Transcriptome-wide isolation and expression profiles of NF-Y gene family in male cone development and hormone treatment of Chinese pine (Pinus tabuliformis)

Abstract

Background Conifers and angiosperms have difference in reproductive development, especially for flowering. It is known that NUCLEAR FACTOR Y (NF-Y) transcription factor play an important role in flowering, drought stress and GA, ABA signaling, but, little known in auxin, salicylic acid, jasmonic acid, etc. Moreover, the NF-Y genes family has been mainly analyzed in angiosperms, but it has not been comprehensively reported in conifers. Results In this study, we identified 9 NF-YA, 9 NF-YB, and 10 NF-YC genes in Pinus tabuliformis using Arabidopsis NF-Y protein sequences as queries. Besides, by comparing conserved regions and phylogenetic relationships of the PtNF-Ys, we found that the NF-Ys were both conserved and altered during evolution. PtTFL2, PtCO, PtNF-YC1 and PtNF-YC4 were exploited by expression profile in male cone development and the correlation analysis. In addition, NF-YC1/4 can interact with DPL by yeast two-hybrid assays and BiFC. The multiple types of phytohormones-responsive cis-elements (ABA, JA, IAA, SA) were present and many NF-Y genes responded positively to SA and as opposed to IAA and JA. Conclusions Twenty-eight PtNF-Ys were identified and bioinformatic characterization of NF-Y genes including conserved regions, phylogenetic relationships, gene-motifs, was carried out. Two candidate genes (NF-YC1 and NF-YC4) were found to be involved in the regulation of conifer flowering and gibberellin signalling. The cis-elements and hormone transcriptome analysis revealed that the potential role of NF-Ys in conifers resistance. This study provides the basis for improved understanding of NF-Y genes function in conifers.