High‐throughput two‐dimensional root system phenotyping platform facilitates genetic analysis of root growth and development

High‐throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyse these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to, rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user‐guided and automated features that increase flexibility and enhance efficiency when measuring root growth traits from specific roots or entire root systems during large‐scale phenotyping studies. To demonstrate the unique capabilities and high‐throughput capacity of this phenotyping platform for studying root systems, genome‐wide association studies on rice (Oryza sativa) and maize (Zea mays) root growth were performed and root traits related to aluminium (Al) tolerance were analysed on the parents of the maize nested association mapping (NAM) population.     

Dissecting spatiotemporal biomass accumulation in barley under different water regimes using high‐throughput image analysis

Phenotyping large numbers of genotypes still represents the rate‐limiting step in many plant genetic experiments and in breeding. To address this issue, novel automated phenotyping technologies have been developed. We investigated for a core set of barley cultivars if high‐throughput image analysis can help to dissect vegetative biomass accumulation in response to two different watering regimes under semi‐controlled greenhouse conditions. We found that experiments, treatments, genotypes and genotype by environment interaction (G × E) can be characterized at any time point by certain digital traits. Biomass accumulation under control and stress conditions was highly heritable. Growth model‐derived maximum vegetative biomass (K_max), inflection point (I) and regrowth rate (k) were identified as promising candidate traits for genome‐wide association studies. Drought stress symptoms can be visualized, dissected and modelled. Especially the highly heritable regrowth rate, which had the biggest influence on biomass accumulation in stress treatment, seems promising for future studies to improve drought tolerance in different crop species. A proof of concept study revealed potential correlations between digital traits obtained from pot experiments under greenhouse conditions and agronomic traits from field experiments. Overall, non‐invasive, imaging‐based phenotyping platforms under greenhouse conditions offer excellent possibilities for trait discovery, trait development and industrial applications.     

Resource allocation to growth or luxury consumption drives mycorrhizal responses

Highly variable phenotypic responses in mycorrhizal plants challenge our functional understanding of plant‐fungal mutualisms. Using non‐invasive high‐throughput phenotyping, we observed that arbuscular mycorrhizal (AM) fungi relieved phosphorus (P) limitation and enhanced growth of Brachypodium distachyon under P‐limited conditions, while photosynthetic limitation under low nitrogen (N) was exacerbated by the fungus. However, these responses were strongly dependent on host genotype: only the faster growing genotype (Bd3‐1) utilised P transferred from the fungus to achieve improved growth under P‐limited conditions. Under low N, the slower growing genotype (Bd21) had a carbon and N surplus that was linked to a less negative growth response compared with the faster growing genotype. These responses were linked to the regulation of N : P stoichiometry, couples resource allocation to growth or luxury consumption in diverse plant lineages. Our results attest strongly to a mechanism in plants by which plant genotype‐specific resource economics drive phenotypic outcomes during AM symbioses.     

Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis

Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf‐level water‐use efficiency (WUE). In Arabidopsis, little is known about the variation of whole‐plant water use (PWU) and whole‐plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large‐scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water‐use strategies, namely, C24 (low PWU) and Col‐0 (high PWU). Subsequent quantitative trait loci mapping and validation through near‐isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ¹³C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ¹³C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf‐level traits.     

The rapid A–Ci response: photosynthesis in the phenomic era

Phenotyping for photosynthetic gas exchange parameters is limiting our ability to select plants for enhanced photosynthetic carbon gain and to assess plant function in current and future natural environments. This is due, in part, to the time required to generate estimates of the maximum rate of ribulose‐1,5‐bisphosphate carboxylase oxygenase (Rubisco) carboxylation (V_c,max) and the maximal rate of electron transport (J_max) from the response of photosynthesis (A) to the CO₂ concentration inside leaf air spaces (C_i). To relieve this bottleneck, we developed a method for rapid photosynthetic carbon assimilation CO₂ responses [rapid A–C_i response (RACiR)] utilizing non‐steady‐state measurements of gas exchange. Using high temporal resolution measurements under rapidly changing CO₂ concentrations, we show that RACiR techniques can obtain measures of V_c,max and J_max in ~5 min, and possibly even faster. This is a small fraction of the time required for even the most advanced gas exchange instrumentation. The RACiR technique, owing to its increased throughput, will allow for more rapid screening of crops, mutants and populations of plants in natural environments, bringing gas exchange into the phenomic era.     

Hyperspectral imaging combined with machine learning as a tool to obtain high‐throughput plant salt‐stress phenotyping

The rapid selection of salinity‐tolerant crops to increase food production in salinized lands is important for sustainable agriculture. Recently, high‐throughput plant phenotyping technologies have been adopted that use plant morphological and physiological measurements in a non‐destructive manner to accelerate plant breeding processes. Here, a hyperspectral imaging (HSI) technique was implemented to monitor the plant phenotypes of 13 okra (Abelmoschus esculentus L.) genotypes after 2 and 7 days of salt treatment. Physiological and biochemical traits, such as fresh weight, SPAD, elemental contents and photosynthesis‐related parameters, which require laborious, time‐consuming measurements, were also investigated. Traditional laboratory‐based methods indicated the diverse performance levels of different okra genotypes in response to salinity stress. We introduced improved plant and leaf segmentation approaches to RGB images extracted from HSI imaging based on deep learning. The state‐of‐the‐art performance of the deep‐learning approach for segmentation resulted in an intersection over union score of 0.94 for plant segmentation and a symmetric best dice score of 85.4 for leaf segmentation. Moreover, deleterious effects of salinity affected the physiological and biochemical processes of okra, which resulted in substantial changes in the spectral information. Four sample predictions were constructed based on the spectral data, with correlation coefficients of 0.835, 0.704, 0.609 and 0.588 for SPAD, sodium concentration, photosynthetic rate and transpiration rate, respectively. The results confirmed the usefulness of high‐throughput phenotyping for studying plant salinity stress using a combination of HSI and deep‐learning approaches.     

Spatio‐temporal variation in the effect of herbaceous layer on woody seedling survival in a Chilean mediterranean ecosystem

Questions: What is the effect of herbaceous layer on seedling establishment of three woody pioneer species in open areas of central Chile under a semi‐arid mediterranean climate? How do inter‐annual and habitat conditions (slope aspect) modulate this effect? Under high stress conditions such as the drier year and habitat (north‐facing slope) do herbs reach low abundance and have neutral effects on woody seedlings? Under medium stress conditions for these woody species, such as the wetter year and south‐facing slope, does the herbaceous layer reach greater abundance and have positive effects on woody seedlings due to increasing soil water content? Location: A watershed on the outskirts of Santiago, Chile, subjected to clearing of woody vegetation through firewood extraction and human‐set fires. Methods: In spring 2007, we set up 20 plots (3 m × 2 m). Half of each plot had herbs removed manually and by application of herbicide. In both halves of each plot, one seedling (8 months old) of each of the three native woody species (Colliguaya odorifera, Schinus polygamus and Quillaja saponaria) was planted and survival monitored subsequently. The experiment was repeated in two consecutive growing seasons (2007–2008 and 2008–2009) that differed significantly in total precipitation (152 and 256.5 mm, respectively), and replicated in two sites that differed in aspect and abiotic conditions: a moister south‐ and a drier north‐facing slope. Results: In the first and drier year, the herbaceous layer had low cover and no significant effect on seedling survival of woody species. During the second year, herbs had greater cover and a significant positive effect on spring survival of C. odorifera in the north‐facing slope, which was lost after summer. During this wetter year on the south‐facing slope, herb cover had a positive effect on survival of S. polygamus (mainly during summer). Conclusions: The role of mostly ruderal herbs on woody seedling establishment depended on the species, rainfall of the current year and slope aspect, and may be explained by soil moisture patterns. This suggests that the effect of ruderal herbs on woody seedlings shifts from neutral under high stress conditions produced by drought to positive under moderate stress conditions. Our results contribute to understand interactions between ruderal herbs and woody species under contrasting abiotic conditions. Therefore, control of the herbaceous layer may not be needed in restoration programmes for this region. Moreover, herbs may benefit restoration of woody cover in mesic habitats.     

Domestication of tomato has reduced the attraction of herbivore natural enemies to pest‐damaged plants

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Community‐level plant–soil feedbacks explain landscape distribution of native and non‐native plants

Plant–soil feedbacks (PSFs) have gained attention for their potential role in explaining plant growth and invasion. While promising, most PSF research has measured plant monoculture growth on different soils in short‐term, greenhouse experiments. Here, five soil types were conditioned by growing one native species, three non‐native species, or a mixed plant community in different plots in a common‐garden experiment. After 4 years, plants were removed and one native and one non‐native plant community were planted into replicate plots of each soil type. After three additional years, the percentage cover of each of the three target species in each community was measured. These data were used to parameterize a plant community growth model. Model predictions were compared to native and non‐native abundance on the landscape. Native community cover was lowest on soil conditioned by the dominant non‐native, Centaurea diffusa, and non‐native community cover was lowest on soil cultivated by the dominant native, Pseudoroegneria spicata. Consistent with plant growth on the landscape, the plant growth model predicted that the positive PSFs observed in the common‐garden experiment would result in two distinct communities on the landscape: a native plant community on native soils and a non‐native plant community on non‐native soils. In contrast, when PSF effects were removed, the model predicted that non‐native plants would dominate all soils, which was not consistent with plant growth on the landscape. Results provide an example where PSF effects were large enough to change the rank‐order abundance of native and non‐native plant communities and to explain plant distributions on the landscape. The positive PSFs that contributed to this effect reflected the ability of the two dominant plant species to suppress each other's growth. Results suggest that plant dominance, at least in this system, reflects the ability of a species to suppress the growth of dominant competitors through soil‐mediated effects.     

Host‐plant use by two Orthomeria (Phasmida: Aschiphasmatini) species feeding on Macaranga myrmecophytes

Myrmecophytes depend on symbiotic ants (plant‐ants) to defend against herbivores. Although these defensive mechanisms are highly effective, some herbivorous insects can use myrmecophytes as their host‐plants. The feeding habits of these phytophages on myrmecophytes and the impacts of the plant‐ants on their feeding behavior have been poorly studied. We examined two phasmid species, Orthomeria alexis and O. cuprinus, which are known to feed on Macaranga (Euphorbiaceae) myrmecophytes in a Bornean primary forest. Our observations revealed that: (i) each phasmid species relied on two closely‐related myrmecophytic Macaranga species for its host‐plants in spite of their normal plant‐ant symbioses; and (ii) there was little overlap between their host‐plant preferences. More O. cuprinus adults and nymphs were found on new leaves, which were attended by more plant‐ants than mature leaves, while most adults and nymphs of O. alexis tended to avoid new leaves. In a feeding choice experiment under ant‐excluded conditions, O. alexis adults chose a non‐host Macaranga myrmecophyte that was more intensively defended by plant‐ants and was more palatable than their usual host‐plants almost as frequently as their usual host‐plant, suggesting that the host‐plant range of O. alexis was restricted by the presence of plant‐ants on non‐host‐plants. Phasmid behavior that appeared to minimize plant‐ant attacks is described.     

Forest understory plant and soil microbial response to an experimentally induced drought and heat‐pulse event: the importance of maintaining the continuum

Drought duration and intensity are expected to increase with global climate change. How changes in water availability and temperature affect the combined plant–soil–microorganism response remains uncertain. We excavated soil monoliths from a beech (Fagus sylvatica L.) forest, thus keeping the understory plant–microbe communities intact, imposed an extreme climate event, consisting of drought and/or a single heat‐pulse event, and followed microbial community dynamics over a time period of 28 days. During the treatment, we labeled the canopy with ¹³CO₂ with the goal of (i) determining the strength of plant–microbe carbon linkages under control, drought, heat and heat–drought treatments and (ii) characterizing microbial groups that are tightly linked to the plant–soil carbon continuum based on ¹³C‐labeled PLFAs. Additionally, we used 16S rRNA sequencing of bacteria from the Ah horizon to determine the short‐term changes in the active microbial community. The treatments did not sever within‐plant transport over the experiment, and carbon sinks belowground were still active. Based on the relative distribution of labeled carbon to roots and microbial PLFAs, we determined that soil microbes appear to have a stronger carbon sink strength during environmental stress. High‐throughput sequencing of the 16S rRNA revealed multiple trajectories in microbial community shifts within the different treatments. Heat in combination with drought had a clear negative effect on microbial diversity and resulted in a distinct shift in the microbial community structure that also corresponded to the lowest level of label found in the PLFAs. Hence, the strongest changes in microbial abundances occurred in the heat–drought treatment where plants were most severely affected. Our study suggests that many of the shifts in the microbial communities that we might expect from extreme environmental stress will result from the plant–soil–microbial dynamics rather than from direct effects of drought and heat on soil microbes alone.     

Seedling recruitment in a semi‐arid Patagonian steppe: Facilitative effects of refuse dumps of leaf‐cutting ants

Question: What is the influence of refuse dumps of leaf‐cutting ants on seedling recruitment under contrasting moisture conditions in a semi‐arid steppe? Location: Northwestern Patagonia, Argentina. Methods: In a greenhouse experiment, we monitored seedling recruitment in soil samples from refuse dumps of nests of the leaf‐cutting ant Acromyrmex lobicornis and non‐nest sites, under contrasting moisture conditions simulating wet and dry growing seasons. Results: The mean number of seedling species and individuals were higher in wet than in dry plots, and higher in refuse dump plots than in non‐nest soil plots. The positive effect of refuse dumps on seedling recruitment was greater under low moisture conditions. Both the accumulation of discarded seeds by leaf‐cutting ants and the passive trapping of blowing‐seeds seems not explain the increased number of seeds in refuse dumps. Conversely, refuse dumps have higher water retention capacity and nutrient content than adjacent non‐nest soils, allowing the recruitment of a greater number of species and individual seedlings. Conclusions: Nests of A. lobicornis may play an important role in plant recruitment in the study area, allowing a greater number of seedlings and species to be present, hence resulting in a more diverse community. Moreover, leaf‐cutting ant nests may function as nurse elements, generating safe sites that enhance the performance of neighbouring seedlings mainly during the driest, stressful periods.     

Plant cell packs: a scalable platform for recombinant protein production and metabolic engineering

Industrial plant biotechnology applications include the production of sustainable fuels, complex metabolites and recombinant proteins, but process development can be impaired by a lack of reliable and scalable screening methods. Here, we describe a rapid and versatile expression system which involves the infusion of Agrobacterium tumefaciens into three‐dimensional, porous plant cell aggregates deprived of cultivation medium, which we have termed plant cell packs (PCPs). This approach is compatible with different plant species such as Nicotiana tabacum BY2, Nicotiana benthamiana or Daucus carota and 10‐times more effective than transient expression in liquid plant cell culture. We found that the expression of several proteins was similar in PCPs and intact plants, for example, 47 and 55 mg/kg for antibody 2G12 expressed in BY2 PCPs and N. tabacum plants respectively. Additionally, the expression of specific enzymes can either increase the content of natural plant metabolites or be used to synthesize novel small molecules in the PCPs. The PCP method is currently scalable from a microtiter plate format suitable for high‐throughput screening to 150‐mL columns suitable for initial product preparation. It therefore combined the speed of transient expression in plants with the throughput of microbial screening systems. Plant cell packs therefore provide a convenient new platform for synthetic biology approaches, metabolic engineering and conventional recombinant protein expression techniques that require the multiplex analysis of several dozen up to hundreds of constructs for efficient product and process development.     

Soil as a mediator in plant‐plant interactions in a semi‐arid community

Abstract. Competition and facilitation may occur simultaneously in plant communities, and the prevalence of either process depends on abiotic conditions. Here we attempt a community‐wide approach in the analysis of plant interactions, exploring whether in a semi‐arid environment positive or negative interactions predominate and whether there are differences among co‐occurring shrub species. Most shrubs in our plot exerted significant effects on their understorey communities, ranging from negative to positive. We found a clear case of interference and another case where the effect was neutral, but facilitation predominated and the biomass of annuals under most shrubs in our community was larger than in gaps. Effects on soil water and fertility were revealed as the primary source of facilitation; the build‐up of soil organic matter changed soil physical properties and improved soil water relations. Facilitation by shrubs involved decoupling of soil temperature and moisture. Sheltering from direct radiation had an effect on productivity, but significant differences in understorey biomass did not parallel understorey light environment. A positive balance of the interaction among plants, essentially mediated by changes in soil properties, is the predominant outcome of plant interactions in this semi‐arid community.     

