The authors would like to thank Dr. Richard Richards and Dr. Shek Hossain at CSIRO, Agriculture, and Food for access to and management of the field plots used for this research. This research was supported by the International Wheat Yield Partnership, through a grant provided by the Grains Research and Development Corporation (US00082). TNB was supported by the Australian Research Council (DP150103863 and LP130100183) and the National Science Foundation (Award #1557906). This work was supported by the USDA National Institute of Food and Agriculture, Hatch projects 1016439 and 1001480.

1. Build and calibrate the PARbars
<ol>
	<li>Gather all parts and tools required for the assembly in a clean workspace.</li>
	<li>Drill a 4 mm diameter hole 20 mm from each end of a white acrylic diffuser bar (1,200 mm length x 30 mm width x 4.5 mm thickness). Drill and tap threaded holes 20 mm from each end of a section of aluminum U-bar to secure diffuser. Drill and tap threaded holes to suit mounting hardware (e.g., a tripod mounting plate).</li>
	<li>Obtain a 1.25 m length of bare copper wire (1.25 mm diameter). If the wire came on a roll, then straighten it by securing one end into a vice or clamp and the other end into the grips of a hand drill, and then turning on the drill at a low speed (100-200 rpm). Repeat with a second 1.25 m length of bare copper wire.</li>
	<li>Mark the intended locations of the photodiodes along the edge of the diffuser using a fine-tip permanent marker, beginning with the first photodiode position at 13.5 cm from one end of the diffuser and the other positions located every 2 cm between the first diode and the far end of the diffuser.
	<ol>
		<li>Mark the position of the first copper wire on the diffuser by centering one photodiode on the diffuser bar with its electrical connection tabs pointing towards the sides of the bar, placing the wire underneath one of the tabs, and marking the wire&#39;s location.</li>
		<li>Repeat the preceding step to mark the wire&#39;s position at the center and the opposite end of the bar.</li>
	</ol>
	</li>
	<li>Use cyanoacrylate glue to glue the first straightened copper wire to the diffuser, using the locations marked in the preceding step to align the wire.
	<ol>
		<li>Use cyanoacrylate glue to glue 50 photodiodes face-down along the diffuser at 20 mm intervals (as marked in the preceding step), ensuring that they are in the center of the diffuser and that all are arranged all in the same orientation such that the large tab sits on the copper wire, and the small tab sits opposite.</li>
		<li>Place the second copper wire such that it sits underneath each of the smaller tabs of the photodiodes, and then glue the wire to the diffuser with cyanoacrylate glue.</li>
	</ol>
	</li>
	<li>Wet both tabs of one photodiode, as well as the adjacent and underlying wires, with flux using a solder flux pen. Solder each tab of the diode to the underlying copper wires using a fine tipped soldering iron at a temperature of approximately 350-400 oC. Test the solder connections by shining a light onto the photodiode and checking for a voltage signal across the wires using a multimeter. Repeat this step for all 50 photodiodes. 
	NOTE: Step 1.7 is optional (if the resistor is not soldered into the PARbar, it can instead later be connected in parallel with the PARbar signal inputs on the datalogger).</li>
	<li>Solder a 1.5 &#937; low temperature coefficient precision resistor in parallel across the copper wires.</li>
	<li>Solder the male end of a waterproof DC connector to the ends of the copper wires (the same ends to which the resistor was soldered, if you followed optional step 1.7) and then seal the connections using glue lined heat shrink tubing.</li>
	<li>Create a continuous silicone barrier around the circuity on the diffuser to form a fluid-tight well, by applying a bead of silicone sealant to the surface of the diffuser, near the edge. Inspect the bead closely to ensure that no air gaps remain between the silicone and the diffuser bar, as gaps will permit epoxy to leak out. Once the sealant has cured, fill the well with epoxy resin.</li>
	<li>When the epoxy resin has hardened (overnight), remove the silicone sealant using a razor blade. Bolt the diffuser to the pre-threaded aluminum U-bar using M4 bolts.</li>
	<li>Use masking tape to secure the diffuser to the aluminum along its whole length, and then fill the void inside the ceptometer with polyurethane foam filler. Once the foam filler has set (overnight), remove the masking tape.</li>
	<li>Solder the female end of the DC connector to a length of two-conductor cable and seal the connections with glue lined heat shrink.</li>
	<li>To calibrate the PARbar against a quantum sensor,
	<ol>
		<li>Connect both sensors to a datalogger or voltmeter capable of measuring a differential voltage output (connect a 1.5 &#937; low temperature-coefficient precision resistor in parallel with the PARbar if a resistor was not integrated into the design in step 1.7),</li>
		<li>Set them outside in full sun on a level plane (level with a spirit level or spirit bubble), record the outputs of both sensors across a period during which solar radiation varies widely, such as a full diurnal cycle, and determine the calibration factor for the PARbar as the slope of a linear regression of PAR reported from the quantum sensor (as the dependent variable) vs. raw voltage output (as the independent variable).</li>
	</ol>
	</li>
</ol>
2. Install in the field
<ol>
	<li>To infer effective plant area index (PAIeff), install one PARbar above the canopy (ensuring that it is not shaded by any light-absorbing elements within the canopy) and another below all light-absorbing elements whose absorptance you wish to measure (typically, below the lowest leaves), with both PARbars aligned at a 45&#176; angle to planting rows. Ensure the upper PARbar is positioned so as not to shade the lower PARbar. Level the PARbars using a spirit level or bubble level.</li>
	<li>Connect the PARbars to a datalogger or voltmeter using cables made in step 1.11. If a 1.5 &#937; low temperature-coefficient precision resistor was not integrated into the PARbar circuit during construction (step 1.7), then connect such a resistor in parallel with each PARbar at this stage.</li>
	<li>Convert differential voltage output to PAR using the calibration factor determined for each PARbar in step 1.13.</li>
</ol>
3. Calculate the effective plant area index (PAIeff)
<ol>
	<li>Calculate PAIeff for each pair of above- and below-canopy PAR measurements using the following equations6: 
	(1) <img alt="Equation 1" src="/files/ftp_upload/59447/59447eq1.jpg" />, 
	where A = 0.283 + 0.0785a &#8211; 0.159a2 (in which a is leaf absorptance), &#964; is the ratio of below- to above-canopy PAR, and K and fb are modeled by Equation 24 and Equation 39, respectively: 
	(2) <img alt="Equation 2" src="/files/ftp_upload/59447/59447eq2.jpg" />, 
	where &#967; is a dimensionless parameter describing leaf angle distribution, &#952; is the solar zenith angle, and 
	(3) <img alt="Equation 3" src="/files/ftp_upload/59447/59447eq3.jpg" />, 
	where r is PAR above the canopy (PARabove) as a fraction of its maximum possible value (PARabove,max = 2550&#8729;cos&#952;); i.e. r = PARabove/PARabove,max. Consult the literature for values of a and c appropriate to your study species (we assumed a = 0.9 and c = 0.9610 for the wheat canopies used for trial measurements presented here). 
	NOTE: A sample R script is provided as a supplementary file to assist users in developing code for automated processing of large datasets.</li>
</ol>

