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Background  The cell cycle and cellular oxidative stress responses are tightly controlled for proper growth and development of Scots pine ( Pinus sylvestris  L.) seed. Programmed cell death (PCD) is an integral part of the embryogenesis during which megagametophyte cells in the embryo surrounding region (ESR) and cells in the nucellar layers face death. In the present study, we show both the tissue and developmental stage specific expression of the genes encoding the autophagy related ATG5, catalase (CAT), and retinoblastoma related protein (RBR) as well as the connection between the gene expressions and cell death programs.    Results  We found strong  CAT  expression in the cells of the developing embryo throughout the embryogenesis as well as in the cells of the megagametophyte and the nucellar layers at the early embryogeny. The  CAT  expression was found to overlap with both the  ATG5  expression and hydrogen peroxide localization. At the late embryogeny,  CAT  expression diminished in the dying cells of the nucellar layers as well as in megagametophyte cells, showing the first signs of incipient cell death. Accumulation of starch and minor  RBR  expression were characteristic of megagametophyte cells in the ESR, whereas strong  RBR  expression was found in the cells of the nucellar layers at the late embryogeny.    Conclusions  Our results suggest that ATG5, CAT, and RBR are involved in the Scots pine embryogenesis and cell death processes. CAT seems to protect cells against hydrogen peroxide accumulation and oxidative stress related cell death especially during active metabolism. The opposite expression of  RBR  in the ESR and nucellar layers alongside morphological characteristics emphasizes the different type of the cell death processes in these tissues. Furthermore, the changes in  ATG5  and  RBR  expressions specifically in the megagametophyte cells dying by necrotic cell death suggest the genetic regulation of developmental necrosis in Scots pine embryogenesis.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0462-0) contains supplementary material, which is available to authorized users.

Expression of catalase and retinoblastoma-related protein genes associates with cell death processes in Scots pine zygotic embryogenesis