Restoring cytonuclear stoichiometry is necessary after whole-genome duplication (WGD) and interspecific/intergeneric hybridization in plants. We investigated this phenomenon in auto- and allopolyploids of the Festuca-Lolium complex providing insights into the mechanisms governing cytonuclear interactions in early polyploid and hybrid generations. Our study examined the main processes potentially involved in restoring the cytonuclear balance after WGD comparing diploids and new and well-established autopolyploids. We uncovered that both the number of chloroplasts and the number of chloroplast genome copies were significantly higher in the newly established autopolyploids and grew further in more established autopolyploids. The increase in the copy number of the chloroplast genome exceeded the rise in the number of chloroplasts and fully compensated for the doubling of the nuclear genome. In addition, changes in nuclear and organelle gene expression were insignificant. Allopolyploid Festuca × Lolium hybrids displayed potential structural conflicts in parental protein variants within the cytonuclear complexes. While biased maternal allele expression has been observed in numerous hybrids, our results suggest that its role in cytonuclear stabilization in the Festuca × Lolium hybrids is limited. This study provides insights into the restoration of the cytonuclear stoichiometry, yet it emphasizes the need for future research to explore post-transcriptional regulation and its impact on cytonuclear gene expression stoichiometry. Our findings may enhance the understanding of polyploid plant evolution, with broader implications for the study of cytonuclear interactions in diverse biological contexts.

Bavarian State Research Center for Agriculture Institute for Crop Science and Plant Breeding Am Gereuth 4 85354 Freising Germany

Department of Crop Genetics John Innes Centre Norwich NR4 7UH UK

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

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

Institute of Experimental Botany of the Czech Academy of Sciences Centre of Plant Structural and Functional Genomics Šlechtitelů 31 77900 Olomouc Czech Republic

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

New Mexico Institute of Mining and Technology Biology Department Socorro New Mexico 87801 USA

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