Mapping crops within the growing season across the United States
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The U.S. Department of Agriculture’s (USDA) Cropland Data Layer (CDL) is a 30 m resolution crop-specific land cover map produced annually to assess crops and cropland area across the conterminous United States. Despite its prominent use and value for monitoring agricultural land use/land cover (LULC), there remains substantial uncertainty surrounding the CDLs’ performance, particularly in applications measuring LULC at national scales, within aggregated classes, or changes across years. To fill this gap, we used state- and land cover class-specific accuracy statistics from the USDA from 2008 to 2016 to comprehensively characterize the performance of the CDL across space and time. We estimated nationwide area-weighted accuracies for the CDL for specific crops as well as for the aggregated classes of cropland and non-cropland. We also derived and reported new metrics of superclass accuracy and within-domain error rates, which help to quantify and differentiate the efficacy of mapping aggregated land use classes (e.g., cropland) among constituent subclasses (i.e., specific crops). We show that aggregate classes embody drastically higher accuracies, such that the CDL correctly identifies cropland from the user’s perspective 97% of the time or greater for all years since nationwide coverage began in 2008. We also quantified the mapping biases of specific crops throughout time and used these data to generate independent bias-adjusted crop area estimates, which may complement other USDA survey- and census-based crop statistics. Our overall findings demonstrate that the CDLs provide highly accurate annual measures of crops and cropland areas, and when used appropriately, are an indispensable tool for monitoring changes to agricultural landscapes.
Understanding the carbon fluxes and dynamics from a broad range of agricultural systems has the potential to improve our ability to increase carbon sequestration while maintaining crop yields. Short-term, single-location studies have limited applicability, but long-term data from a network of many locations can provide a broader understanding across gradients of climate and management choices. Here we examine eddy covariance measured carbon dioxide (CO 2 ) fluxes from cropland sites across the United States Department of Agriculture's Long-Term Agroecosystem Research (LTAR) network. The dataset was collected between 2001 and 2020, spanning 13 sites for a total of 182 site-years. Average seasonal patterns of net ecosystem CO 2 exchange (NEE), gross primary productivity (GPP), and ecosystem respiration (R eco ) were determined, and subsequent regression analysis on these “flux climatologies” was used to identify relationships to mean annual temperature (MAT), mean annual precipitation (MAP), cropping systems, and management practices. At rainfed sites, carbon fluxes were better correlated with MAP (r2 ≤ 0.5) than MAT (r2 ≤ 0.22). Net carbon balance was different among cropping systems (p < 0.001), with the greatest net carbon uptake occurring in sugarcane (Saccharum spp. hybrids) and the least in soybean (Glycine max) fields. Crop type had a greater effect on carbon balance than irrigation management at a Nebraska site. Across cropping systems, grain crops often had higher GPP and were more likely to have net uptake when compared to legume crops. This multi-site analysis highlights the potential of the LTAR network to further carbon flux research using eddy covariance measurements.
We report accurate estimation of cropping intensity (CI), an indicator of food production, is well aligned with the ongoing efforts to achieve sustainable development goals (SDGs) under diminishing natural resources. The advancement in satellite remote sensing provides unprecedented opportunities for capturing CI information in a spatially continuous manner. However, challenges remain due to the lack of generalizable algorithms for accurately and efficiently mapping global CI with a fine spatial resolution. In this study, we developed a 30-m planetary-scale CI mapping framework with the reconstructed time series of Normalized Difference Vegetation Index (NDVI) from multiple satellite images. Using a binary crop phenophase profile indicating growing and non-growing periods, we estimated pixel-by-pixel CI by enumerating the total number of valid cropping cycles during the study years. Based on the Google Earth Engine cloud computing platform, we implemented the framework to estimate CI during 2016–2018 in eight geographic regions across continents that are representative of global cropping system diversity. Comparison with PhenoCam network data in four cropland sites suggests that the proposed framework is capable of capturing the seasonal dynamics of cropping practices. Spatially, overall accuracies based on validation samples range from 80.0% to 98.9% across different regions worldwide. Regarding the CI classes, single cropping systems are associated with more robust and less biased estimations than multiple cropping systems. Finally, our CI estimates reveal high agreement with two widely used land surface phenology products, including Vegetation Index and Phenology V004 (VIP4) and Moderate Resolution Imaging Spectroradiometer Land Cover Dynamics (MCD12Q2), meanwhile providing much more spatial details. Due to its robustness, the developed CI framework can be potentially generalized to produce global fine resolution CI products for food security and other applications.
