Transcriptome profiling and comparison ofRhinanthus majorandRhinanthus minorreciprocal F1hybrids during seed stratification and germination

Background and Aims: Germination is a vital stage in a plant’s life cycle, and a different germination behavior of offspring in comparison to their parents can have fitness consequences. In studies on hybridization between Rhinanthus minor and R. major , low germination rates of F 1 hybrids with R. major as the maternal parent have often been reported. In contrast, the F 1m hybrid, with R. minor as the maternal parent, germinates readily and rapidly. Methods: In order to find the cause of this difference, we used RNA-Seq to obtain transcriptome profiles of F 1a and F 1m seeds during stratification at 4°C and just after germination, after 40 days of stratification for the F 1m seeds and 60 days for the F 1a seeds. Key Results A comparison of the transcriptome of F 1a seeds that had just germinated (60 days) with non-germinated F 1a seeds after 40 and 60 days revealed 2918 and 1349 differentially expressed (DE) genes, respectively. For F 1m seeds, 958 genes showed differential expression in germinated and non-germinated seeds after 40 days. The DE genes of F 1a and F 1m hybrids clustered into two separate groups, even though they had the same parents, and no differentially expression was found for plastid genes. Non-germinated F 1a seeds had an abundance of enzymes and proteins associated with peroxidase activity, peroxiredoxin activity and nutrient reservoir activity. Expression of genes related to seed germination and seed development increased in non-germinated F 1a hybrid seeds between 40 and 60 days of cold stratification. F 1a seeds that had germinated showed an upregulation of genes related to the gibberellic acid-mediated signaling pathway and response to gibberellin, along with a low expression of DELLA superfamily. Conclusions: Although the results demonstrated strong differences in gene expression during stratification between the reciprocal hybrids, we could not identify its cause, since no plastid genes were differentially expressed. It is possible that differences in embryo development after seed formation and before stratification play a role, including epigenetic imprinting.