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A primordium-level ice barrier in Vaccinium corymbosum floral buds is lost as their xylem trace matures

Flower primordia of Vaccinium corymbosum L. (highbush blueberry) exclude ice formation in winter through an unexplained biological barrier despite lignified xylem connecting them to the stem. We asked where this barrier lies and whether the maturation of that connection, rather than its presence, tracks its seasonal loss. On buds collected in fall, winter and spring we combined structure-resolved freezing tests, water content, thermal analysis, cryomicroscopy and xylem anatomy. Whole-bud LT50 was -20 C in fall, -31 C in winter, and -16 C in spring; water content rose only in spring. Buds froze extraorgan, without low-temperature exotherms to -46 C. Ice nucleated in the stem, reached the bud within minutes and accumulated in the scales. The bud axis froze in every season, whereas the primordia stayed ice-free in fall and winter and froze in spring, placing the barrier at each primordium, not the bud base. A continuous xylem trace reached every primordium in every season; its elements were mostly annular and helical until spring, when scalariform, reticulate and pitted elements predominated. Junction conduits stayed narrow (2 to 3 um). The primordium-level barrier was lost as this trace matured; we propose that its immature state is part of the long-unexplained barrier.

plant biology↗

The histone deacetylase HDA15 interacts with MAC3A and MAC3B to regulate intron retention of ABA-responsive genes

Histone deacetylases (HDAs) play an important role in transcriptional regulation involved in multiple biological processes. In this study, we investigate the function of HDA15 in abscisic acid (ABA) responses. Immunopurification coupled with mass spectrometry-based proteomics was used to identify the HDA15 interacting proteins. We found that HDA15 can interact with the core subunits of MOS4-Associated Complex (MAC), MAC3A and MAC3B. In addition, ABA enhances the interaction of HDA15 with MAC3B. hda15 and mac3a/mac3b mutants are ABA-insensitive in seed germination and hyposensitive to salinity. RNA sequencing (RNA-seq) analysis demonstrate that HDA15 and MAC3A/MAC3B not only affect the expression of ABA-related genes, but also regulate ABA-responsive intron retention (IR). Furthermore, HDA15 and MAC3A/MAC3B reduce the histone acetylation level of the genomic regions near ABA-responsive IRs. Our studies uncovered the role of histone deacetylation in ABA-mediated splicing regulation and identified that HDA15-MAC3A/MAC3B acts as an important regulation module to mediate splicing of introns in ABA responses. One Sentence SummaryHDA15 and MAC3A/MAC3B coregulate intron retention and reduce the histone acetylation level of the genomic regions near ABA-responsive retained introns.

plant biology↗

Quantitative variation within a species for traits underpinning C4 photosynthesis

Engineering C4 photosynthesis into C3 crops such as rice or wheat could substantially increase their yield by alleviating photorespiratory losses1,2. This objective is challenging because the C4 pathway involves complex modifications to the biochemistry, cell biology and anatomy of leaves3. Forward genetics has provided limited insight into the mechanistic basis of these characteristics and there have been no reports of significant quantitative intra-specific variation of C4 attributes that would allow trait-mapping4,5. Here we show that accessions of C4 Gynandropsis gynandra collected from locations across Africa and Asia exhibit natural variation in key characteristics of C4 photosynthesis. Variable traits include bundle sheath size and vein density, gas exchange parameters and carbon-isotope discrimination associated with the C4 state, but also abundance of transcripts encoding core enzymes of the C4 cycle. Traits relating to water use showed more quantitative variation than those associated with carbon assimilation. We propose variation in these traits likely adapted the hydraulic system for increased water use efficiency rather than improving carbon fixation, indicating that selection pressure may drive C4 diversity in G. gynandra by acting to modify water use rather than photosynthesis. As these accessions can be easily crossed and produce fertile offspring, our findings indicate that natural variation within a C4 species is sufficiently large to allow genetic-mapping of key anatomical C4 traits and regulators.

plant biology↗

Dual single-nucleus gene expression atlas of grapevine and Erysiphe necator during early powdery mildew infection

We applied dual-organism single-nucleus transcriptomics to study the interaction between grapevine leaves and Erysiphe necator, the causal agent of powdery mildew, at one and five days post-infection, including controls and three biological replicates. We generated a grapevine leaf atlas encompassing over 100,000 nuclei, and a pathogen atlas of more than 3,000 nuclei. We successfully annotated all major grapevine cell types, including mesophyll, epidermis, phloem and xylem parenchyma, companion cells, and guard cells. We identified key E. necator structures, including appressoria, haustoria, and hyphae, and provided a list of novel cell type markers for both species. We reveal structure-specific gene expression programs in E. necator laying a foundation for future studies of fungal development and virulence mechanisms. In the host, we identified spatially distinct expression patterns of defense-related genes. As the infection progressed, we observed the activation of a coordinated immune response involving multiple cell types, mainly epidermal and mesophyll cells. High-dimensional weighted gene co-expression network analysis identified key hubs and networks associated with cell type-specific signaling and defense response. We describe a spatial separation of pattern- and effector-triggered immunity, supporting a model in which pattern-triggered immunity is activated at the site of pathogen contact and effector-triggered immunity is induced in surrounding tissue.

plant biology↗

Growth of Sphagnum riparium is strongly rhythmic: Contribution of the seasonal, circalunar and third rhythmiccomponents

Continuous high-resolution monitoring of Sphagnum growth can provide insights into the biological rhythms of moss growth. Moss Sphagnum riparium is a convenient model for growth monitoring. Application of the method of geotropic curvatures has enabled a three-year monitoring with two to five-day intervals. We measured the increment in ca. 85000 shoots and produced ca. 3500 growth rate estimates, making this study a champion in precision compared to previous efforts. The zeitgeber for seasonal growth rhythms is the temperature seasonal cycle (R2=0.21-0.52). When the temperature changes by 10{degrees}C, moss growth rate is modified by 0.10-0.17cm/day according to the linear model, and 1.47-2.06-fold in the exponential model. The zeitgeber for circalunar rhythms is the lunar synodic cycle (R2=0.14-0.26). The average amplitude of the fluctuations it induces in the growth rate is 0.0425- 0.0572cm/day, which is equivalent to the effect of a 3.43-4.53{degrees}C change in temperature. The third rhythm can be distinguished in periodograms. Its period ranges from 10 to 16 days, but we did not detect the zeitgeber.\n\nIn total, three rhythms explain 51-78% of the growth rate. We believe that the strong rhythmicity in Sphagnum growth is associated with shoot growth synchronization.

plant biology↗

A pistil peptide toxin-pollen antidote system for reproductive barrier

Summary paragraphPrezygotic reproductive barriers in angiosperms are crucial for female-mediated selection of compatible male gametes. In this study, we identified a biological activity within the stylar tissues of Arabidopsis thaliana pistils that inhibits the elongation of heterospecific pollen tubes. Using genome-wide association studies, we identified a cysteine-rich peptide predominantly expressed in the style as the responsible barrier. This secreted peptide, named Femme fatale (FEM), inhibited pollen tube elongation of heterospecific species and some conspecific strains, both in vivo and in vitro. Importantly, FEMs function was independent of the known reproductive barrier component SPRI1 that functions in the stigmatic papilla cell surface. This means two factors act spatially in sequence to create a multilayered reproductive barrier system against pollen in pistils. We also identified a secreted protein expressed in pollen, Homme capable (HOM), which is encoded by a gene next to FEM. HOM interacts with FEM to counteract its barrier effect and allow pollen tube elongation. The FEM-HOM locus has undergone frequent tandem duplications during Brassicaceae evolution. Dosage differences between the two factors can lead to reproductive incompatibility among lineages. Together, our findings suggest that FEM and HOM form a toxin-antidote system that helps establish reproductive barriers.

plant biology↗

The autophagy-related genes AtATG5 and AtATG7 influence reserve mobilisation and responses to ABA during seed germination in Arabidopsis thaliana

Autophagy is an intracellular recycling mechanism that generally degrades cytoplasmic components non-selectively, but it can also target specific substrates under certain conditions. Here, we investigate the impact of autophagy on Arabidopsis seed biology through autophagy-related (ATG) genes AtATG5 and AtATG7, and their role in ABA responses. Seeds of atg5 and atg7 mutants germinate significantly slower than Col-0, especially under ABA, and show transcriptomic differences and histochemical alterations in the organization of lipid droplets and protein storage vacuoles. Notably, immunolocalization of ATG8 is observed in PSV of Col-0, but not in atg mutants. Differentially expressed genes in atg7 compared to Col-0 in response to ABA include reported targets of the transcription factor (TF) ABI5, a master regulator of ABA signalling in the seed. Interestingly, the decrease in ABI5 normally observed in Col-0 seeds after imbibition is delayed in atg mutants, which also show altered accumulation in developing seeds of the bZIP67, an ABI5 homolog that regulates reserve biosynthesis. Yeast two-hybrid and co-immunoprecipitation assays confirmed a direct interaction with the autophagy machinery in vitro and in vivo, mediated through ATG8. Our data highlight the relevance of autophagy in seed reserve mobilization, and seed germination through ABA responses by a TF decay mechanism.

plant biology↗

Successful Predictive Modeling of Pollen Fitness Phenotypes Is Enabled by Measures of Expression Specificity

AO_SCPLOWBSTRACTC_SCPLOWThe ability to predict phenotypes from genotypes in multicellular organisms remains limited despite rapid advances in genotyping and phenotyping methods. Machine learning offers a promising way to model phenotype from genotype, but requires sizable datasets that quantitatively link phenotype to specific genes. Such datasets remain limited; however, maize pollen provides a unique biological system that is especially well suited for this challenge. Because maize pollen is haploid, mutations that affect its function can result in a quantitative phenotypic effect on pollen fitness, measurable as deviations in transmission rate from the expected Mendelian ratio. We leveraged a large set of fluorescently-marked insertional mutations, the Ds-GFP lines, to link fitness effects to specific genes. We then developed a machine learning framework that integrates expression profiling and genomic data to predict genes contributing to pollen fitness in maize. Well performing models that distinguish genes with strong fitness effects from those with little or no fitness effect could be generated using features, such as codon usage, derived solely from genome sequence (auROC 85%). Using expression data enabled even more successful models, achieving auROC values above 90%. Because we used interpretable machine learning methods, we were able to identify expression specificity as a critical feature for strongest model performance. The best performing model was achieved when specificity measures were complemented with certain genomic sequence features. Models that include expression specificity generalize well across the maize genome, as predictions meet expectations of mutational frequencies for thousands of genes in a well characterized mutagenized population.

plant biology↗

Diverse 3D cellular patterns underlie the development of Cardamine hirsuta and Arabidopsis thaliana ovules

A fundamental question in biology is how organ morphogenesis comes about. The ovules of Arabidopsis thaliana have been established as a successful model to study numerous aspects of tissue morphogenesis; however, little is known regarding the relative contributions and dynamics of differential tissue and cellular growth and architecture in establishing ovule morphogenesis in different species. To address this issue, we generated a 3D digital atlas of Cardamine hirsuta ovule development with full cellular resolution. We combined quantitative comparative morphometrics and topological analysis to explore similarities and differences in the 3D cellular architectures underlying ovule development of the two species. We discovered that they show diversity in the way the three radial cell layers of the primordium contribute to its growth, in the formation of a new cell layer in the inner integument and, in certain cases, in the topological properties of the 3D cell architectures of homologous tissues despite their similar shape. Our work demonstrates the power of comparative 3D cellular morphometry and the importance of internal tissues and their cellular architecture in organ morphogenesis. Summary StatementQuantitative morphometric comparison of 3D digital ovules at full cellular resolution reveals diversity in internal 3D cellular architectures between similarly shaped ovules of Cardamine hirsuta and Arabidopsis thaliana.

