Leaf to panicle ratio (LPR): a new physiological trait indicative of source and sink relation in japonica rice based on deep learning

doi:10.21203/rs.3.rs-25185/v2

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Leaf to panicle ratio (LPR): a new physiological trait indicative of source and sink relation in japonica rice based on deep learning

https://doi.org/10.21203/rs.3.rs-25185/v2

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published 26 Aug, 2020

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Background : Identification and characterization of new traits with a sound physiological foundation is essential for crop breeding and management. Deep learning has been widely used in image data analysis to explore spatial and temporal information on crop growth and development, thus strengthening the power of the identification of physiological traits. This study aims to develop a novel trait that indicates source and sink relation in japonica rice based on deep learning.

Results : We applied a deep learning approach to accurately segment leaf and panicle and subsequently developed the procedure of GvCrop to calculate the leaf to panicle ratio (LPR) of rice populations during grain filling. Images of the training dataset were captured in the field experiments, with large variations in camera shooting angle, the elevation angle and the azimuth angle of the sun, rice genotype, and plant phenological stages. Accurately labeled by manually annotating all the panicle and leaf regions, the resulting dataset were used to train FPN-Mask (Feature Pyramid Network Mask) models, consisting of a backbone network and a task-specific sub-network. The model with the highest accuracy is then selected to study the variations in LPR among 192 rice germplasms and among agronomical practices. Despite the challenging field conditions, FPN-Mask models achieved a high detection accuracy, with Pixel Accuracy being 0.99 for panicles and 0.98 for leaves. The calculated LPRs showed large spatial and temporal variations as well as genotypic differences.

Conclusion : Deep learning techniques can achieve high accuracy in simultaneously detecting panicle and leaf data from complex rice field images. The proposed FPN-Mask model is applicable for detecting and quantifying crop performance under field conditions. The newly identified trait of LPR should provide a high throughput protocol for breeders to select superior rice cultivars as well as for agronomists to precisely manage field crops that have a good balance of source and sink.

Plant Physiology and Morphology

Plant Molecular Biology and Genetics

Plant phenotyping

Leaf and panicle detection

Deep learning

Physiological trait

Leaf to panicle ratio (LPR)

Japonica rice

Sustainable improvement in crop production is crucial for supporting the demand from an increasing global population, particularly considering that there are 821 M people who lack sufficient food to support their daily lives [1]. Recent technological advances in genome biology like next-generation sequencing, genome editing and genomic selection have paved the way for crop breeders to identify, characterize, transfer, or modify the genes responsible for grain yield or quality traits in a rapid and precise way [2]. However, there is a huge gap between the fundamental plant sciences and the applied science of crop breeding, as reflected by the limited understanding of the link between genotype and phenotype. Crop physiology is a key interface between the genome and the plant phenotype, and thus is indispensable for hastening crop improvement [3]. Accordingly, physiological breeding, a methodology for selection of physiological traits such as canopy temperature, carbon isotope discrimination, and stomatal conductance, was proposed. This approach has advantages over conventional breeding such as in water stressed Australian environments and in heat and drought stressed conditions of the International Wheat Improvement Network [4].

Chemically, cereal grain yield consists of photosynthetic assimilates first produced in the leaf source organs which are translocated to the sink organ of grain. Therefore, source and sink relations, the core concept of crop physiology, is the critical factor dominating crop yield formation. Improving the source activity of leaf photosynthesis to harness light irradiation more efficiently is one of the major targets of crop breeding. In rice, ideotypes have long been pursued by breeders, resulting in several successfully implemented theories such as the New Plant Type, Super Rice, and Ideal Plant Architecture [5-7]. One common future shared by these new plant types is the emphasis on leaf erectness, especially the top three leaves, which is supposed to be essential for improving source activity. However, some of the main cultivars with this ideotype had problems of incomplete filling of inferior grains, especially for those with large numbers of grains, indicating the importance of optimization of the source-sink ratio [8, 9].

