More eyes on the prize: open-source data, software and hardware for advancing plant science through collaboration

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.

Open source 3D phenotyping of chickpea plant architecture across plant development

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 < 10%. We demonstrate the ability to assess several important architectural traits, including canopy volume and projected area, and estimate relative growth rate in commercial chickpea cultivars and lines from local and international breeding collections. Detailed analysis of individual reconstructions also allowed us to investigate partitioning of plant surface area, and by proxy plant biomass.

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.

Identification of quantitative trait loci for dynamic and steady-state photosynthetic traits in a barley mapping population

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.

Wide variation in the suboptimal distribution of photosynthetic capacity in relation to light across genotypes of wheat

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.

The role of leaf water potential in the temperature response of mesophyll conductance

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

Rate of photosynthetic induction in fluctuating light varies widely among genotypes of wheat

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.

PARbars: Cheap, Easy to Build Ceptometers for Continuous Measurement of Light Interception in Plant Canopies

Ceptometry 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.

A multiplexed gas exchange system for increased throughput of photosynthetic capacity measurements

BACKGROUND

Existing methods for directly measuring photosynthetic capacity (Amax) have low throughput, which creates a key bottleneck for pre-breeding and ecological research. Currently available commercial leaf gas exchange systems are not designed to maximize throughput, on either a cost or time basis.

RESULTS

We present a novel multiplexed semi-portable gas exchange system, OCTOflux, that can measure Amax with approximately 4-7 times the throughput of commercial devices, despite a lower capital cost. The main time efficiency arises from having eight leaves simultaneously acclimate to saturating CO2 and high light levels; the long acclimation periods for each leaf (13.8 min on average in this study) thus overlap to a large degree, rather than occurring sequentially. The cost efficiency arises partly from custom-building the system and thus avoiding commercial costs like distribution, marketing and profit, and partly from optimizing the system's design for Amax throughput rather than flexibility for other types of measurements.

CONCLUSION

Throughput for Amax measurements can be increased greatly, on both a cost and time basis, by multiplexing gas streams from several leaf chambers connected to a single gas analyzer. This can help overcome the bottleneck in breeding and ecological research posed by limited phenotyping throughput for Amax.

Contrasting responses of crop legumes and cereals to nitrogen availability

In nonagricultural systems, the relationship between intrinsic water-use efficiency (WUE_i ) and leaf nitrogen (N_area ) 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 WUE_i (and its component parts, photosynthesis (A_sat ) and stomatal conductance (g_s )) 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, N_area was positively related to photosynthesis in the legumes, explaining nearly half of the variance in A_sat . WUE_i was tightly coupled to N_area for agricultural legumes and nonlegume dicots, but not for cereal crops. Our analysis suggests that breeding efforts to reduce g_s in legumes could increase WUE_i by 120-218% while maintaining A_sat at nonlegume values. Physiologically informed breeding of legumes can enhance sustainable agriculture by reducing requirements for water and N.

Stopped in its tracks: how λ-cyhalothrin can break the aphid transmission of a potato potyvirus

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.