BEAR1, a bHLH transcription factor, controls seedling growth by regulating gibberellins biosynthesis in rice

The genetic pathways of rice seedling growth have a major impact on seedling emergence from soil and development. In this study, we identified a new bHLH transcription factor, BEAR1, from rice RNAi mutant library. Both the BEAR1-RNAi and bear1 CRISPR mutants had accelerated seedling growth. Histological section of leaves showed accelerated development of lacuna and vascular bundles in bear1 mutant. GUS staining revealed that BEAR1 was highly expressed in coleoptiles and leaves at seedling stage. Expression analysis of gibberellin (GA) biosynthesis and metabolic genes and content determination of active GAs indicated that the expression of GA biosynthesis genes, especially OsKS4 and OsCPS2, were upregulated and the GAs content were significantly increased in bear1, which correlated with the seedling phenotype of bear1 mutant. Molecular and biochemical assays revealed that BEAR1 directly binds to the promoter of OsKS4, thereby repressing its expression. Haplotypes analysis showed clear differentiation in indica and japonica rice varieties, and a strong correlation with seedling height. These findings provide novel insights into the regulation of seedling growth in rice.