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BackgroundBoth 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.ResultsWe 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 F2 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/OsBAK1 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.ConclusionsOur 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 materialThe online version of this article (doi:10.1186/s12284-017-0165-2) contains supplementary material, which is available to authorized users.