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Root density sensing allows pro-active modulation of shoot growth to avoid future resource limitation

Plants use environmental cues to determine their optimal root and shoot growth. It is well known to gardeners and horticulturists alike that soil volume - most commonly in the form of pot size - strongly restricts plant growth, but the mechanisms by which this effect occurs remain unclear. Here, we show that shoot growth scales directly with soil volume, independently of the nutritional content of the soil, and that plants can become volume restricted even in the presence of abundant resources. We show that plants can detect their soil volume as early as 3 weeks post germination, and that shoot growth restriction therefore constitutes a pro-active decision by the plant to avoid resource limitation later in the life cycle. Shoot growth restriction is not directly linked to root growth restriction, and does not occur in response to the mechanical detection of the pot walls. Rather, we show that plants detect their soil volume by detecting the density of roots in the proximity of their root system. As such, volume restriction may be intimately connected with the mechanism by which plants sense and respond to the roots of other plants in the rhizosphere. Our work demonstrates the remarkable ability of plants to make pro-active decisions about their growth to ensure they can complete their cycle, and has important implications for agricultural practise regarding both nutrient use efficiency and yield.

plant biology

KAI2 regulates root and root hair development by modulating auxin distribution

Strigolactones (SLs) are endogenous signalling molecules that play important roles in controlling plant development. SL perception is closely related to that of karrikins, smoke-derived compounds presumed to mimic endogenous signalling molecules (KLs). SLs have been suggested to regulate root development. However, perception of both molecules requires the F-box protein MAX2 and the use of max2 mutants has hampered defining the exact role of SLs in roots. Here we dissect the role of SL and KL signalling in Arabidopsis root development using mutants defective in the /{beta} hydrolase receptors D14 and KAI2, which specifically perceive SLs and KLs, respectively. Both pathways together regulate lateral root density (LRD), but contrary to previous reports, KL signalling alone controls root hair density, root hair length and additionally root skewing, straightness and diameter. Members of the SMXL protein family are downstream targets of SL (SMXL6, 7, 8) and KL (SMAX1, SMXL2) signalling. We identified distinct and overlapping roles of these proteins in the regulation of root development. Both SMAX1/SMXL2 and SMXL6/SMXL7/SMXL8 regulate LRD, confirming that SL and KL signalling act together to regulate this trait, while the KL-signalling specific SMAX1 and SMXL2 regulate all other investigated root traits. Finally, we show that KL signalling regulates root hair development by modulating auxin distribution within the root.

plant biology

GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

Transition to flowering at the right time is critical for local adaptation and to maximize seed yield in canola, which is an important oilseed crop. There is extensive variation among canola varieties in flowering time. However, our understanding of underlying genes and their role in canola productivity is still limited. We reveal natural variation in flowering time and response to photoperiod in a diverse GWAS panel (up to 368 accessions) of canola and identify associated SNPs across multiple experiments. Complementary QTL and eQTL mapping studies were also conducted in an Australian doubled haploid (DH) population for flowering time and other grain yield related traits. We show that several associations that were repeatedly detected across experiments map in the vicinity of FLOWERING LOCUS T (FT) paralogues and its known transcriptional regulators. QTL mapping study in a DH population detected consistent genomic regions close to FT paralogs. FT sequences vary between accessions and FT expression in field and controlled environment grown plants was correlated with flowering time. FT paralogs displayed association not only with flowering time, but also with plant emergence, shoot biomass and grain yield. Our findings suggest that FT paralogs not only modulate flowering time but also modulate yield-related productivity traits in canola. HighlightThe genetic association, eQTL and expression analyses suggest that FT paralogs have multifaceted roles in canola flowering time, plant development and productivity traits.

plant biology

GNI-A1 mediates trade-off between grain number and grain weight in tetraploid wheat

