A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana

TANDEM ZINC-FINGER/PLUS3 integrates light signaling and flowering regulatory pathways at the chromatin level

Environmental and endogenous stimuli determine plant developmental transitions including flowering through multiple signaling cascades. Although the key activators and repressors of flowering initiation are defined, the components and mechanisms integrating light signaling and flowering pathways are not fully established. This study investigates the role of TANDEM ZINC-FINGER/PLUS3 (TZP), a light-integrating transcriptional regulator, to elucidate how light cues influence the epigenetic regulation of flowering in Arabidopsis thaliana. To dissect the molecular function of TZP, this study employed a combination of genetics, RNA sequencing, chromatin immunoprecipitation sequencing and phenotypic assays. These approaches were used to determine TZP's genomic binding sites, its downstream gene targets and its influence on flowering time and chromatin modifications. TANDEM ZINC-FINGER/PLUS3 was found to directly associate with the promoter regions of chromatin-modifying genes, including FLOWERING LOCUS D (a histone H3K4 demethylase) and histone deacetylase 6 (a histone deacetylase). This regulation promotes a chromatin environment that represses FLOWERING LOCUS C (FLC) transcription, thereby accelerating flowering. TANDEM ZINC-FINGER/PLUS3 thus functions upstream of multiple pathways integrating photoperiodic and autonomous floral cues. TANDEM ZINC-FINGER/PLUS3 mediates crosstalk between light signaling and flowering pathways by modulating chromatin structure at the FLC locus. This provides a mechanistic framework for understanding how environmental signals dynamically influence epigenetic regulation of developmental transitions.

TANDEM ZINC-FINGER/PLUS3: a multifaceted integrator of light signaling

TANDEM ZINC-FINGER/PLUS3 (TZP) is a nuclear-localized protein with multifaceted roles in modulating plant growth and development under diverse light conditions. The unique combination of two intrinsically disordered regions (IDRs), two zinc-fingers (ZFs), and a PLUS3 domain provide a platform for interactions with the photoreceptors phytochrome A (phyA) and phyB, light signaling components, and nucleic acids. TZP controls flowering and hypocotyl elongation by regulating gene expression and protein abundance in a blue, red, or far-red light-specific context. Recently, TZP was shown to undergo liquid-liquid phase separation through its IDRs, thus promoting phyA phosphorylation. Collectively, TZP is an emerging regulator of diverse light signaling pathways; therefore, understanding its biochemical function in integrating environmental signaling networks is key for optimizing plant adaptation.

What is going on inside of phytochrome B photobodies?

Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.

Protein kinase SnRK2.4 is a key regulator of aquaporins and root hydraulics in Arabidopsis

Soil water uptake by roots is a key component of plant water homeostasis contributing to plant growth and survival under ever-changing environmental conditions. The water transport capacity of roots (root hydraulic conductivity; Lpr ) is mostly contributed by finely regulated Plasma membrane Intrinsic Protein (PIP) aquaporins. In this study, we used natural variation of Arabidopsis for the identification of quantitative trait loci (QTLs) contributing to Lpr . Using recombinant lines from a biparental cross (Cvi-0 x Col-0), we show that the gene encoding class 2 Sucrose-Non-Fermenting Protein kinase 2.4 (SnRK2.4) in Col-0 contributes to >30% of Lpr by enhancing aquaporin-dependent water transport. At variance with the inactive and possibly unstable Cvi-0 SnRK2.4 form, the Col-0 form interacts with and phosphorylates the prototypal PIP2;1 aquaporin at Ser121 and stimulates its water transport activity upon coexpression in Xenopus oocytes and yeast cells. Activation of PIP2;1 by Col-0 SnRK2.4 in yeast also requires its protein kinase activity and can be counteracted by clade A Protein Phosphatases 2C. SnRK2.4 shows all hallmarks to be part of core abscisic acid (ABA) signaling modules. Yet, long-term (>3 h) inhibition of Lpr by ABA possibly involves a SnRK2.4-independent inhibition of PIP2;1. SnRK2.4 also promotes stomatal aperture and ABA-induced inhibition of primary root growth. The study identifies a key component of Lpr and sheds new light on the functional overlap and specificity of SnRK2.4 with respect to other ABA-dependent or independent SnRK2s.

Role of plant microRNAs and their corresponding pathways in fluctuating light conditions

In recent years, it has been established that microRNAs (miRNAs) are critical for various plant physiological regulations in numerous species. Next-generation sequencing technologies have aided to our understandings related to the critical role of miRNAs during environmental stress conditions and plant development. Light influences not just miRNA accumulation but also their biological activities via regulating miRNA gene transcription, biosynthesis, and RNA-induced silencing complex (RISC) activity. Light-regulated routes, processes, and activities can all be affected by miRNAs. Here, we will explore how light affects miRNA gene expression and how conserved and novel miRNAs exhibit altered expression across different plant species in response to variable light quality. Here, we will mainly discuss recent advances in understanding how miRNAs are involved in photomorphogenesis, and photoperiod-dependent plant biological processes such as cell proliferation, metabolism, chlorophyll pigment synthesis and axillary bud growth. The review concludes by presenting future prospects via hoping that light-responsive miRNAs can be exploited in a better way to engineer economically important crops to ensure future food security.

Coordinated regulation of the mitochondrial retrograde response by circadian clock regulators and ANAC017

Mitochondrial retrograde signaling (MRS) supports photosynthetic function under a variety of conditions. Induction of mitochondrial dysfunction with myxothiazol (a specific inhibitor of the mitochondrial bc₁ complex) or antimycin A (an inhibitor of the mitochondrial bc₁ complex and cyclic electron transport in the chloroplast under light conditions) in the light and dark revealed diurnal control of MRS. This was evidenced by (1) significantly enhanced binding of ANAC017 to promoters in the light compared with the dark in Arabidopsis plants treated with myxothiazol (but not antimycin A), (2) overlap in the experimentally determined binding sites for ANAC017 and circadian clock regulators in the promoters of ANAC013 and AOX1a, (3) a diurnal expression pattern for ANAC017 and transcription factors it regulates, (4) altered expression of ANAC017-regulated genes in circadian clock mutants with and without myxothiazol treatment, and (5) a decrease in the magnitude of LHY and CCA1 expression in an ANAC017-overexpressing line and protein-protein interaction between ANAC017 and PIF4. This study also shows a large difference in transcriptome responses to antimycin A and myxothiazol in the dark: these responses are ANAC017 independent, observed in shoots and roots, similar to biotic challenge and salicylic acid responses, and involve ERF and ZAT transcription factors. This suggests that antimycin A treatment stimulates a second MRS pathway that is mediated or converges with salicylic acid signaling and provides a merging point with chloroplast retrograde signaling.

Altering the balance between AOX1A and NDB2 expression affects a common set of transcripts in Arabidopsis

Stress-responsive components of the mitochondrial alternative electron transport pathway have the capacity to improve tolerance of plants to abiotic stress, particularly the alternative oxidase AOX1A but also external NAD(P)H dehydrogenases such as NDB2, in Arabidopsis. NDB2 and AOX1A can cooperate to entirely circumvent the classical electron transport chain in Arabidopsis mitochondria. Overexpression of AOX1A or NDB2 alone can have slightly negative impacts on plant growth under optimal conditions, while simultaneous overexpression of NDB2 and AOX1A can reverse these phenotypic effects. We have taken a global transcriptomic approach to better understand the molecular shifts that occur due to overexpression of AOX1A alone and with concomitant overexpression of NDB2. Of the transcripts that were significantly up- or down- regulated in the AOX1A overexpression line compared to wild type (410 and 408, respectively), the majority (372 and 337, respectively) reverted to wild type levels in the dual overexpression line. Several mechanisms for the AOX1A overexpression phenotype are proposed based on the functional classification of these 709 genes, which can be used to guide future experiments. Only 28 genes were uniquely up- or down-regulated when NDB2 was overexpressed in the AOX1A overexpression line. On the other hand, many unique genes were deregulated in the NDB2 knockout line. Furthermore, several changes in transcript abundance seen in the NDB2 knockout line were consistent with changes in the AOX1A overexpression line. The results suggest that an imbalance in AOX1A:NDB2 protein levels caused by under- or over-expression of either component, triggers a common set of transcriptional responses that may be important in mitochondrial redox regulation. The most significant changes were transcripts associated with photosynthesis, secondary metabolism and oxidative stress responses.