plant biology↗

Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize

MicroRNAs (miRNAs) are endogenous 20-to 24-nucleotide (nt) noncoding RNAs that play important regulatory roles in many biological processes in eukaryotes. miRNAs modulate the expression of target genes at the post-transcriptional level by transcript cleavage or translational inhibition. Identification of miRNA target genes have been extensively investigated in Arabidopsis and rice, but an in-depth global analysis of miRNA-mediated target regulation is still lacking in maize. Here, we report a transcriptome-wide identification of miRNA targets by analyzing Parallel Analysis of RNA Ends (PARE) datasets derived from nine different tissues at five developmental stages of the maize (Zea mays L.) B73 cultivar. 246 targets corresponding to 60 miRNAs from 25 families were identified, including transcription factors and other genes. In addition, PARE analysis revealed that miRNAs guide specific target transcript cleavage in a tissue-preferential manner. Interestingly, primary transcripts of MIR159c and MIR169e were found to be cleaved by mature miR159 and miR169, respectively, indicating a positive-feedback regulatory mechanism in miRNA biogenesis. Moreover, several new miRNA-target gene pairs involved in seed germination were identified and experimentally validated. Our PARE analyses generated a wide and detailed miRNA-target interaction atlas, which provides a valuable resource for investigating the roles of miRNAs and their targets in maize.

plant biology↗

Three-dimensional fruit growth analysis clarifies developmental mechanisms underlying complex shape diversity in persimmon fruit

How fruit size and shape are determined is of research interest in agriculture and developmental biology. Fruit typically exhibits three-dimensional structures with genotype-dependent geometric features. Although minor developmental variations have been recognized, little research has fully visualized and measured these variations throughout fruit growth. In this study, a high-resolution 3D scanner was used to investigate the fruit development of 51 persimmon (Diospyros kaki) cultivars with various complex shapes. We obtained 2,380 3D fruit models that fully represented fruit appearance, and enabled precise and automated measurements of unique geometric features throughout fruit development. The 3D fruit model analysis identified key stages that determined the shape attributes at maturity. Typically, genetic diversity in vertical groove development was found, and such grooves can be filled by tissue expansion in the carpal fusion zone during fruit development. Furthermore, transcriptome analysis of fruit tissues from groove/non-groove tissues revealed gene co-expression networks that were highly associated with groove depth variation. The presence of YABBY homologs was most closely associated with groove depth and indicated the possibility that this pathway is a key molecular contributor to vertical groove depth variation. These results demonstrate the validity of fruit 3D growth analysis, which is a powerful tool for identifying the developmental mechanisms of fruit shape variation and the molecular basis of this diversity.

plant biology↗

Genome-wide association mapping and systems-level analysis reveal genetic architecture and physiological mechanisms linked with tolerance to flooding during germination in rice

Rice is the staple food of more than half of the worlds population; yet, it faces numerous challenges to meet the rising food demands and worsening climates. An urgent global imperative is to address imminent food shortages through intensive and sustainable agri-food systems and steady genetic gains. Intensification of rice production through direct-seeded rice (DSR) has been progressively practiced but is hindered by poor germination of existing high-yielding varieties in flooded soils. Identifying donors of anaerobic germination (AG) tolerance in rice will expedite the development of varieties suitable for DSR and will lead to enhanced and sustained agricultural productivity. This study aims to dissect the genetic architecture and physiological mechanisms of AG tolerance using systems biology and omics approaches. A Rice Diversity Panel (343 accessions) consisting of 5 subpopulations was screened for AG tolerance under greenhouse conditions, mapped through genome-wide association study (GWAS), and profiled for metabolites. Analyses revealed that most of the AG-tolerant varieties are japonicas with few indicas) and aus. Tolerant japonicas employed better root growth or rapid shoot extension, while tolerant indicas exhibited only the latter. A total of 51 significant GWAS peaks were detected across the genome, some of which were co-localized with known quantitative trait loci while others were novel, more so tolerance was found to involve different genetic controls across subpopulations. AG stress causes distinct biochemical signatures for tolerant genotypes and the profiles contrast among subpopulations implicating divergent metabolic adjustments, including shifts in sugars, intermediates, amino acids, antioxidants, and hormones. This study provides a systems-level approach for underpinning physiological mechanisms of AG tolerance; elucidating phenotypic heterogeneity, genetic architecture, transcriptomic networks, and metabolic landscapes from a genome-wide perspective. ONE SENTENCE SUMMARYThe integration of GWA mapping, gene network analysis and, non-targeted metabolite profiling elucidates genetic architecture and physiological mechanisms of tolerance to germination and early seedling growth under anaerobic conditions in rice.

plant biology↗

Five novel ubiquitous totiviruses function as virulence-promoting symbionts in the obligate biotrophic fungus Puccinia triticina

