevated ozone conditions.    Results  Elevated ozone significantly increased the proportion of immature (mainly chalky) kernels in “Koshihikari” but not in “Kasalath”. Scanning electron microscopy of transverse sections of kernels showed that endosperm starch granules of “Koshihikari” ripened under elevated ozone were loosely packed with large spaces and contained irregular rounded granules. Amylose content was increased in “Koshihikari” kernels with ozone exposure, but was unchanged in “Kasalath” kernels. Distribution analysis of amylopectin chain length showed that ozone induces a decrease of long-side chains and alterations of short side-chains in “Koshihikari” kernels. Furthermore,  Starch Synthase (SS) IIIa  transcript levels in “Koshihikari” caryopses were decreased by elevated ozone.    Conclusions  The  japonica  cultivar “Koshihikari” showed significant deterioration in appearance quality of kernels caused by abnormal starch accumulation due to exposure to ozone. The alteration patterns of amylose and amylopectin in ozone-exposed rice kernels are similar to those in rice kernels harvested from  SSIIIa -deficient mutants. These findings suggest that the increase of chalky kernels in ozone-treated “Koshihikari” is partly attributable to the repressed expression of  SSIIIa  involved in amylopectin side-chain elongation with ozone exposure. Elevated ozone reduced appearance quality in “Koshihikari” although it did not impair starch properties contributing to the eating quality of cooked rice.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-016-0079-4) contains supplementary material, which is available to authorized users.

Elevated Ozone Deteriorates Grain Quality of Japonica Rice cv. Koshihikari, Even if it Does Not Cause Yield Reduction