<ol>
	<li>Armbrust, D. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+measurement+of+crop+canopy+cover.">Rapid measurement of crop canopy cover.</a> Agronomy Journal. 82 (6), 1170-1171 (1990).</li><li>Breda, N. J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ground-based+measurements+of+leaf+area+index:+a+review+of+methods,+instruments+and+current+controversies.">Ground-based measurements of leaf area index: a review of methods, instruments and current controversies.</a> Journal of Experimental Botany. 54 (392), 2403-2417 (2003).</li><li>Francone, C., Pagani, V., Foi, M., Cappelli, G., Confalonieri, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+leaf+area+index+estimates+by+ceptometer+and+PocketLAI+smart+app+in+canopies+with+different+structures.">Comparison of leaf area index estimates by ceptometer and PocketLAI smart app in canopies with different structures.</a> Field Crops Research. 155, 38-41 (2014).</li><li>Campbell, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extinction+coefficients+for+radiation+in+plant+canopies+calculated+using+an+ellipsoidal+inclination+angle+distribution.">Extinction coefficients for radiation in plant canopies calculated using an ellipsoidal inclination angle distribution.</a> Agricultural and Forest Meteorology. 36 (4), 317-321 (1986).</li><li>Cohen, S., Rao, R. S., Cohen, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Canopy+transmittance+inversion+using+a+line+quantum+probe+for+a+row+crop.">Canopy transmittance inversion using a line quantum probe for a row crop.</a> Agricultural and Forest Meteorology. 86 (3-4), 225-234 (1997).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> AccuPAR PAR/LAI Ceptometer Model LP-80 Operator&#39;s Manual. , (2017).</li><li>Salter, W. T., Gilbert, M. E., Buckley, T. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Time-dependent+bias+in+instantaneous+ceptometry+caused+by+row+orientation.">Time-dependent bias in instantaneous ceptometry caused by row orientation.</a> The Plant Phenome Journal. , (2018).</li><li>Huang, X. H., Han, B., Merchant, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Annual Review of Plant Biology. 65, 531-551 (2014).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Application Note: Beam fraction calculation in the LP80. , (2009).</li><li>Campbell, G. S., Van Evert, F. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Light interception by plant canopies - efficiency and architecture. , (1994).</li><li>Pask, A., Pietragalla, J., Mullan, D., Reynolds, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Physiological breeding II: a field guide to wheat phenotyping. , (2012).</li><li>Murchie, E. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+the+dynamic+photosynthome.">Measuring the dynamic photosynthome.</a> Annals of Botany. 122 (2), 207-220 (2018).</li><li>Beddows, P. A., Mallon, E. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cave+Pearl+Data+Logger:+a+flexible+Arduino-based+logging+platform+for+long-term+monitoring+in+harsh+environments.">Cave Pearl Data Logger: a flexible Arduino-based logging platform for long-term monitoring in harsh environments.</a> Sensors. 18 (2), 26 (2018).</li><li>Li, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhancement+of+crop+photosynthesis+by+diffuse+light:+quantifying+the+contributing+factors.">Enhancement of crop photosynthesis by diffuse light: quantifying the contributing factors.</a> Annals of Botany. 114 (1), 145-156 (2014).</li><li>Lang, A. R. G., Yueqin, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Estimation+of+leaf-area+index+from+transmission+of+direct+sunlight+in+discontinuous+canopies.">Estimation of leaf-area index from transmission of direct sunlight in discontinuous canopies.</a> Agricultural and Forest Meteorology. 37 (3), 229-243 (1986).</li><li>Cruse, M. J., Kucharik, C. J., Norman, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+a+simple+apparatus+to+measure+direct+and+diffuse+photosynthetically+active+radiation+at+remote+locations.">Using a simple apparatus to measure direct and diffuse photosynthetically active radiation at remote locations.</a> Plos One. 10 (2), 19 (2015).</li><li>Yang, G. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Unmanned+aerial+vehicle+remote+sensing+for+field-based+crop+phenotyping:+current+status+and+perspectives.">Unmanned aerial vehicle remote sensing for field-based crop phenotyping: current status and perspectives.</a> Frontiers in Plant Science. 8, 26 (2017).</li></ol>

The authors confirm that they have no conflicts of interest and nothing to disclose.