Grain yield is a highly polygenic trait determined by the number of grains per unit area, as well as by grain weight. In wheat, grain number and grain weight are usually negatively correlated. Yet, the genetic basis underlying trade-off between the two is mostly unknown. Here, we fine-mapped a grain weight QTL using wild emmer introgressions in a durum wheat background, and showed that grain weight is associated with the GNI-A1 gene, a regulator of floret fertility. In-depth characterization of grain number and grain weight indicated that suppression of distal florets by the wild emmer GNI-A1 allele increase weight of proximal grains in basal and central spikelets due to alteration in assimilate distribution. Re-sequencing of GNI-A1 in tetraploid wheat demonstrated the rich allelic repertoire of the wild emmer gene pool, including a rare allele which was present in two gene copies and contained a non-synonymous mutation in the C-terminus of the protein. Using an F2 population generated from a cross between wild emmer accessions Zavitan, which carries the rare allele, and TTD140, we demonstrated that this unique polymorphism is associated with grain weight, independent of grain number. Moreover, we showed, for the first time, that GNI-A1 proteins are transcriptional activators and that selection in domesticated wheat targeted compromised activity of the protein. Our finding expand the knowledge of the genetic basis underlying trade-off between key yield components and may contribute to breeding efforts for enhanced grain yield.

plant biology

Cyanobacteria is uniquely enriched in the roots of grain amaranths

Plants and microbes have coexisted for millions of years and some have evolved mechanisms to achieve symbiosis driving positive selection. The bartering of chemicals produced by soil microbes and plants favour enrichment of certain types of bacteria near the roots that offers selective advantage to the plant under a given environment. Grain amaranths display certain important agronomic characteristics like C4 dicot, high protein and high lysine grains, resistance to biotic and abiotic stress, which can be translated to other crops. Considering an unusual collection of desirable traits shown by grain amaranths, it is worth pondering if symbiosis with bacteria has played any role in these traits. The objective of this study is to identify bacterial root microflora unique to grain amaranths. Here, by comparing rhizospheric and endophytic composition of 16S rRNA from various sections of roots from selected species under major plant orders including the three varieties of grain amaranths, we report that Cyanobacteria are uniquely enriched by grain amaranths. The diversity in OTUs among the Cyanobacteria also significantly increased among samples from amaranth species compared to negative control. This finding is also validated using root transcriptome of Amaranthus hypochondriacus, where we observe relative increase in Cyanobacterial population between day 15 to day 30 compared to other abundant phylum during this period.

plant biology

Will climate change affect sugar beet establishment of the 21st century? Insights from a simulation study using a crop emergence model

Ongoing climate change has been reported to have far-reaching impact on crop development and yield in many regions of the globe including Europe. However, little is known about the potential impact of climate change on specific stages of the crop cycle including crop establishment, although it is a crucial stage of the annual crop cycles. For the first time, we performed a simulation study to pinpoint how sugar beet sowing conditions of the next eight decades will be altered under future climate change and if these variations will affect sowing dates, germination and emergence as well as bolting rates of this crop. We chose Northern France as an important study site, representative of sugar beet growing basin in Northern Europe. Sugar beet emergence simulations were performed for a period between 2020 and 2100, taking into account five sowing dates (mid-February, 1st March, mid-March, 1st April and mid-April). Soil water contents and temperatures in the 0-10 cm soil horizon were first simulated with the STICS soil-crop model using the most pessimistic IPCC scenario (RCP 8.5) to feed the SIMPLE crop emergence model. We also evaluated the probability of field access for the earlier sowings, based on the amount of cumulated rainfall during February and March. When analyzed by sowing date and for successive 20-year period from 2020 to 2100, there was a significant increase in seedbed temperatures by 2{degrees}C after 2060 while no change in cumulative rainfall was found before and after sowings, compared with the past. Emergence rate was generally higher for 2081-2100, while time to reach the maximum emergence rate decreased by about one week, compared with other periods, due to higher average seedbed temperatures. The rate of non-germinated seeds decreased, especially for the earlier sowing dates, but the frequency of non-emergence due to water stress increased after 2060 for all sowing dates, including the mid-February sowing. Bolting remains a risk for sowings before mid-March although this risk will be markedly decreased after 2060. The changes in seedbed conditions will be significant after 2060 in terms of temperatures. However, the possibility of field access will be a main limiting factor for earlier sowings, as no significant changes in cumulative rainfall, compared with the past, will occur under future climate change. When field access is not a constraint, an anticipation of the sowing date, compared to the currently practiced sowing (i.e. mid-March), will lead to decreased risks for the sugar beet crop establishment and bolting. The use of future climate scenarios coupled with a crop model allows a precise insight into the future sowing conditions, and provide helpful information to better project future farming systems.

plant biology

Comparative transcriptome analysis of Powdery mildew Resistance between two Melon (Cucumis melo L) with Different Thickness Peel

Melon (Cucumis melo L.) is wildly planted in the world and China is a major producer of muskmelon. Powdery mildew is one of the most common fungal diseases in the world and this disease frequently affects melon (Cucumis melo L.) and due to the reduction of melon yield. In this study, one material GanTianmi with thin peel and another material XueLianHua with thick peel were selected. After inoculating the powdery mildew, both materials were used to do the RNA-Seq. In total two RNA-seq libraries were constructed and sequenced separately. The reads per kilobase per Million mapped reads (RPKM) values of all the genes in the two materials were calculated and there were 13828 genes were expressed in the material G and 13944 genes were expressed in the material S (RPKM>1). The differentially expression gene (DEG) analysis result suggested that total 769 the DEGs between the two materials were identified. All the DEGs were annotated with several database and the transcript factors (TFs) that related to disease resistance such as MYB, ERF and WRKY among the DEGs were also identified. This research could not only provide the information about understanding the mechanism of powdery mildew infection but also help researchers breed the varieties with powdery mildew resistance.

plant biology

Multi-allelic APRR2 Gene is Associated with Fruit Pigment Accumulation in Melon and Watermelon

Color and pigment content are important aspects of fruit quality and consumer acceptance of cucurbit crops. Here, we describe the independent mapping and cloning of a common causative APRR2 gene regulating pigment accumulation in melon and watermelon. We initially show that the APRR2 transcription factor is causative for the qualitative difference between dark and light green rind in both crops. Further analyses establish the link between sequence or expression level variations in the CmAPRR2 gene and pigments content in the rind and flesh of mature melon fruits. GWAS of young fruit rind color in a panel composed of 177 diverse melon accessions did not result in any significant association, leading to an earlier assumption that multiple genes are involved in shaping the overall phenotypic variation at this trait. Through resequencing of 25 representative accessions and allelism tests between light rind accessions, we show that multiple independent SNPs in the CmAPRR2 gene are causative for the light rind phenotype. The multi-haplotypic nature of this gene explain the lack of detection power obtained through GBS-based GWAS and confirm the pivotal role of this gene in shaping fruit color variation in melon. This study demonstrates the power of combining bi- and multi-allelic designs with deep sequencing, to resolve lack of power due to high haplotypic diversity and low allele frequencies. Due to its central role and broad effect on pigment accumulation in fruits, the APRR2 gene is an attractive target for carotenoids bio-fortification of cucurbit crops.

plant biology

Transcriptome Dedifferentiation Observed in Animal Primary Cultures is Essential to Plant Reprogramming

Tissue culture environment liberate cells from ordinary laws of multi-cellular organisms. This liberation enables cells several behaviors, such as growth, dedifferentiation, acquisition of pluripotency, immortalization and reprogramming. Each phenomenon is relating to each other and hardly to determine. Recently, dedifferentiation of animal cell was determined and quantified in increasing information entropy of transcriptome. The increasing information entropy of transcriptome induced by tissue culture may reappear in plant cells too. Here we corroborated it. Measuring information entropies of transcriptomes during reprogramming of plant cells suggested that reprogramming is a combined phenomenon of dedifferentiation and re-differentiation.

plant biology

Auxin export from proximal fruits drives arrest in competent inflorescence meristems

