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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.

Cleaved Amplified Polymorphic Sequences (CAPS) markers are applicable in a wide range of tasksin plant biology. They have been developed for plant genetics and breeding and become especially useful. This mini-review analyzes information about the application of CAPS markers within the past3–5 years. In the presented study, special attention is focused on CAPS markers linked with genes controlling important agricultural traits in different crops. The main principles of the developmentand analysis of CAPS markers, as well as advantages and disadvantages of this type of molecular markers, are briefly outlined in the beginning of this review. CAPS markers are based on PCR amplification of DNA fragments with specific primers followed by digestion with restriction enzymes and separation of the products in agarose gel. Functional CAPS markers can be developed on the known sequence of a gene of interest for the analyses of its structure, function, expression, and regulation. CAPS closely linked to the gene of interest are especially helpful for Marker-Assisted Selection, and they are widely used in the breeding of wheat, barley, soybean, potato, tomato, and other crops for tolerance to various pathogens. CAPS markers are often used for the preparation of genetic maps and fine mapping of studied genes. For some plants, first moleculargenetic maps were prepared using CAPS. This method was also successfully used for the mapping of both individual genes and QTLs controlling such important traits as plant growth habit, grain quality, and tolerance to pathogens in cereals, as well as the shape of tomato fruit. CAPS have important applications in the analyses of genetic polymorphism and phylogeny, particularly, in closely related species. Thus, CAPS are an effective tool for molecular-genetic research and plant breeding.

The inheritance of the reaction of sunflower to downy mildew was investigated using resistant and susceptible near isogenic lines (NILs) and their F 3 families. Resistance to race 730 was evaluated using the whole seedling inoculation technique. Seventy-three F 3 families were inoculated, among which 54 families were resistant and 19 susceptible, fitting a 3 : 1 segregation ratio. F 3 families were also studied using several PCR markers. Ten markers at the Pl6 locus, specific for the resistant line, also segregated in F 3 families with a 3 : 1 ratio. The same segregation ratio occurred for microsatellite haplotypes that resembled the resistant parent, and were amplified with ORS 166 and ORS 1043. The only common fragment that was observed between resistant and susceptible parental lines was one of the TIR-NBS-LRR resistance gene analogue markers, having a restriction site. Two co-dominant cleaved amplified polymorphic sequence (CAPS) markers were obtained. The mapping data indicate that several dominant markers and two CAPS markers, developed here, completely co-segregate with the Pl6 gene conferring resistance to race 730. CAPS markers will facilitate efficient marker-assisted selection for sunflower resistance to downy mildew race 730.

Sea Lettuce (Ulva spp. Ulvophyceae, Ulvaceae) has tremendous ecological and industrial impacts, from the negative effects of green tide events to the industrial production of food, feed, and value-added products. Due to the morphological similarities between Ulva species, their identification requires the use of “barcoding”, which relies on the sequencing of short fragments of DNA and the comparison of the obtained sequence to that of sequences present in public repositories. However, Sanger sequencing can be costly when hundreds of samples need to be analysed. In addition, “barcoding”, which uses Sanger sequencing, cannot be applied directly on bulk biomass, and requires independent assessment of the individuals within, which is often not possible in commercial products. Here, we describe a novel “sequencing-free” method for species identification of foliose Ulva species that by-passes the drawbacks associated with Sanger sequencing. The assay uses restriction digestion enzymes which target species-specific Single Nucleotide Polymorphisms (SNPs) present within the ITS1 sequence. Digestion of the ITS1 PCR product with two enzyme mixtures allows for the discrimination of the main foliose Ulva species, as well as U. compressa, which can have a foliose morphotype. Of the species tested, only U. pseudorotundata and U. arasakii show the same digestion pattern. Since those two Ulva species are allopatric, we expect this issue to be of limited impact for the users. In addition to species identification, we demonstrate that the assay can be used for hybrid detection, which can have interests for Ulva breeding and species delimitation. Importantly, the assay can be used to detect at once the different Ulva species present within a bulk of Ulva biomass, which could allow for traceability and characterisation of the purity of Ulva commercial products. This study provides a new quick and cost-effective method for foliose Ulva species identification that could readily be extended to other species.