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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Integrated field phenotyping and management platform for crop development and precision agriculture

A field controller and sensor is presented as an elongate body having a hollow interior and axially opposite first and second ends with a first arm extending outward from the elongate body adjacent to the first axial end and a second arm extending outward from the elongate body adjacent to the second, axially opposite end. Each of the arms has an imaging device. The first arm imaging device is positioned to obtain images in a direction toward the second axial end of the elongate body. The second arm imaging device is positioned to obtain images in a direction toward the first axial end. The first and second arms are spaced apart from one another along a length of the elongate body at a distance sufficient to image a canopy of crop growth in a field in which the field controller and sensor is deployed. The sensor may be formed from modules that allow the operator the ability to vary the height of the sensor by stacking the modules together end to end, which in turn allows users to scale their particular system with varying crop sizes within crop rotations.

Shakoor, Nadia↗
DOE OSTI2023

High-Throughput Field Plant Phenotyping: A Self-Supervised Sequential CNN Method to Segment Overlapping Plants

High-throughput plant phenotyping—the use of imaging and remote sensing to record plant growth dynamics—is becoming more widely used. The first step in this process is typically plant segmentation, which requires a well-labeled training dataset to enable accurate segmentation of overlapping plants. However, preparing such training data is both time and labor intensive. To solve this problem, we propose a plant image processing pipeline using a self-supervised sequential convolutional neural network method for in-field phenotyping systems. This first step uses plant pixels from greenhouse images to segment nonoverlapping in-field plants in an early growth stage and then applies the segmentation results from those early-stage images as training data for the separation of plants at later growth stages. The proposed pipeline is efficient and self-supervising in the sense that no human-labeled data are needed. We then combine this approach with functional principal components analysis to reveal the relationship between the growth dynamics of plants and genotypes. We show that the proposed pipeline can accurately separate the pixels of foreground plants and estimate their heights when foreground and background plants overlap and can thus be used to efficiently assess the impact of treatments and genotypes on plant growth in a field environment by computer vision techniques. This approach should be useful for answering important scientific questions in the area of high-throughput phenotyping.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Plot-level rapid screening for photosynthetic parameters using proximal hyperspectral imaging

Abstract Photosynthesis is currently measured using time-laborious and/or destructive methods which slows research and breeding efforts to identify crop germplasm with higher photosynthetic capacities. We present a plot-level screening tool for quantification of photosynthetic parameters and pigment contents that utilizes hyperspectral reflectance from sunlit leaf pixels collected from a plot (~2 m×2 m) in <1 min. Using field-grown Nicotiana tabacum with genetically altered photosynthetic pathways over two growing seasons (2017 and 2018), we built predictive models for eight photosynthetic parameters and pigment traits. Using partial least squares regression (PLSR) analysis of plot-level sunlit vegetative reflectance pixels from a single visible near infra-red (VNIR) (400–900 nm) hyperspectral camera, we predict maximum carboxylation rate of Rubisco (Vc,max, R2=0.79) maximum electron transport rate in given conditions (J1800, R2=0.59), maximal light-saturated photosynthesis (Pmax, R2=0.54), chlorophyll content (R2=0.87), the Chl a/b ratio (R2=0.63), carbon content (R2=0.47), and nitrogen content (R2=0.49). Model predictions did not improve when using two cameras spanning 400–1800 nm, suggesting a robust, widely applicable and more ‘cost-effective’ pipeline requiring only a single VNIR camera. The analysis pipeline and methods can be used in any cropping system with modified species-specific PLSR analysis to offer a high-throughput field phenotyping screening for germplasm with improved photosynthetic performance in field trials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

PHOTO‐SENSITIVE LEAF ROLLING 1 encodes a polygalacturonase that modifies cell wall structure and drought tolerance in rice

Summary The biosynthesis and modification of cell wall composition and structure are controlled by hundreds of enzymes and have a direct consequence on plant growth and development. However, the majority of these enzymes has not been functionally characterised. Rice mutants with leaf‐rolling phenotypes were screened in a field. Phenotypic analysis under controlled conditions was performed for the selected mutant and the relevant gene was identified by map‐based cloning. Cell wall composition was analysed by glycome profiling assay. We identified a photo‐sensitive leaf rolling 1 ( psl1 ) mutant with ‘napping’ (midday depression of photosynthesis) phenotype and reduced growth. The PSL1 gene encodes a cell wall‐localised polygalacturonase (PG), a pectin‐degrading enzyme. psl1 with a 260‐bp deletion in its gene displayed leaf rolling in response to high light intensity and/or low humidity. Biochemical assays revealed PG activity of recombinant PSL1 protein. Significant modifications to cell wall composition in the psl1 mutant compared with the wild‐type plants were identified. Such modifications enhanced drought tolerance of the mutant plants by reducing water loss under osmotic stress and drought conditions. Taken together, PSL1 functions as a PG that modifies cell wall biosynthesis, plant development and drought tolerance in rice.

Zhang, Guangheng↗
DOE OSTI2021

Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping

Abstract Camelina [ Camelina sativa (L.) Crantz] is an oilseed crop in the Brassicaceae family that is currently being developed as a source of bioenergy and healthy fatty acids. To facilitate modern breeding efforts through marker‐assisted selection and biotechnology, we evaluated genetic variation among a worldwide collection of 222 camelina accessions. We performed whole‐genome resequencing to obtain single nucleotide polymorphism (SNP) markers and to analyze genomic diversity. We also conducted phenotypic field evaluations in two consecutive seasons for variations in key agronomic traits related to oilseed production such as seed size, oil content (OC), fatty acid composition, and flowering time. We determined the population structure of the camelina accessions using 161,301 SNPs. Further, we identified quantitative trait loci (QTL) and candidate genes controlling the above field‐evaluated traits by genome‐wide association studies (GWAS) complemented with linkage mapping using a recombinant inbred line (RIL) population. Characterization of the natural variation at the genome and phenotypic levels provides valuable resources to camelina genetic studies and crop improvement. The QTL and candidate genes should assist in breeding of advanced camelina varieties that can be integrated into the cropping systems for the production of high yield of oils of desired fatty acid composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Integrating crop growth models with remote sensing for predicting biomass yield of sorghum

Abstract Plant phenotypes are often descriptive, rather than predictive of crop performance. As a result, extensive testing is required in plant breeding programmes to develop varieties aimed at performance in the target environments. Crop models can improve this testing regime by providing a predictive framework to (i) augment field phenotyping data and derive hard-to-measure phenotypes and (ii) estimate performance across geographical regions using historical weather data. The goal of this study was to parameterize the Agricultural Production Systems sIMulator (APSIM) crop growth models with remote-sensing and ground-reference data to predict variation in phenology and yield-related traits in 18 commercial grain and biomass sorghum hybrids. Genotype parameters for each hybrid were estimated using remote-sensing measurements combined with manual phenotyping in West Lafayette, IN, in 2018. The models were validated in hybrid performance trials in two additional seasons at that site and against yield trials conducted in Bushland, TX, between 2001 and 2018. These trials demonstrated that (i) maximum plant height, final dry biomass and radiation use efficiency (RUE) of photoperiod-sensitive and -insensitive forage sorghum hybrids tended to be higher than observed in grain sorghum, (ii) photoperiod-sensitive sorghum hybrids exhibited greater biomass production in longer growing environments and (iii) the parameterized and validated models perform well in above-ground biomass simulations across years and locations. Crop growth models that integrate remote-sensing data offer an efficient approach to parameterize larger plant breeding populations.

Yang, Kai-Wei↗
DOE OSTI2022

Deep Convolutional Neural Networks Exploit High-Spatial- and -Temporal-Resolution Aerial Imagery to Phenotype Key Traits in Miscanthus

Miscanthus is one of the most promising perennial crops for bioenergy production, with high yield potential and a low environmental footprint. The increasing interest in this crop requires accelerated selection and the development of new screening techniques. New analytical methods that are more accurate and less labor-intensive are needed to better characterize the effects of genetics and the environment on key traits under field conditions. We used persistent multispectral and photogrammetric UAV time-series imagery collected 10 times over the season, together with ground-truth data for thousands of Miscanthus genotypes, to determine the flowering time, culm length, and biomass yield traits. We compared the performance of convolutional neural network (CNN) architectures that used image data from single dates (2D-spatial) versus the integration of multiple dates by 3D-spatiotemporal architectures. The ability of UAV-based remote sensing to rapidly and non-destructively assess large-scale genetic variation in flowering time, height, and biomass production was improved through the use of 3D-spatiotemporal CNN architectures versus 2D-spatial CNN architectures. The performance gains of the best 3D-spatiotemporal analyses compared to the best 2D-spatial architectures manifested in up to 23% improvements in R2, 17% reductions in RMSE, and 20% reductions in MAE. The integration of photogrammetric and spectral features with 3D architectures was crucial to the improved assessment of all traits. In conclusion, our findings demonstrate that the integration of high-spatiotemporal-resolution UAV imagery with 3D-CNNs enables more accurate monitoring of the dynamics of key phenological and yield-related crop traits. This is especially valuable in highly productive, perennial grass crops such as Miscanthus, where in-field phenotyping is especially challenging and traditionally limits the rate of crop improvement through breeding.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 ( ZmCIPK15 )

Crops with reduced nutrient and water requirements are urgently needed in global agriculture. Root growth angle plays an important role in nutrient and water acquisition. A maize diversity panel of 481 genotypes was screened for variation in root angle employing a high-throughput field phenotyping platform. Genome-wide association mapping identified several single nucleotide polymorphisms (SNPs) associated with root angle, including one located in the root expressed CBL-interacting serine/threonine-protein kinase 15 (ZmCIPK15) gene (LOC100285495). Reverse genetic studies validated the functional importance of ZmCIPK15, causing a approximately 10° change in root angle in specific nodal positions. A steeper root growth angle improved nitrogen capture in silico and in the field. OpenSimRoot simulations predicted at 40 days of growth that this change in angle would improve nitrogen uptake by 11% and plant biomass by 4% in low nitrogen conditions. In field studies under suboptimal N availability, the cipk15 mutant with steeper growth angles had 18% greater shoot biomass and 29% greater shoot nitrogen accumulation compared to the wild type after 70 days of growth. We propose that a steeper root growth angle modulated by ZmCIPK15 will facilitate efforts to develop new crop varieties with optimal root architecture for improved performance under edaphic stress.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Root system architecture in cereals: progress, challenges and perspective

We report roots are essential multifunctional plant organs involved in water and nutrient uptake, metabolite storage, anchorage, mechanical support, and interaction with the soil environment. Understanding of this ‘hidden half’ provides potential for manipulation of root system architecture (RSA) traits to optimize resource use efficiency and grain yield in cereal crops. Unfortunately, root traits are highly neglected in breeding due to the challenges of phenotyping, but could have large rewards if the variability in RSA traits can be fully exploited. Until now, a plethora of genes have been characterized in detail for their potential role in improving RSA. The use of forward genetics approaches to find sequence variations in genes underpinning desirable RSA would be highly beneficial. Advances in computer vision applications have allowed image-based approaches for high-throughput phenotyping of RSA traits that can be used by any laboratory worldwide to make progress in understanding root function and dissection of the genetics. At the same time, the frontiers of root measurement include non-invasive methods like X-ray computer tomography and magnetic resonance imaging that facilitate new types of temporal studies. Root physiology and ecology are further supported by spatiotemporal root simulation modeling. The discovery of component traits providing improved resilience and yield advantage in target environments is a key necessity for mainstreaming root-based cereal breeding. The integrated use of pan-genome resources, now available in most cereals, coupled with new in-field phenotyping platforms has the potential for precise selection of superior genotypes with improved RSA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

DIRT/3D: 3D root phenotyping for field-grown maize ( Zea mays )

The development of crops with deeper roots holds substantial promise to mitigate the consequences of climate change. Deeper roots are an essential factor to improve water uptake as a way to enhance crop resilience to drought, to increase nitrogen capture, to reduce fertilizer inputs, and to increase carbon sequestration from the atmosphere to improve soil organic fertility. A major bottleneck to achieving these improvements is high-throughput phenotyping to quantify root phenotypes of field-grown roots. We address this bottleneck with Digital Imaging of Root Traits (DIRT)/3D, an image-based 3D root phenotyping platform, which measures 18 architecture traits from mature field-grown maize (Zea mays) root crowns (RCs) excavated with the Shovelomics technique. DIRT/3D reliably computed all 18 traits, including distance between whorls and the number, angles, and diameters of nodal roots, on a test panel of 12 contrasting maize genotypes. The computed results were validated through comparison with manual measurements. Overall, we observed a coefficient of determination of r 2 > 0.84 and a high broad-sense heritability of H$_{mean}^{2}$ < 0.6 for all but one trait. The average values of the 18 traits and a developed descriptor to characterize complete root architecture distinguished all genotypes. DIRT/3D is a step toward automated quantification of highly occluded maize RCs. Therefore, DIRT/3D supports breeders and root biologists in improving carbon sequestration and food security in the face of the adverse effects of climate change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The Consortium for Advanced Sorghum Phenomics (CASP). Final report

The goal of CASP was to accelerate breeding of biomass sorghum [Sorghum bicolor (L.) Moench] by identifying genotypes exhibiting high yield under well-watered, pre- or post-drought and/or salinity-stress conditions. We did this by combining high-throughput, non-invasive drone phenotyping with genomics and molecular profiling. Field-based phenotyping utilized a multi-modal sensor suite of LiDAR, multispectral cameras, and thermal cameras mounted on a commercial drone to detect traits required for yield prediction and selection of drought and saline tolerant lines of sorghum. Traits of interest included plant height (PH), leaf area index (LAI), wet biomass (BMW), and biomass at 65% moisture (BM65) and were measured from emergence to harvest on a weekly basis over three growing seasons. The final output were measurements of traits on a plot-by-plot basis, identified by the plot ID used by the Proprietary data processing software enabled raw field data to be turned into plant traits and delivered to the PNNL and JGI within the same workday.

09 BIOMASS FUELS↗
DOE OSTI2025

Phenome‐to‐genome insights for evaluating root system architecture in field studies of maize

Abstract Understanding the genetic basis of root system architecture (RSA) in crops requires innovative approaches that enable both high‐throughput and precise phenotyping in field conditions. In this study, we evaluated multiple phenotyping and analytical frameworks for quantifying RSA in mature, field‐grown maize in three field experiments. We used forward and reverse genetic approaches to evaluate >1700 maize root crowns, including a diversity panel, a biparental mapping population, and maize mutant and wild‐type alleles at two known RSA genes,DEEPER ROOTING 1(DRO1) andRootless1(Rt1). We show the utility of increasing the dimensionality of traditional two‐dimensional (2D) techniques, referred to as the “2D multi‐view” method, to improve the capture of whole root system information for mapping genetic variation influencing RSA. Comparison of univariate and multivariate genome‐wide association study (GWAS) approaches revealed that multivariate traits were effective at dissecting complex RSA phenotypes and identifying pleiotropic quantitative trait loci (QTLs). Overall, three‐dimensional (3D) root models generated from X‐ray computed tomography and digital phenotyping captured a larger proportion of RSA trait variations compared to other methods of root phenotyping, as evidenced by both genome‐wide and single‐gene analyses. Among the individual root traits, root pulling force emerged as a highly heritable estimate of RSA that identified the largest number of shared QTLs with 3D phenotypes. Our study shows that integrating complementary phenotyping technologies helps to provide a more comprehensive understanding of the genetic architecture of RSA in field‐grown maize.

Genetics & Heredity↗
DOE OSTI2022

Installation and imaging of thousands of minirhizotrons to phenotype root systems of field-grown plants

Roots are vital to plant performance because they acquire resources from the soil and provide anchorage. However, it remains difficult to assess root system size and distribution because roots are inaccessible in the soil. Existing methods to phenotype entire root systems range from slow, often destructive, methods applied to relatively small numbers of plants in the field to rapid methods that can be applied to large numbers of plants in controlled environment conditions. Much has been learned recently by extensive sampling of the root crown portion of field-grown plants. But, information on large-scale genetic and environmental variation in the size and distribution of root systems in the field remains a key knowledge gap. Minirhizotrons are the only established, non-destructive technology that can address this need in a standard field trial. Prior experiments have used only modest numbers of minirhizotrons, which has limited testing to small numbers of genotypes or environmental conditions. This study addressed the need for methods to install and collect images from thousands of minirhizotrons and thereby help break the phenotyping bottleneck in the field. Over three growing seasons, methods were developed and refined to install and collect images from up to 3038 minirhizotrons per experiment. Modifications were made to four tractors and hydraulic soil corers mounted to them. High quality installation was achieved at an average rate of up to 84.4 minirhizotron tubes per tractor per day. A set of four commercially available minirhizotron camera systems were each transported by wheelbarrow to allow collection of images of mature maize root systems at an average rate of up to 65.3 tubes per day per camera. This resulted in over 300,000 images being collected in as little as 11 days for a single experiment. The scale of minirhizotron installation was increased by two orders of magnitude by simultaneously using four tractor-mounted, hydraulic soil corers with modifications to ensure high quality, rapid operation. Image collection can be achieved at the corresponding scale using commercially available minirhizotron camera systems. Along with recent advances in image analysis, these advances will allow use of minirhizotrons at unprecedented scale to address key knowledge gaps regarding genetic and environmental effects on root system size and distribution in the field.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Row selection in remote sensing from four-row plots of maize and sorghum based on repeatability and predictive modeling