Mycoviruses modulate fungal fitness and pathogenicity, yet their biological roles in obligate biotrophic phytopathogens remain poorly understood. Here, we report the first functional characterization of totiviruses in rust fungi, identifying five novel totiviruses, designated Puccinia triticina totivirus 1 to 5 (PtTV1?PtTV5), from the wheat leaf rust fungus Puccinia triticina (Pt). All five PtTVs possess the canonical genomic architecture of Totiviridae, including two overlapping ORFs and a conserved ?1 ribosomal frameshifting motif. Transcriptional profiling revealed that PtTVs are highly expressed during early Pt infection. PtTV-encoded proteins suppressed BAX-triggered programmed cell death in Nicotiana benthamiana, indicating immune-suppressive activity. Using BSMV-mediated host-induced gene silencing (HIGS), we showed that knockdown of PtTV transcripts significantly impaired fungal hyphal expansion and uredinial formation, concomitant with enhanced host H?O? accumulation. A survey of 90 Pt field isolates from four major wheat-growing regions of China revealed that PtTVs are ubiquitously distributed in natural rust populations. Collectively, these findings demonstrate that totiviruses function as virulence-promoting symbionts in Pt, establishing for the first time a functional link between totiviral infection and enhanced pathogenicity in cereal rust fungi and identifying candidate targets for RNAi-based disease control.

plant biology↗

Successes of artemisinin elicitation in low-artemisinin producing Artemisia annua cell cultures constrained by repression of biosynthetic genes

The sesquiterpene phytolactone derived from Artemisia annua, artemisinin is associated with a variety of novel biological properties, such as immunoregulatory and anticancer effects, and therapeutic applications, apart from its main function as an antimalarial drug. Emerging from the fact that artemisinin production in planta occurs in trace amounts and its compartmentalized synthesis, the irregular agricultural supply often results in market fluctuations and reductions in artemisinin inventory. Further improvement in artemisinin production calls for approaches that act in a supplementary manner, filling the agricultural production gap. Here we investigated the elicitation efficiency of ultraviolet B (UV-B) and dimethyl sulfoxide (DMSO) independently on a low-artemisinin producing (LAP) chemotype of the species A. annua. The exposure of cell suspension cultures to short-term UV-B radiation and DMSO treatment did not result in significant changes in artemisinin yield. The lack of stimulation has been associated with: (i) the general lack of cytodifferentiation of cell cultures; (ii) negative feedback regulation of artemisinin biosynthesis; and (iii) artemisinin sequestration by cellular detoxification. Further molecular analysis revealed the repression of key genes ADS, DBR2 and ALDH1 which affected artemisinin synthesis. This study provides insights into the complexity of stress-induced responses of A. annua cell suspension cultures in relation to metabolic processes (transportation, accumulation and degradation of secondary products) which are important for artemisinin formation.

plant biology↗

The evolutionary history of the current global Ramularia collo-cygni epidemic

Ramularia Leaf Spot (RLS) has emerged as a threat for barley production in many regions of the world. Late appearance of unspecific symptoms caused that Ramularia collo-cygni could only by molecular diagnostics be detected as the causal agent of RLS. Although recent research has shed more light on the biology and genomics of the pathogen, the cause of the recent global spread remains unclear.\n\nTo address urgent questions, especially on the emergence to a major disease, life-cycle, transmission, and quick adaptation to control measures, we de-novo sequenced the genome of R. collo-cygni (urug2 isolate). Additionally, we sequenced fungal RNA from 6 different conditions, which allowed for an improved genome annotation. This resulted in a high quality draft assembly of about 32 Mb, with only 78 scaffolds with an N50 of 2.1 Mb. The overall annotation enabled the prediction of 12.346 high confidence genes. Genomic comparison revealed that R. collo-cygni has significantly diverged from related Dothidiomycetes, including gain and loss of putative effectors, however without obtaining species-specific genome features.\n\nTo evaluate the species-wide genetic diversity, we sequenced the genomes of 19 R. collo-cygni isolates from multiple geographic locations and diverse hosts and mapped sequences to our reference genome. Admixture analyses show that R. collo-cygni is world-wide genetically uniform and that samples do not show a strong clustering on either geographical location or host species. To date, the teleomorph of R. collo-cygni has not been observed. Analysis of linkage disequilibrium shows that in the world-wide sample set there are clear signals of recombination and thus sexual reproduction, however these signals largely disappear when excluding three outliers samples, suggesting that the main global expansion of R. collo-cygni comes from mixed or clonally propagating populations. We further analysed the historic population size (Ne) of R. collo-cygni using Bayesian simulations.\n\nWe discuss how our genomic data and population genetics analysis can help understand the current R. collo-cygni epidemic and provide different hypothesis that are supported by our data. We specifically highlight how recombination, clonal spreading and lack of host-specificity could further support global epidemics of this increasingly recognized plant disease and suggest specific approaches to combat this pathogen.

