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Automating the analysis of plants using image processing would help remove barriers to phenotyping and large-scale precision agricultural technologies, such as site-specific weed control. The combination of accessible hardware and high-performance deep learning (DL) tools for plant analysis is becoming widely recognised as a path forward for both plant science and applied precision agricultural purposes. Yet, a lack of collaboration in image analysis for plant science, despite the open-source origins of much of the technology, is hindering development. Here, we show how tools developed for specific attributes of phenotyping or weed recognition for precision weed control have substantial overlapping data structure, software/hardware requirements and outputs. An open-source approach to these tools facilitates interdisciplinary collaboration, avoiding unnecessary repetition and allowing research groups in both basic and applied sciences to capitalise on advancements and resolve respective bottlenecks. The approach mimics that of machine learning in its nascence. Three areas of collaboration are identified as critical for improving efficiency, (1) standardized, open-source, annotated dataset development with consistent metadata reporting; (2) establishment of accessible and reliable training and testing platforms for DL algorithms; and (3) sharing of all source code used in the research process. The complexity of imaging plants and cost of annotating image datasets means that collaboration from typically distinct fields will be necessary to capitalize on the benefits of DL for both applied and basic science purposes.

Background Being able to accurately assess the 3D architecture of plant canopies can allow us to better estimate plant productivity and improve our understanding of underlying plant processes. This is especially true if we can monitor these traits across plant development. Photogrammetry techniques, such as structure from motion, have been shown to provide accurate 3D reconstructions of monocot crop species such as wheat and rice, yet there has been little success reconstructing crop species with smaller leaves and more complex branching architectures, such as chickpea. Results In this work, we developed a low-cost 3D scanner and used an open-source data processing pipeline to assess the 3D structure of individual chickpea plants. The imaging system we developed consists of a user programmable turntable and three cameras that automatically captures 120 images of each plant and offloads these to a computer for processing. The capture process takes 5–10 min for each plant and the majority of the reconstruction process on a Windows PC is automated. Plant height and total plant surface area were validated against “ground truth” measurements, producing R2 > 0.99 and a mean absolute percentage error Conclusions Our results show that it is possible to use low-cost photogrammetry techniques to accurately reconstruct individual chickpea plants, a crop with a complex architecture consisting of many small leaves and a highly branching structure. We hope that our use of open-source software and low-cost hardware will encourage others to use this promising technique for more architecturally complex species.

Vulnerability to cavitation in leaves is the result of highly adaptive anatomical and physiological traits that can be linked to water availability in a species’ climate of origin. Despite similar gross leaf morphology, eucalypt species are often confined to specific climate envelopes across the variable rainfall environments of Australia. In this study, we investigate how the progression of cavitation differs among eucalypts and whether this is related to other hydraulic and physical leaf traits. We used the Optical Visualisation technique to capture cavitation progression across the leaves of eight eucalypt species (Angophora crassifolia, Corymbia tessellaris, Eucalyptus atrata, Eucalyptus grandis, Eucalyptus laevopinea, Eucalyptus longifolia, Eucalyptus macrandra, Eucalyptus tereticornis) from a wide range of climates and grown in a common garden setting. Vulnerability to cavitation, represented by the leaf water potential required for 50% cavitation of leaf vessels, varied significantly among species (−3.48 MPa to −8.25 MPa) and correlated linearly with home climate precipitation and leaf SLA (R2 of 0.64 and 0.75, respectively). P12-P88, the range of water potentials between which 12% to 88% of cavitation occurs, was decoupled from P50 but also correlated with leaf SLA (R2 of 0.72). We suggest the magnitude of P12-P88 may be representative of a species’ drought strategy – a large P12-P88 signifying leaves that exhibit drought tolerance (retention of leaves under drought conditions) and a small P12-P88 signifying drought avoidance (leaf shedding after a threshold of drought is reached). Our results agree with other studies that highlight these cavitation metrics as genetically fixed traits. Turgor loss point, on the other hand, may be more plastic, as evidenced by the low variability of this trait across these eucalypt species grown in a common garden environment. Further study will help to establish the SLA-related anatomical traits that impart cavitation resistance and to extend these conclusions to a greater number of species and home climates.

Enhancing the photosynthetic induction response to fluctuating light has been suggested as a key target for improvement in crop breeding programmes, with the potential to substantially increase whole-canopy carbon assimilation and contribute to crop yield potential. Rubisco activation may be the main physiological process that will allow us to achieve such a goal. In this study, we assessed the phenotype of Rubisco activation rate in a doubled haploid (DH) barley mapping population [131 lines from a Yerong/Franklin (Y/F) cross] after a switch from moderate to saturating light. Rates of Rubisco activation were found to be highly variable across the mapping population, with a median activation rate of 0.1 min−1 in the slowest genotype and 0.74 min−1 in the fastest genotype. A unique quantitative trait locus (QTL) for Rubisco activation rate was identified on chromosome 7H. This is the first report on the identification of a QTL for Rubisco activation rate in planta and the discovery opens the door to marker-assisted breeding to improve whole-canopy photosynthesis of barley. This also suggests that genetic factors other than the previously characterized Rubisco activase (RCA) isoforms on chromosome 4H control Rubisco activity. Further strength is given to this finding as this QTL co-localized with QTLs identified for steady-state photosynthesis and stomatal conductance. Several other distinct QTLs were identified for these steady-state traits, with a common overlapping QTL on chromosome 2H, and distinct QTLs for photosynthesis and stomatal conductance identified on chromosomes 4H and 5H, respectively. Future work should aim to validate these QTLs under field conditions so that they can be used to aid plant breeding efforts., Speeding up the photosynthetic induction response to fluctuating light has been highlighted as a key target for crop improvement programmes. We identified significant variation in the photosynthetic induction response after a switch from moderate to saturating light across a barley doubled haploid population. A quantitative trait locus (QTL) for Rubisco activation rate was identified on chromosome 7H, as well as overlapping QTLs for steady-state photosynthesis and stomatal conductance. This is the first report on the identification of a QTL for Rubisco activation rate in planta and the discovery opens the door to marker-assisted breeding to improve whole-canopy photosynthesis of barley.

Suboptimal distribution of photosynthetic capacity in relation to light among leaves reduces potential whole-canopy photosynthesis. We quantified the degree of suboptimality in 160 genotypes of wheat by directly measuring photosynthetic capacity and daily irradiance in flag and penultimate leaves. Capacity per unit daily irradiance was systematically lower in flag than penultimate leaves in most genotypes, but the ratio (γ) of capacity per unit irradiance between flag and penultimate leaves varied widely across genotypes, from less than 0.5 to over 1.2. Variation in γ was most strongly associated with differences in photosynthetic capacity in penultimate leaves, rather than with flag leaf photosynthesis or canopy light penetration. Preliminary genome-wide association analysis identified nine strong marker-trait associations with this trait, which should be validated in future work in other environments and/or materials. Our modelling suggests canopy photosynthesis could be increased by up to 5 % under sunny conditions by harnessing this variation through selective breeding for increased γ., Plants invest nitrogen in photosynthetic enzymes in leaves. Although the optimal investment should be roughly proportional to how much light each leaf receives, plants tend to underinvest N in upper-canopy (sunlit) leaves. We examined, for the first time, whether this suboptimal pattern differs within species, by measuring light capture and photosynthetic capacity in flag and penultimate leaves across 160 wheat genotypes. We found wide variation in suboptimal N distribution, mostly driven by variation in plants’ ability to move N from penultimate to flag leaves as flag leaves develop. Selecting for less-suboptimal N distribution could increase canopy photosynthesis by several percent.

Enhancing the photosynthetic induction response to fluctuating light has been suggested as a key target for improvement in crop breeding programs, with the potential to substantially increase whole canopy carbon assimilation and contribute to crop yield potential. Rubisco activation may be the main physiological process that will allow us to achieve such a goal. In this study, we phenotypically assessed the rubisco activation rate in a doubled haploid (DH) barley mapping population [131 lines from a Yerong/Franklin (Y/F) cross] after a switch from moderate to saturating light. Rates of rubisco activation were found to be highly variable across the mapping population, with a median activation rate of 0.1 min−1 in the slowest genotype and 0.74 min−1 in the fastest genotype. A QTL for rubisco activation rate was identified on chromosome 7H. This is the first report on the identification of a QTL for rubisco activation rate in planta and the discovery opens the door to marker assisted breeding to improve whole canopy photosynthesis of barley. Further strength is given to this finding as this QTL colocalised with QTLs identified for steady state photosynthesis and stomatal conductance. Several other distinct QTLs were identified for these steady state traits, with a common overlapping QTL on chromosome 2H, and distinct QTLs for photosynthesis and stomatal conductance identified on chromosomes 4H and 5H respectively. Future work should aim to validate these QTLs under field conditions so that they can be used to aid plant breeding efforts.HighlightSignificant variation exists in the photosynthetic induction response after a switch from moderate to saturating light across a barley doubled haploid population. A QTL for rubisco activation rate was identified on chromosome 7H, as well as overlapping QTLs for steady state photosynthesis and stomatal conductance.

ABSTRCT Recent literature suggests a shifting paradigm in relation to photobiology associated with ultraviolet (UV) radiation. UV has been repeatedly shown to be less detrimental to plant performance than previously thought. Nonetheless, relatively few plant species have been studied; too few to make definitive statements about effects of UV on plants at the ecosystem scale. We present findings of a field-based study using natural solar radiation, coupled with UV screening films, to determine physiological costs and benefits of exposure to solar UV for three species representative of subalpine Australian flora: a tree (Eucalyptus pauciflora), a forb (Geranium antrorsum), and a grass (Poa hiemata). Photochemical and photosynthetic responses to UV exclusion varied among species; exposure to UV was of no consequence to the structure, chemistry, or incidence of photoinhibition for E. pauciflora. UV was effectively screened at the leaf surface of P. hiemata. The response of G. anstrorsum to UV exclusion sugges...

Variation in temperature (T) is usually accompanied by changes in leaf water potential (Ψleaf ), which may influence mesophyll conductance (gm ). However, the effects of Ψleaf on gm have not yet been considered in models of the gm response to temperature. Temperature responses of gm and Ψleaf and the response of gm to Ψleaf were studied in rice (Oryza sativa) and wheat (Triticum aestivum), and then an empirical model of Ψleaf was incorporated into an existing gm -T model. In wheat, Ψleaf was dramatically decreased with increasing T, whereas in rice Ψleaf was less sensitive or insensitive to T. Without taking Ψleaf into account, gm for wheat showed no response to T. However, at a given Ψleaf , gm was significantly higher at high temperature compared with low. After incorporating the function of Ψleaf into the gm -T model, we suggest that the gm -T relationship can be influenced by the activation and deactivation energy for membrane permeability, Ψleaf gradient between temperatures, and the sensitivity of gm to Ψleaf , below a threshold (Ψleaf,0 ). The data presented here suggest that Ψleaf plays an important role in the gm -T relationship and should be considered in future studies related to the temperature response of gm and photosynthesis.

Short AbstractDetailed instructions on how to build, calibrate and collect research quality data from PARbar ceptometers are presented.Long AbstractCeptometry is a technique used to measure the transmittance of photosynthetically active radiation through a plant canopy using multiple light sensors connected in parallel on a long bar. Ceptometry is often used to infer properties of canopy structure and light interception, notably leaf area index (LAI) and effective plant area index (PAIeff). Due to the high cost of commercially available ceptometers, the number of measurements that can be taken is often limited in space and time. This limits the usefulness of ceptometry for studying genetic variability in light interception, and precludes thorough analysis of, and correction for, biases that can skew measurements depending on the time of day. We developed continuously logging ceptometers (called PARbars) that can be produced for USD $75 each and yield high quality data comparable to commercially available alternatives. Here we provide detailed instruction on how to build and calibrate PARbars, how to deploy them in the field and how to estimate PAI from collected transmittance data. We provide representative results from wheat canopies and discuss further considerations that should be made when using PARbars.

Crop photosynthesis and yield are limited by slow photosynthetic induction in sunflecks. We quantified variation in induction kinetics across diverse genotypes of wheat for the first time. Following a preliminary study that hinted at wide variation in induction kinetics across 58 genotypes, we grew 10 genotypes with contrasting responses in a controlled environment and quantified induction kinetics of carboxylation capacity (Vcmax) from dynamic A versus ci curves after a shift from low to high light (from 50 µmol m–2 s–1 to 1500 µmol m–2 s–1), in five flag leaves per genotype. Within-genotype median time for 95% induction (t95) of Vcmax varied 1.8-fold, from 5.2 min to 9.5 min. Our simulations suggest that non-instantaneous induction reduces daily net carbon gain by up to 15%, and that breeding to speed up Vcmax induction in the slowest of our 10 genotypes to match that in the fastest genotype could increase daily net carbon gain by up to 3.4%, particularly for leaves in mid-canopy positions (cumulative leaf area index ≤1.5 m2 m–2), those that experience predominantly short-duration sunflecks, and those with high photosynthetic capacities., Significant variation exists in the induction time of photosynthesis following near-darkness to light transitions across wheat genotypes. Slow induction reduced daily carbon assimilation by up to 15%.

HighlightSignificant variation exists in the acclimation time of photosynthesis following dark-to-light transitions across wheat genotypes, under field and controlled conditions. Slow acclimation reduced daily carbon assimilation by up to 16%.AbstractCrop photosynthesis and yield are limited by slow photosynthetic induction in sunflecks. We quantified variation in induction kinetics across diverse genotypes of wheat for the first time. In a preliminary study using penultimate leaves of 58 genotypes grown in the field, we measured induction kinetics for maximum assimilation rate (Amax) after a shift from full darkness to saturating light (1700 μmol m−2 s−1) with 1-4 replicates per genotype. We then grew 10 of these genotypes with contrasting responses in a controlled environment and quantified induction kinetics of carboxylation capacity (Vcmax) from dynamic A vs ci curves after a shift from low to high light (50 to 1500 μmol m−2 s−1), with 5 replicates per genotype. Within-genotype median time for 95% induction (t95) varied from 8.4 to 23.7 min across genotypes for Amax in field-grown penultimate leaves, and from 6.7 to 10.4 min for Vcmaxin chamber-grown flag leaves. Our simulations suggested that non-instantaneous acclimation reduces daily net carbon gain by up to 16%, and that breeding to speed up Vcmax induction in the slowest genotype to match that in the fastest genotype could increase daily net carbon gain by more than 4%, particularly for leaves that experience predominantly short-duration sunflecks.

© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust In nonagricultural systems, the relationship between intrinsic water-use efficiency (WUEi) and leaf nitrogen (Narea) is known to be stronger for legumes than for nonlegumes. We tested whether these relationships are retained for major agricultural legumes and nonlegumes. We compared the response to N nutrition of WUEi(and its component parts, photosynthesis (Asat) and stomatal conductance (gs)) for legumes Cicer arietinum, Glycine max, Lupinus alba and Vicia faba, nonlegume dicots Brassica napus and Helianthus annus, and nonlegume cereals Hordeum vulgare and Triticum aestivum. Surprisingly, and in contrast to studied cereals and nonlegume dicots, Nareawas positively related to photosynthesis in the legumes, explaining nearly half of the variance in Asat. WUEiwas tightly coupled to Nareafor agricultural legumes and nonlegume dicots, but not for cereal crops. Our analysis suggests that breeding efforts to reduce gsin legumes could increase WUEiby 120–218% while maintaining Asatat nonlegume values. Physiologically informed breeding of legumes can enhance sustainable agriculture by reducing requirements for water and N.

Replacement of phospholipids with phosphorus (P)-free lipids in cellular membranes has been identified as a mechanism facilitating fast rates of photosynthesis when phosphorus availability is limited. We measured photosynthetic rates, leaf and soil P fractions, and foliar membrane lipid compositions for five species (Geranium antrorsum, Ranunculus graniticola, Poa costiniana, Poa hiemata, and Veronica derwentiana) common to two Australian subalpine ecosystems of contrasting parent material to characterize the extent to which they have adapted to long-term P availability. Our results indicate limited tolerance to reduced P, albeit adaptation strategies differ among species. Under reduced P conditions, phospholipids were replaced in foliage by galactolipids and sulfolipids, but photosynthesis was still impaired owing to reduced stomatal conductance. Accumulation of antioxidants, including carotenoids and alpha-tocopherol, in leaves with limited P supply suggests oxidative stress. Our field study shows that while subalpine Australian plants of a variety of life forms adapt to P availability by replacing phospholipids with P-free lipids in foliar membranes, this adaptation is insufficient to fully mitigate the effects of reduced P on photosynthesis.

BACKGROUND Pyrethroids are one of the most widespread and commonly used classes of insecticide and are used in multiple roles, including protecting potato crops from virus vector aphids. Resistance in some genotypes of a few species is now widespread, but most species remain susceptible. The rate of virus transmission by two genotypes of the peach potato aphid, Myzus persicae, fed on potato virus Y (PVY)-infected leaves of potato treated with the pyrethroid λ-cyhalothrin was evaluated. RESULTS The susceptible genotype, type J, was significantly inhibited from transmitting virus to uninfected seedlings. A genotype containing the M918L super knockdown resistance mutation conferring resistance to pyrethroids, type O, showed no inhibition of transmission. However, when survival of the aphids after exposure was compared, the pyrethroid had not killed the type J aphids. CONCLUSIONS λ-Cyhalothrin in a commercial formulation disrupts PVY transmission by disorienting aphid vectors for a sufficient time for the virus to lose its transmissibility. However, M. persicae genotypes carrying the M918L mutation are not prevented from transmitting. © 2014 Society of Chemical Industry

Pyrethroids are one of the most widespread and commonly used classes of insecticide and are used in multiple roles, including protecting potato crops from virus vector aphids. Resistance in some genotypes of a few species is now widespread, but most species remain susceptible. The rate of virus transmission by two genotypes of the peach potato aphid, Myzus persicae, fed on potato virus Y (PVY)-infected leaves of potato treated with the pyrethroid λ-cyhalothrin was evaluated.The susceptible genotype, type J, was significantly inhibited from transmitting virus to uninfected seedlings. A genotype containing the M918L super knockdown resistance mutation conferring resistance to pyrethroids, type O, showed no inhibition of transmission. However, when survival of the aphids after exposure was compared, the pyrethroid had not killed the type J aphids.λ-Cyhalothrin in a commercial formulation disrupts PVY transmission by disorienting aphid vectors for a sufficient time for the virus to lose its transmissibility. However, M. persicae genotypes carrying the M918L mutation are not prevented from transmitting.

TO DIFFERENTIATE the function of the adrenal cortex from that of the testis has been a main objective of various investigators interested in “androgens.” Recent studies by Heard (22) and Talbot (34) suggest that the excretion of non-ketonic steroids in the urine may afford important information toward this end. The major part of the extant literature on the subject, however, is concerned with 17-ketosteroids; and at this time it seems desirable to inquire how far this basic information can be applied in routine clinical and physiologic problems. Fundamental research by the Callows (6, 7), Marrian (4), Dobriner (10, 12, 13), Baumann (2), Talbot (35) and others have laboriously established the basis for such work. The painstaking isolation of crystalline steroids from the urine of individual mice or even from individual patients, however, is not an attractive prospect for the physiological investigator. Even the colorimetric procedures now available frequently involve tedious extraction procedures employing...

IN STUDIES of iodine metabolism, particularly those involving the blood and the thyroid, it is becoming important to work with small samples. This is especially true in observations on small animals; but in the clinic, e.g., in pediatric studies, it is also essential that blood “hormonal” iodine (Salter, 1940) be determined without drawing too much human blood. This paper describes a method which will give duplicate analyses on 2 cc. of serum, and is adapted to standard photoelectric colorimeters such as are available in many laboratories at the present time. It is now well established that human thyroid function can be easured satisfactorily by serum iodine analysis, even when the serum is transmitted long distances in simple containers (Salter, Bassett and Sappington, 1941; Riggs, Gildea, Man and Peters, 1941). Normally the concentration of the “hormonal” iodine is approximately 5 micrograms per cent, or 0.05 micrograms per cc. in man.

In the preceding paper (1), we described a method whereby the amylolytic activity of mouse sarcoma could be measured. It is the purpose of this paper to present the results of experiments performed upon mice in an attempt to alter the amylolytic activity of such tumors. This activity is expressed in terms of an α-value, the significance of which has been discussed in the previous paper. Possible Factors Affecting Amylolytic Activityof Sarcoma The α-value for amylase in tumors carried by inbred mice was fairly constant, the usual variation being between 9 and 13 per gram of tumor. Occasionally a single tumor with no obvious gross pathological difference from the others would be as low as 6 or as high as 15. The age of the tumor and the rapidity of its growth (the latter probably dependent to some degree on the size of the original implant) had some bearing on the glycogenolytic activity. In general, the older the tumor and the slower its growth, the higher was its α-value. The actual figures may be seen in the control groups presented in Tables I and II. In consequence of these variations, every experiment had its own controls, with mice of approximately the same age, kept under identical conditions, and with tumors of similar size which had been inoculated at the same time as those of the experimental animals. The tumors were all from eighteen to twenty-eight days old when used.

REPEATED STUDY has shown that the blood iodine in hyperthyroid-ism tends to be abnormally high (Salter, 1944). Furthermore the “organic” or “hormonal” iodine accounts for most of the increase (Bassett, Coons and Salter, 1941). This finding suggests that the cir-culation contains an excess of a physiologically active iodine com-pound. It is the purpose of this communication to show that such blood can increase the respiration of surviving tissues. The time factor looms large in experimental attempts to demon-strate such stimulation of metabolism in vitro. Thus Davis and Has-tings (1936), using the heart of Limulus polyphemus, obtained an elevation of respiration only after 10 to 15 hours’ exposure to thyroxine in vitro. Hopping Scott (1935), however, reported in some instances a prompt increase in oxygen consumption by the nucleated red cells of alligator blood when thyroxine was added in vitro. In the present communication emphasis will be laid upon the prompt respiratory response of mammalian tissues (wh...

The significance of the protein constituents of muscle for the contractile process has long been recognized. The instability of these bodies, however, has rendered difficult their characterization. Danilewsky1 described the extraction of muscle protein with sal ammoniac in 1881. The older method of expression, despite rigid precautions, often led to “denaturation” or “clotting of muscle plasma.” The properties of muscle globulin, as of other globulins, are altered both by too low salinity and by too high acidity.2 Howe3 has employed phosphate buffers as solvents to overcome these difficulties. In the present investigation an ammonium chloride solution, rendered alkaline by excess of ammonia, was used as solvent and yielded solutions of muscle protein which, for several months, retained solubility in neutral salt solutions.A globulin-like fraction of ox muscle protein was studied, which presumably corresponded to the “myosin” of von Furth4 and the “paramyosinogen” of Halliburton.5 The method of preparation...

ACHIEF function of the thyroid gland is to convert inorganic iodine (iodide) to a state of higher oxidation, equivalent to elementary iodine. When various animal proteins, except gelatine which is nearly devoid of tyrosine, are treated with elementary iodine, thyroxine is formed in vitro. In myxedema, the patient's own serum when combined with iodine (1) (2) will restore his health; whereas sodium iodide usually will not. A more striking demonstration is the relief of myxedema by the parenteral administration of elementary iodine (3) (4). The higher state of oxidation allows iodine to form the essential organic iodine complex (5) present in all tissues (“thyrenzyme,” so-called). As this is degraded in the course of metabolism, it reverts to the inorganic form. Therefore, in broad terms, a large section of thyroid physiology may be described as the reciprocal metabolism of organic versus inorganic iodine. It is the purpose of this communication to report observations on the mutual interconversion of organi...

DURING the last fifteen years estimations of the urinary excretion of 17-ketosteroids and androgens have been made in a variety of clinical disturbances with the hope that they might give some indication of the functional status of the testis and the suprarenal cortex (1, 2, 3, 4). The question of the relative significance of biologic assay for androgens and chemical analysis for 17–ketosteroids, when applied to suitably prepared urine extracts, has been raised repeatedly. It is the primary purpose of this paper to compare, in several distinct clinical syndromes, the results obtained by the two methods with the same urine extracts. We were particularly interested to learn whether the decreased urinary 17–ketosteroid excretion in gynecomastia previously observed by Salter, Klatskin and Humm (5) would be reflected in lower excretion of androgens also. EXPERIMENTAL PLAN Three groups were selected among male patients who might be expected to exhibit evidence of androgenic disturbance. In addition, a group of ...