New PhotosynQ Related Publication

Check out the new publication in Nature Communications Biology, using the MultispeQ and PhotosynQ Platform (10.1038/s42003-019-0561-9)

Overexpression of the Rieske FeS protein of the Cytochrome b6f complex increases C4 photosynthesis in Setaria viridis.

Maria Ermakova, Patricia E. Lopez-Calcagno, Christine A. Raines, Robert T. Furbank & Susanne von Caemmerer

C4 photosynthesis is characterized by a CO2 concentrating mechanism that operates between mesophyll and bundle sheath cells increasing CO2 partial pressure at the site of Rubisco and photosynthetic efficiency. Electron transport chains in both cell types supply ATP and NADPH for C4 photosynthesis. Cytochrome b6f is a key control point of electron transport in C3 plants. To study whether C4 photosynthesis is limited by electron transport we constitutively overexpressed the Rieske FeS subunit in Setaria viridis. This resulted in a higher Cytochrome b6f content in mesophyll and bundle sheath cells without marked changes in the abundances of other photosynthetic proteins. Rieske overexpression plants showed better light conversion efficiency in both Photosystems and could generate higher proton-motive force across the thylakoid membrane underpinning an increase in CO2 assimilation rate at ambient and saturating CO2 and high light. Our results demonstrate that removing electron transport limitations can increase C4 photosynthesis.

More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in The Plant Journal, using the MultispeQ and PhotosynQ Platform (10.1111/tpj.14190)

Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency.

Roel F. H. M. van Bezouw, Joost J. B. Keurentjes, Jeremy Harbinson, Mark G. M. Aarts

In recent years developments in plant phenomic approaches and facilities have gradually caught up with genomic approaches. An opportunity lies ahead to dissect complex, quantitative traits when both genotype and phenotype can be assessed at a high level of detail. This is especially true for the study of natural variation in photosynthetic efficiency, for which forward genetics studies have yielded only a little progress in our understanding of the genetic layout of the trait. High‐throughput phenotyping, primarily from chlorophyll fluorescence imaging, should help to dissect the genetics of photosynthesis at the different levels of both plant physiology and development. Specific emphasis should be directed towards understanding the acclimation of the photosynthetic machinery in fluctuating environments, which may be crucial for the identification of genetic variation for relevant traits in food crops. Facilities should preferably be designed to accommodate phenotyping of photosynthesis‐related traits in such environments. The use of forward genetics to study the genetic architecture of photosynthesis is likely to lead to the discovery of novel traits and/or genes that may be targeted in breeding or bio‐engineering approaches to improve crop photosynthetic efficiency. In the near future, big data approaches will play a pivotal role in data processing and streamlining the phenotype‐to‐gene identification pipeline.

More PhotosynQ related publications are available here

PhotosynQ Workshop Recap

On Tuesday April, 30th 2019 the first annual PhotosynQ workshop was held in East Lansing, MI. We would like to thank all the attendees for joining us, for their feedback, participation and making this day a success! It helped us tremendously, understanding what the needs of our community are and how we can support them. Thank you for your support!

After a short welcome, Prabode Weebadde presented how PhotosynQ has developed over the years and announced new products. The PhotosynQ Academic Subscription for the PhotosynQ platform, allowing Projects to be private, as well as CaliQ, a device to calibrate the MultispeQ’s PAR (Photosynthetically Active Radiation) sensor. Both will be available in Q3 this year. He also presented PhotosynQ Enterprise, a separate cloud instance of the PhotosynQ platform, helping enterprises to keep their data private.

Prabode announcing new products coming in Q3
Prabode announcing new products coming in Q3


Following the introduction, David Kramer presented an overview of possible use cases and how to use the PhotosynQ platform. Further, he gave an introduction into photosynthesis and the most important photosynthetic parameters that can be measured using the MultispeQ v2.0. Another important part of his presentation was on how to avoid bias when planning and collecting field data.

Dave presenting on comparing experimental approaches
Dave presenting on comparing experimental approaches


After that, Sebastian Kuhlgert gave an overview on how to set up a Project using the PhotosynQ platform. The focus was on how to use the MultispeQ in combination with the mobile application to collect measurements successfully together with meta data that can be used to analyze the subsequent dataset more efficiently. He also presented on some of the experiences reported from users who have already collected large amounts of data in the field.

Next, David Kramer started a hands on Project, that allowed all attendees to collect data comparing cowpea plants (Vigna unguiculata) grown in low or bright light. After the data was collected in groups, the analysis tools were presented, doing a “live” data analysis of the data that had just been collected.

