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Background  In flowering plants, the male gametophyte (pollen) is one of the most vulnerable cells to temperature stress. In  Arabidopsis thaliana , a pollen-specific   C   yclic    N   ucleotide-   G   ated cation    C   hannel 16  ( cngc16 ), is required for plant reproduction under temperature-stress conditions. Plants harboring a  cncg16  knockout are nearly sterile under conditions of hot days and cold nights. To understand the underlying cause, RNA-Seq was used to compare the pollen transcriptomes of wild type (WT) and  cngc16  under normal and heat stress (HS) conditions.    Results  Here we show that a heat-stress response (HSR) in WT pollen resulted in 2102 statistically significant transcriptome changes (≥ 2-fold changes with adjusted  p -value ≤0.01), representing approximately 15% of 14,226 quantified transcripts. Of these changes, 89 corresponded to transcription factors, with 27 showing a preferential expression in pollen over seedling tissues. In contrast to WT,  cngc16  pollen showed 1.9-fold more HS-dependent changes (3936 total, with 2776 differences between WT and  cngc16 ). In a quantitative direct comparison between WT and  cngc16  transcriptomes, the number of statistically significant differences increased from 21 pre-existing differences under normal conditions to 192 differences under HS. Of the 20 HS-dependent changes in WT that were most different in  cngc16 , half corresponded to genes encoding proteins predicted to impact cell wall features or membrane dynamics.    Conclusions  Results here define an extensive HS-dependent reprogramming of approximately 15% of the WT pollen transcriptome, and identify at least 27 transcription factor changes that could provide unique contributions to a pollen HSR. The number of statistically significant transcriptome differences between WT and  cngc16  increased by more than 9-fold under HS, with most of the largest magnitude changes having the potential to specifically impact cell walls or membrane dynamics, and thereby potentiate  cngc16  pollen to be hypersensitive to HS. However, HS-hypersensitivity could also be caused by the extensive number of differences throughout the transcriptome having a cumulative effect on multiple cellular pathways required for tip growth and fertilization. Regardless, results here support a model in which a functional HS-dependent reprogramming of the pollen transcriptome requires a specific calcium-permeable  Cyclic Nucleotide-Gated cation Channel, CNGC16.Electronic supplementary material  The online version of this article (10.1186/s12864-018-4930-4) contains supplementary material, which is available to authorized users.

bmc genomics

A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)