Successful implementation of the protocol outlined here for building ceptometers (PARbars) depends most sensitively on two steps: 1.5 (gluing photodiodes in place) and 1.6 (soldering photodiodes to the copper wire). Step 1.5 is prone to error by aligning the photodiodes incorrectly with respect to their intrinsic polarity. For the photodiodes that we used, and which we recommend as essential specific items, the polarity is identified by virtue of the two electrical connector tabs on the diode having clearly different sizes. Thus, before applying cyanoacrylate glue and soldering the photodiodes in place, it is strongly advised to double-check that all diodes are placed with the large connector tabs facing in one direction and the small tabs facing in the other direction. Step 1.6 is prone to failure due to poor soldering technique and formation of a cold soldered junction. This can be avoided by applying thin solder flux using a flux pen immediately before soldering and ensuring that both the wire and the photodiode tab are heated with the solder tip (at approximately 350-400 oC) before soldering itself is applied to the junction. Problems with electrical connections in a PARbar typically manifest in the form of a calibration slope distinctly different from those of other PARbars. Such problems can be caught early by testing each electrical connection during construction (as described in Step 1.6), and again after all connections have been soldered, but before they have been encased in epoxy (Step 1.9). A third potential source of error arises from the failure to use a low temperature-coefficient precision resistor, whose resistance is insensitive to temperature; using an ordinary resistor will cause the error as the resistance, and hence the voltage output per unit of light absorbed by the diodes, changes with ambient temperature. The final major source of error is not unique to PARbars, but applies to all ceptometry measurements: namely, the inference of effective plant area index or leaf area index from light capture depends on features of canopy structure (notably mean leaf absorptance and leaf angle distribution; a and c in Eqns 1 and 2) that may vary during plant development and between genotypes.
There are two main areas in which the protocol described here could be modified or adapted. First, the PARbars that we present here were designed specifically for use in row crops, such as wheat and barley, but the design could easily be modified for other applications. For example, a shunt resistor with larger resistance could be used to enhance gain (mV output per unit PAR) at lower PAR ranges. For versatility, a low-temperature coefficient precision potentiometer (variable resistor) could be used to modify the PARbar&#39;s sensitivity range as needed or to make small adjustments to gain so that each of many PARbars have identical calibration slopes. Second, the photodiodes could also be used individually as quantum sensors, allowing the user to capture spatial as well as temporal variation within individual canopies for a much lower cost than possible using commercially available quantum sensors. This could be particularly valuable given the growing interest in dynamic photosynthesis under fluctuating light conditions12. Third, although we used a conventional (and expensive) datalogger for the data presented in this study, there is scope for dataloggers to instead be built using off-the-shelf componentry, enabling the creation of a combined ceptometry and datalogger system on a limited budget. The popularity of so-called maker platforms, such as Arduino and Raspberry Pi, offer great promise in this area; we suggest the open-source Arduino-based Cave Pearl project13 as a starter for further development. Cave Pearl dataloggers were designed for environmental monitoring of cave ecosystems, so ruggedness and low power demand were key considerations in their design. Similar considerations are relevant for implementation to plant phenotyping work. Cave Pearl datalogger components are inexpensive (less than USD $50 per unit) and small, which could enable them to be directly incorporated into PARbars.
Application of the PARbars described here faces three main limitations. First, the inference of plant area index or leaf area index from measured light capture is hampered by strong time-dependent biases, particularly in row crops7. This can be overcome by making repeated or continuous measurements over a day. Second, inexpensive photodiodes do not have a spectral output that is exactly proportional to photon flux (the variable of greatest interest in photosynthesis research). This can cause bias when light quality changes greatly through a canopy, although previous estimates of the resulting error indicate that it is on the order of a few percent7. Third, PARbars cannot distinguish between the direct beam and diffuse components of incoming PAR above the canopy. As diffuse radiation penetrates deeper into the canopy than direct sunlight14, transmittance will be increased and PAIeff will be underestimated as the diffuse fraction of total irradiance increases. When all radiation is diffuse, PAIeff is directly proportional to the logarithm of 1/&#964;&#160; rather than the relationship shown in Equation 115. Cruse et al. (2015)16 noted that currently available commercial instruments that can measure direct and diffuse PAR are expensive and require regular maintenance, so they designed a simple and inexpensive apparatus to address this issue. Their system consists of a quantum sensor that is routinely shaded by a motorized, moving shadowband and allows for continuous measurement of total, direct and diffuse PAR. The sensor used in the Cruse et al.16 system could be replaced with the same photodiode used in PARbars to further reduce cost and may be easily incorporated into the existing PARbar setup. These measurements could be integrated into the data processing pipeline and would further enhance the reliability of estimates of PAIeff.
The major advantage of PARbars relative to existing commercial ceptometers is their low cost, which makes it feasible to produce them in large numbers. Recently, there has been a growing interest in novel high-throughput plant phenotyping technologies for the estimation of canopy traits (for review see Yang et al., 201717). Whilst these methods are promising in that they produce huge amounts of data they are typically very indirect and require validation against conventional techniques. PARbars could serve as a cost-effective, ground-based validation tool for these new techniques.
The low production cost of PARbars also make them a viable option for continuous measurements in the field. This could be useful for several reasons. For example, continuous measurements can be used to characterize row-orientation biases to develop time-specific correction functions for instantaneous measurements (for more information see Salter et al. 20187). Continuous ceptometry can also capture short fluctuations in canopy light capture over time (sunflecks and shadeflecks) caused by clouds passing overhead, movement of the canopy, etc. Photosynthesis is known to be highly sensitive to small changes in environmental conditions and &#8216;dynamic&#8217; changes in photosynthesis are now thought to be important in driving crop yield (for review see Murchie et al., 201812). PARbars installed in the field with a suitably short logging interval could be used to capture these short fluctuations and provide better understanding of the dynamic nature of plant canopies.

