Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance

Summary Allopolyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being “dominant.” Such “genome dominance” can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k‐mer–based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans‐acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent‐specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies. Significance Statement Establishment of genome dominance is observed immediately after hybridization between plant species from two different genera using a novel RNA‐sequencing approach. This dominance is largely heritable, only marginally modified by cold stress and plant age and at least partly caused by more efficient trans‐acting regulatory factors of the dominant parent. Uncovering the nature and mechanisms of genome dominance contributes to the understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.