In addition to storing photosynthetic assimilates from leaves, sink organs like glumes and awns have photosynthetic activity. Cumulative evidence favors the sizable contribution of spike or panicle to grain filling in terms of providing carbohydrates as well as nitrogen (N), magnesium, and zinc [10, 11]. In wheat and barley, contribution of spikes to grain filling has a range of 10% to 76% [12]. In rice, gross photosynthetic rate of the panicle is 30% of that of the flag leaf, and it was estimated that panicle photosynthesis contributed 20% to 30% of the dry matter in grain [13]. Thus light interception of the ear or panicle should be integrated into the breeding programmes aiming for source-sink balance.

Technical advances in high throughput field phenotyping on a breeding scale in realistic field environments have strengthened the power of physiological breeding [4]. Concurrently, methods for data mining of the big data acquired by various phenotyping platforms are developed. Among them, deep learning has been widely used in image data analysis to explore spatial and temporal information concerning crop growth and development [14]. Leaf area and number indicate the photosynthetic capacity of the crop canopy, and the precise segmentation and counting of leaves has been one of the objectives of image processing. Studies have resulted in robust methodology of deep learning for quantifying leaf number from 2D images [15] and 3D images [16-18], providing effective tools for growth estimation and yield prediction of crop plants. Spike (wheat) or panicle (rice) number per square meter is the key component of cereal grain yield. Numerous attempts have been made to segment and count this reproductive organ accurately in rice [19-21] and wheat [22-24]. Collectively, these robust, low-cost and efficient methods to assess the number of economic organs are of high relevance for phenotyping efforts towards increases in cereal grain yield. However, to our knowledge, method development is still necessary to simultaneously extract both leaf and panicle from the background of a field crop population, as required by the breeder to adopt physiological strategies to balance source and sink.

In this study, we applied a deep learning approach to accurately extract leaf and panicle image data and subsequently calculate the leaf to panicle ratio (LPR) of rice populations during grain filling stage. Of note, the LPR is proposed as a proximate estimation of the distribution of light interception between leaf and panicle, with an assumption that the light captured by the camera is the sunlight directly reflected by the leaf or panicle. Images of the training dataset were captured in the field experiments, with large variations in camera shooting angle, the elevation angle and the azimuth angle of the sun, rice genotype, and plant phenological stages. Accurately labeled by manually annotating all the panicle and leaf regions, the resulting dataset were used to train FPN-Mask models, consisting of a backbone network and a task-specific sub-network. The model with the highest accuracy was then selected to study the variations in LPR among 192 japonica rice germplasms and among agronomical practices. Our aim was to provide a high throughput protocol and new physiological trait for breeders to select superior rice cultivars as well as for agronomists to precisely manage field crops that have a good balance of source and sink.

We explored an end-to-end semantic segmentation method to label each pixel as panicle, leaf or background automatically under natural field conditions, and then generated the leaf to panicle ratio (LPR) by division of the number of pixels assigned for each class in each field image. Figure 1 shows the overall work-flow of this method, including two parts. Part 1 is the offline training workflow, which builds a deep learning network called FPN-Mask to segment panicle and leaf from field RGB images. Part 2 is the procedure of GvCrop to develop a software system for calculating LPR.

Experimental setup

In 2018, plots of ongoing field experiments at Danyang (31°54′31″N, 119°28′21″E), Jiangsu Province, China were selected to take pictures for the training dataset. Of note, these experiments were not specially designed for a phenotyping study. In brief, the plant materials of these experiments were highly diverse in genotypic variation, containing seven main japonica cultivars of Jiangsu and 195 mutants with contrasting agronomical traits as reported by Abacar et al [25]. Further, the seven cultivars had two sowing dates, resulting in obviously different phenotypes for a certain genotype. Thus the diversity in plant architecture and canopy structure of the tested materials can provide as many kinds of phenotypes as possible for image analysis.

In 2019, three experiments were conducted to test and apply the proposed FPN-Mask model. (1) Genotypic variations in LPR. A total of 192 mutants were investigated. The plot area was 2.4 m × 1.4 m with a row spacing of 30 cm and plant spacing 20 cm. Nitrogen, phosphate (P₂O₅) and potassium (K₂O) fertilizers were applied at a rate of 240 kg ha^-1, 120 kg ha^-1and 192 kg ha^-1, respectively, and were equally separated into basic fertilizers (before transplanting) and topdressing (at 4th leaf age in reverse order). (2) N fertilization effects on LPR. A japonica rice cultivar, Wuyunjing 30, was selected for field experiments with a randomized complete-block design. It had three replications and a plot area of 2.4 m ×1.4 m. Total N fertilizer was 240 kg ha^-1 N, and two N fertilization modes with different base/topdressing ratios were applied: (1) N5-5: base/topdressing, 5/5; (2) N10-0: base/topdressing, 10/0. (3) Regulation of plant growth regulators on LPR. Solutions of 100 mM gibberellin, 100 mM uniconazole, 25 mM 2, 4-epibrassinolide, 25 mM brassinazole as well as the control, water, were made up in distilled water with 0.5 % TWEEN-20. One cultivar, Ningjing 8, from the N treatment was used as material. Spraying was conducted at the rate of 500 mL m^-2 after sunset, with three times starting at booting stage on August 22 and with a 2-day interval.

In addition, a dynamic canopy light interception simulating device (DCLISD) was designed for capturing images from the sun’s position installed on a supporting track (Fig. 2). The bottom part consists of four pillars with wheels and the upper part is comprised of two arches consolidated by two steel pipes, and a moveable rail for mounting the RGB camera. The sun’s trajectory is simulated by two angles, the elevation angle and the azimuth angle, which is calculated according to the latitude, longitude, as well as the growth periods at the experimental site.

Image acquisition

Images of the training dataset were captured in the field experiments in 2018, reflecting the large variations in camera shooting angle, the elevation angle and the azimuth angle of the sun, rice genotype, and plant phenological stages (Fig. 3). Images for validation and application of the proposed model were acquired in 2019. For the three treatments of genotypes, N fertilization, and spraying, an angle of 40° was selected for the tripod. The height of the camera (Canon EOS 750D, 24.2 megapixels) was 167.1 cm, the average height of a Chinese adult, and the distance between the central point of the target area and vertical projection of the camera on the ground was 90 cm. The camera settings were as follows: focal length, 18 mm; aperture, automatic; ISO, automatic; and exposure time, automatic. In the experiment with DCLISD, the camera model was SONY DSC-QX100, with settings were as follows: focal length, 10 mm; aperture, automatic; ISO, automatic; and exposure time, automatic.

Dataset preparation

Training dataset: Taking into consideration camera angle, solar angle, panicle type and growth stage (Fig. 3), we prepared a training dataset with 360 representative images from the 2018 dataset (Table S1). The GG (green panicle with green leaf) growth stage, YG (yellow panicle with green leaf) growth stage and YY (yellow panicle with yellow leaf) growth stage were represented by 113, 104, and 143 images, respectively. Fig. 1(1)-(3) shows the preparation of the training data. Considering that the original size of these field images is as large as 4864×3648 pixels, they were cropped to a size between [150,150] and [600,600] using the Paint.Net software. After obtaining these patches, we labeled pixels of each patch as panicle, leaf and background manually using the Fluid Mask software. Finally, a total of 1896 representative patches were selected as the final training sample set. Among them, 1210 samples were added continuously during the late daily tests of the model. Further, to increase the diversity of the training dataset and avoid overfitting, we performed basic data enhancements to the training set, including random horizontal/vertical flips, rotations by 90 degrees, and histogram equalizations. To reduce illumination effects, we performed random brightness enhancements on the image. All the input images were resized to 256×256 pixels. And for a faster and more stable training model, all the input images were normalized to [0, 1] [27,28].

Testing dataset：We divided all 2018 collected images into three groups based on the rice growth stage during the image acquisition. From each group, we randomly selected 30 testing images and finally selected 90 images as the testing dataset (Table S2). Many of the field images in the testing dataset included extraneous objects, such as tracks, chains, neighbor plots, color-charts and sky, which were not required for our approach. Therefore, only a significant region from the plot was selected as the region of interest (ROI) and all selected testing images were cropped manually to exclude the area outside the ROI.

