Using High-Resolution Hyperspectral and Thermal Airborne Imagery to Assess Physiological Condition in the Context of Wheat Phenotyping

Remote Sens. 2015, 7, 13586-13605; doi:10.3390/rs71013586 remote sensing ISSN 2072-4292 www.mdpi.com/journal/remotesensing Article Using High-Resolution Hyperspectral and Thermal Airborne Imagery to Assess Physiological Condition in the Context of Wheat Phenotyping Victoria Gonzalez-Dugo 1, Pilar Hernandez 1, Ignacio Solis 2 and Pablo J. Zarco-Tejada 1,* 1 Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14004 Cordoba, Spain; E-Mails: victoria.gonza[email protected] (V.G.-D.); [email protected] (P.H.) 2 Agrovegetal S.A., Demetrio de los Rios 15, 41003 Sevilla, Spain; E-Mail: [email protected] * Author to whom correspondence should be ssed; E-Mail: [email protected]; Tel.: +34-957-499-280; Fax: +34-957-499-252. Academic Editors: Mutlu Ozdogan, Clement Atzberger and Prasad S. Thenkabail Received: 28 July 2015 / Accepted: 1 October 2015 / Published: 19 October 2015 Abstract: There is a growing need for developing high-throughput tools for crop phenotyping that would increase the rate of genetic improvement. In most cases, the indicators used for this purpose are related with canopy structure (often acquired with RGB cameras and multispectral sensors allowing the calculation of NDVI), but using approaches related with the crop physiology are rare. High-resolution hyperspectral remote sensing imagery provides optical indices related to physiological condition through the quantification of photosynthetic pigment and chlorophyll fluorescence emission. This study demonstrates the use of narrow-band indicators of stress as a potential tool for phenotyping under rainfed conditions using two airborne datasets acquired over a wheat experiment with 150 plots comprising two species and 50 varieties (bread and durum wheat). The flights were performed at the early stem elongation stage and during the milking stage. Physiological measurements made at the time of flights demonstrated that the second flight was made during the terminal stress, known to largely determine final yield under rainfed conditions. The hyperspectral imagery enabled the extraction of thermal, radiance, and reflectance spectra from 260 spectral bands from each plot for the calculation of indices related to photosynthetic pigment absorption in the visible and red-edge regions, the quantification of chlorophyll fluorescence emission, as well as structural indices related to canopy structure. Under the conditions of this study, the structural indices OPEN ACCESS Remote Sens. 2015, 7 13587 (i.e., NDVI) did not show a good performance at predicting yield, probably because of the large effects of terminal water stress. Thermal indices, indices related to chlorophyll fluorescence (calculated using the FLD method), and carotenoids pigment indices (PRI and CAR) demonstrated to be better suited for screening complex traits such as crop yield. The study concludes that the indicators derived from high-resolution thermal and hyperspectral airborne imagery are efficient tools for field-based phenotyping providing additional information to standard NDVI imagery currently used. Keywords: hyperspectral; water stress; field-based phenotyping; chlorophyll fluorescence; thermal imaging 1. Introduction Wheat provides 20% of the global population s calorie intake and a similar percentage of its daily protein [1]. The global average rate of yield increase for wheat is 0.9% per year, while predictions of increase in demand reach 2.4% [2]. This means that the rate of genetic improvement required in the near future is greater than those currently being achieved [3]. Well-focused high-throughput phenotyping will be crucially important in developing new avenues for genetic improvement [4]. When the number of lines is limited or the studies are conducted under controlled environments, this task should be afforded by technologies such as high-throughput phenotyping platforms [5]. However, the performance of breeding programs on crop yield and productivity must be assessed under natural conditions [6,7]. Field-based phenotyping (FBP) is recognized as the only approach capable of delivering the required throughput and an accurate description of trait expression in real-world cropping systems [6,8]. A review of the approaches available for FBP and sensors commonly used can be found in