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Background  Grain filling rates (GFRs) of  indica  rice cultivars are often higher than those of  japonica  cultivars. Although GFR is mainly determined by the starch accumulation rate (SAR) in endosperm, the genetic basis for SAR during the ripening period has not been well studied in rice. To elucidate the factors influencing the differing SARs between typical  indica  and  japonica  cultivars, we focused on differences in sink potentials, especially on starch synthesis in the endosperm.    Results  SAR in  indica  rice cultivar IR36 was significantly higher than in  japonica  cultivar T65. Although enzymes for both amylose and amylopectin syntheses had higher activity in IR36, amylopectin synthesis was seemingly more important for accelerating SAR because an elevation of amylose synthesis ability alone in the T65 genetic background did not result in the same level of SAR as IR36. In IR36, most starch-synthetic genes (SSGs) in the endosperm were more highly expressed during ripening than in T65. In panicle culture experiments, the SSGs in rice endosperm were regulated in either sucrose-dependent or -independent manners, or both. All SSGs except  SSI  and  BEIIa  were responsive to sucrose in both cultivars, and  GBSSI, AGPS2b  and  PUL  were more responsive to sucrose in IR36. Interestingly, the  GBSSI  gene ( Wx    a  ) in IR36 was highly activated by sucrose, but the  GBSSI  gene ( Wx    b  ) in T65 was insensitive. In sucrose-independent regulation,  AGPL2 ,  SSIIIa ,  BEI ,  BEIIb  and  ISA1  genes in IR36 were upregulated 1.5 to 2 times more than those in T65. Additionally, at least  SSI  and  BEIIa  might be regulated by unknown signals; that regulation pathway should be more activated in IR36 than T65.    Conclusions  In this study, at least three regulatory pathways seem to be involved in SSG expression in rice endosperm, and all pathways were more active in IR36. One of the factors leading to the high SAR of IR36 seemed to be an increase in the sink potential.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-017-0146-5) contains supplementary material, which is available to authorized users.

Differential Regulation of Starch-synthetic Gene Expression in Endosperm Between Indica and Japonica Rice Cultivars