Ceptometers (linear arrays of light sensors) are used to measure the proportion of photosynthetically active radiation (PAR) intercepted by plant canopies. Ceptometers are used widely for agricultural crop research due to the relatively straightforward nature of measurements and simplicity of data interpretation. The basic principle of ceptometry is that the transmittance of light to the base of a plant canopy (&#964;) is dependent on the projected area of light absorbing materials above. Measurements of PAR above and below the canopy can, therefore, be used to estimate canopy traits such as leaf area index (LAI) and effective plant area index (PAIeff) (which includes stems, culms and reproductive structures in addition to leaves)1,2,3. Reliability of PAIeff estimates inferred from &#964; is improved by modeling the effects of the beam fraction of incoming PAR (fb), the leaf absorptance (a) and the effective canopy extinction coefficient (K); K, in turn, depends on both the solar zenith angle (&#952;) and the leaf angle distribution (&#967;)1,4,5,6. It is a common practice to correct for these effects. However, there are other biases that have not received due consideration in the past due to methodological and cost limitations.
We recently identified significant time-dependent bias in instantaneous ceptometry measurements of row crops, such as wheat and barley7. This bias is caused by an interaction between row planting orientation and solar zenith angle. To overcome this bias, continuously logging ceptometers can be mounted in the field to monitor diurnal cycles of canopy light interception and then daily averages of &#964; and PAIeff can be calculated. However, continuous measurements are often infeasible due to the prohibitively high cost of commercially available ceptometers &#8211; often several thousand US dollars for a single instrument &#8211; and the requirement for measurements of many field plots. The latter is particularly evident in the -omics era where many hundreds of genotypes are required for genomic analyses, such as genome wide association studies (GWAS) and genomic selection (GS) (for review see Huang &#38; Han, 20148). We recognized that there was a need for cost-effective ceptometers that could be produced in large numbers and be used for continuous measurements across many genotypes.
As a solution, we designed easy-to-build, high-accuracy ceptometers (PARbars) at a cost of USD $75 per unit and requiring approximately one hour of labor to construct. PARbars are built using 50 photodiodes that are sensitive only in the PAR waveband (wavelengths 390 &#8211; 700 nm), with very little sensitivity outside this range, obviating the use of costly filters. The photodiodes are connected in parallel across a 1 m length to produce an integrated differential voltage signal that can be recorded with a datalogger. The circuitry is encased in epoxy for waterproofing and the sensors operate over a large temperature range (-40 to +80 &#176;C), allowing the PARbars to be deployed in the field for extended periods of time. With the exception of the photodiodes and a low-temperature-coefficient resistor, all parts required to build a PARbar can be purchased from a hardware store. A full list of required parts and tools is provided in the Table of Materials. Here we present detailed instructions on how to build and use PARbars for the estimation of PAIeff and present representative results from wheat canopies.

<table>
	<tbody>
		<tr>
			<td>1.5 &#937; low temperature coefficient precision resistor</td>
			<td>TE Connectivity Ltd., Schaffhausen, Switzerland.</td>
			<td>UPW25 series</td>
			<td>Could be made using multiple larger resistors in parallel but they need to have low temperature coefficient (i.e. &#177; 3 ppm/&#176;C). 
			URL for commercial source: https://bit.ly/2DFuPpm</td>
		</tr>
		<tr>
			<td>Acrylic diffuser</td>
			<td>Plastix Australia Pty. Ltd., Arncliffe, NSW, Australia.</td>
			<td>445 - Opal White</td>
			<td>1200 mm length x 30 mm width x 4.5 mm thick. 
			URL for commercial source: https://bit.ly/2Bq0fyc</td>
		</tr>
		<tr>
			<td>Aluminum U-bar</td>
			<td>Capral Ltd., Bundamba, QLD, Australia.</td>
			<td>EK9160</td>
			<td>1220 mm length x 35 mm width x 25 mm depth. 
			URL for commercial source: https://bit.ly/2PPfJou</td>
		</tr>
		<tr>
			<td>Bare solid core copper wire</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Bolts</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Clamps</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Clear epoxy potting resin</td>
			<td>Solid Solutions, East Bentleigh, VIC, Australia.</td>
			<td>651 - Universal Epoxy Potting Resin</td>
			<td>Clear epoxy resin for electrical applications. 
			URL for commercial source: https://bit.ly/2qY0pHa</td>
		</tr>
		<tr>
			<td>Cyanoacrylate glue</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Datalogger</td>
			<td>Campbell Scientific, Logan, Utah, USA.</td>
			<td>CR5000</td>
			<td>Other dataloggers that record differential voltages could be used. 
			URL for commercial source: https://bit.ly/2U7Io5H</td>
		</tr>
		<tr>
			<td>Drill or drill press</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Glue lined heat shrink</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Heat gun</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>LED torch</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Masking tape</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Photodiodes (50)</td>
			<td>Everlight Americas Inc., Carrollton, Texas, USA.</td>
			<td>EAALSDSY6444A</td>
			<td>It is important that this specific component is used due to spectral response. 
			URL for commercial source: https://bit.ly/2FzVnuH</td>
		</tr>
		<tr>
			<td>Polyurethane foam filler</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Quantum sensor</td>
			<td>LI-COR, Lincoln, Nebraska, USA.</td>
			<td>LI-190R</td>
			<td>For calibration of PARbars only. 
			URL for commercial source: https://bit.ly/2HEfKbh</td>
		</tr>
		<tr>
			<td>Screwdrivers</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Silicone sealant</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Solder</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Solder flux pen</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Soldering iron</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Spirit/bubble level</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Tap and die set</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Two-core cable</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Voltmeter</td>
			<td>Non-specific part</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Waterproof connectors</td>
			<td>Core Electronics, Adamstown, NSW, Australia.</td>
			<td>ADA743</td>
			<td>2 core waterproof connector. DC power connectors work well. 
			URL for commercial source: https://bit.ly/2Brcrik</td>
		</tr>
	</tbody>
</table>

