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Background  In cereal crops such as wheat, an optimal timing of developmental transitions is required to maximize grain yield. Many of these developmental changes are precisely regulated by changes in the duration, intensity or quality of light. Phytochromes are dimeric photoreceptors that absorb light maximally in the red and far-red wavelengths and induce large-scale transcriptional changes in response to variation in light quality. In wheat,  PHYC  is required for early flowering under long days. However, it is currently unknown whether this function requires the presence of  PHYB . In this study, we characterized the role of  PHYB  in wheat development and used RNA-seq to analyze and compare the transcriptomes of  phyB -null and  phyC- null TILLING mutants.    Results  Under long-day photoperiods,  phyB- null plants exhibit a severe delay in flowering comparable to the delay observed in  phyC -null plants. These results demonstrate that both genes are required for the induction of wheat flowering under long days. Using replicated RNA-seq studies we identified 82 genes that are significantly up or down regulated in both the  phyB- null and  phyC- null mutant relative to their respective wild-type controls. Among these genes are several well-characterized positive regulators of flowering, including  PPD1, FT1  and  VRN1 . Eight-fold more genes were differentially regulated only in the  phyB -null mutant (2202) than only in the  phyC- null mutant (261). The  PHYB- regulated genes were enriched in components of the auxin, gibberellin and brassinosteroid biosynthesis and signaling pathways, and in transcription factors with putative roles in regulating vegetative development and shade-avoidance responses. Several genes involved in abiotic stress tolerance pathways were also found to be regulated by  PHYB .    Conclusions   PHYB  and  PHYC  are both required for the photoperiodic induction of wheat flowering, whereas  PHYB  alone regulates a large number of genes involved in hormone biosynthesis and signaling, shade-avoidance response, and abiotic stress tolerance. Our analysis provides a comprehensive overview of the PHYB- and PHYC-mediated transcriptional changes during light signaling, and an initial step towards the dissection of this regulatory gene network in wheat. This further dissection will be required to explore the individual phytochrome-mediated developmental responses and to evaluate their potential to improve wheat adaptation to changing environments.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-016-0831-3) contains supplementary material, which is available to authorized users.

bmc plant biology

RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways