Twan Rutten

Local metabolic programs can determine whether developing organs maintain growth, differentiate, or degenerate. However, the spatial establishment of such programs during reproductive development remains poorly understood. In cereal inflorescences, this question is closely tied to grain number because the fate of initiated floral primordia is shaped by the developmental position, metabolic support, genotype, and environmental stress. To understand the metabolic logic underlying floral fate in barley ( Hordeum vulgare L.), we mapped the spatial distribution of metabolites across the inflorescence in wild-type Bowman and in hvcmf4 , a mutant that undergoes premature apical inflorescence degeneration. Amino acid-, carbohydrate-, and chlorophyll-associated metabolites form clear developmental gradients along the inflorescence axis. These gradients are progressively remodeled during developmental pre-anthesis tip degeneration but are both accelerated and spatially distorted in hvcmf4 . Within this broader metabolic landscape, two discrete domains stand out. First, spermidine-associated domains specifically marked reproductive meristems, a pattern corroborated by the meristem-enriched expression of polyamine biosynthetic genes. This polyamine-rich meristem state declined as developmental tip degeneration proceeded and was prematurely lost in hvcmf4 , where polyamine metabolism appeared to shift toward oxidative breakdown via the polyamine oxidase pathway. Second, lysophosphatidylcholine accumulated specifically at floral attachment and vascular supply zones. The developmental reduction of this bioactive lysophospholipid-associated domain in the apical regions, and its stronger disruption in hvcmf4 , coincided with the reprogramming of lipid-remodeling and auxin transport-associated genes, suggesting impaired coordination of lipid signaling, auxin canalization, and vascular support. Together, our study reveals spatial polyamine and lysophospholipid domains that couple meristem maintenance with vascular support, providing a metabolic framework for the fate of developing cereal inflorescences.

Hybrid wheat breeding is constrained by the predominantly self-pollinating nature of wheat florets, which limits cross-pollination efficiency and increases grain production costs. Enhancing hybridization requires a better understanding of male reproductive traits, particularly pollen quantity and viability. We combined developmental staging, environmental assays, and genetic mapping to dissect these traits in European winter bread wheat. Anther and pollen maturation, characterized using an enhanced high-resolution Waddington scale, followed a proximo-distal gradient across the spike and an acropetal gradient within spikelets, with stage W10 marking peak pollen maturation and viability stage. Time-lapse imaging revealed that anthesis follows the same coordinated spatial pattern, indicating tightly synchronized reproductive development across the spike. Importantly, pollen viability was best maintained at room temperature (22 °C) for up to 8 h; however, unexpectedly, it declined more rapidly under cooler storage conditions (15 °C and 8 °C). To investigate the genetic basis of pollen viability and pollen number, we performed quantitative trait locus (QTL) analysis and identified seven loci, including a major QTL for pollen number on chromosome 2A and a distinct QTL for pollen viability on 5A. In both cases, alleles from the cultivar ‘Piko’ consistently conferred beneficial trait effects. These findings refine anther staging, highlight environmental sensitivity of wheat pollen, and identify genomic regions that can improve reproductive efficiency for hybrid wheat production and breeding.

The kinetochore is an essential protein complex that ensures proper chromosome segregation during cell division. Kinetochore assembly is initiated by the incorporation of centromere-specific Histone H3 (CENP-A/CENH3) into centromeric nucleosomes. This process depends on KNL2/M18BP1 and CENP-C proteins. In eudicots, two variants of KNL2 are present, namely αKNL2 and βKNL2. Both possess the conserved SANTA domain, while αKNL2 additionally has the centromere-targeting CENPC-k motif. Despite lacking the CENPC-like motif, the plant-specific βKNL2 localizes to centromeres and aids in CENP-A/CENH3 loading. We found that efficient centromeric targeting of βKNL2 requires the SANTA domain and the C-terminal part, while nuclear localization is regulated by a conserved C-terminal motif-III, which undergoes SUMOylation. Independent experiments supported by structural analysis suggest that βKNL2 can interact multivalently with αKNL2, with DNA, and itself. We show that the centromeric targeting of βKNL2 depends on αKNL2 in a tissue-dependent manner. Our findings provide crucial insights into the unique mechanisms of plant-specific kinetochore assembly, highlighting βKNL2’s essential role in this process.