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 schematic for the PARbar build is shown in Figure 1. A representative calibration curve for a PARbar is shown in Figure 2. The differential voltage output of a PARbar is linearly proportional to the PAR output from a quantum sensor, with R2 = 0.9998. PARbars were deployed in wheat canopies and logged every 20 s across the development of the plants. A typical diurnal time course of the canopy light environment collected using a PARbar on a clear sunny day is shown in Figure 3 (raw transmittance data and corrected PAIeff are shown for comparison). Figures 3b and 3c demonstrate the bias that could be introduced by taking instantaneous ceptometry measurements at various times of day (as per Salter et al. 20187). The wheat plots used for the collection of this data had a row planting orientation due north-south with the transmission of light to the lower canopy peaking at 12:30 (Figure 3b). If an instantaneous measurement were to be taken at this point, PAIeff would be underestimated, whereas if it were taken in the morning or afternoon it may be overestimated. The weatherproof PARbars can also be deployed in the field for long time periods; Figure 4 demonstrates how PARbars could be used to monitor how canopy light environment changes as plants develop.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/59447/59447fig1.jpg" /> 
Figure 1. Schematics for the PARbar build. (a) Location and arrangement of the waterproof connector and the internal shunt resistor; (b) arrangement and spacing of the photodiodes; (c) drilling locations on the acrylic diffuser bar; (d) drilling locations on the aluminum U-bar; and (e) electronic circuit diagram of a PARbar. <a href="https://www.jove.com/files/ftp_upload/59447/59447fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/59447/59447fig2.jpg" /> 
Figure 2. Representative PARbar calibration curve. The relationship between the differential voltage output of a PARbar (mV) and the photosynthetic photon flux density or PAR (&#956;mol m-2 s-1) from a quantum sensor. Each point represents a single pair of measurements from the PARbar and quantum sensor, recorded once every 20 seconds over a period of 4 hours for one day. <a href="https://www.jove.com/files/ftp_upload/59447/59447fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/59447/59447fig3.jpg" /> 
Figure 3. Representative daily timecourse of PARbar output. Data collected on a clear day using PARbars in wheat canopies at anthesis in Canberra, Australia (-35&#176;12&#39;00.1008&#34;, 149&#176;05&#39;17.0988&#34;). (a) PAR measured above the canopy (&#956;mol m-2 s-1), (b) uncorrected transmittance (the ratio of PARabove/PARbelow) (unitless), and (c) the effective plant area index (PAIeff, m2 m-2), calculated from Equation 1. Data points shown in (b) and (c) are means (n = 30), solid lines are LOESS local regressions fitted in R (a = 0.5), shaded areas are standard errors of the fit and the dashed horizontal lines represent the daily means. The shaded area between the dotted lines is the time window (1100 &#8211; 1400h) recommended for instantaneous ceptometer measurements in wheat by CIMMYT11. <a href="https://www.jove.com/files/ftp_upload/59447/59447fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/59447/59447fig4.jpg" /> 
Figure 4. Representative data collected across a growing season. PARbar data collected from early tillering to anthesis in wheat canopies in Canberra, Australia (-35&#176;12&#39;00.1008&#34;, 149&#176;05&#39;17.0988&#34;). (a) Uncorrected transmittance data (unitless), and (b) effective plant area index (PAIeff, m2 m-2) calculated from Equation 1. Data points shown represent daily means for the period 1,000 &#8211; 1,400h (n = 30). Solid lines are LOESS local regressions fitted in R (a = 0.75), shaded areas are standard errors of the fit. Raw data was not included in further analysis if PARabove was &#60; 1,500 &#181;mol m-2 s-1 and if PARbelow/PARabove was &#62; 1. <a href="https://www.jove.com/files/ftp_upload/59447/59447fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about PARbars: Cheap, Easy to Build Ceptometers for Continuous Measurement of Light Interception in Plant Canopies at JoVE.com

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

Here, we present detailed instructions on how to build and calibrate research quality ceptometers (light sensors that integrate light intensity across many sensors arrayed linearly along a horizontal bar).

Ceptometry is a technique used to measure the transmittance of photosynthetically active radiation through a plant canopy using multiple light sensors ...

parbars-cheap-easy-to-build-ceptometers-for-continuous-measurement

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9.3K Views.  University of Sydney. Here, we present detailed instructions on how to build and calibrate research quality ceptometers (light sensors that integrate light intensity across many sensors arrayed linearly along a horizontal bar).

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

Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail millet. Recently, the 510 Mb genome of foxtail millet, S. italica, has been sequenced 1,2 and a 25x coverage genome sequence of the weedy relative S. viridis is in progress. S. viridis has a number of characteristics that make it a potentially excellent model genetic system including a rapid generation time, small stature, simple growth requirements, prolific seed production 3 and developed systems for both transient and stable transformation 4. However, the genetics of S. viridis is largely unexplored, in part, due to the lack of detailed methods for performing crosses. To date, no standard protocol has been adopted that will permit rapid production of seeds from controlled crosses.
The protocol presented here is optimized for performing genetic crosses in S. viridis, accession A10.1. We have employed a simple heat treatment with warm water for emasculation after pruning the panicle to retain 20-30 florets and labeling of flowers to eliminate seeds resulting from newly developed flowers after emasculation. After testing a series of heat treatments at permissive temperatures and varying the duration of dipping, we have established an optimum temperature and time range of 48 &deg;C for 3-6 min. By using this method, a minimum of 15 crosses can be performed by a single worker per day and an average of 3-5 outcross progeny per panicle can be recovered. Therefore, an average of 45-75 outcross progeny can be produced by one person in a single day. Broad implementation of this technique will facilitate the development of recombinant inbred line populations of S. viridis X S. viridis or S. viridis X S. italica, mapping mutations through bulk segregant analysis and creating higher order mutants for genetic analysis.

Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

We have developed a methodology for performing crosses in Setaria viridis (S. viridis). The method involves pruning the panicle prior to a hot water treatment to kill viable pollen. Crosses are performed following a well-controlled growth regime and typically result in the recovery of 1 to 7 cross-pollinated seed/s per panicle.

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail ...

Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling

Tracing rare stable isotopes from plant material through the ecosystem provides the most sensitive information about ecosystem processes; from CO2 fluxes and soil organic matter formation to small-scale stable-isotope biomarker probing. Coupling multiple stable isotopes such as 13C with 15N, 18O or&#160;2H has the potential to reveal even more information about complex stoichiometric relationships during biogeochemical transformations. Isotope labeled plant material has been used in various studies of litter decomposition and soil organic matter formation1-4. From these and other studies, however, it has become apparent that structural components of plant material behave differently than metabolic components (i.e. leachable low molecular weight compounds) in terms of microbial utilization and long-term carbon storage5-7. The ability to study structural and metabolic components separately provides a powerful new tool for advancing the forefront of ecosystem biogeochemical studies. Here we describe a method for producing 13C and 15N labeled plant material that is either uniformly labeled throughout the plant or differentially labeled in structural and metabolic plant components.
Here, we present the construction and operation of a continuous 13C and 15N labeling chamber that can be modified to meet various research needs. Uniformly labeled plant material is produced by continuous labeling from seedling to harvest, while differential labeling is achieved by removing the growing plants from the chamber weeks prior to harvest. Representative results from growing Andropogon gerardii Kaw demonstrate the system&#39;s ability to efficiently label plant material at the targeted levels. Through this method we have produced plant material with a 4.4 atom%13C and 6.7 atom%15N uniform plant label, or material that is differentially labeled by up to 1.29 atom%13C and 0.56 atom%15N in its metabolic and structural components (hot water extractable and hot water residual components, respectively). Challenges lie in maintaining proper temperature, humidity, CO2 concentration,&#160;and light levels in an airtight 13C-CO2 atmosphere for successful plant production. This chamber description represents a useful research tool to effectively produce uniformly or differentially multi-isotope labeled plant material for use in experiments on ecosystem biogeochemical cycling.

Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling

This method explains how to build and operate a continuous 13C and 15N isotope labeling chamber for uniform or differential plant tissue labeling. Representative results from metabolic and structural labeling of Andropogon gerardii are discussed.

Tracing rare stable isotopes from plant material through the ecosystem provides the most sensitive information about ecosystem processes; from CO2 fluxes ...

Experimental Protocol for Manipulating Plant-induced Soil Heterogeneity

Coexistence theory has often treated environmental heterogeneity as being independent of the community composition; however biotic feedbacks such as plant-soil feedbacks (PSF) have large effects on plant performance, and create environmental heterogeneity that depends on the community composition. Understanding the importance of PSF for plant community assembly necessitates understanding of the role of heterogeneity in PSF, in addition to mean PSF effects. Here, we describe a protocol for manipulating plant-induced soil heterogeneity. Two example experiments are presented: (1) a field experiment with a 6-patch grid of soils to measure plant population responses and (2) a greenhouse experiment with 2-patch soils to measure individual plant responses. Soils can be collected from the zone of root influence (soils from the rhizosphere and directly adjacent to the rhizosphere) of plants in the field from conspecific and heterospecific plant species. Replicate collections are used to avoid pseudoreplicating soil samples. These soils are then placed into separate patches for heterogeneous treatments or mixed for a homogenized treatment. Care should be taken to ensure that heterogeneous and homogenized treatments experience the same degree of soil disturbance. Plants can then be placed in these soil treatments to determine the effect of plant-induced soil heterogeneity on plant performance. We demonstrate that plant-induced heterogeneity results in different outcomes than predicted by traditional coexistence models, perhaps because of the dynamic nature of these feedbacks. Theory that incorporates environmental heterogeneity influenced by the assembling community and additional empirical work is needed to determine when heterogeneity intrinsic to the assembling community will result in different assembly outcomes compared with heterogeneity extrinsic to the community composition.

Understanding the role of environmental heterogeneity in species coexistence has typically focused on types of heterogeneity that are extrinsic to the community&#8217;s species composition. We provide novel detailed methods for creating soil heterogeneity treatments using soils subject to plant-soil feedback conditioning, or heterogeneity intrinsic to the community composition.

Coexistence theory has often treated environmental heterogeneity as being independent of the community composition; however biotic feedbacks such as ...

A New Application of the Electrical Penetration Graph (EPG) for Acquiring and Measuring Electrical Signals in Phloem Sieve Elements

Electrophysiological properties of cells are often studied in vitro, after dissociating them from their native environments. However, the study of electrical transmission between distant cells in an organism requires in vivo, artifact-free recordings of cells embedded within their native environment. The transmission of electrical signals from wounded to unwounded areas in a plant has since long piqued the interest of botanists. The phloem, the living part of the plant vasculature that is spread throughout the plant, has been postulated as a major tissue in electrical transmission in plants. The lack of suitable electrophysiological methods poses many challenges for the study of the electrical properties of the phloem cells in vivo. Here we present a novel approach for intracellular electrophysiology of sieve elements (SEs) that uses living aphids, or other phloem-feeding hemipteran insects, integrated in the electrical penetration graph (EPG) circuit. The versatility, robustness, and accuracy of this method made it possible to record and study in detail the wound-induced electrical signals in SEs of central veins of the model plant Arabidopsis thaliana1. Here we show that EPG-electrodes can be easily implemented for intracellular electrophysiological recordings of SEs in marginal veins, as well as to study the capacity of SEs to respond with electrical signals to several external stimuli. The EPG approach applied to intracellular electrophysiology of SEs can be implemented to a wide variety of plant species, in a large number of plant/insect combinations, and for many research aims.

