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Summary: Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse‐transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S‐genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D‐genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage. Significance Statement: Nucleolar dominance (ND) can be present in both hybrids and allopolyploids, and consists of the reversible selective suppression of the 35S rRNA genes that are inherited from one of the ancestral species. We showed that in the allotetraploid Brachypodium hybridum ND is stabilized towards the Brachypodium distachyon‐like rDNA units, irrespectively of species polyphyletic origin and genetic changes influencing homoeologue 35S rRNA gene ratios. [ABSTRACT FROM AUTHOR]

Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines. [ABSTRACT FROM AUTHOR]

Bromus erectus Huds. (erect brome) and B. variegatus M. Bieb. are Eurasian Bromus species that have been tentatively identified as potential progenitors of smooth bromegrass (B. inermis Leyss) which is the principal cultivated bromegrass in North America. The objective of this study was to characterize the genome of diploid accessions of B. erectus (2n = 2x = 14) and B. variegatus (2n = 2x = 14) using nuclear DNA content and cytogenetic analysis using Giemsa C-banding. The nuclear DNA content for B. erectus (6.19 ± 0.08 pg 2C-1) was less than that of B. variegatus (6.76 ± 0.05 pg 2C-1). These two species can be distinguished cytogenetically with the karyotypes that were developed. Complete karyotypes were not developed for both species because within species, multiple chromosomes were similar in size and C-banding. Both species had two pairs of chromosomes with satellites but the size of the satellites and the number and position of C-bands on these chromosomes differed between species. Bromus variegatus had five pairs of chromosomes with telomeric C-bands on both arms, while B. erectus had four pairs of chromosomes with a single telomeric band on the long arm and a single pair with telomeric bands on both arms. Comparison with the previously reported karyotypes and nuclear DNA contents for tetraploid and octaploid B. inermis suggest that if the diploid species B. erectus and B. varlegatus were the donor species for these polyploids, significant evolutionary changes have occurred since the initial formation of these species including chromosome loss and re-arrangement. [ABSTRACT FROM AUTHOR]

Smooth bromegrass (Bromus inermis Leyss.) has both tetraploid (2n = 28) and octaploid (2n = 56) ploidy levels that have been difficult to characterize cytogenetically because of similar chromosome morphology. Objectives of this study were to identify individual chromosomes of tetraploid and octaploid B. inermis with C-banding procedures along with chromosome length and arm length ratios, develop more detailed karyotypes than those previously available, and use the karyotypes to examine the genomic relationship of tetraploid and octaploid B. inermis. Root tips of the plants from four tetraploid and three octaploid accessions were used to produce chromosome squash preparations for cytogenetic analysis. The tetraploid B. inermis genome consisted of 12 chromosomes with a telomeric band on each arm and sixteen chromosomes with only one telomeric band on one arm. All of the chromosomes of the tetraploid form, except for four chromosomes, were identified by C-banding patterns, chromosome length, and arm length ratio. The octaploid B. inermis genome consisted of four chromosomes with no C-bands, ≈14 chromosomes with two telomeric bands, and ≈38 chromosomes with only one telomeric band on either the short or long arm. The combined use of C-banding, chromosome size, and arm length ratio only enabled groups of 2, 4, 6, or 8 similar chromosomes to be identified because of similarities in chromosome morphology of the octaploids. Results indicate that tetraploid B. inermis is an allotetraploid since all chromosomes except four could be separated into identifiable pairs. Because of differences between expected and actual numbers of satellite chromosomes and chromosomes with specific C-banding patterns, octaploid B. inermis is probably not a doubled form of the tetraploid B. inermis. [ABSTRACT FROM AUTHOR]

Determines the nuclear DNA content of bromegrass accessions in the United States Department of Agriculture National Plant Germplasm System by flow cytometry. Correlation of DNA content with ploidy level; Effect of the colchine treatment on the root tips; Detection of aneuploid plants.

Analyzes karyotype and C-banding patterns of mitotic chromosomes in diploid bromegrass. Location of C-bands; Differences of telomeric bands on chromosomes; Total length of individual chromosomes; Assigned numbers in paired homologous chromosomes; Construction of a karyotype.