New PhotosynQ Related Publication

Check out the new publication in the Journal of Plant Breeding and Crop Sciences, using the MultispeQ and PhotosynQ Platform (10.5897/JPBCS2017.0679 )

Evaluation of Cowpea Genotypes for Resistance to Fusarium redolens in Uganda

Namasaka Roy Wanjala, Geoffrey Tusiime, Orawu Martin, Paul Gibson, Symphorien Agbahoungba, Alladassi Mahule Elyse Boris, Richard Edema

Fusarium related root rots have been associated with reduced cowpea productivity in Uganda. Sources of genetic resistance to Fusarium redolens which was found to be the most virulent have been identified but the mode of inheritance of the genes conferring the resistance is unknown. This study aims to investigate how the genes for resistance to F. redolens are inherited in cowpea. Four F. redolens root rot resistant cowpea genotypes were crossed with four intermediately resistant and 2 susceptible cowpea genotypes using North Carolina mating design II. The F1 and the parents were evaluated and data were collected on resistance to seed rot, leaf chlorophyll amount, produced lateral roots, response to plant mortality and root rot severity. Results revealed that additive gene effects were significant for all evaluated traits and non-additive genetic effects were significant in resistance to seed rot and chlorophyll amount. General combining ability (GCA) effects showed that the Asontem genotype was a good combiner for increased lateral roots production and resistance to root rot. Degree of dominance estimates revealed that response to plant mortality, root rots and increased lateral root production traits were recessively inherited while seed rot and amount of leaf chlorophyll were dominantly inherited.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in Photosynthesis Research, using the MultispeQ and PhotosynQ Platform (10.1007/s11120-017-0449-9)

Faster photosynthetic induction in tobacco by expressing cyanobacterial flavodiiron proteins in chloroplasts

Rodrigo Gómez, Néstor Carrillo, María P. Morelli, Suresh Tula, Fahimeh Shahinnia, Mohammad-Reza Hajirezaei, Anabella F. Lodeyro

Plants grown in the field experience sharp changes in irradiation due to shading effects caused by clouds, other leaves, etc. The excess of absorbed light energy is dissipated by a number of mechanisms including cyclic electron transport, photorespiration, and Mehler-type reactions. This protection is essential for survival but decreases photosynthetic efficiency. All phototrophs except angiosperms harbor flavodiiron proteins (Flvs) which relieve the excess of excitation energy on the photosynthetic electron transport chain by reducing oxygen directly to water. Introduction of cyanobacterial Flv1/Flv3 in tobacco chloroplasts resulted in transgenic plants that showed similar photosynthetic performance under steady-state illumination, but displayed faster recovery of various photosynthetic parameters, including electron transport and non-photochemical quenching during dark–light transitions. They also kept the electron transport chain in a more oxidized state and enhanced the proton motive force of dark-adapted leaves. The results indicate that, by acting as electron sinks during light transitions, Flvs contribute to increase photosynthesis protection and efficiency under changing environmental conditions as those found by plants in the field.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in Plant Physiology, using the MultispeQ and PhotosynQ Platform (10.1104/pp.17.01624)

The Impacts of Phosphorus Deficiency on the Photosynthetic Electron Transport Chain

Andreas Carstensen, Andrei Herdean, Sidsel Birkelund Schmidt, Anurag Sharma, Cornelia Spetea, Mathias Pribil, Søren Husted

Phosphorus (P) is an essential macronutrient, and P deficiency limits plant productivity. Recent work showed that P deficiency affects electron transport to photosystem I (PSI), but the underlying mechanisms are unknown. Here, we present a comprehensive biological model describing how P deficiency disrupts the photosynthetic machinery and the electron transport chain through a series of sequential events in barley (Hordeum vulgare). P deficiency reduces the orthophosphate concentration in the chloroplast stroma to levels that inhibit ATP synthase activity. Consequently, protons accumulate in the thylakoids and cause lumen acidification, which inhibits linear electron flow. Limited plastoquinol oxidation retards electron transport to the cytochrome b6f complex, yet the electron transfer rate of PSI is increased under steady-state growth light and is limited under high-light conditions. Under P deficiency, the enhanced electron flow through PSI increases the levels of NADPH, whereas ATP production remains restricted and, hence, reduces CO2 fixation. In parallel, lumen acidification activates the energy-dependent quenching component of the nonphotochemical quenching mechanism and prevents the overexcitation of photosystem II and damage to the leaf tissue. Consequently, plants can be severely affected by P deficiency for weeks without displaying any visual leaf symptoms. All of the processes in the photosynthetic machinery influenced by P deficiency appear to be fully reversible and can be restored in less than 60 min after resupply of orthophosphate to the leaf tissue.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

