The production and analysis of a synthetic hybrid: Trifolium pallescens x Trifolium occidentale

White clover (Trifolium repens L.) is a globally important stoloniferous agricultural crop. It is an allopolyploid; T. occidentale is generally accepted as the male progenitor, while T. pallescens and T. nigrescens have been proposed as one of the possible female progenitors. This work depicts a synthetic cross between T. pallescens and T. occidentaleand a preliminary analysis of the effect of the hybridization on the transcriptome.Two hybrids (H1 and H2) of the same cross were produced, these were stoloniferous, had viable pollen, and were back-crossed successfully to the male parent. A polyploid was produced, but it died due to technical difficulties. Trait measurements were taken, these showed characteristics from both parents. AFLP analysis displayed different inheritance patterns. Sequencing of some AFLP fragments showed these differences were due to retrotransposon movement and white clover SSR mutations in the hybrids. NGS of transcriptome via Illumina HiScan detected SNP and indicated differing expression patterns between the hybrids and parents.Phenotypically the hybrids are more like the female, but with stolons and leaf markings from the male. AFLP analysis showed equal numbers of T. occidentale alleles in H1 and H2, but H2 had far fewer T. pallescensalleles. This is unexpected from the trait data. PCA analysis of normalized expression values revealed an intermediate expression of the hybrids to the parents, as was expected. The hybrid will be a useful resource for evolutionary studies, for mapping agriculturally important traits, and ultimately in the clover breeding program, as novel genotypes may be generated by hybridization and polyploidization