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Background  Both grain size and grain number are significant for rice yield. In the past decade, a number of genes related to grain size and grain number have been documented, however, the regulatory mechanisms underlying them remains ambiguous.    Results  We identified a rice  small grain  ( sg2 ) mutant in an EMS mutant library generated from an  indica  variety,  Shuhui498 . Using the MutMap gene mapping strategy, we identified two linkage regions on chromosome 7 and 8, respectively, consistent with the segregation ratios in the F 2  population. We focused on the linkage region on chromosome 8, and named this locus as  08sg2 . One of three SNPs identified in the linkage region was located in an exon of  OsBAK1 , leading to a nonsynonymous mutation in the kinase domain. The plant harboring the mutant version  08sg2  locus exhibited a decreased grain size, grain number and plant height. Cytological analysis indicated that  08SG2  regulated spikelet hull development by affecting cell proliferation. The grain size and number of knockout mutants of  OsBAK1  in the  japonica  background were significantly decreased, but less so than in  08sg2 , supporting the idea that the SNP in  OsBAK1  was responsible for the  08sg2  phenotype, but that  08SG2/OsBAK 1 function differently in  indica  and  japonica  backgrounds.  08sg2  was insensitive to 24-epiBL, and the expression of BR-related genes was obviously altered in  08sg2 . The proportionally decreased grain length when  08sg2  and  GS3  were combined indicate that  08SG2  and  GS3  regulate grain length independently.    Conclusions  Our work shows that  08SG2/OsBAK1  is important for rice yield in both  indica  and  japonica  backgrounds, by regulating grain size and grain number, and the function of  08SG2/OsBAK1  is obviously affected by genetic background. The amino acid substituted in  08sg2  is highly conserved among different species, supporting the idea that it is important for the molecular function of  08SG2/OsBAK1 . Together, our work is helpful for fully understanding the function of  08SG2/OsBAK1 .    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-017-0165-2) contains supplementary material, which is available to authorized users.

08SG2/OsBAK1 regulates grain size and number, and functions differently in Indica and Japonica backgrounds in rice