A New Application of the Electrical Penetration Graph EPG for Acquiring and Measuring Electrical Signals in Phloem Sieve Elements

Electrical Penetration Graph (EPG) is a well-established technique for studying the feeding behavior of stylet-bearing insects. Here we show a new application of EPG as a non-invasive tool for the acquisition of intracellular electrophysiology recordings of sieve elements (SEs), the cells that form the phloem vasculature in plants.

Electrophysiological properties of cells are often studied in vitro, after dissociating them from their native environments. However, the study of ...

Continuous Instream Monitoring of Nutrients and Sediment in Agricultural Watersheds

Pollutant concentrations and loads in watersheds vary considerably with time and space. Accurate and timely information on the magnitude of pollutants in water resources is a prerequisite for understanding the drivers of the pollutant loads and for making informed water resource management decisions. The commonly used &#34;grab sampling&#34; method provides the concentrations of pollutants at the time of sampling (i.e., a snapshot concentration) and may under- or overpredict the pollutant concentrations and loads. Continuous monitoring of nutrients and sediment has recently received more attention due to advances in computing, sensing technology, and storage devices. This protocol demonstrates the use of sensors, sondes, and instrumentation to continuously monitor in situ nitrate, ammonium, turbidity, pH, conductivity, temperature, and dissolved oxygen (DO) and to calculate the loads from two streams (ditches) in two agricultural watersheds. With the proper calibration, maintenance, and operation of sensors and sondes, good water quality data can be obtained by overcoming challenging conditions such as fouling and debris buildup. The method can also be used in watersheds of various sizes and characterized by agricultural, forested, and/or urban land.

With the advancement of technology and the rise in end-user expectations, the need and use of higher temporal resolution data for pollutant load estimation has increased. This protocol describes a method for continuous in situ water quality monitoring to obtain higher temporal resolution data for informed water resource management decisions.

Pollutant concentrations and loads in watersheds vary considerably with time and space. Accurate and timely information on the magnitude of pollutants in ...

Adherence of Bacteria to Plant Surfaces Measured in the Laboratory

This manuscript describes a method to measure bacterial binding to axenic plant surfaces in the light microscope and through the use of viable cell counts. Plant materials used include roots, sprouts, leaves, and cut fruits. The methods described are inexpensive, easy, and suitable for small sample sizes. Binding is measured in the laboratory and a variety of incubation media and conditions can be used. The effect of inhibitors can be determined. Situations that promote and inhibit binding can also be assessed. In some cases it is possible to distinguish whether various conditions alter binding primarily due to their effects on the plant or on the bacteria.

An easy method for measuring and characterizing bacterial adhesion to plants, particularly roots and sprouts, is described in this article.

This manuscript describes a method to measure bacterial binding to axenic plant surfaces in the light microscope and through the use of viable cell ...

Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions

Beneficial plant-microbe interactions offer a sustainable biological solution with the potential to boost low-input food and bioenergy production. A better mechanistic understanding of these complex plant-microbe interactions will be crucial to improving plant production as well as performing basic ecological studies investigating plant-soil-microbe interactions. Here, a detailed description for ecosystem fabrication is presented, using widely available 3D printing technologies, to create controlled laboratory habitats (EcoFABs) for mechanistic studies of plant-microbe interactions within specific environmental conditions. Two sizes of EcoFABs are described that are suited for the investigation of microbial interactions with various plant species, including Arabidopsis thaliana, Brachypodium distachyon, and Panicum virgatum. These flow-through devices allow for controlled manipulation and sampling of root microbiomes, root chemistry as well as imaging of root morphology and microbial localization. This protocol includes the details for maintaining sterile conditions inside EcoFABs and mounting independent LED light systems onto EcoFABs. Detailed methods for addition of different forms of media, including soils, sand, and liquid growth media coupled to the characterization of these systems using imaging and metabolomics are described. Together, these systems enable dynamic and detailed investigation of plant and plant-microbial consortia including the manipulation of microbiome composition (including mutants), the monitoring of plant growth, root morphology, exudate composition, and microbial localization under controlled environmental conditions. We anticipate that these detailed protocols will serve as an important starting point for other researchers, ideally helping create standardized experimental systems for investigating plant-microbe interactions.

Ecosystem Fabrication EcoFAB Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions

This article describes detailed protocols for ecosystem fabrication of devices (EcoFABs) that enable the studies of plants and plant-microbe interactions in highly controlled laboratory conditions.

Beneficial plant-microbe interactions offer a sustainable biological solution with the potential to boost low-input food and bioenergy production. A ...

A Strain Gauge Monitor (SGM) for Continuous Valve Gape Measurements in Bivalve Molluscs in Response to Laboratory Induced Diel-cycling Hypoxia and pH

An inexpensive, laboratory-based, strain gauge valve gape monitor (SGM) was developed to monitor the valve gape behavior of bivalve molluscs in response to diel-cycling hypoxia. A Wheatstone bridge was connected to strain gauges that were attached to the shells of oysters (Crassostrea virginica). The recorded signals allowed for the opening and closing of the bivalves to be recorded continuously over two-day periods of experimentally-induced diel-cycling hypoxia and diel-cycling changes in pH. Here, we describe a protocol for developing an inexpensive strain gauge monitor and describe, in an example laboratory experiment, how we used it to measure the valve gape behavior of Eastern oysters (C. virginica), in response to diel-cycling hypoxia and cyclical changes in pH. Valve gape was measured on oysters subjected to cyclical severe hypoxic (0.6 mg/L) dissolved oxygen conditions with and without cyclical changes in pH, cyclical mild hypoxic (1.7 mg/L) conditions and normoxic (7.3 mg/L) conditions. We demonstrate that when oysters encounter repeated diel cycles, they rapidly close their shells in response to severe hypoxia and close with a time lag to mild hypoxia. When normoxia is restored, they rapidly open again. Oysters did not respond to cyclical pH conditions superimposed on diel cycling severe hypoxia. At reduced oxygen conditions, more than one third of the oysters closed simultaneously. We demonstrate that oysters respond to diel-cycling hypoxia, which must be considered when assessing the behavior of bivalves to dissolved oxygen. The valve SGM can be used to assess responses of bivalve molluscs to changes in dissolved oxygen or contaminants. Sealing techniques to better seal the valve gape strain gauges from sea water need further improvement to increase the longevity of the sensors.