TANDEM ZINC-FINGER/PLUS3 regulates phytochrome B abundance and signaling to fine-tune hypocotyl growth

TANDEM ZINC-FINGER/PLUS3 (TZP) is a transcriptional regulator that acts at the crossroads of light and photoperiodic signaling. Here, we unveil a role for TZP in fine-tuning hypocotyl elongation under red light and long-day conditions. We provide genetic evidence for a synergistic action between TZP and PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) in regulating the protein abundance of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and downstream gene expression in response to red light and long days (LDs). Furthermore, we show that TZP is a positive regulator of the red/far-red light receptor and thermosensor phytochrome B (phyB) by promoting phyB protein abundance, nuclear body formation, and signaling. Our data therefore assign a function to TZP in regulating two key red light signaling components, phyB and PIF4, but also uncover a new role for PCH1 in regulating hypocotyl elongation in LDs. Our findings provide a framework for the understanding of the mechanisms associated with the TZP signal integration network and their importance for optimizing plant growth and adaptation to a changing environment.

Cellular localization of Arabidopsis EARLY FLOWERING3 is responsive to light quality

Circadian clocks facilitate the coordination of physiological and developmental processes to changing daily and seasonal cycles. A hub for environmental signaling pathways in the Arabidopsis (Arabidopsis thaliana) circadian clock is the evening complex (EC), a protein complex composed of EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRYTHMO (LUX). Formation of the EC depends on ELF3, a scaffold protein that recruits the other components of the EC and chromatin remodeling enzymes to repress gene expression. Regulating the cellular distribution of ELF3 is thus an important mechanism in controlling its activity. Here, we determined that the cellular and sub-nuclear localization of ELF3 is responsive to red (RL) and blue light and that these two wavelengths have apparently competitive effects on where in the cell ELF3 localizes. We further characterized the RL response, revealing that at least two RL pathways influence the cellular localization of ELF3. One of these depends on the RL photoreceptor phytochrome B (phyB), while the second is at least partially independent of phyB activity. Finally, we investigated how changes in the cellular localization of ELF3 are associated with repression of EC target-gene expression. Our analyses revealed a complex effect whereby ELF3 is required for controlling RL sensitivity of morning-phased genes, but not evening-phased genes. Together, our findings establish a previously unknown mechanism through which light signaling influences ELF3 activity.

Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling

Phytochrome A (phyA) is the far-red (FR) light photoreceptor in plants that is essential for seedling de-etiolation under FR-rich environments, such as canopy shade. TANDEM ZINC-FINGER/PLUS3 (TZP) was recently identified as a key component of phyA signal transduction in Arabidopsis thaliana; however, how TZP is integrated into the phyA signaling networks remains largely obscure. Here, we demonstrate that ELONGATED HYPOCOTYL5 (HY5), a well-characterized transcription factor promoting photomorphogenesis, mediates FR light induction of TZP expression by directly binding to a G-box motif in the TZP promoter. Furthermore, TZP physically interacts with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), an E3 ubiquitin ligase targeting HY5 for 26S proteasome-mediated degradation, and this interaction inhibits COP1 interaction with HY5. Consistent with those results, TZP post-translationally promotes HY5 protein stability in FR light, and in turn, TZP protein itself is destabilized by COP1 in both dark and FR light conditions. Moreover, tzp hy5 double mutants display an additive phenotype relative to their respective single mutants under high FR light intensities, indicating that TZP and HY5 also function in largely independent pathways. Together, our data demonstrate that HY5 and TZP mutually upregulate each other in transmitting the FR light signal, thus providing insights into the complicated but delicate control of phyA signaling networks.

Transcriptome and Degradome Profiling Reveals a Role of miR530 in the Circadian Regulation of Gene Expression in Kalanchoë marnieriana

Crassulacean acid metabolism (CAM) is an important photosynthetic pathway for plant adaptation to dry environments. CAM plants feature a coordinated interaction between mesophyll and epidermis functions that involves refined regulations of gene expression. Plant microRNAs (miRNAs) are crucial post-transcription regulators of gene expression, however, their roles underlying the CAM pathway remain poorly investigated. Here, we present a study characterizing the expression of miRNAs in an obligate CAM species Kalanchoë marnieriana. Through sequencing of transcriptome and degradome in mesophyll and epidermal tissues under the drought treatments, we identified differentially expressed miRNAs that were potentially involved in the regulation of CAM. In total, we obtained 84 miRNA genes, and eight of them were determined to be Kalanchoë-specific miRNAs. It is widely accepted that CAM pathway is regulated by circadian clock. We showed that miR530 was substantially downregulated in epidermal peels under drought conditions; miR530 targeted two tandem zinc knuckle/PLU3 domain encoding genes (TZPs) that were potentially involved in light signaling and circadian clock pathways. Our work suggests that the miR530-TZPs module might play a role of regulating CAM-related gene expression in Kalanchoë.

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.

ACCELERATED CELL DEATH 6 Acts on Natural Leaf Senescence and Nitrogen Fluxes in Arabidopsis

As the last step of leaf development, senescence is a molecular process involving cell death mechanism. Leaf senescence is trigged by both internal age-dependent factors and environmental stresses. It must be tightly regulated for the plant to adopt a proper response to environmental variation and to allow the plant to recycle nutrients stored in senescing organs. However, little is known about factors that regulate both nutrients fluxes and plant senescence. Taking advantage of variation for natural leaf senescence between Arabidopsis thaliana accessions, Col-0 and Ct-1, we did a fine mapping of a quantitative trait loci for leaf senescence and identified ACCELERATED CELL DEATH 6 (ACD6) as the causal gene. Using two near-isogeneic lines, differing solely around the ACD6 locus, we showed that ACD6 regulates rosette growth, leaf chlorophyll content, as well as leaf nitrogen and carbon percentages. To unravel the role of ACD6 in N remobilization, the two isogenic lines and acd6 mutant were grown and labeled with ¹⁵N at the vegetative stage in order to determine ¹⁵N partitioning between plant organs at harvest. Results showed that N remobilization efficiency was significantly lower in all the genotypes with lower ACD6 activity irrespective of plant growth and productivity. Measurement of N uptake at vegetative and reproductive stages revealed that ACD6 did not modify N uptake efficiency but enhanced nitrogen translocation from root to silique. In this study, we have evidenced a new role of ACD6 in regulating both sequential and monocarpic senescences and disrupting the balance between N remobilization and N uptake that is required for a good seed filling.

