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Background  Grain length, as a critical trait for rice grain size and shape, has a great effect on grain yield and appearance quality. Although several grain size/shape genes have been cloned, the genetic interaction among these genes and the molecular mechanisms of grain size/shape architecture have not yet to be explored.    Results  To investigate the genetic interaction between two major grain length loci of rice,  GS3  and  qGL3 , we developed two near-isogenic lines (NILs), NIL- GS3  ( GS3 / qGL3 ) and NIL- qgl 3 ( gs3 / qgl3 ), in the genetic background of 93–11 ( gs3 / qGL3 ) by conventional backcrossing and marker-assisted selection (MAS). Another NIL- GS3 / qgl3  ( GS3/qgl3 ) was developed by crossing NIL- GS3  with NIL- qgl3  and using MAS. By comparing the grain lengths of 93–11, NIL- GS3 , NIL- qgl3  and NIL- GS3 / qgl3 , we investigated the effects of  GS3 ,  qGL3  and  GS3  ×  qGL3  interaction on grain length based on two-way ANOVA. We found that  GS3  and  qGL3  had additive effects on rice grain length regulation. Comparative analysis of primary panicle transcriptomes in the four NILs revealed that the genes affected by  GS3  and  qGL3  partially overlapped, and both loci might be involved in brassinosteroid signaling.    Conclusion  Our data provide new information to better understand the rice grain length regulation mechanism and help rice breeders improve rice yield and appearance quality by molecular design breeding.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0515-4) contains supplementary material, which is available to authorized users.

The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons