Guoxing Chen

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits.

Plant phenomics and high-throughput phenotyping accelerating rice functional genomics using multidisciplinary technologies

The functional analysis of the rice genome has entered into a high-throughput stage, and a project named RICE2020 has been proposed to determine the function of every gene in the rice genome by the year 2020. However, as compared with the robustness of genetic techniques, the evaluation of rice phenotypic traits is still performed manually, and the process is subjective, inefficient, destructive and error-prone. To overcome these limitations and help rice phenomics more closely parallel rice genomics, reliable, automatic, multifunctional, and high-throughput phenotyping platforms should be developed. In this article, we discuss the key plant phenotyping technologies, particularly photonics-based technologies, and then introduce their current applications in rice (wheat or barley) phenomics. We also note the major challenges in rice phenomics and are confident that these reliable high-throughput phenotyping tools will give plant scientists new perspectives on the information encoded in the rice genome.

Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer

Highlight A combination of high-throughput leaf phenotyping and genome-wide association analysis provides valuable insights into the genetic basis of rice leaf traits.

High-throughput phenotyping and QTL mapping reveals the genetic architecture of maize plant growth

Combining high-throughput phenotyping and large-scale QTL mapping dissects the dynamic genetic architecture of maize development by using a RIL population. With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction.

A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

BackgroundThe fitness of the rape leaf is closely related to its biomass and photosynthesis. The study of leaf traits is significant for improving rape leaf production and optimizing crop management. Canopy structure and individual leaf traits are the major indicators of quality during the rape seedling stage. Differences in canopy structure reflect the influence of environmental factors such as water, sunlight and nutrient supply. The traits of individual rape leaves traits indicate the growth period of the rape as well as its canopy shape.ResultsWe established a high-throughput stereo-imaging system for the reconstruction of the three-dimensional canopy structure of rape seedlings from which leaf area and plant height can be extracted. To evaluate the measurement accuracy of leaf area and plant height, 66 rape seedlings were randomly selected for automatic and destructive measurements. Compared with the manual measurements, the mean absolute percentage error of automatic leaf area and plant height measurements was 3.68 and 6.18%, respectively, and the squares of the correlation coefficients (R2) were 0.984 and 0.845, respectively. Compared with the two-dimensional projective imaging method, the leaf area extracted using stereo-imaging was more accurate. In addition, a semi-automatic image analysis pipeline was developed to extract 19 individual leaf shape traits, including 11 scale-invariant traits, 3 inner cavity related traits, and 5 margin-related traits, from the images acquired by the stereo-imaging system. We used these quantified traits to classify rapes according to three different leaf shapes: mosaic-leaf, semi-mosaic-leaf, and round-leaf. Based on testing of 801 seedling rape samples, we found that the leave-one-out cross validation classification accuracy was 94.4, 95.6, and 94.8% for stepwise discriminant analysis, the support vector machine method and the random forest method, respectively.ConclusionsIn this study, a nondestructive and high-throughput stereo-imaging system was developed to quantify canopy three-dimensional structure and individual leaf shape traits with improved accuracy, with implications for rape phenotyping, functional genomics, and breeding.

Panicle-SEG: a robust image segmentation method for rice panicles in the field based on deep learning and superpixel optimization

BackgroundRice panicle phenotyping is important in rice breeding, and rice panicle segmentation is the first and key step for image-based panicle phenotyping. Because of the challenge of illumination differentials, panicle shape deformations, rice accession variations, different reproductive stages and the field’s complex background, rice panicle segmentation in the field is a very large challenge.ResultsIn this paper, we propose a rice panicle segmentation algorithm called Panicle-SEG, which is based on simple linear iterative clustering superpixel regions generation, convolutional neural network classification and entropy rate superpixel optimization. To build the Panicle-SEG-CNN model and test the segmentation effects, 684 training images and 48 testing images were randomly selected, respectively. Six indicators, including Qseg, Sr, SSIM, Precision, Recall and F-measure, are employed to evaluate the segmentation effects, and the average segmentation results for the 48 testing samples are 0.626, 0.730, 0.891, 0.821, 0.730, and 76.73%, respectively. Compared with other segmentation approaches, including HSeg, i2 hysteresis thresholding and jointSeg, the proposed Panicle-SEG algorithm has better performance on segmentation accuracy. Meanwhile, the executing speed is also improved when combined with multithreading and CUDA parallel acceleration. Moreover, Panicle-SEG was demonstrated to be a robust segmentation algorithm, which can be expanded for different rice accessions, different field environments, different camera angles, different reproductive stages, and indoor rice images. The testing dataset and segmentation software are available online.ConclusionsIn conclusion, the results demonstrate that Panicle-SEG is a robust method for panicle segmentation, and it creates a new opportunity for nondestructive yield estimation.