Network structure

In this study, we proposed a deep learning-based method for rice panicle segmentation, called FPN-Mask. The method consists of a backbone network and a task-specific subnetwork. The Feature Pyramid Network (FPN) [29] was selected as the backbone network for extracting features over the entire input data. Originally designed for object detection, it has the advantages of extracting a multi-level feature pyramid from an input image with a single scale. The subnetwork is referenced from the Unified Perceptual Parsing Network [30], which performs semantic segmentation based on the output of the backbone network (Fig. 4).

Backbone network for feature extraction: The FPN [29] is a standard feature extractor with a top-down architecture and lateral connections. The top-down architecture is based on Residual Networks (ResNet) [31], which consists of four stages. Each stage is denoted as C₂, C₃, C₄ and C₅, respectively. For a detailed description of the FPN structure, please refer to reference [29]. A detailed description of the ResNet structure can be found in [31]. We denoted the last feature map of each stage in ResNet as {C₂, C₃, C₄, C₅}. In our backbone network, we removed the global max pooling layer before C₂, because it will drop out semantic information. Therefore, the rates of each stage {C₂, C₃, C₄, C₅} were down-sampled from {4,8,16,32} to {1,2,4,8}. The down-sampling rates of the feature maps derived by FPN {P₂, P₃, P₄, P₅} are {1, 2, 4, 8}, respectively; this means that the size of P₂is the same as the original image size of 256×256, the size of P₃is 128×128; the size of P₄ is 64×64 and the size of P₅is 32×32. The number of feature maps output for each stage in ResNet is equal to 32.

Subnetwork for semantic segmentation: the subnetwork is based on the multi-level features extracted from the backbone network introduced above. Each level of the features will be fused together as an input feature map for semantic segmentation, which has been proved to outperform semantic segmentation compared to using only the highest resolution feature map [30, 32]. To up-sample the low-level feature maps {p₃, p₄, p₅} to get the same size feature as the original image, we directly adopted the bilinear interpolation layer instead of the time-consuming deconvolution layer, and attached a convolution layer followed by each interpolation layer to refine the interpolation result. After up-sampling, different levels of the features were concatenated as the final semantic feature. The concatenated multi-level features were convoluted by a convolution layer to refine the result and a convolution layer to reduce the channel dimensions. The convolution layer was attached to a batch normal layer and a relu layer. Finally, we obtained a 3-channel semantic segmentation result, representing background, leaf and panicle, respectively.

Loss function for semantic segmentation

The cross-entropy loss function is a standard classification method [33]. In practical applications, due to the uneven number of pixels in different categories, the loss calculated by the cross-entropy loss function is not realistic [34]. For this reason, our paper used the focal loss, which is specifically designed to solve the imbalance problem [34] and focuses on the more difficult classification locations by changing the weight of different categories. For specific descriptions refer to [34].

Training

We experimented with ResNet-18 as the FPN backbone. All convolutional layers were initialized as in He et al [35]. Batch layers were simply initialized with bias and weight . The mini-batch size was 24, optimization was according to the Adam method, and training lasted for 7 days with the base learning rate of 0.001. All the experiments in this article were conducted on a high-performance computer with Intel 3.50 GHz processor and 128 GB of memory. Two NVIDIA 1080 GeForce graphics processing unit (GPU) has a 12 GB memory used to accelerate the training of our model.

During the training, we tested the model performance with all the collected images and selected supplementary training samples for the images that did not perform well to make sure that the training samples covered all the cases of the 6 GB images obtained in 2018 (except the 90 testing images). There were 60 field images which generated 302 patches which were added as supplementary training samples, about 40 samples per day. The performance standards (good or bad) were determined through observation. The training period continued until the testing performance of all images visually met the accuracy requirements and the loss function curve was smooth without fluctuations.

PostProcess

Although a deep network is well suited for processing semantic segmentation problems, it is impossible to achieve 100% accuracy based only on auto segmentation methods. Therefore, developing a tool for manually modifying the segmentation results is a necessity. To solve that problem, we developed a software called GvCrop, which not only integrates the pixel-wise segmentation method (Fig. 1(6)), but also integrates the ability to modify the segmentation results by human interaction (Fig. 1(7)). Because pixel-level labelling of the wrong location is time consuming, processing the image regions with homogeneous characteristics instead of single pixels can help us accelerate the manual labelling speed (Fig. 1(7)). According to the image color space and boundary cues, we used the gSLICr [36] algorithm to group pixels into perceptually homogeneous regions. gSLICr is the Simple Linear Iterative Clustering (SLIC) [37] implemented on GPU using the NVIDIA CUDA framework, 83 × faster than the SLIC CPU implementation. The gSLICr has three parameters: S, C and N. S stands for super pixel size, C is the compact coefficient degree, N is the number of iterations. In our paper, S was set to 15, C was set to 0.2, and N was set to 50. After super pixel segmentation, users can modify the auto-segmentation results based on super pixels.

Accuracy assessment

To quantify the performance of our method, we evaluated our semantic segmentation calculating Pixel Accuracy (P.A.) (1) and mean IoU (mIoU) (2). These are standard metrics used to quantify semantic segmentation tasks [30]. P.A. indicates the proportion of correctly classified pixels to the total number of pixels and mIoU indicates the intersection-over-union (IoU) between the ground truth and the predicted pixels, averaged over all classes:

where n is the number of classes, p_ij is the number of pixels of class i predicted to belong to class j, p_ii is the true positive, p_ijis the false negative, p_ji is the false positive, p_jj is the true negative.

Calculation of leaf-panicle ratio (LPR)

The software GvCrop was developed to calculate LPR based on the quantity of pixels contained in the leaf (L) and panicle (P) regions in an image and is calculated as: LPR = L / P.

1. Accuracy verification

The semantic segmentation of the 90 field images was assessed both visually (Fig. 5) and quantitatively (Table 1).

Figure 5 shows some examples of semantic segmentation results. Visual assessment suggested that the tested results and real data were very similar in different conditions. However, we still found some subtle segmentation errors: 1) The background and shadow pixels of the leaves were very similar visually, resulting in some shadow pixels being misclassified as background; 2) The segmentation was a little poor at the edges of the plant parts. Pixels at the junction between leaf and panicle were misclassified into error categories; 3) Some scattered small patches on the leaves were misclassified as panicle.

Table 1 provides a quantitative evaluation of the complete test set, indicating the accuracy of all the testing images exhibited high accuracy and differences between each image were quite small. Difference between each stage was also very small. Table S3 shows the model can reach 99 % accuracy for panicles pixels, followed by leaf pixels (97.6 % to 98.3 %), while the worse was for background pixels, ranging from 81.4 % to 89.4 %.

The efficiency of a training model can also be described in terms of training data loss. Figure S1 exhibits that there was a rapid decline in loss over subsequent epochs of training, although the loss was initially high. To avoid overfitting and improve the robustness of our model, we iteratively added samples to the training dataset (Fig. 1(5)) and performed basic data enhancements randomly to the training set before put into the model so that the curve did not decrease smoothly.

2. Verification and application of the FPN-Mask model

The most important output of this FPN-Mask model is to estimate the distribution of light interception between leaf and panicle. Using GvCrop, we calculated the LPR values of the crop stand for various field experiments and detected large spatial and temporal variations as well as genotypic differences. Overall, these results suggest the feasibility of the model in detecting and quantifying crop performance under field conditions.

(1) Daily changes of LPR

LPR showed an obvious pattern of daily change, being higher after sunrise and before sunset but lower at noon (Fig. 6). The larger values of LPR in the morning or afternoon can be explained by the shading of leaves when the solar angle of incidence is lower.

(2) Genotypic variations in LPR

Large genotypic differences in LPR were detected among the 192 mutants, ranging from 1.37 to 5.60 (Table S4). As shown in Fig. 7, the six panicle types showed marked differences in LPR. Generally, cultivars with compact panicle (CP) had the highest value, while those with loose panicle and awns (LPA) had the lowest. The former can be associated with the high density of spikelets on the panicle that caused smaller panicle area. The latter can be explained by the large panicle area due to sparse spikelets. Temporal variations of LPR were revealed showing a diminishing trend from the early stage to the late stage of grain filling. This means the relative area of leaf was reduced, as it is partly due to the increased area of panicle that changes its shape from erect and dense at early stage to loose and drooping at late stage.

(3) N effect on LPR

N fertilization mode exerted substantial influence on LPR. On average, N topdressing of the N5-5 increased LPR by 0.45 and 0.76 at middle and late stage, respectively (Fig. 8), compared with N10-0. The promoting effect of N topdressing is associated with the elongation of flag leaf (Fig. 8). Similarly, LPR decreased gradually as grain filling progressed for both N treatments.

(4) Modification of LPR by plant growth regulators

Plant growth regulators brassinolide, brassinazole, gibberellin, and uniconazole obviously reshaped plant architecture (Fig. 9). The effects of these regulators agreed well with their well-documented phenotypes, for example, the drooping flag leaf caused by brassinolide spraying [38, 39] and the elongated upper internode caused by gibberellin [40]. More importantly, LPR can be either up-regulated or down-regulated by these regulators, depending on growth stages. As shown in Fig. 9, LPR at grain filling stage was increased by brassinazole and uniconazole, whereas reduced by brassinolide and gibberellin. In addition, the degree of increase or decrease depended on regulators, with uniconazole having the most significant influence.

1. Weakness of the methodology and improvement

In this study, we built a robust and highly accurate deep learning network, FPN-Mask, which can easily segment panicle, leaf and background at a pixel level from a field RGB image. For this study we also developed the GvCrop software, which not only included some basic image processing functions such as I/O, cut, rotation, zoom in/out, translation, but also integrated the above-mentioned auto semantic segmentation method, manual modification of auto-segmentation result function and export of LPR report function.

This work represents a proof of concept that deep learning can be used for accurate organ level (panicle, leaf) pixel-wise segmentation of field rice images. However, there are several challenges which should be resolved in future work.

First, segmentation accuracy was quite high for these 6 GB datasets, but if objects were not included in the training dataset, it would have not performed as well. In other words, the robustness of a deep learning model is partially dependent on the diversity of the training dataset. In the future, we will seek to improve the robustness of FPN-Mask by collecting a wider range of field data. Second, the shadow on leaves and background exhibited very similar visual patterns. It is difficult to distinguish red, green and blue in the visible band. The junctions between different parts of plants are also quite difficult to distinguish. This explained most of the low precision for the semantic segmentation, and these types of errors occurred in every image in the testing dataset. Other studies also met the same problem [18].

Third, perspective photography can cause the deformation of objects projected into 2D images, which in turn affects the accuracy of LPR. However, our method has an advantage of reliably calculating the relative value of leaf to panicle ratio using 2D photos, on which the leaf and panicle in the 3D stand is compressed proportionally according to the imaging principle of the camera. Recently, light detection and ranging (LiDAR) has shown its advantages for showing high resolution 3-dimensional (3D) structural information of terrain and vegetation [41-43] and the advantage for segmentation of plant organs [16, 44, 45]. Shi et al [18] also showed that a multi-view 3D system can avoid these errors. In the future, we will combine plant height provided by LiDAR to texture and color information provided by the RGB image to distinguish object categories more effectively and accurately.