Crop water productivity (CWP) metrics can reveal how the dynamics of crop production and water use change across space and time. We use field-scale satellite inputs from 2016–2021 to estimate potential water savings for four crops (almonds, grapes, walnuts, and citrus—which collectively account for approximately one-third of California’s cropland area), within critically overdrafted groundwater sub-basins of California’s San Joaquin Valley. These annual estimates of field-level water savings potential are based on locally achievable CWP values for each crop type. Our findings show considerable spatial variation in CWP and potential water savings within each sub-basin. We find that increasing CWP to peak efficiency (defined as improving fields to the 95th percentile of observed CWP) for four crops could meet up to 36% of the estimated annual overdraft in San Joaquin Valley. For comparison, fallowing 5% of the four crop type fields in the same study area could potentially reduce annual overdraft by 11%. By delivering results at the field scale, our work can inform targeted interventions by irrigation district managers and more efficient allocation of state incentives for improved water management. For example, we estimate that state grant funding for water efficiency upgrades could have amplified potential water savings threefold by targeting investments to the least efficient fields.
The BioSiting Tool provides a geospatial interface for analyzing bioeconomy resources and infrastructure across the continental U.S. The tool integrates empirical and modeled data from a broad range of sources. Bioeconomy resources mapped in the tool include agricultural residues, forest residues, municipal solid waste streams, food waste, manure, fats, oils and greases and potential yields of energy crops. Infrastructure mapped in the tool includes biorefineries, material recovery facilities, anaerobic digesters, wastewater treatment plants, combustion plants, district energy systems, crude oil pipelines, petroleum pipelines, natural gas pipelines, railways and freight terminals. Additional data layers include environmental justice indicators at the census tract level and carbon dioxide geologic storage potential. Users can select a location on the map, define a buffer radius in kilometers and generate an inventory of all bioecomony resources within the buffer zone. Data from the tool can be downloaded from individual buffer zones, or at the state or national level.
Solar-induced chlorophyll fluorescence (SIF) observed by satellites has advanced the monitoring of terrestrial photosynthesis regionally and globally. The relationship between SIF and gross primary production (GPP) at leaf, canopy, and ecosystem scales has received tremendous attention in recent years. It remains controversial whether the SIF-GPP relationship at the ecosystem scale is universal or dependent upon vegetation type. New SIF observations from the TROPOspheric Monitoring Instrument (TROPOMI) with unprecedented high spatial and temporal resolution provide a new opportunity to elucidate the SIF-GPP relationship. Here, we examine the SIF-GPP relationship for seven major vegetation types across the U.S. with TROPOMI SIF and in-situ GPP data for 83 eddy covariance flux sites. We find that TROPOMI SIF shows a strong and consistent relationship with tower-based GPP at both satellite footprint and grid-cell levels. The slope of the SIF-GPP relationship is similar among all the vegetation types except croplands, demonstrating a nearly universal (converging to ~13.5 g C m -2 d -1 /W m -2 μm -1 sr -1) rather than vegetation type-specific SIF-GPP relationship. This confirms that TROPOMI SIF can be used as a proxy for GPP across a wide variety of vegetation types and can also be used to quantify GPP by avoiding uncertainty associated with land cover maps. The C 4 crops have a much higher slope than the C 3 crops, and therefore croplands tend to have a higher slope than C 3 -dominated vegetation types (e.g., forests, shrublands, savannas). We also find that the TROPOMI SIF is well correlated with GPP under normal or wetter conditions, while their relationship becomes weaker under water stress. In conclusion, our TROPOMI-based study could improve our understanding of the SIF-GPP relationship at the ecosystem scale and advance the mapping of GPP globally with SIF observations from space.
Starch accumulated in the endosperm of cereal grains as reserve energy for germination serves as a staple in human and animal nutrition. Unraveling genetic control for starch metabolism is important for breeding grains with high starch content. In this study, we used a sorghum association panel with 389 individuals and 141,557 single nucleotide polymorphisms (SNPs) to fit linear mixed models (LMM) for identifying genomic regions and potential candidate genes associated with starch content. Three associated genomic regions, one in chromosome (chr) 1 and two novel associations in chr-8, were identified using combination of LMM and Bayesian sparse LMM. All significant SNPs were located within protein coding genes, with SNPs ∼ 52 Mb of chr-8 encoding a Casperian strip membrane protein (CASP)-like protein (Sobic.008G111500) and a heat shock protein (HSP) 90 (Sobic.008G111600) that were highly expressed in reproductive tissues including within the embryo and endosperm. The HSP90 is a potential hub gene with gene network of 75 high-confidence first interactors that is enriched for five biochemical pathways including protein processing. The first interactors of HSP90 also showed high transcript abundance in reproductive tissues. The candidates of this study are likely involved in intricate metabolic pathways and represent candidate gene targets for source-sink activities and drought and heat stress tolerance during grain filling.
Abstract Genotyping‐by‐sequencing (GBS) is a widely used strategy for obtaining large numbers of genetic markers in model and non‐model organisms. In crop plants, GBS‐derived marker datasets are frequently used to perform quantitative trait locus (QTL) mapping. In some plant species, however, high heterozygosity and complex genome structure mean that researchers must use care in handling GBS data to conduct QTL mapping most effectively. Such outbred crops include most of the perennial grass and tree species used for bioenergy. To identify strategies for increasing accuracy and precision of QTL mapping using GBS data in outbred crops, we conducted an empirical study of SNP‐calling and genetic map‐building pipeline parameters in a Miscanthus sinensis population, and a complementary simulation study to estimate the relationship between genome‐wide error rate, read depth, and marker number. The bioenergy grass Miscanthus is an obligate outcrossing species with a recent (diploidized) whole‐genome duplication. For the study of empirical M. sinensis data, we compared two SNP‐calling methods (one non‐reference‐based and one reference‐based), a series of depth filters (12×, 20×, 30×, and 40×) and two map‐construction methods (i.e., marker ordering: linkage‐only and order‐corrected based on a reference genome). We found that correcting the order of markers on a linkage map by using a high‐quality reference genome improved QTL precision (shorter confidence intervals). For typical GBS datasets of between 1000 and 5000 markers to build a genetic map for biparental populations, a depth filter set at 30× to 40× applied to outbred populations provided a genome‐wide genotype‐calling error rate of less than 1%, improved accuracy of QTL point estimates and minimized type I errors for identifying QTL. Based on these results, we recommend using a reference genome to correct the marker order of genetic maps and a robust genotype depth filter to improve QTL mapping for outbred crops.