A hyperspectral imaging system for an accurate prediction of the above-ground biomass of individual rice plants.

Biomass is an important component of the plant phenomics, and the existing methods for biomass estimation for individual plants are either destructive or lack accuracy. In this study, a hyperspectral imaging system was developed for the accurate prediction of the above-ground biomass of individual rice plants in the visible and near-infrared spectral region. First, the structure of the system and the influence of various parameters on the camera acquisition speed were established. Then the system was used to image 152 rice plants, which selected from the rice mini-core collection, in two stages, the tillering to elongation (T-E) stage and the booting to heading (B-H) stage. Several variables were extracted from the images. Following, linear stepwise regression analysis and 5-fold cross-validation were used to select effective variables for model construction and test the stability of the model, respectively. For the T-E stage, the R(2) value was 0.940 for the fresh weight (FW) and 0.935 for the dry weight (DW). For the B-H stage, the R(2) value was 0.891 for the FW and 0.783 for the DW. Moreover, estimations of the biomass using visible light images were also calculated. These comparisons showed that hyperspectral imaging performed better than the visible light imaging. Therefore, this study provides not only a stable hyperspectral imaging platform but also an accurate and nondestructive method for the prediction of biomass for individual rice plants.

Accurate Digitization of the Chlorophyll Distribution of Individual Rice Leaves Using Hyperspectral Imaging and an Integrated Image Analysis Pipeline

Pigments absorb light, transform it into energy, and provide reaction sites for photosynthesis; thus, the quantification of pigment distribution is vital to plant research. Traditional methods for the quantification of pigments are time-consuming and not suitable for the high-throughput digitization of rice pigment distribution. In this study, using a hyperspectral imaging system, we developed an integrated image analysis pipeline for automatically processing enormous amounts of hyperspectral data. We also built models for accurately quantifying 4 pigments (chlorophyll a, chlorophyll b, total chlorophyll and carotenoid) from rice leaves and determined the important bands (700-760 nm) associated with these pigments. At the tillering stage, the R2 values and mean absolute percentage errors of the models were 0.827–0.928 and 6.94–12.84%, respectively. The hyperspectral data and these models can be combined for digitizing the distribution of the chlorophyll with high resolution (0.11 mm/pixel). In summary, the integrated hyperspectral image analysis pipeline and selected models can be used to quantify the chlorophyll distribution in rice leaves. The use of this technique will benefit rice functional genomics and rice breeding.

A nondestructive method for estimating the total green leaf area of individual rice plants using multi-angle color images

Total green leaf area (GLA) is an important trait for agronomic studies. However, existing methods for estimating the GLA of individual rice plants are destructive and labor-intensive. A nondestructive method for estimating the total GLA of individual rice plants based on multi-angle color images is presented. Using projected areas of the plant in images, linear, quadratic, exponential and power regression models for estimating total GLA were evaluated. Tests demonstrated that the side-view projected area had a stronger relationship with the actual total leaf area than the top-projected area. And power models fit better than other models. In addition, the use of multiple side-view images was an efficient method for reducing the estimation error. The inclusion of the top-view projected area as a second predictor provided only a slight improvement of the total leaf area estimation. When the projected areas from multi-angle images were used, the estimated leaf area (ELA) using the power model and the actual leaf area had a high correlation coefficient (R2 > 0.98), and the mean absolute percentage error (MAPE) was about 6%. The method was capable of estimating the total leaf area in a nondestructive, accurate and efficient manner, and it may be used for monitoring rice plant growth.

High-Throughput Estimation of Yield for Individual Rice Plant Using Multi-angle RGB Imaging

Modern breeding technologies are capable of producing hundreds of new varieties daily, so fast, simple and effective methods for screening valuable candidate plant materials are urgently needed. Final yield is a significant agricultural trait in rice breeding. In the screening and evaluation of the rice varieties, measuring and evaluating rice yield is essential. Conventional means of measuring rice yield mainly depend on manual determination, which is tedious, labor-intensive, subjective and error-prone, especially when large-scale plants were to be investigated. This paper presented an in vivo, automatic and high-throughput method to estimate the yield of individual pot-grown rice plant using multi-angle RGB imaging and image analysis. In this work, we demonstrated a new idea of estimating rice yield from projected panicle area, projected area of leaf and stem and fractal dimension. 5-fold cross validation showed that the predictive error was 7.45%. The constructed model achieved promising results on rice plants grown both in-door and out-door. The presented work has the potential of accelerating yield estimation and would be a promising impetus for plant phenomics.