 

Check out the new publication in the American Journal of Plant Sciences, using the MultispeQ and PhotosynQ Platform (10.4236/ajps.2017.89154)

Evaluation of Cowpea Genotypes for Resistance to Fusarium redolens in Uganda

Roy Wanjala Namasaka, Geoffrey Tusiime, Martin Orawu, Paul Gibson, Josiane Nyiramugisha, Richard Edema

Fusarium redolens, a virulent fungus which causes damping off, leaf yellowing, wilting and root rots has recently been devastating cowpea fields in Uganda. This study aimed at identifying cowpea genotypes that are resistant to Fusarium redolens. Therefore, ninety cowpea genotypes were evaluated two times against a highly virulent Fusarium redolens (isolate from Zombo in Paidha district) in the screen house in 2016. Genotype effect was highly significant (P < 0.001) for root rot severity. Based on the Index of Susceptibility (IS), three genotypes (Asontem, Dan1 LA and IT89KD-88) remained resistant (IS < 3.5) over the two screening periods, 72 moderately resistant (3.5 ≤ IS < 6.5) and 11 susceptible (IS ≥ 6.5). Resistance was found to be enhanced by presence of lateral roots above or at the ground level. Further results suggested a difference in genetic control of resistance to root rots and seed rots caused by Fusarium redolens. All the released varieties tested (SECOW 1 T, SECOW 2 W, SECOW 3 B, SECOW 4 W and SECOW 5 T) had moderate resistance to Fusarium redolens. Correlation analysis revealed root rot severity was strongly correlated to disease incidence (+0.64, P < 0.001), to proportion of plants with lateral roots (−0.56, P < 0.001), to amount of leaf chlorophyll (−0.53, P < 0.001) and to proportion of plants that died prematurely due to Fusarium redolens infection (+0.45, P < 0.001). No significant correlation was detected between root rot severity and proportion of plants that germinated. The established resistance could be exploited for improvement of farmer preferred cowpea varieties towards Fusarium redolens resistance in Uganda.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in Physiologia Planatarum, using the MultispeQ and PhotosynQ Platform (10.1111/ppl.12689)

Chlorophyll fluorescence imaging reveals genetic variation and loci for a photosynthetic trait in diploid potato

Aina E. Prinzenberg, Marcela Víquez-Zamora, Jeremy Harbinson, Pim Lindhout, Sjaak van Heusden

Physiology and genetics are tightly interrelated. Understanding the genetic basis of a physiological trait such as the quantum yield of the photosystem II, or photosynthetic responses to environmental changes will benefit the understanding of these processes. By means of chlorophyll fluorescence imaging “CF”, the quantum yield of photosystem II can be determined rapidly, precisely and non-invasively. In this article, the genetic control and variation in the steady-state quantum yield of PSII “ΦPSII” is analysed for diploid potato plants. Current progress in potato research and breeding is slow due to high levels of heterozygosity and complexity of tetraploid genetics. Diploid potatoes offer the possibility of overcoming this problem and advance research for one of the globally most important staple foods. With the help of a diploid genetic mapping population two genetic loci that were strongly associated with differences in ΦPSII were identified. This is a proof of principle that genetic analysis for ΦPSII can be done on potato. The effects of three different stress conditions that are important in potato cultivation were also tested: salt stress, low temperature and deficiency in the macronutrient phosphate. For the last two stresses, significant decreases in photosynthetic activity could be shown, revealing potential for stress detection with CF based tools. In general, our findings show the potential of high-throughput phenotyping for physiological research and breeding in potato.


More PhotosynQ related publications are available here

User Page | PhotosynQ Website

User Page | Website Update

We are working on making your user page the central hub for all the information regarding your work with PhotosynQ.

We have found that one of the most useful features for any PhotosynQ project is the Dashboard, which allows you to quickly view important project results on one page.

We are currently using the same approach to allow users to have a personal dashboard that makes all of their PhotosynQ information (e.g. projects, protocols, macro’s etc) available in one place.

If you haven’t visited your user page recently, you should try it now, we think you’ll be pleasantly surprised! To get there, click on your name in the top right hand corner of the PhotosynQ webpage, this leads to your user page.

Over the past couple of months we have made a number of changes to this page that should really help you navigate through your PhotosynQ projects and collaborations.

user page image

Recent Activity

This change has been around for a while, but if you haven’t been checking in you may have missed it. We have now added your most recent projects, collaborations and comments to your user homepage. This should help you navigate quickly to your most active projects, instead of always going through the PhotosynQ search bar.

