Summary• Leaf senescence can be described as the dismantling of cellular components during a specific time interval before cell death. This has the effect of remobilizing N in the form of amino acids that can be relocalized to developing seeds. High levels of carbohydrates have previously been shown to promote the onset of the senescence process.• Carbohydrate accumulation in barley ( Hordeum vulgare ) plants was induced experimentally by steam-girdling at the leaf base, occluding the phloem, and gene regulation under these conditions was investigated using the Affymetrix Barley GeneChip array and quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR).• Transcript levels of plastidial (aminopeptidases, cnd41) and vacuolar (thiol and serine) proteases clearly increase in girdled leaves. Of special interest are cnd41, a plastidial aspartyl peptidase that has been implicated in Rubisco degradation in tobacco; and cp-mIII, a highly upregulated carboxypeptidase. SAG12 , hexokinases and other senescence-specific genes are also upregulated under these conditions.• Applying a genomic approach to the innovative experimental system described here significantly enhances our knowledge of leaf proteolysis and whole-plant N recycling.

Summary• To identify genes involved in the regulation and execution of leaf senescence and whole-plant nitrogen reallocation, near-isogenic barley germplasm divergent in senescence timing and protein concentration of mature grains was contrasted.• Barley lines differing in allelic state at a major locus on chromosome six, controlling grain protein concentration, were obtained after four generations of backcrossing. Based on physiological data indicating major differences between low-and high-grain protein germplasm at 14-21 d past anthesis, the flag leaf and kernel transcriptomes of the low-protein parent and one high-protein near-isogenic line were compared at these time points, using the 22-k Barley1 Affymetrix microarray.• Our data associate several genes with both known (based on sequence comparisons) and unknown functions with the senescence process. These include leucine-rich repeat transmembrane protein kinases, a glycine-rich RNA-binding protein with homology to AtGRP7 and a 'mother of FT/TF1' gene. Our data also indicate upregulation of genes coding for both plastidial and extraplastidial proteases in germplasm with accelerated leaf senescence.• Functional characterization of candidate genes identified by this research may contribute to our understanding of the molecular network underlying leaf senescence and nitrogen reallocation.

Leaf senescence is characterized by nitrogen remobilization to developing seeds of annual plants, or surviving organs of perennial species. It has been demonstrated that high carbohydrate levels (carbon "feast") are associated with the onset of the senescence process. Therefore, the development of model systems allowing the manipulation of leaf carbohydrates constitutes a logical first step in the investigation of processes important during early phases of senescence, such as plastidial protein degradation. In this study, sugar accumulation was induced either by the incubation of excised, mature barley (Hordeum vulgare L.) leaves under relatively strong light, or by the interruption of sieve tubes at the base of the leaf lamina by "steam-girdling". Accelerated chlorophyll degradation and net proteolysis confirmed successful senescence induction in both model systems, but suggested that girdled leaves are more useful than excised leaves to study proteolysis. Activities or transcript levels of several proteolytic enzymes, including plastidial (aminopeptidases, Clp protease), cytosolic (proteasome) and vacuolar (thiol proteases, an aspartic protease and a serine carboxypeptidase) proteases were clearly induced under these conditions; some of these genes also reacted to other stimuli such as leaf excision. The most interesting finding was the specific induction of a carboxypeptidase gene (cp-mIII) in girdled leaves accumulating high carbohydrate levels. As a previous study from our laboratory, using a genetic approach, has indicated that one or several carboxypeptidases are involved in leaf N remobilization, the detailed characterization of cp-mIII (and, possibly, closely related genes) may considerably improve our understanding of whole-plant N recycling.

BackgroundRibosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arabidopsis thaliana, 45S rRNA genes are found in two large ribosomal DNA (rDNA) clusters and little is known about the contribution of each to the overall transcription pattern in the species.ResultsBy taking advantage of genome sequencing data from the 1001 Genomes Consortium, we characterize rRNA gene sequence variation within and among accessions. Notably, variation is not restricted to the pre-rRNA sequences removed during processing, but it is also present within the highly conserved ribosomal subunits. Through linkage mapping we assign these variants to a particular rDNA cluster unambiguously and use them as reporters of rDNA cluster-specific expression. We demonstrate that rDNA cluster-usage varies greatly among accessions and that rDNA cluster-specific expression and silencing is controlled via genetic interactions between entire rDNA cluster haplotypes (alleles).ConclusionsWe show that rRNA gene cluster expression is controlled via complex epistatic and allelic interactions between rDNA haplotypes that apparently regulate the entire rRNA gene cluster. Furthermore, the sequence polymorphism we discovered implies that the pool of rRNA in a cell may be heterogeneous, which could have functional consequences.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1209-z) contains supplementary material, which is available to authorized users.