Nucleolar dominance (ND) is an epigenetic, developmentally regulated phenomenon that describes the selective inactivation of 35S rDNA loci derived from one progenitor of a hybrid or allopolyploid. The presence of ND was documented in an allotetraploid grass, Brachypodium hybridum (genome composition DDSS), which is a polyphyletic species that arose from crosses between two putative ancestors that resembled the modern B. distachyon (DD) and B. stacei (SS). In this work, we investigated the developmental stability of ND in B. hybridum genotype 3-7-2 and compared it with the reference genotype ABR113. We addressed the question of whether the ND is established in generative tissues such as pollen mother cells (PMC). We examined condensation of rDNA chromatin by fluorescence in situ hybridization employing state-of-art confocal microscopy. The transcription of rDNA homeologs was determined by reverse-transcription cleaved amplified polymorphic sequence analysis. In ABR113, the ND was stable in all tissues analyzed (primary and adventitious root, leaf, and spikes). In contrast, the 3-7-2 individuals showed a strong upregulation of the S-genome units in adventitious roots but not in other tissues. Microscopic analysis of the 3-7-2 PMCs revealed extensive decondensation of the D-genome loci and their association with the nucleolus in meiosis. As opposed, the S-genome loci were always highly condensed and localized outside the nucleolus. These results indicate that genotype-specific loss of ND in B. hybridum occurs probably after fertilization during developmental processes. This finding supports our view that B. hybridum is an attractive model to study ND in grasses.

Department of Molecular Epigenetics Institute of Biophysics Academy of Sciences of the Czech Republic Brno Czechia

Plant Cytogenetics and Molecular Biology Group Institute of Biology Biotechnology and Environmental Protection Faculty of Natural Sciences University of Silesia in Katowice Katowice Poland

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Front Plant Sci. 2022 Apr 28;13:917940. doi: 10.3389/fpls.2022.917940. PubMed

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Amado L., Abranches R., Neves N., Viegas W. (1997). Development-dependent inheritance of 5-azacytidine-induced epimutations in triticale: analysis of rDNA expression patterns. Chromosome Res. 5 445–450. 10.1023/a:1018460828720 PubMed DOI

Bass H. W., Marshall W. F., Sedat J. W., Agard D. A., Cande W. Z. (1997). Telomeres cluster de novo before the initiation of synapsis: a three-dimensional spatial analysis of telomere positions before and during meiotic prophase. J. Cell Biol. 137 5–18. 10.1083/jcb.137.1.5 PubMed DOI PMC

Bellini C., Pacurar D. I., Perrone I. (2014). Adventitious roots and lateral roots: similarities and differences. Annu. Rev. Plant Biol. 65 639–666. 10.1146/annurev-arplant-050213-035645 PubMed DOI

Borowska-Zuchowska N., Hasterok R. (2017). Epigenetics of the preferential silencing of Brachypodium stacei-originated 35S rDNA loci in the allotetraploid grass Brachypodium hybridum. Sci. Rep. 7:5260. 10.1038/s41598-017-05413-x PubMed DOI PMC

Borowska-Zuchowska N., Kovarik A., Robaszkiewicz E., Tuna M., Tuna G. S., Gordon S., et al. (2020). The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum. Plant J. 103 1810–1825. 10.1111/tpj.14869 PubMed DOI PMC

Borowska-Zuchowska N., Kwasniewski M., Hasterok R. (2016). Cytomolecular analysis of ribosomal DNA evolution in a natural allotetraploid Brachypodium hybridum and its putative ancestors - dissecting complex repetitive structure of intergenic spacers. Front. Plant Sci. 7:1499. 10.3389/fpls.2016.01499 PubMed DOI PMC

Borowska-Zuchowska N., Robaszkiewicz E., Wolny E., Betekhtin A., Hasterok R. (2019). Ribosomal DNA loci derived from Brachypodium stacei are switched off for major parts of the life cycle of Brachypodium hybridum. J. Exp. Bot. 70 805–815. 10.1093/jxb/ery425 PubMed DOI PMC

Castilho A., Queiroz A., Neves N., Barao A., Silva M., Viegas W. (1995). The developmental stage of inactivation of rye origin rRNA genes in the embryo and endosperm of wheat x rye F1 hybrids. Chromosome Res. 3 169–174. 10.1007/BF00710710 PubMed DOI