A Strain Gauge Monitor SGM for Continuous Valve Gape Measurements in Bivalve Molluscs in Response to Laboratory Induced Diel-cycling Hypoxia and pH

Understanding the behavioral responses of bivalve suspension-feeders to environmental variables, such as dissolved oxygen, can explain some ecosystem processes. We have developed an inexpensive, laboratory-based, strain gauge monitor (SGM) to measure valve gape responses of oysters, Crassostrea virginica, to diel-cycling hypoxia and cyclical pH.

An inexpensive, laboratory-based, strain gauge valve gape monitor (SGM) was developed to monitor the valve gape behavior of bivalve molluscs in response ...

The Plant Infection Test: Spray and Wound-Mediated Inoculation with the Plant Pathogen Magnaporthe Grisea

Plants possess a powerful system to defend themselves against potential threats by pathogenic fungi. For agriculturally important plants, however, current measures to combat such pathogens have proved too conservative and, thus, not sufficiently effective, and they can potentially pose environmental risks. Therefore, it is extremely necessary to identify host-resistance factors to assist in controlling plant diseases naturally through the identification of resistant germplasm, the isolation and characterization of resistance genes, and the molecular breeding of resistant cultivars. In this regard, there is need to establish an accurate, rapid, and large-scale inoculation method to breed and develop plant resistance genes. The rice blast fungal pathogen Magnaporthe grisea causes severe disease symptoms and yield losses. Recently, M. grisea has emerged as a model organism for studying the mechanisms of plant-fungal pathogen interactions. Hence, we report the development of a plant virulence test method that is specific for M. grisea. This method provides for both spray inoculation with a conidial suspension and wounding inoculation with mycelium cubes or droplets of conidial suspension. The key step of the wounding inoculation method for detached rice leaves is to make wounds on plant leaves, which avoids any interference caused by host penetration resistance. This spray/wounding protocol contributes to the rapid, accurate, and large-scale screening of the pathotypes of M. grisea isolates. This integrated and systematic plant infection method will serve as an excellent starting point for gaining a broad perspective of issues in plant pathology.

The Plant Infection Test: Spray and Wound-Mediated Inoculation with the Plant Pathogen Magnaporthe Grisea

Here, we present a protocol to test plant virulence with the plant pathogen Magnaporthe grisea. This report will contribute to the large-scale screening of the pathotypes of fungi isolates and serve as an excellent starting point for understanding the resistant mechanisms of plants during molecular breeding.

Plants possess a powerful system to defend themselves against potential threats by pathogenic fungi. For agriculturally important plants, however, current ...

A Flexible Low Cost Hydroponic System for Assessing Plant Responses to Small Molecules in Sterile Conditions

A wide range of studies in plant biology are performed using hydroponic cultures. In this work, an in vitro hydroponic growth system designed for assessing plant responses to chemicals and other substances of interest is presented. This system is highly efficient in obtaining homogeneous and healthy seedlings of the C3 and C4 model species Arabidopsis thaliana and Setaria viridis, respectively. The sterile cultivation avoids algae and microorganism contamination, which are known limiting factors for plant normal growth and development in hydroponics. In addition, this system is scalable, enabling the harvest of plant material on a large scale with minor mechanical damage, as well as the harvest of individual parts of a plant if desired. A detailed protocol demonstrating that this system has an easy and low-cost assembly, as it uses pipette racks as the main platform for growing plants, is provided. The feasibility of this system was validated using Arabidopsis seedlings to assess the effect of the drug AZD-8055, a chemical inhibitor of the target of rapamycin (TOR) kinase. TOR inhibition was efficiently detected as early as 30 min after an AZD-8055 treatment in roots and shoots. Furthermore, AZD-8055-treated plants displayed the expected starch-excess phenotype. We proposed this hydroponic system as an ideal method for plant researchers aiming to monitor the action of plant inducers or inhibitors, as well as to assess metabolic fluxes using isotope-labeling compounds which, in general, requires the use of expensive reagents.

A simple, versatile, and low-cost in vitro hydroponic system was successfully optimized, enabling large-scale experiments under sterile conditions. This system facilitates the application of chemicals in a solution and their efficient absorption by roots for molecular, biochemical, and physiological studies.

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

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Chapters in this video

Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

Design and Operation of a Continuous ¹³C and ¹⁵N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling

Experimental Protocol for Manipulating Plant-induced Soil Heterogeneity

A New Application of the Electrical Penetration Graph (EPG) for Acquiring and Measuring Electrical Signals in Phloem Sieve Elements

Continuous Instream Monitoring of Nutrients and Sediment in Agricultural Watersheds

Adherence of Bacteria to Plant Surfaces Measured in the Laboratory

Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions

A Strain Gauge Monitor (SGM) for Continuous Valve Gape Measurements in Bivalve Molluscs in Response to Laboratory Induced Diel-cycling Hypoxia and pH

The Plant Infection Test: Spray and Wound-Mediated Inoculation with the Plant Pathogen Magnaporthe Grisea

A Flexible Low Cost Hydroponic System for Assessing Plant Responses to Small Molecules in Sterile Conditions