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.

Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany of the Czech Academy of Sciences Šlechtitelů 31 77900 Olomouc Czech Republic

Department of Botany Faculty of Science Palacký University in Olomouc Šlechtitelů 27 78371 Olomouc Czech Republic

Department of Ecology Evolution and Organismal Biology Iowa State University Ames IA 50011 USA

Department of Environmental Stress Biology Institute of Plant Genetics Polish Academy of Sciences Strzeszyńska 34 60 479 Poznań Poland

Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland

Molecular Plant Breeding Institute of Agricultural Sciences ETH Zurich Universitaetstrasse 2 8092 Zurich Switzerland

National Centre for Biomolecular Research Faculty of Science Masaryk University Kotlářská 2 61137 Brno Czech Republic

Plant Sciences Unit Flanders Research Institute for Agriculture Fisheries and Food Caritasstraat 39 9090 Melle Belgium

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Uniparental expression of ribosomal RNA in ×Festulolium grasses: a link between the genome and nucleolar dominance

Genome Dominance in Allium Hybrids (A. cepa × A. roylei)