Catalan P., Muller J., Hasterok R., Jenkins G., Mur L. A., Langdon T., et al. (2012). Evolution and taxonomic split of the model grass Brachypodium distachyon. Ann. Bot. 109 385–405. 10.1093/aob/mcr294 PubMed DOI PMC

Cermeno M. C., Orellana J., Santos J. L., Lacadena J. R. (1984). Nucleolar organizer activity in wheat, rye and derivatives analyzed by a silver-staining procedure. Chromosoma 89 370–376. 10.1007/Bf00331254 DOI

Chandrasekhara C., Mohannath G., Blevins T., Pontvianne F., Pikaard C. S. (2016). Chromosome-specific NOR inactivation explains selective rRNA gene silencing and dosage control in Arabidopsis. Genes Dev. 30 177–190. 10.1101/gad.273755.115 PubMed DOI PMC

Chen Z. J., Pikaard C. S. (1997a). Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Gene Dev. 11 2124–2136. PubMed PMC

Chen Z. J., Pikaard C. S. (1997b). Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica. Proc. Natl. Acad. Sci. U S A 94 3442–3447. PubMed PMC

Chester M., Gallagher J. P., Symonds V. V., da Silva A. V. C., Mavrodiev E. V., Leitch A. R., et al. (2012). Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc. Natl. Acad. Sci. U S A 109 1176–1181. 10.1073/pnas.1112041109 PubMed DOI PMC

Costa-Nunes P., Pontes O., Preuss S. B., Pikaard C. S. (2010). Extra views on RNA-dependent DNA methylation and MBD6-dependent heterochromatin formation in nucleolar dominance. Nucleus 1 254–259. 10.4161/nucl.1.3.11741 PubMed DOI PMC

Diaz-Perez A., Lopez-Alvarez D., Sancho R., Catalan P. (2018). Reconstructing the origins and the biogeography of species’ genomes in the highly reticulate allopolyploid-rich model grass genus Brachypodium using minimum evolution, coalescence and maximum likelihood approaches. Mol. Phylogenet. Evol. 127 256–271. 10.1016/j.ympev.2018.06.003 PubMed DOI

Dolezel J., Cizkova J., Simkova H., Bartos J. (2018). One major challenge of sequencing large plant genomes is to know how big they really are. Internat. Mole. Sci. 19:11. 10.3390/ijms19113554 PubMed DOI PMC

Earley K., Lawrence R. J., Pontes O., Reuther R., Enciso A. J., Silva M., et al. (2006). Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Gene Dev. 20 1283–1293. 10.1101/gad.1417706 PubMed DOI PMC

Ge X. H., Ding L., Li Z. Y. (2013). Nucleolar dominance and different genome behaviors in hybrids and allopolyploids. Plant Cell Rep. 32 1661–1673. 10.1007/s00299-013-1475-5 PubMed DOI

Gordon S. P., Contreras-Moreira B., Levy J. J., Djamei A., Czedik-Eysenberg A., Tartaglio V. S., et al. (2020). Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nat. Comm. 11:1. 10.1038/s41467-020-17302-5 PubMed DOI PMC

Guo X., Han F. P. (2014). Asymmetric Epigenetic Modification and Elimination of rDNA Sequences by Polyploidization in Wheat. Plant Cell 26 4311–4327. 10.1105/tpc.114.129841 PubMed DOI PMC

Hasterok R., Draper J., Jenkins G. (2004). Laying the cytotaxonomic foundations of a new model grass, Brachypodium distachyon (L.) Beauv. Chromosome Res. 12 397–403. 10.1023/B:CHRO.0000034130.35983.99 PubMed DOI

Hasterok R., Dulawa J., Jenkins G., Leggett M., Langdon T. (2006). Multi-substrate chromosome preparations for high throughput comparative FISH. BMC Biotechnol. 6:20. 10.1186/1472-6750-6-20 PubMed DOI PMC

Hasterok R., Langdon T., Taylor S., Jenkins G. (2002). Combinatorial labelling of DNA probes enables multicolour fluorescence in situ hybridisation in plants. Folia Histochem. Cytobiol. 40, 319–323. PubMed