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Abstract. With increasing crop water demands and drought threats, mapping andmonitoring of cropland evapotranspiration (ET) at high spatial and temporalresolutions become increasingly critical for water management andsustainability. However, estimating ET from satellites for precise waterresource management is still challenging due to the limitations in bothexisting ET models and satellite input data. Specifically, the process of ETis complex and difficult to model, and existing satellite remote-sensing datacould not fulfill high resolutions in both space and time. To address theabove two issues, this study presents a new high spatiotemporal resolution ETmapping framework, i.e., BESS-STAIR, which integrates a satellite-drivenwater–carbon–energy coupled biophysical model, BESS (Breathing Earth SystemSimulator), with a generic and fully automated fusion algorithm, STAIR(SaTallite dAta IntegRation). In this framework, STAIR provides daily 30'mmultispectral surface reflectance by fusing Landsat and MODIS satellite datato derive a fine-resolution leaf area index and visible/near-infrared albedo,all of which, along with coarse-resolution meteorological and CO 2 data, are used to drive BESS to estimate gap-free 30 m resolution daily ET.We applied BESS-STAIR from 2000 through 2017 in six areas across the US CornBelt and validated BESS-STAIR ET estimations using flux-tower measurementsover 12 sites (85 site years). Results showed that BESS-STAIR daily ETachieved an overall R2=0.75, with root mean square error RMSE=0.93 mm d -1 and relative error RE =27.9 % when benchmarkedwith the flux measurements. In addition, BESS-STAIR ET estimations capturedthe spatial patterns, seasonal cycles, and interannual dynamics well indifferent sub-regions. The high performance of the BESS-STAIR frameworkprimarily resulted from (1) the implementation of coupled constraints onwater, carbon, and energy in BESS, (2) high-quality daily 30 m data from theSTAIR fusion algorithm, and (3) BESS's applicability under all-skyconditions. BESS-STAIR is calibration-free and has great potentials to be areliable tool for water resource management and precision agricultureapplications for the US Corn Belt and even worldwide given the globalcoverage of its input data.
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.
Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ~1920 bin markers spanning ~875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.
Abstract Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.
Respiration in the light (R L ) releases CO 2 in photosynthesizing leaves and is a phenomenon that occurs independently from photorespiration. Since R L lowers net carbon fixation, understanding R L could help improve plant carbon-use efficiency and models of crop photosynthesis. Although R L was identified more than 75 years ago, its biochemical mechanisms remain unclear. To identify reactions contributing to R L , we mapped metabolic fluxes in photosynthesizing source leaves of the oilseed crop and model plant camelina (Camelina sativa). We performed a flux analysis using isotopic labeling patterns of central metabolites during 13 CO 2 labeling time course, gas exchange, and carbohydrate production rate experiments. To quantify the contributions of multiple potential CO 2 sources with statistical and biological confidence, we increased the number of metabolites measured and reduced biological and technical heterogeneity by using single mature source leaves and quickly quenching metabolism by directly injecting liquid N 2 ; we then compared the goodness-of-fit between these data and data from models with alternative metabolic network structures and constraints. Our analysis predicted that R L releases 5.2 μmol CO2 g –1 FW h –1 of CO 2 , which is relatively consistent with a value of 9.3 μmol CO 2 g –1 FW h –1 measured by CO 2 gas exchange. The results indicated that ≤10% of R L results from TCA cycle reactions, which are widely considered to dominate R L . Further analysis of the results indicated that oxidation of glucose-6-phosphate to pentose phosphate via 6-phosphogluconate (the G6P/OPP shunt) can account for >% of CO 2 released by R L .
We report photosynthesis is a key target to improve crop production in many species including soybean [Glycine max (L.) Merr.]. A challenge is that phenotyping photosynthetic traits by traditional approaches is slow and destructive. There is proof-of-concept for leaf hyperspectral reflectance as a rapid method to model photosynthetic traits. However, the crucial step of demonstrating that hyperspectral approaches can be used to advance understanding of the genetic architecture of photosynthetic traits is untested. To address this challenge, we used full-range (500–2,400 nm) leaf reflectance spectroscopy to build partial least squares regression models to estimate leaf traits, including the rate-limiting processes of photosynthesis, maximum Rubisco carboxylation rate, and maximum electron transport. In total, 11 models were produced from a diverse population of soybean sampled over multiple field seasons to estimate photosynthetic parameters, chlorophyll content, leaf carbon and leaf nitrogen percentage, and specific leaf area (with R 2 from 0.56 to 0.96 and root mean square error approximately <10% of the range of calibration data). We explore the utility of these models by applying them to the soybean nested association mapping population, which showed variability in photosynthetic and leaf traits. Genetic mapping provided insights into the underlying genetic architecture of photosynthetic traits and potential improvement in soybean. Notably, the maximum Rubisco carboxylation rate mapped to a region of chromosome 19 containing genes encoding multiple small subunits of Rubisco. We also mapped the maximum electron transport rate to a region of chromosome 10 containing a fructose 1,6-bisphosphatase gene, encoding an important enzyme in the regeneration of ribulose 1,5-bisphosphate and the sucrose biosynthetic pathway. The estimated rate-limiting steps of photosynthesis were low or negatively correlated with yield suggesting that these traits are not influenced by the same genetic mechanisms and are not limiting yield in the soybean NAM population. Leaf carbon percentage, leaf nitrogen percentage, and specific leaf area showed strong correlations with yield and may be of interest in breeding programs as a proxy for yield. This work is among the first to use hyperspectral reflectance to model and map the genetic architecture of the rate-limiting steps of photosynthesis.