Hands on, taking measurements with the MultispeQ for a test Project and subsequent analysis
“Hands on”, taking measurements with the MultispeQ for a test Project and subsequent analysis


In the afternoon, the attendees were able to gain a more detailed look into how to create protocols and macros to take measurements, analyzing collected data and on how MultispeQs are calibrated.

Sebastian explaining on how to create protocols for the MultispeQ and build a macro to analyze the data coming from the instrument
Sebastian explaining how to create protocols for the MultispeQ and build a macro to analyze the data coming from the instrument


During the last session, Isaac Osei-Bonsu, who collected more than 40,000 measurements at this point, was presenting datasets he had collected using the MultispeQ in combination with the PhotosynQ platform and a new method to account for collection bias he is developing to analyze his massive dataset.

We hope we were able to give insights into how the PhotosynQ platform can accelerate your research and how versatile and flexible it is, when it comes to data collection and analysis. The workshop was intended to be as interactive as possible and we would like to thank all the attendees for their questions and participation!

Feedback from the Workshop

When planning the workshop we wanted to offer a very broad program, that would touch topics that are relevant to experienced as well as inexperienced users and we hope we were able to accomplish that. We would like to thank everyone for giving us such positive feedback as well as providing ideas and requests when it comes to improving the workshop. The most frequent ones are listed below. Please feel free to contact us, if you have more ideas and suggestions.

  1. More insights into how to data analysis, statistical analysis and removing bias from data collection
  2. More details on the theory behind measurements, how to read them and how the instrument works
  3. More training on taking measurements and using the instrument, more time in general

Impressions from the Workshop

All Photos by Annie Barker

New PhotosynQ Related Publication

Check out the new publication in the journal Crop Science, using the MultispeQ and PhotosynQ Platform (10.2135/cropsci2018.04.0275)

Screening for Heat Tolerance in Phaseolus spp. Using Multiple Methods.

Jesse Traub, Timothy Porch, Muhammad Naeem, Carlos A. Urrea, Greg Austic, James D. Kelly and Wayne Loescher

Common bean (Phaseolus vulgaris L.) is a nutritious crop grown around the world, a staple that provides high levels of protein and iron in the diets of Central and South Americans and East Africans. Heat stress negatively affects common bean seed yields and prevents cultivation in certain areas. Furthermore, under field conditions, heat stress often coincides with and exacerbates drought stress effects. Breeding more heat-tolerant cultivars would stabilize seed yield and open new regions to field production. To support these efforts, we examined a variety of methods for screening large numbers of bean germplasm exposed to heat stress at the vegetative growth stage as opposed to the reproductive stage, which would prolong the screening process. Tepary bean (P. acutifolius A. Gray), a closely related species to common bean, was used as a heat-stress-tolerant check. Plants exposed to day/night temperatures of 45/36°C for 2 d showed measurable signs of heat stress, but tepary bean outperformed the common beans on all stress tolerance measures. Gas exchange, chlorophyll fluorescence, and oxidative stress were only affected by this high temperature and not by temperatures below 45/36°C. Heat stress measurements also correlated well with visual signs of leaf tissue damage. Gradually raising temperatures was useful for screening large number of entries for heat tolerance, but this heat tolerance was only partially related to drought tolerance in the field. Plant breeders can use some of these methods to supplement field data and to further characterize the stress tolerance of bean lines.

More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in the journal Planta, using the MultispeQ and PhotosynQ Platform (10.1007/s00425-018-3014-7)

DOTAP, a lipidic transfection reagent, triggers Arabidopsis plant defense responses

Carolina Grandellis, Betiana S. Garavaglia, Natalia Gottig, Caroline Lonez, Jean-Marie Ruysschaert, Jorgelina Ottado

DOTAP is a cationic lipid widely used as a liposomal transfection reagent and it has recently been identified as a strong activator of the innate immune system in animal cells. Plants are sessile organisms and unlike mammals, that have innate and acquired immunity, plants possess only innate immunity. A key feature of plant immunity is the ability to sense potentially dangerous signals, as it is the case for microbe-associated, pathogen-associated or damage-associated molecular patterns and by doing so, trigger an active defense response to cope with the perturbing stimulus. Here, we evaluated the effect of DOTAP in plant basal innate immunity. An initial plant defense response was induced by the cationic lipid DOTAP in the model plant Arabidopsis thaliana, assessed by callose deposition, reactive oxygen species production, and plant cell death. In addition, a proteomic analysis revealed that these responses are mirrored by changes in the plant proteome, such as up-regulation of proteins related to defense responses, including proteins involved in photorespiration, cysteine and oxylipin synthesis, and oxidative stress response; and down-regulation of enzymes related to photosynthesis. Furthermore, DOTAP was able to prime the defense response for later pathogenic challenges as in the case of the virulent bacterial pathogen Pseudomonas syringae pv. tomato. Disease outcome was diminished in DOTAP-pre-treated leaves and bacterial growth was reduced 100 times compared to mock leaves. Therefore, DOTAP may be considered a good candidate as an elicitor for the study of plant immunity.