Hasterok R., Maluszynska J. (2000a). Different rRNA gene expression in primary and adventitious roots of Allium cepa L. Folia Histochem. Cytobiol. 38 181–184. PubMed

Hasterok R., Maluszynska J. (2000b). Nucleolar dominance does not occur in root tip cells of allotetraploid Brassica species. Genome 43 574–579. PubMed

Houchins K., O’Dell M., Flavell R. B., Gustafson J. P. (1997). Cytosine methylation and nucleolar dominance in cereal hybrids. Mol. Gen. Genet. 255 294–301. PubMed

IBI (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463 763–768. 10.1038/nature08747 PubMed DOI

Idziak D., Betekhtin A., Wolny E., Lesniewska K., Wright J., Febrer M., et al. (2011). Painting the chromosomes of Brachypodium-current status and future prospects. Chromosoma 120 469–479. 10.1007/s00412-011-0326-9 PubMed DOI PMC

Idziak D., Hasterok R. (2008). Cytogenetic evidence of nucleolar dominance in allotetraploid species of Brachypodium. Genome 51:5. 10.1139/G08-017 PubMed DOI

Jenkins G., Hasterok R. (2007). BAC ‘landing’ on chromosomes of Brachypodium distachyon for comparative genome alignment. Nat. Protoc. 2 88–98. 10.1038/nprot.2006.490 PubMed DOI

Komarova N. Y., Grabe T., Huigen D. J., Hemleben V., Volkov R. A. (2004). Organization, differential expression and methylation of rDNA in artificial Solanum allopolyploids. Plant Mole. Biol. 56 439–463. 10.1007/s11103-004-4678-x PubMed DOI

Kovarik A., Pires J. C., Leitch A. R., Lim K. Y., Sherwood A. M., Matyasek R., et al. (2005). Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics 169 931–944. 10.1534/genetics.104.032839 PubMed DOI PMC

Lacadena J. R., Cermeno M. C., Orellana J., Santos J. L. (1984). Evidence for wheat-rye nucleolar competition (amphiplasty) in triticale by silver-staining procedure. Theor. Appl. Genet. 67 207–213. 10.1007/BF00317037 PubMed DOI

Lawrence R. J., Earley K., Pontes O., Silva M., Chen Z. J., Neves N., et al. (2004). A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol. Cell 13 599–609. PubMed

Lusinska J., Majka J., Betekhtin A., Susek K., Wolny E., Hasterok R. (2018). Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon. B. stacei and B. hybridum. Ann. Bot. 122 445–459. 10.1093/aob/mcy086 PubMed DOI PMC

Mason A. S., Wendel J. F. (2020). Homoeologous exchanges, segmental allopolyploidy, and polyploid genome evolution. Front. Genet. 11:1014. 10.3389/fgene.2020.01014 PubMed DOI PMC

Matyasek R., Dobesova E., Huska D., Jezkova I., Soltis P. S., Soltis D. E., et al. (2016). Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus. Plant J. 85 362–377. 10.1111/tpj.13110 PubMed DOI

McKinlay A., Fultz D., Wang F., Pikaard C. S. (2021). Targeted Enrichment of rRNA Gene Tandem Arrays for Ultra-Long Sequencing by Selective Restriction Endonuclease Digestion. Front. Plant Sci. 12:656049. 10.3389/fpls.2021.656049 PubMed DOI PMC

Mohannath G., Pontvianne F., Pikaard C. S. (2016). Selective nucleolus organizer inactivation in Arabidopsis is a chromosome position-effect phenomenon. Proc. Natl. Acad. Sci. U S A 113 13426–13431. 10.1073/pnas.1608140113 PubMed DOI PMC

Navashin M. (1934). Chromosomal alterations caused by hybridization and their bearing upon certain general genetic problems. Cytologia 5 169–203.