Remote sensing enables the rapid assessment of many traits that provide valuable information to plant breeders throughout the growing season to improve genetic gain. These traits are often extracted from remote sensing data on a row segment (rows within a plot) basis enabling the quantitative assessment of any row-wise subset of plants in a plot, rather than a few individual representative plants, as is commonly done in field-based phenotyping. Nevertheless, which rows to include in analysis is still a matter of debate. The objective of this experiment was to evaluate row selection and plot trimming in field trials conducted using four-row plots with remote sensing traits extracted from RGB (red-green-blue), LiDAR (light detection and ranging), and VNIR (visible near infrared) hyperspectral data. Uncrewed aerial vehicle flights were conducted throughout the growing seasons of 2018 to 2021 with data collected on three years of a sorghum experiment and two years of a maize experiment. Traits were extracted from each plot based on all four row segments (RS) (RS1234), inner rows (RS23), outer rows (RS14), and individual rows (RS1, RS2, RS3, and RS4). Plot end trimming of 40 cm was an additional factor tested. Repeatability and predictive modeling of end-season yield were used to evaluate performance of these methodologies. Plot trimming was never shown to result in significantly different outcomes from non-trimmed plots. Significant differences were often observed based on differences in row selection. Plots with more row segments were often favorable for increasing repeatability, and excluding outer rows improved predictive modeling. These results support long-standing principles of experimental design in agronomy and should be considered in breeding programs that incorporate remote sensing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

UAV remote sensing imagery - Miscanthus trials 2020 - Energy Farm - UIUC

Aerial imagery utilized as input in the manuscript "Deep convolutional neural networks exploit high spatial and temporal resolution aerial imagery to predict key traits in miscanthus" . Data was collected over M. Sacchariflorus and Sinensis breeding trials at the Energy Farm, UIUC in 2020. Flights were performed using a DJI M600 mounted with a Micasense Rededge multispectral sensor at 20 m altitude around solar noon. Imagery is available as tif file by field trial and date (10). The post-processing of raw images into orthophoto was performed in Agisoft Metashape software. Each crop surface model and multispectral orthophoto was stacked into an unique raster stack by date and uploaded here. Each raster stack includes 6 layers in the following order: Layer 1 = crop surface model, Layer 2 = Blue, Layer 3 = Green, Layer 4 = Red, Layer 5 = Rededge, and Layer 6 = NIR multispectral bands. Msa raster stacks were resampled to 1.67 cm spatial resolution and Msi raster stacks were resampled to 1.41 cm spatial resolution to ease their integration into further analysis. 'MMDDYYYY' is the date of data collection, 'MSA' is M. Sacchariflorus trial, 'MSI' is Miscanthus Sinensis trial, 'CSM' is crop surface model layer, and 'MULTSP' are the five multispectral bands.

bioenergy↗
DOE OSTI2021

Sustainability Trait Modeling of Field-Grown Switchgrass ( Panicum virgatum ) Using UAV-Based Imagery

Unmanned aerial vehicles (UAVs) provide an intermediate scale of spatial and spectral data collection that yields increased accuracy and consistency in data collection for morphological and physiological traits than satellites and expanded flexibility and high-throughput compared to ground-based data collection. In this study, we used UAV-based remote sensing for automated phenotyping of field-grown switchgrass (Panicum virgatum), a leading bioenergy feedstock. Using vegetation indices calculated from a UAV-based multispectral camera, statistical models were developed for rust disease caused by Puccinia novopanici, leaf chlorophyll, nitrogen, and lignin contents. For the first time, UAV remote sensing technology was used to explore the potentials for multiple traits associated with sustainable production of switchgrass, and one statistical model was developed for each individual trait based on the statistical correlation between vegetation indices and the corresponding trait. Also, for the first time, lignin content was estimated in switchgrass shoots via UAV-based multispectral image analysis and statistical analysis. The UAV-based models were verified by ground-truthing via correlation analysis between the traits measured manually on the ground-based with UAV-based data. The normalized difference red edge (NDRE) vegetation index outperformed the normalized difference vegetation index (NDVI) for rust disease and nitrogen content, while NDVI performed better than NDRE for chlorophyll and lignin content. Overall, linear models were sufficient for rust disease and chlorophyll analysis, but for nitrogen and lignin contents, nonlinear models achieved better results. As the first comprehensive study to model switchgrass sustainability traits from UAV-based remote sensing, these results suggest that this methodology can be utilized for switchgrass high-throughput phenotyping in the field.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Discovering useful genetic variation in the seed parent gene pool for sorghum improvement

Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F 6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.

59 BASIC BIOLOGICAL SCIENCES↗