Conservation actions are urgently needed to tackle biodiversity loss in intensively managed agricultural landscapes. Production lands are usually heterogeneous and contain low-yield areas that can be set aside for biodiversity conservation without serious yield losses. Here, we introduce Ecologically-Informed Precision Conservation, a framework that integrates yield mapping and ecological theory to select the best areas to create new set-asides while ensuring high crop yields at the farm/landscape level. Long-term yield maps can be generated using globally available satellite data and basic information on field/farm crop yield from farmers. Ecological principles are then used to select the subset of areas with the highest potential for biodiversity conservation by prioritising those that increase connectivity, maximise habitat heterogeneity and decrease landscape grain size. Here, the created non-crop habitats can be permanent and thus ensure biodiversity support over time. In addition, agricultural management efficiency can be enhanced by improving field shapes. The framework provides the basis for a practical, user-friendly tool that informs all interested stakeholders on how to rationalise existing agricultural landscapes using already-existing farming systems and available technologies. High cost-effectiveness from an economic and conservation perspective, along with the creation of heterogeneous non-crop habitats, make our framework a promising solution to re-design agricultural landscapes.
The European Space Agency’s Sentinel satellites have laid the foundation for global land use land cover (LULC) mapping with unprecedented detail at 10 m resolution. We present a cross-comparison and accuracy assessment of Google’s Dynamic World (DW), ESA’s World Cover (WC) and Esri’s Land Cover (Esri) products for the first time in order to inform the adoption and application of these maps going forward. For the year 2020, the three global LULC maps show strong spatial correspondence (i.e., near-equal area estimates) for water, built area, trees and crop LULC classes. However, relative to one another, WC is biased towards over-estimating grass cover, Esri towards shrub and scrub cover and DW towards snow and ice. Using global ground truth data with a minimum mapping unit of 250 m 2 , we found that Esri had the highest overall accuracy (75%) compared to DW (72%) and WC (65%). Across all global maps, water was the most accurately mapped class (92%), followed by built area (83%), tree cover (81%) and crops (78%), particularly in biomes characterized by temperate and boreal forests. The classes with the lowest accuracies, particularly in the tundra biome, included shrub and scrub (47%), grass (34%), bare ground (57%) and flooded vegetation (53%). When using European ground truth data from LUCAS (Land Use/Cover Area Frame Survey) with a minimum mapping unit of <100 m 2 , we found that WC had the highest accuracy (71%) compared to DW (66%) and Esri (63%), highlighting the ability of WC to resolve landscape elements with more detail compared to DW and Esri. Although not analyzed in our study, we discuss the relative advantages of DW due to its frequent and near real-time data delivery of both categorical predictions and class probability scores. We recommend that the use of global LULC products should involve critical evaluation of their suitability with respect to the application purpose, such as aggregate changes in ecosystem accounting versus site-specific change detection in monitoring, considering trade-offs between thematic resolution, global versus. local accuracy, class-specific biases and whether change analysis is necessary. We also emphasize the importance of not estimating areas from pixel-counting alone but adopting best practices in design-based inference and area estimation that quantify uncertainty for a given study area.