Neves N., Heslop-Harrison J. S., Viegas W. (1995). rRNA gene activity and control of expression mediated by methylation and imprinting during embryo development in wheat x rye hybrids. Theor. Appl. Genet. 91 529–533. 10.1007/BF00222984 PubMed DOI

Nicolas S. D., Leflon M., Monod H., Eber F., Coriton O., Huteau V., et al. (2009). Genetic Regulation of Meiotic Cross-Overs between Related Genomes in Brassica napus Haploids and Hybrids. Plant Cell 21 373–385. 10.1105/tpc.108.062273 PubMed DOI PMC

Ozkan H., Levy A. A., Feldman M. (2001). Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13 1735–1747. 10.1105/Tpc.010082 PubMed DOI PMC

Pikaard C. S. (2000). Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids. Plant Mol. Biol. 43 163–177. PubMed

Pontes O., Lawrence R. J., Silva M., Preuss S., Costa-Nunes P., Earley K., et al. (2007). Postembryonic establishment of megabase-scale gene silencing in nucleolar dominance. PLoS One 2:e1157. 10.1371/journal.pone.0001157 PubMed DOI PMC

Preuss S. B., Costa-Nunes P., Tucker S., Pontes O., Lawrence R. J., Mosher R., et al. (2008). Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol. Cell 32 673–684. 10.1016/j.molcel.2008.11.009 PubMed DOI PMC

Reeder R. H. (1985). Mechanisms of nucleolar dominance in animals and plants. J. Cell Biol. 101 2013–2016. 10.1083/jcb.101.5.2013 PubMed DOI PMC

Shaked H., Kashkush K., Ozkan H., Feldman M., Levy A. A. (2001). Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13 1749–1759. 10.1105/tpc.010083 PubMed DOI PMC

Shaw P. (2013). The Plant Nucleolus. Plant Gen. Div. Vol. 2 65–76.

Silva M., Queiroz A., Neves N., Barao A., Castilho A., Morais-Cecilio L., et al. (1995). Reprogramming of rye rDNA in triticale during microsporogenesis. Chromosome Res. 3 492–496. 10.1007/BF00713964 PubMed DOI

Sims J., Rabanal F. A., Elgert C., von Haeseler A., Schlögelhofer P. (2021). It is just a matter of time: balancing homologous recombination and non-homologous end joining at the rDNA locus during meiosis. Front. Plant Sci. 12:773052. 10.3389/fpls.2021.773052 PubMed DOI PMC

Sochorova J., Coriton O., Kuderova A., Lunerova J., Chevre A. M., Kovarik A. (2017). Gene conversion events and variable degree of homogenization of rDNA loci in cultivars of Brassica napus. Ann. Bot. 119 13–26. 10.1093/aob/mcw187 PubMed DOI PMC

Soltis P. S., Marchant D. B., Van de Peer Y., Soltis D. E. (2015). Polyploidy and genome evolution in plants. Curr. Opin. Genet. Dev. 35 119–125. 10.1016/j.gde.2015.11.003 PubMed DOI

Symonova R. (2019). Integrative rDNAomics-Importance of the oldest repetitive fraction of the eukaryote genome. Genes 10:5. 10.3390/genes10050345 PubMed DOI PMC

Unfried I., Gruendler P. (1990). Nucleotide sequence of the 5.8S and 25S rRNA genes and of the internal transcribed spacers from Arabidopsis thaliana. Nucleic Acids Res. 18:4011. 10.1093/nar/18.13.4011 PubMed DOI PMC

Vieira R., Mellosampayo T., Viegas W. S. (1990). 1R chromosome nucleolus organizer region activation by 5-azacytidine in wheat x rye hybrids. Genome 33 707–712.

Volkov R. A., Komarova N. Y., Hemleben V. (2007). Ribosomal DNA in plant hybrids: Inheritance, rearrangement, expression. Systemat. Biodiv. 5 261–276. 10.1017/S1477200007002447 DOI

Volkov R. A., Medina F. R., Zentgraf U., Hemleben V. (2004). Molecular Cell Biology: Organization and molecular evolution of rDNA, nucleolar dominance, and nucleolus structure. Prog. Bot. 65 106–146. 10.1007/978-3-642-18819-0 DOI

Wendel J. F., Lisch D., Hu G., Mason A. S. (2018). The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation. Curr. Opin. Genet. Dev. 49 1–7. 10.1016/j.gde.2018.01.004 PubMed DOI

Yoo M. J., Liu X., Pires J. C., Soltis P. S., Soltis D. E. (2014). Nonadditive gene expression in polyploids. Annu. Rev. Genet. 48 485–517. 10.1146/annurev-genet-120213-092159 PubMed DOI

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