Deery et al. [7]. Nevertheless, and in spite of recent progress, FBP remains a bottleneck for future advance in breeding [9]. The development of improved varieties relies on the ability to identify the best genetic variations for advancement, but the spatial variability that is generally observed in fields and the interaction with the environment (G × E) add more complexity to the analysis of crop performance [8]. Several features, related to crop physiology and agronomy, are involved, making difficult the identification of simple traits for phenotyping purposes [4]. Spatial variability must be taken into account when the results of phenotyping experiments are being evaluated. For this reason, plant breeders have been displaying a growing interest in high-resolution remote sensing for phenotyping purposes [5,6,9,10]. Remote sensing has proven useful for monitoring vegetation in the context of plant phenotyping [9]. Most efforts in this field employ RGB (visible) or CIR (color infrared) cameras to produce high-resolution maps of the Normalized Difference Vegetation Index (NDVI) or pseudo-NDVI as an indicator of plant vigor and structure both from near-field and airborne scales [11 13]. The development of techniques and methodologies to assess crop performance by such structural indices has been favored by its direct link with the interception of solar radiation and thus with potential yield [14] along with the relatively simple and inexpensive sensors required to acquire the imagery. Nevertheless, under rainfed growing conditions in arid environments such as the Mediterranean area, the combination of limited availability Remote Sens. 2015, 7 13588 of water and high temperatures, especially during grain filling, tends to seriously limit yields below their potential. In such environments, the unpredictable and variable rainfall season is largely responsible for the variation in yield [15]. Under these conditions, interactions between genotype, year, and location tend to mask the genetic variations affecting yield. This is the reason why the genetic advances in wheat yield in dry areas have not been as successful as in high-yielding environments [15]. In this context, hyperspectral remote sensing has the potential to provide much richer datasets by the collection of several narrow spectral bands that are sensitive to the absorption of specific photosynthetic pigments [16], which are also capable of quantifying the chlorophyll fluorescence naturally emitted by vegetation [17]. Evidence exists of the usefulness of hyperspectral data for phenotyping crops using hand-held spectroradiometers for near-field data acquisition [18 21]. Nevertheless, the potential of hyperspectral cameras installed on manned or unmanned vehicles for plant phenotyping purposes remains uncertain. In another spectral domain, thermal remote sensing has been shown to detect small changes in stress levels caused by reduced transpiration under water-stress conditions, and it has also displayed potential for yield screening [22]. Therefore, high-resolution (i.e. below 50 cm pixels) thermal and hyperspectral imagery (mainly deployed on-board aircraft or unmanned vehicles) is capable of providing information over small plots typically used by crop breeders to calculate several vegetation and spectral indices at the canopy level. Such indices derived from both thermal and hyperspectral imagery are related to specific leaf biochemical and canopy biophysical parameters related to crop growth and function. The application of chlorophyll fluorescence in this context is still at a very early stage but recent results indicate that fluorescence quantification from hyperspectral imagers were able to detect stress levels [17,23]. Some authors have suggested the application of one or more imaging technique in a multi-sensor approach where thermal sensing in combined with reflectance, fluorescence, and other sensing technique [24,25]. The aim of this study was to determine whether the airborne hyperspectral and thermal-derived indicators acquired from an aircraft can be used to assess physiologically-based plot variability in the context of plant phenotyping, evaluating the effects on wheat yield under rainfed conditions in the Mediterranean area. Specifically, the study evaluated narrow-band hyperspectral indices and the quantification of chlorophyll fluorescence emission as indicators of yield variations under water-stress conditions. 2. Materials and Methods 2.1. Study Area A field trial site for wheat selection was established by Agrovegetal S.A. in Ecija, Seville, Spain (37°32 29 N, 5°05 29 W) under rainfed conditions. The trial site comprised 300 individual plots of 6 m2 each (1.2 m × 5 m) (Figures 1 and 2). The field was sown on 4 December 2013 at a density of 360 seed/m2. This study concentrated on the 150 central plots in order to avoid the edges of the images. These 150 plots comprised 25 varieties of durum wheat (Triticum turgidum L. var. durum) and 25 of bread wheat (Triticum aestivum L.), each replicated three times on a balanced square lattice design. Regarding fertilization, pest and disease management, all plots received the same treatment. Remote Sens. 2015, 7 13589 2.2. Water Relations Measurements Water relations in selected cultivars were measured on DOY 76 and DOY 126, 2014 at noon. The first date corresponded to the early stem elongation stage (Z31); and the second date to grain filling (milk stage Z77). Leaf water potential (LWP; MPa) was measured using a pressure chamber (Model 3000, Soil Moisture Equipment Corp., Santa Barbara, USA) on two sunlit leaves per plot. Assimilation rate and stomatal conductance were measured with a portable photosynthesis measurement system (LCpro-SD, ADC Bioscientific Ltd., Herts, UK) on two sunlit leaves per plot. 2.3. Assessment of Yield Every plot was individually harvested using a Wintersteiger Classic plot combine and yield per plot was determined on 7 June 2014. 2.4. Airborne Campaigns A thermal camera (FLIR SC655, FLIR Systems, Wilsonville, OR, USA) and a micro-hyperspectral imager (Micro-Hyperspec VNIR model, Headwall Photonics, Fitchburg, MA, USA) were installed on a Cessna aircraft operated by the Laboratory for Research Methods in Quantitative Remote Sensing (IAS, CSIC, Spain). The thermal camera has a 640 × 480 pixel resolution with a 24.5 mm f1.0 lens, with radiometric performance assessed in the laboratory using a black body (model P80P, Land Instruments, Dronfield, UK) and through vicarious calibrations using surface temperature measurements (Figure 1). (a) (b) Figure 1. (a) Thermal imagery acquired from the study area; (b) Detail of a single plot. The hyperspectral sensor used in this experiment is the micro-hyperspectral instrument operating in the spectral mode of 260 bands at 1.85 nm/pixel and 12-bit radiometric resolution, yielding 6.4 nm FWHM with a 25-micron slit in the 400 885 nm region (Figures 2 and 3). No spectral binning was performed during the acquisition of the imagery. The frame storage rate on board the aircraft was set to 50 fps with an integration time of 18 ms. The 8-mm focal length lens yielded an IFOV of 0.93 mrad and an angular FOV of 50°. The hyperspectral sensor was radiometrically calibrated in the laboratory Remote Sens. 2015, 7 13590 using coefficients derived from a calibrated uniform light source and an integrating sphere (CSTMUSS2000C Uniform Source System, LabSphere, North Sutton, NH, USA) using four levels of illumination and six integration times. Ortho-rectification of the hyperspectral imagery was performed using PARGE (ReSe Applications Schläpfer, Wil, Switzerland). Inputs were obtained from an inertial measuring unit (IMU) (MTiG model, Xsens, Enschede, The Netherlands), installed on board, and synchronized with the micro-hyperspectral imager (as described by [17]). Two flights were carried out at noon on the solar plane on DOY 76 and DOY 126, 2014 over the experimental field. Flight altitude was 345 m. It delivered a ground resolution of 30 and 20 cm for the thermal and the hyperspectral imagery, respectively. (a) (b) Figure 2. (a) Hyperspectral imagery acquired from the study area; (b) Detail of a single plot. Figure 3. Airborne hyperspectral reflectance (a) and radiance (b) extracted from pure vegetation pixels obtained on DOY 76. 