2. Significance of LPR for crop breeding and management

To some degree, the essence of crop sciences is the knowledge of selection (by breeders) or regulation (by agronomists) of agronomical traits. Traditionally, crop scientists heavily depend on visual inspection of crops in the field as well as their evaluation of target traits based on their experience and expertise of the crop, which is labor intensive, time consuming, relatively subjective, and prone to errors [14, 46]. In addition, the target traits are mainly morphological traits including leaf senescence, plant height, tillering capacity, panicle or spike size, and growth periods, while fewer physiological traits are monitored and analyzed. With the development of plant phenotyping techniques, image-based methods have been successfully applied to obtain phenotypic data related to crop morphology and physiology [16]. In wheat, high throughput methods for a large array of traits are available for the breeders, including canopy temperature, normalized difference vegetation index (NDVI), and chlorophyll fluorescence [47]. However, the capacity for undertaking precision phenotyping of physiological traits is lagging far behind the requirement of crop sciences.

In this study, we propose a new physiological trait, LPR, based on deep learning. Physiologically, LPR indicates the distribution of light interception within the canopy between the source organ leaf and the sink organ panicle. Historically, breeders and agronomists focused on improvement in source activity, with traits of the leaf such as photosynthesis, erectness, and stay-green as the main targets. On the other hand, the role of panicle was largely overlooked, with less attention except for grain number per panicle or erectness of the panicle [7]. The significance of the panicle has been increasingly recognized in terms of its substantial contribution of carbohydrates, nitrogen, and minerals to grain filling. Therefore, light interception of panicles is dispensable for yield formation, and there should be a suitable LPR value for a crop stands growing in a given ecological condition.

The trait of LPR should provide crop scientists with new insights into the physiological status of the crop stand from the perspective of source and sink balance. For breeders, large genotypic variations in LPR are detected among the 192 germplasms, with a range of 1.37 to 5.60, indicating the possibility to select elite parents for target hybridization and future studies on the morphological and physiological foundations of LPR. For agronomists, LPR is affected by nitrogen fertilization mode, and high yielding practice of N5-5 showed a relatively higher LPR value than that of N10-0, explaining the yield promotion effect of nitrogen topdressing in terms of source-sink relations. Further, LPR was sensitive to foliar application of plant growth regulators like BR and GA, and can be increased by brassinazole and uniconazole, or reduced by brassinolide and gibberellin. Thus it is possible to develop methods for targeted regulation of crop stands with a desirable LPR by chemical intervention. In addition, LPR can be easily measured by digital camera and even a smartphone camera (data not shown), and we are currently conducting an experiment to identify the timing that can represent the average or general value of LPR for the whole daytime, which could facilitate the use of LPR by crop scientists. Nevertheless, more work is needed when applying LPR in crop breeding or management, in particular elucidating the inherent link between LPR and yield, and proposing a set of suitable LPR values for different environments or plant types.

The work represents a proof of the concept that the deep learning can achieve high accuracy in simultaneously detecting panicle and leaf data from complex rice field images. The FPN-Mask model is applicable for detecting and quantifying crop performance under field conditions. The proposed trait of LPR should provide a high throughput protocol for breeders to select superior rice cultivars as well as for agronomists to precisely manage field crops to have a good balance of source and sink. However, there are several challenges which should be resolved in future work, in particular combining plant height by LiDAR with the texture and color information from RGB image to distinguish object categories more effectively and accurately.

BR: Brassinolide; BRZ: Brassinazole; CP: Compact panicle; CT: Chicken toe; CTP: Chicken toe panicle; 3D: 3-dimensional; 2D: 2-dimensional; DAA: Days after anthesis; DCLISD: Dynamic canopy light interception simulating device; EP: Erect panicle; FPN: Feature Pyramid Network; FPN-Mask: Feature Pyramid Network Mask; GA: Gibberellin; GG: Green panicle with Green leaf; GPU: GeForce graphics processing unit; IoU: Intersection-over-union; IP: Intermediate panicle; L: Leaf; LiDAR: Light detection and ranging; LP: Loose panicle; LPA: Loose panicle with awns; LPR: Leaf to panicle ratio; Max: Maximum; Min: Minimum; mIoU: Mean intersection-over-union; N: Nitrogen; NDVI: Normalized difference vegetation index; N5-5: N fertilization mode with base/topdressing ratio of 5/5; N10-0: N fertilization mode with base/topdressing ratio of 10/0; Panicle; PA: Pixel accuracy; ResNet: Residual Networks; RGB: Red-Green-Blue; ROI: Region of interest; SLIC: Simple Linear Iterative Clustering; Std: Standard error of mean; UNI: Uniconazole; WT: Wild type; YG: Yellow panicle with Green leaf; YY: Yellow panicle with Yellow leaf.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Availability of data and materials

The data used in this study is available from the corresponding author on reasonable request.