plant biology↗

A fast neutron mutant resource for Ipomoea purpurea reveals dose-dependent genomic and phenotypic variation

A central goal in evolutionary biology is to understand the genomic basis of phenotypic traits, yet this pursuit is often constrained by a lack of accessible phenotypic and genetic variation, particularly in non-model organisms. Fast neutron irradiation offers a powerful approach for generating such variation, as it does not require prior genomic resources, established transformation systems, or reference mutant collections. Here, we describe the development and characterization of the first fast neutron mutant library in Ipomoea purpurea (common morning glory), a noxious agricultural weed and established model system in evolutionary ecology. We exposed an I. purpurea reference genotype to three levels of irradiation and developed 1,043 lines third generation lines and characterized the phenotypic and genetic variation in a subset of 200. Phenotypic screens identified seven mutant lines exhibiting eleven distinct phenotypes, and revealed higher phenotypic variance for anther-stigma distance, flower number, and pollen count relative to a non-irradiated control line. We further identified genetic variation across eight phenotypic traits among the mutant lines. Together, these results show that fast neutron mutagenesis generates novel phenotypic and genetic variation in ecologically relevant traits, offering the research community a new genomic resource for an established model in evolutionary ecology.

plant biology↗

Dual reference method for high precision infrared measurement of leaf surface temperature under field conditions

O_LITemperature is a key control over biological activities from the cellular to the ecosystem scales. However, direct, high precision measurements of surface temperature of small objects such as leaves under field conditions with large variations in ambient conditions remain rare. Contact methods such as thermocouples are prone to large errors. The use of non-contact remote sensing methods such as thermal infrared measurements provides an ideal solution, but their accuracy has been low (in the order of ~2 {degrees}C) due to necessity for corrections for material emissivity and fluctuations in background radiation (Lbg). C_LIO_LIA novel dual-reference method was developed to increase the accuracy of infrared needle-leaf surface temperature measurements in the field. It accounts for variations in Lbg and corrects for the systematic camera offset using two reference plates. C_LIO_LIWe accurately captured surface temperature and leaf-to-air temperature differences of needle-leaves in a forest ecosystem with large diurnal and seasonal temperature fluctuations with an uncertainty of {+/-}0.23 and {+/-}0.25 {degrees}C, respectively. C_LIO_LIRoutine high precision leaf temperature measurements even under harsh field conditions, such as demonstrated here, opens the way for investigating a wide range of leaf-scale processes and its dynamics. C_LI

plant biology↗

A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule

A fundamental question in biology is how morphogenesis integrates the multitude of distinct processes that act at different scales, ranging from the molecular control of gene expression to cellular coordination in a tissue. Investigating morphogenesis of complex organs strongly benefits from three-dimensional representations of the organ under study. Here, we present a digital analysis of ovule development from Arabidopsis thaliana as a paradigm for a complex morphogenetic process. Using machine-learning-based image analysis we generated a three-dimensional atlas of ovule development with cellular resolution. It allows quantitative stage- and tissue-specific analysis of cellular patterns. Exploiting a fluorescent reporter enabled precise spatial determination of gene expression patterns, revealing subepidermal expression of WUSCHEL. Underlying the power of our approach, we found that primordium outgrowth progresses evenly, discovered a novel mode of forming a new cell layer, and detected a new function of INNER NO OUTER in restricting cell proliferation in the nucellus. Moreover, we identified two distinct subepidermal cell populations that make crucial contributions to ovule curvature. Our work demonstrates the expedience of a three-dimensional digital representation when studying the morphogenesis of an organ of complex cellular architecture and shape that eventually consists of 1,900 cells.

plant biology↗