A well-defined set of regulatory pathways control entry into the reproductive phase in flowering plants [1]. Conversely, little is known about the mechanisms that control the end of the reproductive phase ( floral arrest), despite this being a critical process for optimising fruit and seed production. Complete fruit removal or lack of fertile fruit-set in male sterile mutants, for example male sterile1 (ms1), prevents timely floral arrest in the model plant Arabidopsis [2]. These observations formed the basis for Hensel and colleagues model in which end-of-flowering was proposed to result from a cumulative fruit/seed-derived signal that caused simultaneous global proliferative arrest (GPA) in all inflorescences [2]. Recent studies have suggested that end-of-flowering involves gene expression changes at the floral meristem which are at least in part controlled by the FRUITFULL-APETELA2 pathway [3,4], however there is limited understanding of how this process is controlled and the communication needed at the whole plant level. Here, we provide new information providing a framework for the fruit-to-meristem (F-M) communication implied by the GPA model [5]. We show that floral arrest in Arabidopsis is not global and does not occur synchronously between branches, but rather that the arrest of each inflorescence is a local process, driven by auxin export from fruit proximal to the inflorescence meristem (IM). Furthermore, we show that inflorescence meristems are only competent for floral arrest once they reach a certain developmental age. Understanding the regulation of floral arrest is of major importance for the future manipulation of flowering to extend and maximise crop yields.

plant biology

Moisture-dependent morphing tunes the dispersal of dandelion diaspores

Animal migration is highly sensitised to environmental cues, but plant dispersal is considered largely passive. The common dandelion, Taraxacum officinale, bears an intricate haired pappus facilitating flight. The pappus enables the formation of a separated vortex ring during flight; however, the pappus structure is not static but reversibly changes shape by closing in response to moisture. We hypothesised that this leads to changed dispersal properties in response to environmental conditions. Using wind tunnel experiments for flow visualisation, particle image velocimetry, and flight tests we characterised the fluid mechanics effects of the pappus morphing. We also modelled dispersal to understand the impact of pappus morphing on diaspore distribution. Pappus morphing dramatically alters the fluid mechanics of diaspore flight. We found that when the pappus closes in moist conditions, the drag coefficient decreases and thus the falling velocity is greatly increased. Detachment of diaspores from the parent plant also substantially decreases. The change in detachment when the pappus closes increases dispersal distances by reducing diaspore release when wind speeds are low. We propose that moisture-dependent pappus-morphing is a form of informed dispersal allowing rapid responses to changing conditions.

plant biology

HydroShoot: a functional-structural plant model for simulating hydraulic structure, gas and energy exchange dynamics of complex plant canopies under water deficit - application to grapevine (Vitis vinifera L.)

This paper aims at presenting HydroShoot, a functional-structural plant model (FSPM) that is developed to simulate gas-exchange rates of complex plant canopies under water deficit conditions, by scaling up gas-exchange rates from the leaf to the canopy levels. The main hypothesis is that simulating both the hydraulic structure of the shoot together with the energy budget of individual leaves is the asset for successfully achieving this up-scaling task. HydroShoot was hence built as the ensemble of three interacting modules: hydraulic which calculates the distribution of xylem water potential across shoot hydraulic segments, energy which calculates the complete energy budget of individual leaves, and exchange which calculates net assimilation and transpiration rates of individual leaves. HydroShoot was coupled with irradiance interception and soil water balance models, and was evaluated on virtual and real grapevines having strongly contrasted canopies, under well-watered and water-deficit conditions. HydroShoot captured accurately the impact of canopy architecture and the varying soil water deficit conditions on plant-scale gas-exchange rates and leaf-scale temperature and water potential distributions. Both shoot hydraulic structure and leaf energy budget simulations were, as postulated, required to adequately scaling-up leaf to canopy gas-exchange rates. Notwithstanding, simulating the hydraulic structure of the shoot was found far more necessary to adequately performing this scaling task than simulating leaf energy balance. That is, the intra-canopy variability of leaf water potential was a better predictor of the reduction of whole plant gas-exchange rates under water deficit than the intra-canopy variability of leaf temperature. We conclude therefore that simulating the shoot hydraulic structure is a prerequisite if FSPM's are to be used to assess gas-exchange rates of complex plant canopies as those of grapevines. Finally HydroShoot is available through the OpenAlea platform (https://github.com/openalea/hydroshoot) as a set of reusable modules.