Ultra-High-Density QTL Marker Mapping for Seedling Photomorphogenesis Mediating Arabidopsis Establishment in Southern Patagonia

Arabidopsis thaliana shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, Arabidopsis has a high potential for the identification of genes underlying ecologically important complex traits, thus providing new insights on genome evolution. Previous research suggested that distinct light responses were crucial for Arabidopsis establishment in a peculiar ecological niche of southern Patagonia. The aim of this study was to explore the genetic basis of contrasting light-associated physiological traits that may have mediated the rapid adaptation to this new environment. From a biparental cross between the photomorphogenic contrasting accessions Patagonia (Pat) and Columbia (Col-0), we generated a novel recombinant inbred line (RIL) population, which was entirely next-generation sequenced to achieve ultra-high-density saturating molecular markers resulting in supreme mapping sensitivity. We validated the quality of the RIL population by quantitative trait loci (QTL) mapping for seedling de-etiolation, finding seven QTLs for hypocotyl length in the dark and continuous blue light (Bc), continuous red light (Rc), and continuous far-red light (FRc). The most relevant QTLs, Rc1 and Bc1, were mapped close together to chromosome V; the former for Rc and Rc/dark, and the latter for Bc, FRc, and dark treatments. The additive effects of both QTLs were confirmed by independent heterogeneous inbred families (HIFs), and we explored TZP and ABA1 as potential candidate genes for Rc1 and Bc1QTLs, respectively. We conclude that the Pat × Col-0 RIL population is a valuable novel genetic resource to explore other adaptive traits in Arabidopsis.

Characterization of near-isogenic lines confirmed QTL and revealed candidate genes for plant height and yield-related traits in common wheat

Plant height (PH) is closely associated with yield-related traits and environmental adaptation. Seven pairs of near-isogenic lines (NILs) targeting four QTL on 3AL, 4BL, 4AS, and 7AL wheat chromosome arms were assessed for PH and four yield-related traits including yield per plant (Y/P), grain number per spike (G/S), thousand kernel weight (TKW), and biomass per plant (B/P). Significant differences were observed in the NIL pairs for the measured traits. NIL pairs targeting the 3AL QTL differed significantly in PH, G/S, and TKW; NILs targeting the 4BL QTL differed significantly in PH, Y/P, and B/P; NIL pairs targeting the 4AS QTL differed significantly in all the traits; and NIL pairs targeting the 7AL QTL differed significantly in PH. A 90 K SNP genotyping assay of the NILs detected nineteen SNPs associated with fourteen functional genes. Among them, eight candidate genes are related to Rht proteins, four genes are related to hormone pathways and two genes are related to carbohydrate synthesis and transport. By searching the interval marker physical positions, it was found that the four targeted QTL in this study overlapped with eight previously reported QTL for PH, TKW, biomass, and yield. Correlation analysis revealed that PH significantly and positively correlated with B/P and G/S. The SNP and candidate gene information is potentially useful for marker-assisted selection in breeding programs, and the four targeted QTL are proved to be critical genomic regions controlling the investigated agronomic traits, which can be further fine mapped to identify the underlying genes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-020-01196-8.

Nucleo-plastidic PAP8/pTAC6 couples chloroplast formation with photomorphogenesis

The initial greening of angiosperms involves light activation of photoreceptors that trigger photomorphogenesis, followed by the development of chloroplasts. In these semi-autonomous organelles, construction of the photosynthetic apparatus depends on the coordination of nuclear and plastid gene expression. Here, we show that the expression of PAP8, an essential subunit of the plastid-encoded RNA polymerase (PEP) in Arabidopsis thaliana, is under the control of a regulatory element recognized by the photomorphogenic factor HY5. PAP8 protein is localized and active in both plastids and the nucleus, and particularly required for the formation of late photobodies. In the pap8 albino mutant, phytochrome-mediated signalling is altered, degradation of the chloroplast development repressors PIF1/PIF3 is disrupted, HY5 is not stabilized, and the expression of the photomorphogenesis regulator GLK1 is impaired. PAP8 translocates into plastids via its targeting pre-sequence, interacts with the PEP and eventually reaches the nucleus, where it can interact with another PEP subunit pTAC12/HMR/PAP5. Since PAP8 is required for the phytochrome B-mediated signalling cascade and the reshaping of the PEP activity, it may coordinate nuclear gene expression with PEP-driven chloroplastic gene expression during chloroplast biogenesis.

Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans

The diverse eukaryotic proteins that contain zinc fingers participate in many aspects of nucleic acid metabolism, from DNA transcription to RNA degradation, post-transcriptional gene silencing, and small RNA biogenesis. These proteins can be classified into at least 30 types based on structure. In this review, we focus on the CCHC-type zinc fingers (ZCCHC), which contain an 18-residue domain with the CX2CX4HX4C sequence, where C is cysteine, H is histidine, and X is any amino acid. This motif, also named the "zinc knuckle", is characteristic of the retroviral Group Antigen protein and occurs alone or with other motifs. Many proteins containing zinc knuckles have been identified in eukaryotes, but only a few have been studied. Here, we review the available information on ZCCHC-containing factors from three evolutionarily distant eukaryotes-Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens-representing fungi, plants, and metazoans, respectively. We performed systematic searches for proteins containing the CX2CX4HX4C sequence in organism-specific and generalist databases. Next, we analyzed the structural and functional information for all such proteins stored in UniProtKB. Excluding retrotransposon-encoded proteins and proteins harboring uncertain ZCCHC motifs, we found seven ZCCHC-containing proteins in yeast, 69 in Arabidopsis, and 34 in humans. ZCCHC-containing proteins mainly localize to the nucleus, but some are nuclear and cytoplasmic, or exclusively cytoplasmic, and one localizes to the chloroplast. Most of these factors participate in RNA metabolism, including transcriptional elongation, polyadenylation, translation, pre-messenger RNA splicing, RNA export, RNA degradation, microRNA and ribosomal RNA biogenesis, and post-transcriptional gene silencing. Several human ZCCHC-containing factors are derived from neofunctionalized retrotransposons and act as proto-oncogenes in diverse neoplastic processes. The conservation of ZCCHCs in orthologs of these three phylogenetically distant eukaryotes suggests that these domains have biologically relevant functions that are not well known at present.

OsmiR530 acts downstream of OsPIL15 to regulate grain yield in rice

MicroRNAs (miRNAs) are a class of small noncoding RNAs that play important roles in plant growth and development as well as in stress responses. However, little is known about their regulatory functions affecting rice grain yield. We functionally characterized a novel miRNA in rice, OsmiR530, its target OsPL3, and its upstream regulator phytochrome-interacting factor-like 15 (OsPIL15). Their effects on rice yield were dissected comprehensively. We determined that OsmiR530 negatively regulates grain yield. Blocking OsmiR530 increases grain yield, whereas OsmiR530 overexpression significantly decreases grain size and panicle branching, leading to yield loss. Additionally, OsPL3, which encodes a PLUS3 domain-containing protein, is targeted directly by OsmiR530. Knocking out OsPL3 decreases the grain yield. In-depth analyses indicated that OsPIL15 activates OsMIR530 expression by directly binding to the G-box elements in the promoter. Analyses of genetic variations suggested that the OsMIR530 locus has likely been subjected to artificial selection during rice breeding. The results presented herein reveal a novel OsPIL15-OsmiR530 module controlling rice grain yield, thus providing researchers with a new target for the breeding of high-yielding rice.

The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana

One of the main outcomes of quantitative genetics approaches to natural variation is to reveal the genetic architecture underlying the phenotypic space. Complex genetic architectures are described as including numerous loci (or alleles) with small-effect and/or low-frequency in the populations, interactions with the genetic background, environment or age. Linkage or association mapping strategies will be more or less sensitive to this complexity, so that we still have an unclear picture of its extent. By combining high-throughput phenotyping under two environmental conditions with classical QTL mapping approaches in multiple Arabidopsis thaliana segregating populations as well as advanced near isogenic lines construction and survey, we have attempted to improve our understanding of quantitative phenotypic variation. Integrative traits such as those related to vegetative growth used in this work (highlighting either cumulative growth, growth rate or morphology) all showed complex and dynamic genetic architecture with respect to the segregating population and condition. The more resolutive our mapping approach, the more complexity we uncover, with several instances of QTLs visible in near isogenic lines but not detected with the initial QTL mapping, indicating that our phenotyping accuracy was less limiting than the mapping resolution with respect to the underlying genetic architecture. In an ultimate approach to resolve this complexity, we intensified our phenotyping effort to target specifically a 3Mb-region known to segregate for a major quantitative trait gene, using a series of selected lines recombined every 100kb. We discovered that at least 3 other independent QTLs had remained hidden in this region, some with trait- or condition-specific effects, or opposite allelic effects. If we were to extrapolate the figures obtained on this specific region in this particular cross to the genome- and species-scale, we would predict hundreds of causative loci of detectable phenotypic effect controlling these growth-related phenotypes.

ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis

Light coordinates energy production, growth, and survival throughout plant development. In Arabidopsis, light stimulates transcriptional reprogramming during developmental transitions such as photomorphogenesis and flowering through the action of photoreceptors, transcription factors, and signaling components. Here we assign a function to a member of the zinc-finger homeodomain (ZFHD) transcription factor family in regulating light-induced development. Our findings reveal ZFHD10 to be a missing link in understanding how the recently discovered integrator of light and photoperiodic flowering, TANDEM ZINC-FINGER PLUS3 (TZP), controls the expression of growth-promoting transcriptional regulators via direct association with light-regulated promoter elements. Elucidating how such novel protein complexes coordinate gene expression will allow scientists and breeders to optimize plant growth and development in response to unfavorable environmental conditions.

Integration of environmental signals and interactions among photoreceptors and transcriptional regulators is key in shaping plant development. TANDEM ZINC-FINGER PLUS3 (TZP) is an integrator of light and photoperiodic signaling that promotes flowering in Arabidopsis thaliana. Here we elucidate the molecular role of TZP as a positive regulator of hypocotyl elongation. We identify an interacting partner for TZP, the transcription factor ZINC-FINGER HOMEODOMAIN 10 (ZFHD10), and characterize its function in coregulating the expression of blue-light–dependent transcriptional regulators and growth-promoting genes. By employing a genome-wide approach, we reveal that ZFHD10 and TZP coassociate with promoter targets enriched in light-regulated elements. Furthermore, using a targeted approach, we show that ZFHD10 recruits TZP to the promoters of key coregulated genes. Our findings not only unveil the mechanism of TZP action in promoting hypocotyl elongation at the transcriptional level but also assign a function to an uncharacterized member of the ZFHD transcription factor family in promoting plant growth.

TANDEM ZINC-FINGER/PLUS3 Is a Key Component of Phytochrome A Signaling

Phytochrome A (phyA) is the primary plant photoreceptor responsible for perceiving and mediating various responses to far-red (FR) light and is essential for survival in canopy shade. In this study, we identified two Arabidopsis thaliana mutants that grew longer hypocotyls in FR light. Genetic analyses showed that they were allelic and their FR phenotypes were caused by mutations in the gene named TANDEM ZINC-FINGER/PLUS3 (TZP), previously shown to encode a nuclear protein involved in blue light signaling and phyB-dependent regulation of photoperiodic flowering. We show that the expression of TZP is dramatically induced by light and that TZP proteins are differentially modified in different light conditions. Furthermore, we show that TZP interacts with both phyA and FAR-RED ELONGATED HYPOCOTYL1 (FHY1) and regulates the abundance of phyA, FHY1, and ELONGATED HYPOCOTYL5 proteins in FR light. Moreover, our data indicate that TZP is required for the formation of a phosphorylated form of phyA in the nucleus in FR light. Together, our results identify TZP as a positive regulator of phyA signaling required for phosphorylation of the phyA photoreceptor, thus suggesting an important role of phosphorylated phyA in inducing the FR light response.

Under a New Light: Regulation of Light-Dependent Pathways by Non-coding RNAs

The biological relevance of non-protein coding RNAs in the regulation of critical plant processes has been firmly established in recent years. This has been mostly achieved with the discovery and functional characterization of small non-coding RNAs, such as small interfering RNAs and microRNAs (miRNAs). However, recent next-generation sequencing techniques have widened our view of the non-coding RNA world, which now includes long non-coding RNAs (lncRNAs). Small and lncRNAs seem to diverge in their biogenesis and mode of action, but growing evidence highlights their relevance in developmental processes and in responses to particular environmental conditions. Light can affect MIRNA gene transcription, miRNA biogenesis, and RNA-induced silencing complex (RISC) activity, thus controlling not only miRNA accumulation but also their biological function. In addition, miRNAs can mediate several light-regulated processes. In the lncRNA world, few reports are available, but they already indicate a role in the regulation of photomorphogenesis, cotyledon greening, and photoperiod-regulated flowering. In this review, we will discuss how light controls MIRNA gene expression and the accumulation of their mature forms, with a particular emphasis on those miRNAs that respond to different light qualities and are conserved among species. We will also address the role of small non-coding RNAs, particularly miRNAs, and lncRNAs in the regulation of light-dependent pathways. We will mainly focus on the recent progress done in understanding the interconnection between these non-coding RNAs and photomorphogenesis, circadian clock function, and photoperiod-dependent flowering.

Unraveling the microRNA of Caragana korshinskii along a precipitation gradient on the Loess Plateau, China, using high-throughput sequencing

Drought remains one of the main factors that negatively affect plant growth and development. Caragana korshinskii is widely distributed on the Loess Plateau, China, where it mediates soil and water loss and helps prevent desertification. However, little is known about the stress response mechanisms of C. korshinskii in water-starved environments. MicroRNAs (miRNAs) have been implicated in the regulation of plant responses to several types of biotic and abiotic stress. Here, we describe the miRNAs of wild C. korshinskii from Huangling, Yulin, and Dalad Banner, which occur along a precipitation gradient. Using next-generation sequencing technology, we obtained a total of 13 710 681, 15 048 945, and 15 198 442 reads for each location, respectively; after filtering and BLAST analysis, 490 conserved miRNAs and 96 novel miRNAs were characterized from the sRNAome data, with key functions determined using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. We also designed stem-loop qRT-PCR to validate the expression patterns of 5 conserved miRNAs (miR390, miR398, miR530, miR2119, and miR5559) that obviously responded to water stress in plants grown both under natural and experimental water stress conditions and found that the expression levels of miR2119 and miR5559 were negatively correlated with their predicted target genes. This study is the first to identify miRNAs from wild C. korshinskii and provides a basis for future studies of miRNA-mediated gene regulation of stress responses in C. korshinskii.

Light behind the curtain: photoregulation of nuclear architecture and chromatin dynamics in plants

Light is a powerful stimulus regulating many aspects of plant development and phenotypic plasticity. Plants sense light through the action of specialized photoreceptor protein families that absorb different wavelengths and intensities of light. Recent discoveries in the area of photobiology have uncovered photoreversible changes in nuclear organization correlated with transcriptional regulation patterns that lead to de-etiolation and photoacclimation. Novel signalling components bridging photoreceptor activation with chromatin remodelling and regulation of gene expression have been discovered. Moreover, coregulated gene loci have been shown to relocate to the nuclear periphery in response to light. The study of photoinduced changes in nuclear architecture is a flourishing area leading to major discoveries that will allow us to better understand how highly conserved mechanisms underlying genomic reprogramming are triggered by environmental and endogenous stimuli. This review aims to discuss fundamental and innovative reports demonstrating how light triggers changes in chromatin and nuclear architecture during photomorphogenesis.

Transcriptional analysis of the conidiation pattern shift of the entomopathogenic fungus Metarhizium acridum in response to different nutrients

Background

Most fungi, including entomopathogenic fungi, have two different conidiation patterns, normal and microcycle conidiation, under different culture conditions, eg, in media containing different nutrients. However, the mechanisms underlying the conidiation pattern shift are poorly understood.