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 400 500 600 700 800 Wavelength (nm) a 0 20 40 60 80 100 400 500 600 700 800 Wavelength (nm) b Remote Sens. 2015, 7 13591 2.5. Hyperspectral-Derived Indices The indicators described in Table 1 were calculated from the hyperspectral imagery. These indices have been shown to be closely related to certain specific features of plant physiology [17,23]. We selected four types of indices, related to: (i) fluorescence emission by PS-I photosystem, (ii) structural effects, (iii) chlorophyll content, and (iv) carotenoid content. The fluorescence emission was assessed from the radiance spectra by the Fraunhofer Line Depth (FLD) principle calculated from a total of three bands for the in (L763 nm) and out bands (L750 nm; L780 nm) (FLD3), using the equation described in Zarco-Tejada et al. [17]. Some other indices related to the emission of chlorophyll fluorescence as described in Zarco-Tejada et al. [26] were also included in the analysis. The structural indices were calculated to assess whether final yield in wheat could be captured by the Normalized Difference Vegetation Index, NDVI [27], with a modification of NDVI to increase its sensitivity, in the form of the Renormalized Difference Vegetation Index, RDVI [28]. Soil-adjusted indices (OSAVI and MSAVI) that minimize the background influence were included in the analysis as well as MCARI1, which has demonstrated a great potential for LAI predictions [29]. The selected chlorophyll a + b indices were the Transformed Chlorophyll Absorption in Reflectance Index (TCARI) [30], the aforementioned TCARI, normalized by OSAVI to obtain TCARI/OSAVI, as proposed by Haboudane et al. [30] and used by Meggio et al. [31]. Other indices related with the pigment content were also included in the analysis (Table 1). The Photochemical Reflectance Index (PRI) was calculated using the 570 nm band as a reference [32] also using the 515 nm band as reference as proposed by Hernandez-Clemente et al. [33] and normalized by structural and chlorophyll effects (PRIn, [34]). Some other indices related with the carotenes content were included (CAR, [35]). RARS is related to the carotenoids content, as well as chlorophyll a + b [36]. Table 1. Hyperspectral indices used in this study. Index Equation Reference Fluorescence indices FLD [17,37,38] UR [26] R690/R630 [26] DPi (R) [26] R685/R655 [26] Structural indices NDVI [27] RDVI [28] Remote Sens. 2015, 7 13592 Table 1. Cont. Index Equation Reference OSAVI [39] MCARI1 [29] MSAVI [40] Chlorophyll indices TCARI [30] TCARI/OSAVI COMBINED TCARI/OSAVI [30] TVI [41] SIPI [42] G - ZTM [43] VOG [44] Carotenoid indices CAR [35] LIC3 [45] RARS [36] PRI [32] PRI515 [33] PRIn [34] 2.6. Determination of the Crop Water Stress Index (CWSI) and Water Stress Index (WSI) Two indices were derived from the thermal imagery obtained over the experiment. The Crop Water Stress Index (CWSI) was calculated by normalizing the canopy temperature (Tc) with the air temperature (Ta) and vapor pressure deficit (VPD), according to the methodology proposed by Idso et al. ([46]; Equation (1)). (1) where (Tc Ta)LL is the lower limit and corresponds to the Tc Ta value of a canopy that is transpiring at its potential rate and (Tc Ta)UL is the upper limit and corresponds to the Tc Ta value of a canopy where the transpiration is completely halted. The lower limit was determined by the Non-Water Stress Baseline proposed by Idso [47], with the following equation: (Tc Ta)LL = 3.25·DPV + 3.38. Remote Sens. 2015, 7 13593 The Water Deficit Index (WDI) was calculated according to the procedure developed by Moran et al. [48]. It is based on the vegetation index/temperature trapezoid (VIT) and has been developed to combine the spectral vegetation indices with temperature measurements in order to apply CWSI theory to partially-vegetated fields without knowledge of foliage temperature. 2.7. Climatic Conditions during the Experiment Climate during the growing season was close to the average for the past 10 years on the site. The previous autumn and winter were rainy, with a total of 260 mm rainfall. During the spring season, the amount of rainfall was 82 mm (Figure 4a). At the time of the flights, ETo and mean Ta were 3.3 mm and 15.5 °C on DOY 76 and 5.7 mm and 22.6 °C. Maximum Ta achieved on these days were 26.6 and 33.3 °C on DOY 76 and 126, respectively (Figure 4b). (a) (b) Figure 4. (a) Temporal evolution of ETo (mm), solar radiation (MJ·m 2), and rainfall (mm) during the growing season; (b) Maximum, average, and minimum daily temperature (°C) for the same period. Arrows indicate the times of flights (on DOY 76 and 126). 2.8. Statistical Analyses Data were analyzed using SPSS® software (IBM Corporation, Armonk, NY, USA). In order to obtain insight into the relative weight of each of the indices derived from the thermal and hyperspectral imagery, a stepwise multiple regression analysis was employed. The multiple regression model was run with yield as dependent variables and one index per category (categories are defined in Table 1) as independent variables. 