Affordable and robust phenotyping framework to analyse root system architecture of soil‐grown plants

The phenotypic analysis of root system growth is important to inform efforts to enhance plant resource acquisition from soils; however, root phenotyping remains challenging because of the opacity of soil, requiring systems that facilitate root system visibility and image acquisition. Previously reported systems require costly or bespoke materials not available in most countries, where breeders need tools to select varieties best adapted to local soils and field conditions. Here, we report an affordable soil‐based growth (rhizobox) and imaging system to phenotype root development in glasshouses or shelters. All components of the system are made from locally available commodity components, facilitating the adoption of this affordable technology in low‐income countries. The rhizobox is large enough (approximately 6000 cm² of visible soil) to avoid restricting vertical root system growth for most if not all of the life cycle, yet light enough (approximately 21 kg when filled with soil) for routine handling. Support structures and an imaging station, with five cameras covering the whole soil surface, complement the rhizoboxes. Images are acquired via the Phenotiki sensor interface, collected, stitched and analysed. Root system architecture (RSA) parameters are quantified without intervention. The RSAs of a dicot species (Cicer arietinum, chickpea) and a monocot species (Hordeum vulgare, barley), exhibiting contrasting root systems, were analysed. Insights into root system dynamics during vegetative and reproductive stages of the chickpea life cycle were obtained. This affordable system is relevant for efforts in Ethiopia and other low‐ and middle‐income countries to enhance crop yields and climate resilience sustainably.     

The vascular plant‐pathogenic bacterium Ralstonia solanacearum produces biofilms required for its virulence on the surfaces of tomato cells adjacent to intercellular spaces

The mechanism of colonization of intercellular spaces by the soil‐borne and vascular plant‐pathogenic bacterium Ralstonia solanacearum strain OE1‐1 after invasion into host plants remains unclear. To analyse the behaviour of OE1‐1 cells in intercellular spaces, tomato leaves with the lower epidermis layers excised after infiltration with OE1‐1 were observed under a scanning electron microscope. OE1‐1 cells formed microcolonies on the surfaces of tomato cells adjacent to intercellular spaces, and then aggregated surrounded by an extracellular matrix, forming mature biofilm structures. Furthermore, OE1‐1 cells produced mushroom‐type biofilms when incubated in fluids of apoplasts including intercellular spaces, but not xylem fluids from tomato plants. This is the first report of biofilm formation by R. solanacearum on host plant cells after invasion into intercellular spaces and mushroom‐type biofilms produced by R. solanacearum in vitro. Sugar application led to enhanced biofilm formation by OE1‐1. Mutation of lecM encoding a lectin, RS‐IIL, which reportedly exhibits affinity for these sugars, led to a significant decrease in biofilm formation. Colonization in intercellular spaces was significantly decreased in the lecM mutant, leading to a loss of virulence on tomato plants. Complementation of the lecM mutant with native lecM resulted in the recovery of mushroom‐type biofilms and virulence on tomato plants. Together, our findings indicate that OE1‐1 produces mature biofilms on the surfaces of tomato cells after invasion into intercellular spaces. RS‐IIL may contribute to biofilm formation by OE1‐1, which is required for OE1‐1 virulence.     

Preference–performance relationship in the gall midge Rabdophaga rosaria: insights from a common‐garden experiment with nine willow clones

1. Oviposition preferences of herbivorous insects are predicted to match offspring performance on different host taxa or on conspecific host genotypes. In gall‐inducing insects, host‐plant properties such as growth rate and gall size, which are determined by plant genotype and growing conditions, may have a significant impact on offspring performance and, hence, should influence oviposition site selection. 2. The present study investigated host preference of the European rosette willow gall midge Rabdophaga rosaria (Loew) in relation to offspring success on seven clones of Salix myrsinifolia Salisb. and two naturally hybridised S. myrsinifolia × phylicifolia L. clones growing in a replicated design in an experimental field under two fertilisation regimes. For each clone, the average growth rate, number of shoot tips, and leaf and gall size were determined, and their effects on midge preference and larval survival were examined. 3. Main shoot height, number of shoot tips, and gall size were significantly affected by clone. The midges clearly preferred certain clones over the others, but preferences were not related to willow growth traits or to gall size. Survival probability was higher in large than in small galls, but females did not prefer large‐leaved clones that produced the biggest rosette galls. Midge oviposition was also uncorrelated with prior rates of leaf‐rust infection and with feeding preferences of voles and folivorous insects. 4. The weak preference–performance relationship of R. rosaria within S. myrsinifolia is probably explained by evolutionary constraints that prevent generalist insects from achieving an ability to discriminate among conspecific hosts of variable quality.     

Computational aspects underlying genome to phenome analysis in plants

Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high‐throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait?trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.