Side Menu

The side menu now contains a link to the instrument page (see below), your invitations, and the last two updates posted on PhotosynQ.

About – Contributions

We replaced the bar chart showing your contributions over the past year and doughnut chart with a calendar histogram. This view will provide more details about when and how many contributions you made over the last year.

Contributions over the last 12 months, shown as a calendar heat map.
Contributions over the last 12 months, shown as a calendar heat map.

Protocols & Macros

Do you make any of your own protocols and macros? If you do, now you can see all of your protocols and macros, sorted alphabetically and by their category, right from your user page.

Instruments

Now you can see all the instruments you have used in the past. It will show some basic information, based on the last measurement, including the firmware version, the total number of contributions (you and others, if you borrowed/lent the instrument) and the last time the instrument was seen (based on the latest submitted measurement).

Basic information panel for an instrument
Basic information panel for an instrument

If you have questions or need support, please check our forum or send us an email to support@photosynq.org.

New Data Selection & Plotting | Website Update

Data Selection & Plotting | Website Update

This is just a small update to the data viewing tool on https://photosynq.org, but we think, it will be very helpful for your data analysis.

Data Selection

Plots

With switching the plotting library to Plotly we introduced selecting a series by using the lasso tool or box selection tool to generate a new series, instead of using the filters (Goodbye Flot, Hello Plotly | Other Website Updates). Now you can also use the inverse of a selection as a new series or generate both at the same time. Just check the appropriate box in the dialog before you create a new series or download selection.

The new selection dialog allows you to not only select a range of markers as a new series, but also the inverse of your selection or even both as new series.
The new selection dialog allows you to not only select a range of markers as a new series, but also the inverse of your selection or even both as new series.

Map

Now you can also generate a new series by drawing a rectangle or a polygon around markers on the map. When viewing graphs you can use the selection tools to create new series of data selected, or the inverse.

Select a group of markers by dragging a rectangle or polygon to create a new series (buttons in the center top). Similar to the plot, the map as well allows you to use the selection, the inverse selection or both as new series.
Select a group of markers by dragging a rectangle or polygon to create a new series (buttons in the center top). Similar to the plot, the map allows you to use the selection, the inverse selection or both as new series.

Dashboard

A new panel is available, which lists all the Data Quality Issues, which were found in your project, listing each issue with a count of affected measurements. You can now generate a series containing these measurements for an easier screening and potential flagging.

Plotting

What’s in my selection?

When you are working with a scatter plot and you are using a color gradient as a third dimension, it might be hard to tell, if for example, a certain crop variety is enriched in your selection. Now you can use the Enrichment feature to plot fractions of a category for each series.

Just select the bar-graph tab, check Enrichment and choose a category. The bar-graph will display the fractions as to the following selections:

  • category / series Will show the fraction of category appearances in each series compared to the total appearances in each series.
  • category / total Will show the fraction of category appearances in each series compared to the total appearances.

2D Heat-Map

The 2D Heat-Map will now adjust based on the selected series and not only show the map for all all series combined.


Spreadsheet

If you save photos along with your measurements, no matter if it is a project question or if you take them as notes, inside the spreadsheet you see a small image icon. When you hover over the icon, you will see the picture instead on top of your list of series. The same is true for long arrays of numbers. Instead of those, you now see a chart icon and hovering over it, will bring up a line graph.

Copying the data still works the same. You will get all the data or the link to the picture.

The “ID” and “Series” columns are now sticky and will stay visible when scrolling vertically in the table.

Statistics: Chi Square Test

We added another statistical test, the Chi Square test. This allows you to compare categorical data.

Dashboard

The functionality of the dashboard got extended a little bit. The graphs you save to the dashboard are now images, so you can simply save them to you hard-drive.

Hiding Advanced Parameters

As I am sure you’ve noticed by now, we at PhotosynQ like to provide you with a lot of data. Not just the primary parameters (e.g. Phi2, PhiNPQ, Light Intensity (PAR), time, etc) that you are interested in, but also many other parameters that may go into calculating those parameters. However, viewing all of this data in the plotting tool or spreadsheet view may be a bit much for some users.

We have now added a feature that allows users to decide whether or not they want to view the primary parameters and Project questions together with the Advanced parameters (e.g. absorbance_420, FvP_over_FmP, etc) or if they would prefer to hide the advanced parameters. The new default setting is to hide the advance parameters. If you want to view these parameters, select the settings icon near the Add Series and click the Show Advanced Parameters checkbox. Now all of the parameters output by the MultispeQ will be available in the Plot Data, Spreadsheet, Map and Statistics tabs.

Advanced data

If you have questions or need support, please check our forum or send us an email to support@photosynq.org.