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Background   In situ  hybridization is a general molecular method typically used for the localization of mRNA transcripts in plants. The method provides a valuable tool to unravel the connection between gene expression and anatomy, especially in species such as pines which show large genome size and shortage of sequence information.    Results  In the present study, expression of the catalase gene ( CAT ) related to the scavenging of reactive oxygen species (ROS) and the polyamine metabolism related genes, diamine oxidase ( DAO ) and arginine decarboxylase ( ADC ), were localized in developing Scots pine ( Pinus sylvestris  L.) seeds. In addition to specific signals from target mRNAs, the probes continually hybridized non-specifically in the embryo surrounding region (ESR) of the megagametophyte tissue, in the remnants of the degenerated suspensors as well as in the cells of the nucellar layers, i.e. tissues exposed to cell death processes and extensive nucleic acid fragmentation during Scots pine seed development.    Conclusions  In plants, cell death is an integral part of both development and defence, and hence it is a common phenomenon in all stages of the life cycle. Our results suggest that extensive nucleic acid fragmentation during cell death processes can be a considerable source of non-specific signals in traditional  in situ  mRNA hybridization. Thus, the visualization of potential nucleic acid fragmentation simultaneously with the  in situ  mRNA hybridization assay may be necessary to ensure the correct interpretation of the signals in the case of non-specific hybridization of probes in plant tissues.

Dealing with the problem of non-specific in situ mRNA hybridization signals associated with plant tissues undergoing programmed cell death