Gene Expression Changes in First Generations of Reciprocal Interspecific Grass Hybrids

Interspecific hybridization plays a key role in plant evolution. Interspecific hybrids arise from a cross between two different species, frequently followed by polyploidization. As a consequence, such hybrids carry two or even more sub-genomes, which contribute to their phenotype. Some interspecific hybrids, including Festulolium (Festuca × Lolium hybrids), were created artificially to combine favourable characteristics of two species. However, only little is known about the underlying mechanisms of interactions between the two sub-genomes in hybrid plants. We studied gene expression in reciprocal Festuca pratensis × Lolium multiflorum hybrids. First, the transcriptome of both parental genotypes was sequenced and assembled using Orthologous Guided Assembly, resulting in 19,036 and 18,952 transcripts, respectively. Then, interspecific SNPs that discriminate Festuca and Lolium alleles of specific transcripts in the hybrid progeny were identified. These SNPs were used to quantify differential and allele specific expression in the parental genotypes and the two following hybrid generations. Only 135 (out of 6647) orthologous genes display differential expression between the parental genotypes. Similarly, equal expression for the two parental alleles was found in hybrids for the majority of genes. About 9% of the ≈6800 analysed genes analysed in each reciprocal hybrid show allele specific expression in F1 generation and this number increased to about 15% in F2 plants. While maternity did not affect gene expression, effect of species was clearly recognized. Lolium alleles were over-expressed for six times more genes than Festuca alleles in both reciprocal crosses. Our work will significantly contribute to understand hybridisation processes between two important grass species and genome interaction in allopolyploid species in general.