plant biology

Genome wide analysis of Ga1-s modifiers in maize

A one way reproductive barrier exists between most popcorn varieties and dent corn varieties grown in the United States. This barrier is predominantly controlled by the ga1 locus. Using data from a diverse population of popcorn accessions pollinated by a dent corn tester, we found that the non-reciprocal pollination barrier conferred by ga1 is more complex than previously described. Individual accessions ranged from 0% to 100% compatible with dent corn pollen. Using conventional genotyping-by-sequencing data from 371 popcorn accessions carrying Ga1-s, seven significant modifiers of dent pollen compatibility were identified on five chromosomes. One locus may either be a nonfunctional ga1 allele present within popcorn, or second necessary gene for the reproductive barrier in genetic linkage with ga1, while the other modifiers are clearly genetically unlinked. The existence of ga1 modifiers segregating in a popcorn genetic background may indicate selective pressure to allow gene flow between populations, which should be incorporated into future models of the impact of genetic incompatibility loci on gene flow in natural and agricultural plant populations.

plant biology

Cell wall integrity signaling regulates cell wall regeneration via transcriptional activation in Chlamydomonas reinhardtii

An intact cell wall is critical for protecting the cell from osmotic challenges and harmful environments. Signaling mechanisms are necessary to monitor cell wall integrity and to regulate cell wall production and remodeling during growth and division cycles. The green alga, Chlamydomonas, has a proteinaceous cell wall of defined structure that is readily removed by gametolysin (g-lysin), a metalloprotease released during sexual mating. Naked cells treated with g-lysin induce the mRNA accumulation of > 100 cell wall-related genes within an hour, offering a system to study signaling and regulatory mechanisms for de novo cell wall assembly. Combining quantitative RT-PCR and luciferase reporter assays to probe transcript accumulation and promoter activity, we revealed that up to 500-fold upregulation of cell wall-related genes was driven at least partly by transcriptional activation upon g-lysin treatment. To investigate how naked cells trigger this rapid transcriptional activation, we tested whether osmotic stress and cell wall integrity are involved in this process. Under a constant hypotonic condition, comparable levels of cell wall-gene activation were observed by g-lysin treatment. In contrast, cells in an iso- or hypertonic condition showed up to 80% reduction in the g-lysin-induced gene activation, suggesting that hypotonic conditions are required for full-scale responses to g-lysin treatment. To test whether mechanical perturbation is involved, we isolated and examined a new set of cell wall mutants with defective or little cell walls. All cell wall mutants examined showed a constitutive upregulation of cell wall-related genes at the level, which would only be achieved by the g-lysin treatment in wild-type cells. Our study suggests a signaling that monitors mechanical defects of cell walls and regulates cell wall-gene expression in Chlamydomonas, which may relate to cell wall integrity signaling mechanisms in plants.

plant biology

Prediction of prospective leaf morphology in lettuce based on intracellular chloroplast position

In the accumulation response, chloroplasts move toward weak blue light, staying at positions along the periclinal cell wall. By contrast, in the avoidance response, chloroplasts move away from strong blue light, escaping to positions along the anticlinal cell wall. The accumulation response maximizes light capture and the avoidance response reduces photodamage. The intracellular positioning of chloroplasts is important for optimizing photosynthesis and may have common signals with the regulators that determine leaf morphology, another factor that affects photosynthesis. Here, we propose that intracellular chloroplast position can be used to predict prospective leaf morphology in lettuce (Lactuca sativa). To test this, we induced the accumulation or avoidance response in lettuce cells through exposure to the appropriate strength of blue light and observed the growth of the plants. Our results indicated that leaf area increased in response to weak blue light inducing the accumulation response, and leaf thickness increased in response to strong blue light inducing the avoidance response.