3. Results 3.1. Water Relations Two durum and two bread wheat cultivars were chosen to assess the water relations under the conditions described above. The first measurements were made on DOY 76 and corresponded with the early stem elongation stage. The leaf water potential was maintained close to 1.1 MPa for the four cultivars, although the stomatal conductance varied between 245 and 485 mmol·m 2·s 1 (Figure 5a). Remote Sens. 2015, 7 13594 On DOY 126, due to water stress, the water potential ranged from 2.4 to 3.5 MPa. At this moment, the crop was at the milking stage (grain filling). Stomatal conductance was kept below 120·mmol·m 2·s 1. The assimilation rate was linearly related to stomatal conductance for the two measurement dates (Figure 5b). (a) (b) Figure 5. Relationships between stomatal conductance (Gs; mmol·m 2·s 1) and leaf water potential (LWP; MPa) (a); and net assimilation (A; mol·m 2·s 1) (b) for two selected varieties of bread wheat and two of durum wheat. Each point represented a single plot. A linear regression was fitted to both dates in Figure 5b. 3.2. Variability of Grain Yield The average grain yield was 2466 kg·ha 1for the 25 bread wheat genotypes and 1670 kg·ha 1 for the 25 durum wheat genotypes. The ranges of variability among the analyzed varieties were large for both wheat species (Figure 6), despite the severe heat and water stress at the time of grain filling. Mean grain yield was higher for bread wheat than for durum wheat varieties (Figure 6), which is the typical performance in this area. The coefficient of variation (CV) was calculated for each cultivar, taking into consideration the three replicates per cultivar. The CVs were separately averaged for bread and durum wheat. The results demonstrated that bread cultivars displayed a higher CV (10%) than durum wheat cultivars (7.2%). Figure 6. Mean, upper and lower quartile values for bread and durum wheat yield (kg ha 1). Maximum and minimum values are also indicated by whiskers. Each group corresponded to a single species and 25 varieties were used for the calculation. Remote Sens. 2015, 7 13601 separate dates. The imagery enabled the calculation of vegetation and spectral indices related to canopy structure, photosynthetic pigment absorption, the quantification of chlorophyll fluorescence emission, as well as indices derived from canopy temperature. These physiological indices designed to minimize the sensitivity to structural changes while maximizing a rapid response to environmental conditions could be of paramount importance for plant breeding in variable climates such as the Mediterranean, and especially under rainfed conditions. Under the settings of this study, the thermal index CWSI demonstrated the best relationship with yield (R2 = 0.53), the fluorescence emission quantification carried through the FLD method (R2 = 0.47) and the xanthophyll index PRI (R2 = 0.49). The multiple regression model built for the three indices explained 77% of the total variability in yield and was statistically significant (p < 0.001). On the contrary, NDVI, a standard vegetation index widely used in plant phenotyping, showed a weaker relationship for both durum and bread wheat (R2 = 0.10). These results may be explained by the terminal stress that is usually observed in semi-arid regions, as crops displaying higher values of NDVI deplete soil reserves during vegetative growth and are more sensitive to water stress during yield formation. This study showed promising results on the use of new high-resolution remote sensing indices suitable for field-based phenotyping under rainfed conditions. The use of the remote sensing physiological indicators enables the evaluation of crop performance over wider areas, allowing high throughput phenotyping assessments while still taking spatial variability into account. Acknowledgments Authors would acknowledge A. Gomez, K. Gutierrez, D. Notario, and A. Vera for their technical support. Funding from Junta de Andalucia project P12-AGR-0482 and MINECO project AGL2012-40053-C03-01 is gratefully acknowledged. Author Contributions Ignacio Solis and Pilar Hernandez did the experimental design and collected grain yield data. Pablo J. 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