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Background  Blueberry cultivars require a fixed quantity of chilling hours during winter endo-dormancy for vernalization. In this study, transcriptome analysis using RNA sequencing data from nonchilled, chilled, and late pink buds of southern highbush blueberry ‘Legacy’ was performed to reveal genes associated with chilling accumulation and bud break.    Results  Fully chilled ‘Legacy’ plants flowered normally whereas nonchilled plants could not flower. Compared to nonchilled flower buds, chilled flower buds showed differential expression of 89% of flowering pathway genes, 86% of MADS-box genes, and 84% of cold-regulated genes. Blueberry orthologues of  FLOWERING LOCUS T  ( FT ) did not show a differential expression in chilled flower buds (compared to nonchilled flower bud) but were up-regulated in late-pink buds (compared to chilled flower bud). Orthologoues of major MADS-box genes were significantly up-regulated in chilled flower buds and down-regulated in late-pink buds. Functional orthologues of  FLOWERING LOCUS C  ( FLC ) were not found in blueberry. Orthologues of  Protein FD (FD), TERMINAL FLOWER 1 (TFL1) , and  LEAFY (LFY)  were down-regulated in chilled flower buds and in late-pink buds compared to nonchilled flower bud.    Conclusions  The changes from nonchilled to chilled and chilled to late-pink buds are associated with transcriptional changes in a large number of differentially expressed (DE) phytohormone-related genes and DE flowering pathway genes. The profile of DE genes suggests that orthologues of  FT, FD ,  TFL1 ,  LFY , and MADS-box genes are the major genes involved in chilling-mediated blueberry bud-break. The results contribute to the comprehensive investigation of the vernalization-mediated flowering mechanism in woody plants.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1311-8) contains supplementary material, which is available to authorized users.

bmc plant biology

Comparative transcriptome analysis of nonchilled, chilled, and late-pink bud reveals flowering pathway genes involved in chilling-mediated flowering in blueberry