Awns of wild barley ( Hordeum vulgare ssp. spontaneum L.) are rough by default due to silicified upward-oriented trichomes on the awn’s epidermis, forming a ratcheted surface, which is advantageous for seed dispersal and burial. Cultivated barley, however, may carry smooth awns covered by smaller barbs or lacking barbs completely. The gene Raw1 on chromosome 5H is a major factor controlling barley awn roughness and was shown to encode a LONG AND BARBED AWN1 (LABA1) homolog. Here we report, by using quantitative analysis of the barb trait, map-based cloning and Cas9-mediated gene knock-out, a second gene Raw7 , located on barley chromosome 7H, encoding a putative two-component response regulator. We propose that Raw7 acts downstream of Raw1 in a cytokinin signaling pathway underlying cell cycle control in epidermal barb primordia cells. Raw1 and Raw7 show epistatic interaction, suggesting that Raw1 acts as the primary driver of barb initiation, while Raw7 modulates barb size and frequency. Our findings provide the foundation to study the selection and domestication history of the awn roughness trait in barley, and thus to dissect if awn roughness is providing an advantage in cultivated barley or if the trait persisted after domestication due to linkage drag. Summary: The presence of silicified upward-oriented trichomes or barbs arising from the epidermis of barley awns is a prominent trait. They form a ratcheted surface which is advantageous for seed dispersal and burial and defense against herbivory. Previous work identified Raw1 on chromosome 5H as a major determinant of awn roughness in barley. Here, we identify a second awn roughness gene, Raw7 on chromosome 7H, combining quantitative phenotyping of barb traits, map-based cloning and Cas9-mediated targeted mutagenesis for functional analyses. Genetic and functional evidence suggests a complex epistatic interaction in which Raw1 primarily drives barb formation and Raw7 fine-tunes endoreduplication-dependent epidermal cell expansion and patterning in barb primordia cells. Raw1 and Raw7 likely act in a cytokinin-dependent two-component signaling pathway, where Raw1 promotes local cytokinin activation and Raw7 , a type-B response regulator, mediates downstream transcriptional responses. The proposed pathway suggests additional undetected loci may contribute to awn roughness, and emerging barley pangenome and pan-transcriptome resources provide a framework to identify and functionally validate new candidates.

Integrating spatial morphogens with temporal developmental clocks is fundamental to optimizing plant architecture and crop yield, yet their molecular interface remains elusive. Here, we characterize Branched shoot 1 (Bsh1), a semi-dominant wheat mutant exhibiting non-canonical upper-aerial branching and aberrant spike development, caused by a T265I substitution in the DNA-binding domain of the auxin response factor TaARF4-A2. Unlike flanking mutations governing protein stability in basal land plants, this central substitution uniquely converts TaARF4-A2 into an auxin-insensitive hypermorphic repressor. The mutant protein disrupts auxin-cytokinin homeostasis and markedly enhances the native repression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, the core timers of developmental phase transitions. This spatial and temporal uncoupling unleashes upper axillary buds from dormancy, promoting aerial branching and diverting resources from reproductive development. Our findings demonstrate how a conserved spatial morphogen effector was evolutionarily rewired in polyploid wheat to dictate the temporal SPL clock, orchestrating species-specific shoot architectural innovation.

Kinetochores are large protein complexes that serve as attachment sites for spindle microtubules, ensuring proper chromosome segregation during cell division. KINETOCHORE NULL2 (αKNL2) is a key kinetochore protein required for the incorporation of the centromeric histone variant CENH3. The precise regulation of αKNL2 levels is crucial, but the molecular mechanisms controlling this process remain largely unexplored. In this study, we demonstrated that the Anaphase-Promoting Complex/Cyclosome (APC/C) mediates the ubiquitin-dependent proteolysis of αKNL2 during mitosis. Our findings revealed that αKNL2 accumulates in the presence of 26S proteasome inhibitors, and our yeast 2-hybrid and proteomic screens showed that proteins from the ubiquitin-proteasome pathway interact with KNL2 in Arabidopsis (Arabidopsis thaliana) and nematode (Caenorhabditis elegans). Arabidopsis αKNL2 directly interacts with Anaphase-Promoting Complex subunit 10 (APC10) and Cell Division Cycle 20.1 (CDC20.1), 2 substrate recognition components of the APC/C. RNAi-mediated depletion of APC/C resulted in the accumulation and mislocalization of endogenous αKNL2. Additionally, mutation or deletion of the D-box1 region, or substitution of residues K336 and K339, impaired αKNL2 degradation. The expression of a proteasome-resistant αKNL2 variant in planta caused severe defects in growth, fertility, and mitotic division. These findings show that APC/CCDC20-mediated degradation of αKNL2 is critical for proper kinetochore function and centromere integrity.