Competing interest

The authors declare that they have no conflicts of interest.

Funding

The research was supported by the National Key R&D Program, Ministry of Science and Technology, China [2017YFD0300103], the National Natural Science Foundation of China (31771719), and National High Technology Research and Development Program of China (2014AA10A605). Rothamsted Research receives strategic funding from the Biological and Biotechnological Sciences Research Council of the United Kingdom. Matthew Paul acknowledges the Designing Future Wheat Strategic Programme (BB/P016855/1).

Author contributions

Zongfeng Yang and Shang Gao had the main responsibility for data collection and analysis, Feng Xiao contributed to data collection and analysis, Ganghua Li, Yangfeng Ding, and Matthew Paul revised the manuscript, Qinghua Guo and Zhenghui Liu (the corresponding authors) had the overall responsibility for experimental design, project management and manuscript preparation.

Acknowledgements

Not applicable.

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Table 1 Accuracy assessments of the leaf-panicle segmentation

ID	GG		YG		YY
ID	mIoU	PA	mIoU	PA	mIoU	PA
1	0.861	0.937	0.846	0.912	0.900	0.950
2	0.851	0.945	0.860	0.921	0.899	0.952
3	0.840	0.946	0.830	0.902	0.866	0.933
4	0.849	0.958	0.844	0.915	0.861	0.934
5	0.842	0.959	0.845	0.919	0.854	0.936
6	0.837	0.954	0.846	0.921	0.850	0.940
7	0.833	0.954	0.850	0.927	0.856	0.944
8	0.822	0.948	0.847	0.923	0.837	0.933
9	0.825	0.950	0.847	0.924	0.842	0.936
10	0.881	0.987	0.887	0.959	0.890	0.945
11	0.869	0.984	0.864	0.943	0.874	0.931
12	0.857	0.978	0.855	0.934	0.887	0.942
13	0.846	0.979	0.845	0.925	0.889	0.941
14	0.837	0.978	0.841	0.928	0.881	0.935
15	0.847	0.976	0.851	0.936	0.880	0.938
16	0.851	0.978	0.856	0.938	0.885	0.943
17	0.852	0.978	0.860	0.942	0.872	0.937
18	0.863	0.974	0.863	0.946	0.875	0.938
19	0.825	0.962	0.867	0.948	0.880	0.942
20	0.824	0.961	0.871	0.949	0.873	0.938
21	0.824	0.961	0.871	0.950	0.871	0.938
22	0.831	0.960	0.870	0.949	0.871	0.939
23	0.838	0.959	0.868	0.947	0.874	0.941
24	0.837	0.960	0.876	0.948	0.874	0.942
25	0.836	0.961	0.880	0.948	0.874	0.942
26	0.833	0.962	0.879	0.947	0.874	0.942
27	0.833	0.963	0.877	0.947	0.872	0.940
28	0.832	0.962	0.877	0.947	0.871	0.940
29	0.831	0.962	0.869	0.942	0.870	0.941
30	0.833	0.963	0.867	0.942	0.871	0.942
Mean	0.841	0.963	0.860	0.936	0.872	0.940
Min	0.822	0.937	0.830	0.902	0.837	0.931
Max	0.881	0.987	0.887	0.959	0.900	0.952
Std	0.014	0.012	0.014	0.014	0.014	0.005

Note: GG, Green panicle with Green leaf; YG, Yellow panicle with Green leaf; YY, Yellow panicle with Yellow leaf; mIoU, mean intersection-over-union; PA, Pixel accuracy；Min, Minimum; Max, Maximum; Std, Standard error of mean.

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Leaf to panicle ratio (LPR): a new physiological trait indicative of source and sink relation in japonica rice based on deep learning

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