Results

In this study, Metarhizium acridum undergoing microcycle conidiation on sucrose yeast extract agar (SYA) medium shifted to normal conidiation when the medium was supplemented with sucrose, nitrate, or phosphate. By linking changes in nutrients with the conidiation pattern shift and transcriptional changes, we obtained conidiation pattern shift libraries by Solexa/Illumina deep-sequencing technology. A comparative analysis demonstrated that the expression of 137 genes was up-regulated during the shift to normal conidiation, while the expression of 436 genes was up-regulated at the microcycle conidiation stage. A comparison of subtractive libraries revealed that 83, 216, and 168 genes were related to sucrose-induced, nitrate-induced, and phosphate-induced conidiation pattern shifts, respectively. The expression of 217 genes whose expression was specific to microcycle conidiation was further analyzed by the gene expression profiling via multigene concatemers method using mRNA isolated from M. acridum grown on SYA and the four normal conidiation media. The expression of 142 genes was confirmed to be up-regulated on standard SYA medium. Of these 142 genes, 101 encode hypothetical proteins or proteins of unknown function, and only 41 genes encode proteins with putative functions. Of these 41 genes, 18 are related to cell growth, 10 are related to cell proliferation, three are related to the cell cycle, three are related to cell differentiation, two are related to cell wall synthesis, two are related to cell division, and seven have other functions. These results indicate that the conidiation pattern shift in M. acridum mainly results from changes in cell growth and proliferation.

Conclusions

The results indicate that M. acridum shifts conidiation pattern from microcycle conidiation to normal conidiation when there is increased sucrose, nitrate, or phosphate in the medium during microcycle conidiation. The regulation of conidiation patterning is a complex process involving the cell cycle and metabolism of M. acridum. This study provides essential information about the molecular mechanism of the induction of the conidiation pattern shift by single nutrients.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2971-0) contains supplementary material, which is available to authorized users.

RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways

BACKGROUND

In cereal crops such as wheat, an optimal timing of developmental transitions is required to maximize grain yield. Many of these developmental changes are precisely regulated by changes in the duration, intensity or quality of light. Phytochromes are dimeric photoreceptors that absorb light maximally in the red and far-red wavelengths and induce large-scale transcriptional changes in response to variation in light quality. In wheat, PHYC is required for early flowering under long days. However, it is currently unknown whether this function requires the presence of PHYB. In this study, we characterized the role of PHYB in wheat development and used RNA-seq to analyze and compare the transcriptomes of phyB-null and phyC-null TILLING mutants.

RESULTS

Under long-day photoperiods, phyB-null plants exhibit a severe delay in flowering comparable to the delay observed in phyC-null plants. These results demonstrate that both genes are required for the induction of wheat flowering under long days. Using replicated RNA-seq studies we identified 82 genes that are significantly up or down regulated in both the phyB-null and phyC-null mutant relative to their respective wild-type controls. Among these genes are several well-characterized positive regulators of flowering, including PPD1, FT1 and VRN1. Eight-fold more genes were differentially regulated only in the phyB-null mutant (2202) than only in the phyC-null mutant (261). The PHYB-regulated genes were enriched in components of the auxin, gibberellin and brassinosteroid biosynthesis and signaling pathways, and in transcription factors with putative roles in regulating vegetative development and shade-avoidance responses. Several genes involved in abiotic stress tolerance pathways were also found to be regulated by PHYB.

CONCLUSIONS

PHYB and PHYC are both required for the photoperiodic induction of wheat flowering, whereas PHYB alone regulates a large number of genes involved in hormone biosynthesis and signaling, shade-avoidance response, and abiotic stress tolerance. Our analysis provides a comprehensive overview of the PHYB- and PHYC-mediated transcriptional changes during light signaling, and an initial step towards the dissection of this regulatory gene network in wheat. This further dissection will be required to explore the individual phytochrome-mediated developmental responses and to evaluate their potential to improve wheat adaptation to changing environments.

Natural variation involving deletion alleles of FRIGIDA modulate temperature-sensitive flowering responses in Arabidopsis thaliana

Ambient temperature is one of the major environmental factors that modulate plant growth and development. There is extensive natural genetic variation in thermal responses of plants exemplified by the variation exhibited by the accessions of Arabidopsis thaliana. In this work we have studied the enhanced temperature response in hypocotyl elongation and flowering shown by the Tsu-0 accession in long days. Genetic mapping in the Col-0 × Tsu-0 recombinant inbred line (RIL) population identified several QTLs for thermal response including three major effect loci encompassing candidate genes FRIGIDA (FRI), FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). We confirm and validate these QTLs. We show that the Tsu-0 FRI allele, which is the same as FRI-Ler is associated with late flowering but only at lower temperatures in long days. Using transgenic lines and accessions, we show that the FRI-Ler allele confers temperature-sensitive late flowering confirming a role for FRI in photoperiod-dependent thermal response. Through quantitative complementation with heterogeneous inbred families, we further show that cis-regulatory variation at FT contributes to the observed hypersensitivity of Tsu-0 to ambient temperature. Overall our results suggest that multiple loci that interact epistatically govern photoperiod-dependent thermal responses of A. thaliana.

PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis

Plants react to seasonal change in day length through altering physiology and development. Factors that function to harmonize growth with photoperiod are poorly understood. Here we characterize a new protein that associates with both circadian clock and photoreceptor components, named PHOTOPERIODIC CONTROL OF HYPOCOTYL1 (PCH1). pch1 seedlings have overly elongated hypocotyls specifically under short days while constitutive expression of PCH1 shortens hypocotyls independent of day length. PCH1 peaks at dusk, binds phytochrome B (phyB) in a red light-dependent manner, and co-localizes with phyB into photobodies. PCH1 is necessary and sufficient to promote the biogenesis of large photobodies to maintain an active phyB pool after light exposure, potentiating red-light signaling and prolonging memory of prior illumination. Manipulating PCH1 alters PHYTOCHROME INTERACTING FACTOR 4 levels and regulates light-responsive gene expression. Thus, PCH1 is a new factor that regulates photoperiod-responsive growth by integrating the clock with light perception pathways through modulating daily phyB-signaling.

DOI:http://dx.doi.org/10.7554/eLife.13292.001

Most living things possess an internal “circadian” clock that synchronizes many behaviors, such as eating, resting or growing, with the day-night cycle. With the help of proteins that can detect light, known as photoreceptors, the clock also coordinates these behaviors as the number of daylight hours changes during the year. However, it is not known how the clock and photoreceptors are able to work together.

The circadian clocks of animals and plants have evolved separately and use different proteins. In plants, a photoreceptor called phytochrome B responds to red light and regulates the ability of plants to grow. Most plants harness sunlight during the day, but grow fastest in the dark just before dawn. In 2015, researchers identified a new protein in a plant called Arabidopsis that is associated with several plant clock proteins and photoreceptors, including phytochrome B. However, the role of this new protein was not clear.

Now, Huang et al. – including many of the researchers from the 2015 work – studied the new protein, named PCH1, in more detail. The experiments show that PCH1 is a critical link that regulates the daily growth of Arabidopsis plants in response to the number of daylight hours. PCH1 stabilizes the structure of phytochrome B so that it remains active, even in the dark. This prolonged activity acts as a molecular memory of prior exposure to light and helps to prevent plants from growing too much in the winter when there are fewer hours of daylight. Since PCH1 is also found in other species of plants, it may play the same role in regulating growth of major crop plants.

The next challenge is to understand how the binding of PCH1 to phytochrome B alters the photoreceptor’s activity. In the future, Huang et al. hope to find out if manipulating the activity of PCH1 can improve the growth of crops in places where there is a large change in day length across the seasons.