More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in the journal Front. Plant Sci., using the MultispeQ and PhotosynQ Platform (10.3389/fpls.2018.00767)

Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.)

Soltani A, MafiMoghaddam S, Oladzad-Abbasabadi A, Walter K, Kearns PJ, Vasquez-Guzman J, Mamidi S, Lee R, Shade AL, Jacobs JL, Chilivers MI, Lowry DB, McClean P and Osorno JM

Climate change models predict temporal and spatial shifts in precipitation resulting in more frequent incidents of flooding, particularly in regions with poor soil drainage. In these flooding conditions, crop losses are inevitable due to exposure of plants to hypoxia and the spread of root rot diseases. Improving the tolerance of bean cultivars to flooding is crucial to minimize crop losses. In this experiment, we evaluated the phenotypic responses of 277 genotypes from the Andean Diversity Panel to flooding at germination and seedling stages. A randomized complete block design, with a split plot arrangement, was employed for phenotyping germination rate, total weight, shoot weight, root weight, hypocotyl length, SPAD index, adventitious root rate, and survival score. A subset of genotypes (n = 20) were further evaluated under field conditions to assess correlations between field and greenhouse data and to identify the most tolerant genotypes. A genome-wide association study (GWAS) was performed using ~203 K SNP markers to understand the genetic architecture of flooding tolerance in this panel. Survival scores between field and greenhouse data were significantly correlated (r = 0.55, P = 0.01). Subsequently, a subset of the most tolerant and susceptible genotypes were evaluated under pathogenic Pythium spp. pressure. This experiment revealed a potential link between flooding tolerance and Pythium spp. resistance. Several tolerant genotypes were identified that could be used as donor parents in breeding pipelines, especially ADP-429 and ADP-604. Based on the population structure analysis, a subpopulation consisting of 20 genotypes from the Middle American gene pool was detected that also possessed the highest root weight, hypocotyl length, and adventitious root development under flooding conditions. Genomic regions associated with flooding tolerance were identified including a region on Pv08/3.2 Mb, which is associated with germination rate and resides in vicinity of SnRK1.1, a central gene involved in response of plants to hypoxia. Furthermore, a QTL at Pv07/4.7 Mb was detected that controls survival score of seedlings under flooding conditions. The association of these QTL with the survivability traits including germination rate and survival score, indicates that these loci can be used in marker-assisted selection breeding to improve flooding tolerance in the Andean germplasm.

More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in the Biocontrol Science and Technology, using the MultispeQ and PhotosynQ Platform (10.1080/09583157.2017.1376035)

Genotype-specific responses to the effects of commercial Trichoderma formulations in lentil (Lens culinaris ssp. culinaris) in the presence and absence of the oomycete pathogen Aphanomyces euteiches

Pratibha Prashar & Albert Vandenberg

Members of the endophytic fungal genus Trichoderma have been established as plant-beneficial microbes and are most successful commercial biologicals in the form of bio-fertilisers, biocontrol agents, and growth stimulators. We report the variable interactions among different lentil genotypes and Trichoderma strains in both the presence and absence of biotic stress (root-rot pathogen Aphanomyces euteiches). Two commercial Trichoderma formulations, namely RootShield® (RS) and RootShield® Plus (RSP) based on T. harzianum T22 and T. virens G41, respectively, were evaluated for control of Aphanomyces root rot and plant growth promotion in 23 wild and cultivated lentil genotypes. No significant disease control was recorded with either formulation in any lentil genotype. Significant genotype-specific plant growth promotion was observed in terms of root and shoot development and leaf parameters in a genotype-specific manner. Genotypes of Lens culinaris and Lens tomentosus, both in the primary lentil gene pool, demonstrated the maximum response. The overall effect of Trichoderma treatment was markedly higher under biotically stressed conditions in comparison to unstressed conditions. In many cases, negative responses were recorded, particularly in the absence of root-rot disease. L. tomentosus PI 572390 exhibited positive responses for most of the tested parameters. Our findings clearly indicate that, in the case of lentil, plant genotype plays a major role in interactions among the tested Trichoderma strains and the plant. Moreover, the influence of Trichoderma was greater and more favourable under conditions of biotic stress vs. the absence of stress.

More PhotosynQ related publications are available here