Background: The two-component system (TCS) serves as a common intracellular signal transduction pathway implicated in various processes of plant development and response to abiotic stress. With regard to the important cereal crop barley, only partial information about the occurrence of TCS signaling elements in the genome and putative functions is available. Results: In this study, we identified a total of 67 non-redundant TCS genes from all subgroups of the phosphorelay in the latest barley reference genome. Functional annotation and phylogenetic characterization was combined with a comprehensive gene expression analysis of the signaling components. Expression profiles hint at potential functions in vegetative and reproductive organs and tissue types as well as diverse stress responses. Apparently, a distinct subset of TCS genes revealed a stringent grain-specificity not being expressed elsewhere in the plant. By using laser capture microdissection (LCM)-based transcript analysis of barley grain tissues, we refined expression profiles of selected TCS genes and attributed them to individual cell types within the grain. Distinct TCS elements are exclusively expressed in the different maternal and filial cell types, particularly in the endosperm transfer cell (ETC) region. These genes are deemed to be selected in the domestication process of modern cultivars. Moreover, barley plants transformed with a synthetic sensor (TCSn::GFP) showed a high and specific activity in the ETC region of grains monitoring transcriptional output of the signaling system. Conclusions: The results provide comprehensive insights into the TCS gene family in the temperate cereal crop barley and indicate implications in various agronomic traits. The dataset is valuable for future research in different aspects of plant development and will be indispensable not only for barley, but also for other crops of the Poaceae.

In eukaryotes, accurate chromosome segregation during cell division relies on the centromeric histone H3 variant, CENH3. Our previous work identified KINETOCHORE NULL2 (αKNL2) as a plant CENH3 assembly factor, which contains a centromere-targeting motif, CENPC-k, analogous to the CENPC motif found in CENP-C. We also demonstrated that αKNL2 can bind DNA in vitro in a sequence-independent manner, without the involvement of its CENPC-k motif. In this study, we show that the CENPC-k and CENPC motifs alone are insufficient for centromere targeting in Nicotiana benthamiana and Arabidopsis thaliana. In silico analysis identified adjacent DNA-binding regions near the CENPC-k and CENPC motifs, suggesting their role in centromeric DNA interaction. We further demonstrated that protein fragments containing these motifs effectively target centromeres. Deletion of these DNA-binding domains reduced the centromeric localization of αKNL2-C, while fusing CENPC-k to the non-specific DNA-binding domain of histone-like nucleoid structuring protein from Escherichia coli successfully targeted it to centromeres. Our findings suggest that the centromeric targeting of αKNL2 and CENP-C proteins relies on the CENPC-k/CENPC motifs, and that their sequence-independent DNA-binding activity enhances their centromere anchoring. These insights into the mechanisms of αKNL2 and CENP-C targeting may facilitate the engineering of kinetochore structures by directing chromatin-modifying proteins to centromeres.

Understanding the spatial organization of genomes within chromatin is crucial for deciphering gene regulation. A recently developed CRISPR–dCas9-based genome labeling tool, known as CRISPR–FISH, allows efficient labeling of repetitive sequences. Unlike standard fluorescence in situ hybridization (FISH), CRISPR–FISH eliminates the need for global DNA denaturation, allowing for superior preservation of chromatin structure. Here, we report on further development of the CRISPR–FISH method, which has been enhanced for increased efficiency through the engineering of a recombinant dCas9 protein containing an ALFA-tag. Using an ALFA-tagged dCas9 protein assembled with an Arabidopsis centromere-specific guide RNA, we demonstrate target-specific labeling with a fluorescence-labeled NbALFA nanobody. The dCas9 protein possessing multiple copies of the ALFA-tag, in combination with a minibody and fluorescence-labeled anti-rabbit secondary antibody, resulted in enhanced target-specific signals. The dCas9–ALFA-tag system was also instrumental in live cell imaging of telomeres in Nicotiana benthamiana. This method will further expand the CRISPR imaging toolkit, facilitating a better understanding of genome organization. Furthermore, we report the successful integration of the highly sensitive tyramide signal amplification method with CRISPR–FISH, demonstrating effective labeling of Arabidopsis centromeres.

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles—sharp epidermal projections—that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum . Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.