DOI:http://dx.doi.org/10.7554/eLife.13292.002

Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry

Many species possess an endogenous circadian clock to synchronize internal physiology with an oscillating external environment. In plants, the circadian clock coordinates growth, metabolism and development over daily and seasonal time scales. Many proteins in the circadian network form oscillating complexes that temporally regulate myriad processes, including signal transduction, transcription, protein degradation and post-translational modification. In Arabidopsis thaliana, a tripartite complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX), named the evening complex, modulates daily rhythms in gene expression and growth through transcriptional regulation. However, little is known about the physical interactions that connect the circadian system to other pathways. We used affinity purification and mass spectrometry (AP-MS) methods to identify proteins that associate with the evening complex in A. thaliana. New connections within the circadian network as well as to light signaling pathways were identified, including linkages between the evening complex, TIMING OF CAB EXPRESSION1 (TOC1), TIME FOR COFFEE (TIC), all phytochromes and TANDEM ZINC KNUCKLE/PLUS3 (TZP). Coupling genetic mutation with affinity purifications tested the roles of phytochrome B (phyB), EARLY FLOWERING 4, and EARLY FLOWERING 3 as nodes connecting the evening complex to clock and light signaling pathways. These experiments establish a hierarchical association between pathways and indicate direct and indirect interactions. Specifically, the results suggested that EARLY FLOWERING 3 and phytochrome B act as hubs connecting the clock and red light signaling pathways. Finally, we characterized a clade of associated nuclear kinases that regulate circadian rhythms, growth, and flowering in A. thaliana. Coupling mass spectrometry and genetics is a powerful method to rapidly and directly identify novel components and connections within and between complex signaling pathways.

Integration of Light and Photoperiodic Signaling in Transcriptional Nuclear Foci

Light regulates major plant developmental transitions by orchestrating a series of nuclear events. This study uncovers the molecular function of the natural variant, TZP (Tandem Zinc-finger-Plus3), as a signal integrator of light and photoperiodic pathways in transcriptional nuclear foci. We report that TZP acts as a positive regulator of photoperiodic flowering via physical interactions with the red-light receptor phytochrome B (phyB). We demonstrate that TZP localizes in dynamic nuclear domains regulated by light quality and photoperiod. This study shows that phyB is indispensable not only for localizing TZP to transcriptionally active nuclear photobodies, but also for recruiting TZP on the promoter of the floral inducer FLOWERING LOCUS T (FT). Our findings signify a unique transcriptional regulatory role to the highly enigmatic plant nuclear photobodies, where TZP directly activates FT gene expression and promotes flowering.

Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry

Many species possess an endogenous circadian clock to synchronize internal physiology with an oscillating external environment. In plants, the circadian clock coordinates growth, metabolism and development over daily and seasonal time scales. Many proteins in the circadian network form oscillating complexes that temporally regulate myriad processes, including signal transduction, transcription, protein degradation and post-translational modification. In Arabidopsis thaliana, a tripartite complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX), named the evening complex, modulates daily rhythms in gene expression and growth through transcriptional regulation. However, little is known about the physical interactions that connect the circadian system to other pathways. We used affinity purification and mass spectrometry (AP-MS) methods to identify proteins that associate with the evening complex in A. thaliana. New connections within the circadian network as well as to light signaling pathways were identified, including linkages between the evening complex, TIMING OF CAB EXPRESSION1 (TOC1), TIME FOR COFFEE (TIC), all phytochromes and TANDEM ZINC KNUCKLE/PLUS3 (TZP). Coupling genetic mutation with affinity purifications tested the roles of phytochrome B (phyB), EARLY FLOWERING 4, and EARLY FLOWERING 3 as nodes connecting the evening complex to clock and light signaling pathways. These experiments establish a hierarchical association between pathways and indicate direct and indirect interactions. Specifically, the results suggested that EARLY FLOWERING 3 and phytochrome B act as hubs connecting the clock and red light signaling pathways. Finally, we characterized a clade of associated nuclear kinases that regulate circadian rhythms, growth, and flowering in A. thaliana. Coupling mass spectrometry and genetics is a powerful method to rapidly and directly identify novel components and connections within and between complex signaling pathways.

Genome-wide identification of microRNAs and their targets in wild type and phyB mutant provides a key link between microRNAs and the phyB-mediated light signaling pathway in rice

Phytochrome B (phyB), a member of the phytochrome family in rice, plays important roles in regulating a range of developmental processes and stress responses. However, little information about the mechanisms involved in the phyB-mediated light signaling pathway has been reported in rice. MicroRNAs (miRNAs) also perform important roles in plant development and stress responses. Thus, it is intriguing to explore the role of miRNAs in the phyB-mediated light signaling pathway in rice. In this study, comparative high-throughput sequencing and degradome analysis were used to identify candidate miRNAs and their targets that participate in the phyB-mediated light signaling pathway. A total of 720 known miRNAs, 704 novel miRNAs and 1957 target genes were identified from the fourth leaves of wild-type (WT) and phyB mutant rice at the five-leaf stage. Among them, 135 miRNAs showed differential expression, suggesting that the expression of these miRNAs is directly or indirectly under the control of phyB. In addition, 32 out of the 135 differentially expressed miRNAs were found to slice 70 genes in the rice genome. Analysis of these target genes showed that members of various transcription factor families constituted the largest proportion, indicating miRNAs are probably involved in the phyB-mediated light signaling pathway mainly by regulating the expression of transcription factors. Our results provide new clues for functional characterization of miRNAs in the phyB-mediated light signaling pathway, which should be helpful in comprehensively uncovering the molecular mechanisms of phytochrome-mediated photomorphogenesis and stress responses in plants.

Circadian clock and photoperiodic response in Arabidopsis: from seasonal flowering to redox homeostasis

Many of the developmental responses and behaviors in plants that occur throughout the year are controlled by photoperiod; among these, seasonal flowering is the most characterized. Molecular genetic and biochemical analyses have revealed the mechanisms by which plants sense changes in day length to regulate seasonal flowering. In Arabidopsis thaliana, induction of the expression of a florigen, FLOWERING LOCUS T (FT) protein, is a major output of the photoperiodic flowering pathway. The circadian clock coordinates the expression profiles and activities of the components in this pathway. Light-dependent control of CONSTANS (CO) transcription factor activity is a crucial part of the induction of the photoperiodic expression of FT. CO protein is stabilized only in the long day afternoon, which is when FT is induced. In this review, we summarize recent progress in the determination of the molecular architecture of the circadian clock and mechanisms underlying photoperiodic flowering. In addition, we introduce the molecular mechanisms of other biological processes, such as hypocotyl growth and reactive oxygen species production, which are also controlled by alterations in photoperiod.

Variation in sulfur and selenium accumulation is controlled by naturally occurring isoforms of the key sulfur assimilation enzyme ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE2 across the Arabidopsis species range

Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis (Arabidopsis thaliana) accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction, and its reduced activity in the loss-of-function allele apr2-1 and the two Arabidopsis accessions Hodonín and Shahdara leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Shahdara accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by 4 orders of magnitude across the Arabidopsis species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored.

Identification and characterization of Wilt and salt stress-responsive microRNAs in chickpea through high-throughput sequencing

Chickpea (Cicer arietinum) is the second most widely grown legume worldwide and is the most important pulse crop in the Indian subcontinent. Chickpea productivity is adversely affected by a large number of biotic and abiotic stresses. MicroRNAs (miRNAs) have been implicated in the regulation of plant responses to several biotic and abiotic stresses. This study is the first attempt to identify chickpea miRNAs that are associated with biotic and abiotic stresses. The wilt infection that is caused by the fungus Fusarium oxysporum f.sp. ciceris is one of the major diseases severely affecting chickpea yields. Of late, increasing soil salinization has become a major problem in realizing these potential yields. Three chickpea libraries using fungal-infected, salt-treated and untreated seedlings were constructed and sequenced using next-generation sequencing technology. A total of 12,135,571 unique reads were obtained. In addition to 122 conserved miRNAs belonging to 25 different families, 59 novel miRNAs along with their star sequences were identified. Four legume-specific miRNAs, including miR5213, miR5232, miR2111 and miR2118, were found in all of the libraries. Poly(A)-based qRT-PCR (Quantitative real-time PCR) was used to validate eleven conserved and five novel miRNAs. miR530 was highly up regulated in response to fungal infection, which targets genes encoding zinc knuckle- and microtubule-associated proteins. Many miRNAs responded in a similar fashion under both biotic and abiotic stresses, indicating the existence of cross talk between the pathways that are involved in regulating these stresses. The potential target genes for the conserved and novel miRNAs were predicted based on sequence homologies. miR166 targets a HD-ZIPIII transcription factor and was validated by 5′ RLM-RACE. This study has identified several conserved and novel miRNAs in the chickpea that are associated with gene regulation following exposure to wilt and salt stress.

