The general framework of this work is study of hybridization between two Rhinanthus
species (Orobanchaceae), Rhinanthus minor L. and Rhinanthus major using advanced
genomics tools. These species are annual hemi-parasitic plants in which hybridization
and introgression have been documented before. In naturally mixed populations of
both species, hybridization leads predominantly to introgression from R. minor into R.
major. Furthermore, hybrids with R. major as the maternal parent (F1a) have often
been reported to have low germination rates in comparison with hybrids with R.
minor as maternal parent (F1m). Therefore, in order to better estimate the degree of
introgression between both species, a large panel of SNP markers was developed in
this thesis project and used on samples collected from several mixed populations. In
order to understand the mechanisms behind the low germination rate of F1a seeds, a
differential gene expression study was conducted during dormancy and germination.
Using species-specific SNP markers for both species and tracked in nine mixed
populations. Introgression was much more frequent than could be detected with
previously used ISSR and RAPD makers. Further investigation of our species-specific
markers in R. major individuals with a low admixture rate with R. minor showed that
only a few of the loci tended to introgress frequently, while the others had low
introgression rates. Although with ddRAD sequencing we only covered a small part of
the genome, we were still able to find similarity and dissimilarity of introgressed loci
among the populations.
Using RNA-seq in F1a and F1m seeds during cold stratification and after germination
revealed that there were large transcriptome differences between seeds with
different maternal plants, but we could not detect any differentially expressed genes
in the plastid genome, what would be expected in case of a nuclear-cytoplasmic
incompatibility. In F1m seeds, genes active in the development of seeds and
seedlings were upregulated, but in F1a seeds, upregulation of genes related to stress
and enduring dormancy were observed. The main cause of this maternal effect is still
unclear and further investigation is needed to find out how these differences in gene
expression are caused.
The combined action of this thesis has opened the way towards a full understanding
of hybridization and introgression between R. major and R. minor.