plant biology

Salicylic acid-driven association of LENRV and NIMIN1/NIMIN2 binding domain regions in the C-terminus of tobacco NPR1 transduces SAR signal

O_LINONEXPRESSOR OF PATHOGENESIS-RELATED (PR) GENES1 (NPR1) is the central regulator of salicylic acid (SA)-induced PR-1 gene expression and systemic acquired resistance (SAR). The mechanism how SA is transduced through NPR1 is discussed controversially. Previously, we showed that Arabidopsis and tobacco (Nt) NPR1 contain two domains in their C-terminal thirds with relevance to SA signaling. SA sensitivity of NPR1 relies on the arginine residue in the LENRV motif, and SA-induced NIM1-INTERACTING (NIMIN, N) proteins bind to a highly conserved sequence termed N1/N2 binding domain (BD). C_LIO_LIWe demonstrate that LENRV and N1/N2BD regions of tobacco NPR1, separated from each other, interact in yeast, in vitro, in plant and in animal cells. Physical association of LENRV and N1/N2BD parts is enhanced considerably by SA and functional analogs, but not by a non-functional analog. Furthermore, physical association requires R431 and is most effective with intact LENRV and N1/N2BD interfaces. C_LIO_LIAssociation of separated LENRV and N1/N2BD parts by SA reconstitutes a functional NtNPR1 C-terminus, displaying transcription activity and able to interact with TGA transcription factors at two distinct sites. C_LIO_LITobacco NIMIN proteins can assemble LENRV and N1/N2BD parts into ternary complexes suggesting that NIMINs shape the NPR1 C-terminus to modulate SA signaling. C_LI

plant biology

The cloud forest in the Dominican Republic: diversity and conservation status

The study of the forest in rainy environments of the Dominican Republic reveals the presence of four types of vegetation formations, clearly differentiated from each other in terms of their floristic and biogeographical composition, and also significantly different from the rainforests of Cuba. This leads us to propose two new alliances and four plant associations located in northern mountain areas exposed to moisture-laden winds from the Atlantic: All. Rondeletio ochraceae-Clusion roseae (Ass. Cyatheo furfuracei-Prestoetum motanae; Ass. Ormosio krugii-Prestoetum montanae); and All. Rondeletio ochraceae-Didymopanion tremuli (Ass. Hyeronimo montanae-Magnolietum pallescentis; Hyeronimo dominguensis-Magnolietum hamorii). Due to human activity, some areas are very poorly conserved, as evidenced by the diversity index and the presence of endemic tree and plant elements. The worst conserved in terms of the relationship between characteristic plants vegetation (cloud forest) in areas with high rainfall in the Dominican Republic, along with its floristic diversity and state of conservation. Thanks to this study it has been possible to significantly increase the botanical knowledge of this important habitat.

plant biology

Molecular Mechanisms Driving Bistable Switch Behavior in Xylem Cell Differentiation

Plant xylem cells conduct water and mineral nutrients. Although most plant cells are totipotent, xylem cells are unusual and undergo terminal differentiation. Many genes regulating this process are well characterized, including the VASCULAR-RELATED NAC DOMAIN7 (VND7), MYB46 and MYB83 transcription factors which are proposed to act in interconnected feed-forward loops. Much less is known regarding the dynamic behavior underlying the terminal transition to xylem cell differentiation. Here we utilize whole root and single cell data to mathematically model this relationship. These provide evidence for VND7 regulating bistable switching of cells in the root to a xylem cell identity, with additional features of hysteresis. We further determine that although MYB46 responds to VND7 induction, it is not inherently involved in executing the binary switch. A novel regulatory architecture is proposed that involves four downstream targets of VND7 that act in a cycle. These data provide an important model to study the emergent properties that may give rise to totipotency relative to terminal differentiation and reveal novel xylem cell subtypes.

plant biology