Conserved histidine of metal transporter AtNRAMP1 is crucial for optimal plant growth under manganese deficiency at chilling temperatures

Manganese (Mn) is an essential nutrient required for plant growth, in particular in the process of photosynthesis. Plant performance is influenced by various environmental stresses including contrasting temperatures, light or nutrient deficiencies. The molecular responses of plants exposed to such stress factors in combination are largely unknown. Screening of 108 Arabidopsis thaliana (Arabidopsis) accessions for reduced photosynthetic performance at chilling temperatures was performed and one accession (Hog) was isolated. Using genetic and molecular approaches, the molecular basis of this particular response to temperature (G × E interaction) was identified. Hog showed an induction of a severe leaf chlorosis and impaired growth after transfer to lower temperatures. We demonstrated that this response was dependent on the nutrient content of the soil. Genetic mapping and complementation identified NRAMP1 as the causal gene. Chlorotic phenotype was associated with a histidine to tyrosine (H239Y) substitution in the allele of Hog NRAMP1. This led to lethality when Hog seedlings were directly grown at 4°C. Chemical complementation and hydroponic culture experiments showed that Mn deficiency was the major cause of this G × E interaction. For the first time, the NRAMP-specific highly conserved histidine was shown to be crucial for plant performance.

Identifying genotype-by-environment interactions in the metabolism of germinating arabidopsis seeds using generalized genetical genomics

A complex phenotype such as seed germination is the result of several genetic and environmental cues and requires the concerted action of many genes. The use of well-structured recombinant inbred lines in combination with "omics" analysis can help to disentangle the genetic basis of such quantitative traits. This so-called genetical genomics approach can effectively capture both genetic and epistatic interactions. However, to understand how the environment interacts with genomic-encoded information, a better understanding of the perception and processing of environmental signals is needed. In a classical genetical genomics setup, this requires replication of the whole experiment in different environmental conditions. A novel generalized setup overcomes this limitation and includes environmental perturbation within a single experimental design. We developed a dedicated quantitative trait loci mapping procedure to implement this approach and used existing phenotypical data to demonstrate its power. In addition, we studied the genetic regulation of primary metabolism in dry and imbibed Arabidopsis (Arabidopsis thaliana) seeds. In the metabolome, many changes were observed that were under both environmental and genetic controls and their interaction. This concept offers unique reduction of experimental load with minimal compromise of statistical power and is of great potential in the field of systems genetics, which requires a broad understanding of both plasticity and dynamic regulation.

The receptor-like kinase ERECTA contributes to the shade-avoidance syndrome in a background-dependent manner

BACKGROUND AND AIMS

Plants growing at high densities perceive a decrease in the red to far-red (R/FR) ratio of incoming light. These changes in light quality trigger a suite of responses collectively known as the shade-avoidance syndrome (SAS) including hypocotyl and stem elongation, inhibition of branching and acceleration of flowering.

METHODS

Quantitative trait loci (QTLs) were mapped for hypocotyl length to end-of-day far-red (EOD), a simulated shade-avoidance response, in recombinant inbred line (RIL) populations of Arabidopsis thaliana seedlings, derived from Landsberg erecta (Ler) and three accessions (Columbia, Col; Nossen, No-0; and Cape Verde Islands, Cvi-0).

KEY RESULTS

Five loci were identified as being responsible for the EOD response, with a positive contribution of Ler alleles on the phenotype independently of the RIL population. Quantitative complementation analysis and transgenic lines showed that PHYB is the candidate gene for EODRATIO5 in the Ler × Cvi-0 RIL population, but not for two co-localized QTLs, EODRATIO1 and EODRATIO2 mapped in the Ler × No-0 and Ler × Col RIL populations, respectively. The ERECTA gene was also implicated in the SAS in a background-dependent manner. For hypocotyl length EOD response, a positive contribution of erecta alleles was found in Col and Van-0, but not in Ler, Cvi-0, Hir-1 or Ws. Furthermore, pleiotropic effects of ERECTA in the EOD response were also detected for petiole and lamina elongation, hyponastic growth, and flowering time.

CONCLUSIONS

The results show that the analysis of multiple mapping populations leads to a better understanding of the SAS genetic architecture. Moreover, the background- and trait-dependent contribution of ERECTA in the SAS suggest that its function in shaded natural environments may be relevant for some populations in different phases of plant development. It is proposed that ERECTA is involved in canalization processes buffering the genetic variation of the SAS against environmental light fluctuations.

Phenoscope: an automated large-scale phenotyping platform offering high spatial homogeneity

Increased phenotyping accuracy and throughput are necessary to improve our understanding of quantitative variation and to be able to deconstruct complex traits such as those involved in growth responses to the environment. Still, only a few facilities are known to handle individual plants of small stature for non-destructive, real-time phenotype acquisition from plants grown in precisely adjusted and variable experimental conditions. Here, we describe Phenoscope, a high-throughput phenotyping platform that has the unique feature of continuously rotating 735 individual pots over a table. It automatically adjusts watering and is equipped with a zenithal imaging system to monitor rosette size and expansion rate during the vegetative stage, with automatic image analysis allowing manual correction. When applied to Arabidopsis thaliana, we show that rotating the pots strongly reduced micro-environmental disparity: heterogeneity in evaporation was cut by a factor of 2.5 and the number of replicates needed to detect a specific mild genotypic effect was reduced by a factor of 3. In addition, by controlling a large proportion of the micro-environmental variance, other tangible sources of variance become noticeable. Overall, Phenoscope makes it possible to perform large-scale experiments that would not be possible or reproducible by hand. When applied to a typical quantitative trait loci (QTL) mapping experiment, we show that mapping power is more limited by genetic complexity than phenotyping accuracy. This will help to draw a more general picture as to how genetic diversity shapes phenotypic variation.

Global identification of miRNAs and targets in Populus euphratica under salt stress

Populus euphratica, a typical hydro-halophyte, is ideal for studying salt stress responses in woody plants. MicroRNAs (miRNAs) are endogenous non-coding small RNAs that fulfilled an important post-transcriptional regulatory function. MiRNA may regulate tolerance to salt stress but this has not been widely studied in P. euphratica. In this investigation, the small RNAome, degradome and transcriptome were studied in salt stress treated P. euphratica by deep sequencing. Two hundred and eleven conserved miRNAs between Populus trichocarpa and P. euphratica have been found. In addition, 162 new miRNAs, belonging to 93 families, were identified in P. euphratica. Degradome sequencing experimentally verified 112 targets that belonged to 51 identified miRNAs, few of which were known previously in P. euphratica. Transcriptome profiling showed that expression of 15 miRNA-target pairs displayed reverse changing pattern under salt stress. Together, these results indicate that, in P. euphratica under salt stress, a large number of new miRNAs could be discovered, and both known and new miRNA were functionally cleaving to their target mRNA. Expression of miRNA and target were correspondingly induced by salt stress but that it was a complex process in P. euphratica.

An overview of natural variation studies in the Arabidopsis thaliana circadian clock

Circadian clocks are ubiquitous mechanisms that provide an adaptive advantage by predicting subsequent environmental changes. In the model plant Arabidopsis thaliana (Arabidopsis), our understanding of the complex genetic network among clock components has considerably increased during these past years. Modeling has predicted the possibility of additional component to systematically and functionally complete the clock system. Mutagenesis screens have in the past been successfully employed to detect such novel components. With the advancement in sequencing technologies and improvements in statistical approaches, the extensive natural variation present in Arabidopsis accessions has emerged as a powerful alternative in functional gene discovery. In this review article, we review the previous efforts in mapping natural alleles affecting various clock parameters and will discuss further potentials of such natural-variation studies in physiological and ecological contexts.

Natural variation in seed very long chain fatty acid content is controlled by a new isoform of KCS18 in Arabidopsis thaliana

Oil from oleaginous seeds is mainly composed of triacylglycerols. Very long chain fatty acids (VLCFAs) are major constituents of triacylglycerols in many seed oils and represent valuable feedstock for industrial purposes. To identify genetic factors governing natural variability in VLCFA biosynthesis, a quantitative trait loci (QTL) analysis using a recombinant inbred line population derived from a cross between accessions Bay-0 and Shahdara was performed in Arabidopsis thaliana. Two fatty acid chain length ratio (CLR) QTL were identified, with one major locus, CLR.2, accounting for 77% of the observed phenotypic variation. A fine mapping and candidate gene approach showed that a key enzyme of the fatty acid elongation pathway, the β-ketoacyl-CoA synthase 18 (KCS18), was responsible for the CLR.2 QTL detected between Bay-0 and Shahdara. Association genetics and heterologous expression in yeast cells identified a single point mutation associated with an alteration of KCS18 activity, uncovering the molecular bases for the modulation of VLCFA content in these two natural populations of Arabidopsis. Identification of this kcs18 mutant with altered activity opens new perspectives for the modulation of oil composition in crop plants.

Plant developmental biologists meet on stairways in Matera

The third EMBO Conference on Plant Molecular Biology, which focused on ‘Plant development and environmental interactions’, was held in May 2012 in Matera, Italy. Here, we review some of the topics and themes that emerged from the various contributions; namely, steering technologies, transcriptional networks and hormonal regulation, small RNAs, cell and tissue polarity, environmental control and natural variation. We intend to provide the reader who might have missed this remarkable event with a glimpse of the recent progress made in this blossoming research field.

The regulation of plant growth by the circadian clock

Circadian regulated changes in growth rates have been observed in numerous plants as well as in unicellular and multicellular algae. The circadian clock regulates a multitude of factors that affect growth in plants, such as water and carbon availability and light and hormone signalling pathways. The combination of high-resolution growth rate analyses with mutant and biochemical analysis is helping us elucidate the time-dependent interactions between these factors and discover the molecular mechanisms involved. At the molecular level, growth in plants is modulated through a complex regulatory network, in which the circadian clock acts at multiple levels.

DNA fingerprinting and new tools for fine-scale discrimination of Arabidopsis thaliana accessions

One of the main strengths of Arabidopsis thaliana as a model species is the impressive number of public resources available to the scientific community. Exploring species genetic diversity--and therefore adaptation--relies on collections of individuals from natural populations taken from diverse environments. Nevertheless, due to a few mislabeling events or genotype mixtures, some variants available in stock centers have been misidentified, causing inconsistencies and limiting the potential of genetic analyses. To improve the identification of natural accessions, we genotyped 1311 seed stocks from our Versailles Arabidopsis Stock Center and from other collections to determine their molecular profiles at 341 single nucleotide polymorphism markers. These profiles were used to compare genotypes at both the intra- and inter-accession levels. We confirmed previously described inconsistencies and revealed new ones, and suggest likely identities for accessions whose lineage had been lost. We also developed two new tools: a minimal fingerprint computation to quickly verify the identity of an accession, and an optimized marker set to assist in the identification of unknown or mixed accessions. These tools are available on a dedicated web interface called ANATool (https://www.versailles.inra.fr/ijpb/crb/anatool) that provides a simple and efficient means to verify or determine the identity of A. thaliana accessions in any laboratory, without the need for any specific or expensive technology.

Visualizing the genetic landscape of Arabidopsis seed performance

Perfect timing of germination is required to encounter optimal conditions for plant survival and is the result of a complex interaction between molecular processes, seed characteristics, and environmental cues. To detangle these processes, we made use of natural genetic variation present in an Arabidopsis (Arabidopsis thaliana) Bayreuth × Shahdara recombinant inbred line population. For a detailed analysis of the germination response, we characterized rate, uniformity, and maximum germination and discuss the added value of such precise measurements. The effects of after-ripening, stratification, and controlled deterioration as well as the effects of salt, mannitol, heat, cold, and abscisic acid (ABA) with and without cold stratification were analyzed for these germination characteristics. Seed morphology (size and length) of both dry and imbibed seeds was quantified by using image analysis. For the overwhelming amount of data produced in this study, we developed new approaches to perform and visualize high-throughput quantitative trait locus (QTL) analysis. We show correlation of trait data, (shared) QTL positions, and epistatic interactions. The detection of similar loci for different stresses indicates that, often, the molecular processes regulating environmental responses converge into similar pathways. Seven major QTL hotspots were confirmed using a heterogeneous inbred family approach. QTLs colocating with previously reported QTLs and well-characterized mutants are discussed. A new connection between dormancy, ABA, and a cripple mucilage formation due to a naturally occurring mutation in the MUCILAGE-MODIFIED2 gene is proposed, and this is an interesting lead for further research on the regulatory role of ABA in mucilage production and its multiple effects on germination parameters.

Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice

Background

In rice, the major part of the post-embryonic root system is made of stem-derived roots named crown roots (CR). Among the few characterized rice mutants affected in root development, crown rootless1 mutant is unable to initiate crown root primordia. CROWN ROOTLESS1 (CRL1) is induced by auxin and encodes an AS2/LOB-domain transcription factor that acts upstream of the gene regulatory network controlling CR development.

Results

To identify genes involved in CR development, we compared global gene expression profile in stem bases of crl1 mutant and wild-type (WT) plants. Our analysis revealed that 250 and 236 genes are down- and up-regulated respectively in the crl1 mutant. Auxin induces CRL1 expression and consequently it is expected that auxin also alters the expression of genes that are early regulated by CRL1. To identify genes under the early control of CRL1, we monitored the expression kinetics of a selected subset of genes, mainly chosen among those exhibiting differential expression, in crl1 and WT following exogenous auxin treatment. This analysis revealed that most of these genes, mainly related to hormone, water and nutrient, development and homeostasis, were likely not regulated directly by CRL1. We hypothesized that the differential expression for these genes observed in the crl1 mutant is likely a consequence of the absence of CR formation. Otherwise, three CRL1-dependent auxin-responsive genes: FSM (FLATENNED SHOOT MERISTEM)/FAS1 (FASCIATA1), GTE4 (GENERAL TRANSCRIPTION FACTOR GROUP E4) and MAP (MICROTUBULE-ASSOCIATED PROTEIN) were identified. FSM/FAS1 and GTE4 are known in rice and Arabidopsis to be involved in the maintenance of root meristem through chromatin remodelling and cell cycle regulation respectively.

Conclusion

Our data showed that the differential regulation of most genes in crl1 versus WT may be an indirect consequence of CRL1 inactivation resulting from the absence of CR in the crl1 mutant. Nevertheless some genes, FAS1/FSM, GTE4 and MAP, require CRL1 to be induced by auxin suggesting that they are likely directly regulated by CRL1. These genes have a function related to polarized cell growth, cell cycle regulation or chromatin remodelling. This suggests that these genes are controlled by CRL1 and involved in CR initiation in rice.