Estimation of maize yield and effects of variable-rate nitrogen application using UAV-based RGB imagery

Accurate crop yield estimation is important for agronomic and economic decision-making. This study evaluated the performance of imagery data acquired using a unmanned aerial vehicle (UAV)-based imaging system for estimating yield of maize (Zea mays L.) and the effects of variable-rate nitrogen (N) application on crops. Images of a 27-ha maize field were captured using a UAV with a consumer-grade RGB camera flying at ~100 m above ground level at three maize growth stages. The collected sequential images were stitched and the Excess Green (ExG) colour feature was extracted to develop prediction models for maize yield and to examine the effect of the variable-rate N application. Various linear regression models between ExG and maize yield were developed for three sample area sizes (21, 106, and 1058 m2). The model performance was evaluated using coefficient of determination (R2), F-test and the mean absolute percentage error (MAPE) between estimated and actual yield. All linear regression models between ExG and yield were significant (p ≤ 0.05). The MAPE ranged from 6.2 to 15.1% at the three sample sizes, although R2 values were all \u3c0.5. Prediction error was lower at the later growth stages, as the crop approached maturity, and at the largest sample level. The ExG image feature showed potential for evaluating the effect of variable-rate N application on crop growth. Overall, the low-cost UAV imaging system provided useful information for field management

Estimating corn emergence date using UAV-based imagery

Assessing corn (Zea Mays L.) emergence uniformity soon after planting is important for relating to grain production and for making replanting decisions. Unmanned aerial vehicle (UAV) imagery has been used for determining corn densities at vegetative growth stage 2 (V2) and later, but not as a tool for detecting emergence date. The objective of this study was to estimate days after corn emergence (DAE) using UAV imagery. A field experiment was designed with four planting depths to obtain a range of corn emergence dates. UAV imagery was collected during the first, second and third weeks after emergence. Acquisition height was approximately 5m above ground level resulted in a ground sampling distance 1.5 mm pixel-1. Seedling size and shape features derived from UAV imagery were used for DAE classification based on the Random Forest machine learning model. Results showed image features were distinguishable for different DAE (single day) within the first week after initial corn emergence with a moderate overall classification accuracy of 0.49. However, for the second week and beyond the overall classification accuracy diminished (0.20 to 0.35). When estimating DAE within a three-day window (± 1 DAE), overall 3-day classification accuracies ranged from 0.54 to 0.88. Diameter, area, and major axis length/area were important image features to predict corn DAE. Findings demonstrated that UAV imagery can detect newly-emerged corn plants and estimate their emergence date to assist in establishing emergence uniformity. Additional studies are needed for fine-tuning image collection procedures and image feature identification in order to improve accuracy

Early corn stand count of different cropping systems using UAV-imagery and deep learning

Optimum plant stand density and uniformity is vital in order to maximize corn (Zea mays L.) yield potential. Assessment of stand density can occur shortly after seedlings begin to emerge, allowing for timely replant decisions. The conventional methods for evaluating an early plant stand rely on manual measurement and visual observation, which are time consuming, subjective because of the small sampling areas used, and unable to capture field-scale spatial variability. This study aimed to evaluate the feasibility of an unmanned aerial vehicle (UAV)-based imaging system for estimating early corn stand count in three cropping systems (CS) with different tillage and crop rotation practices. A UAV equipped with an on-board RGB camera was used to collect imagery of corn seedlings (~14 days after planting) of CS, i.e., minimum-till corn-soybean rotation (MTCS), no-till corn-soybean rotation (NTCS), and no-till corn-corn rotation with cover crop implementation (NTCC). An image processing workflow based on a deep learning (DL) model, U-Net, was developed for plant segmentation and stand count estimation. Results showed that the DL model performed best in segmenting seedlings in MTCS, followed by NTCS and NTCC. Similarly, accuracy for stand count estimation was highest in MTCS (R2 = 0.95), followed by NTCS (0.94) and NTCC (0.92). Differences by CS were related to amount and distribution of soil surface residue cover, with increasing residue generally reducing the performance of the proposed method in stand count estimation. Thus, the feasibility of using UAV imagery and DL modeling for estimating early corn stand count is qualified influenced by soil and crop management practices

Environmental Implications of Increased Bioenergy Production on Midwest Soil Landscapes [abstract]

Only abstract of poster available.Track III: Energy InfrastructurePrairie soil landscapes encompass over 16 million acres in Missouri and surrounding states. Much of this area has been degraded by erosion but is still used for grain production. Erosion has caused variable topsoil depth within fields which in turn has resulted in greater within-field variability of crop yield, magnified the drought-prone nature of these soils, and lowered the overall soil productivity and ecosystem function. In recent years, pressure on these sensitive soils has risen due to higher demand for grain production, in part for ethanol and biodiesel. In some areas, highly erodible fields which were historically managed as CRP and pasture are being turned into grain crop acres. Thus as new and fluctuating feed and bioenergy markets develop, land management practices will also shift, resulting in changes in soil and water quality of watersheds. This presentation will explore the likely environmental implications of different types of bioenergy production on the soil resource. Further, the positive benefits of potential changes in land use will be in explored. For example, one alternative for sensitive soils is production of perennial grass as a feedstock for coal co-burning plants and for potential future use in cellulosic ethanol production. Perennial grass yields are likely to be less variable than grain yields, both year-to-year and within fields, primarily because of greater resistance to drought. Grass production systems also provide environmental services not obtained from annual grain crops. We will also discuss our work on developing ways to target the most appropriate places in the landscape for grain or perennial production so as to enhance ecosystem services and improve soil and water quality

A long‑term precision agriculture system sustains grain profitability

After two decades of availability of grain yield-mapping technology, long-term trends in field-scale profitability for precision agriculture (PA) systems and conservation practices can now be assessed. Field-scale profitability of a conventional or ‘business-as-usual’ system with an annual corn (Zea mays L.)-soybean (Glycine max [L.]) rotation and annual tillage was assessed for 11 years on a 36 ha field in central Missouri during 1993 to 2003. Following this, a ‘precision agriculture system’ (PAS) with conservation practices was implemented for the next 11 years to address production, profit and environmental concerns. The PAS was multifaceted and temporally dynamic. It included no-till, cover crops, crop rotation changes, site-specific N and variable-rate or zonal P, K and lime. Following a recent evaluation of differences in yield and yield variability, this research compared profitability of the two systems. Results indicated that PAS sustained profits in the majority (97%) of the field without subsidies for cover crops or payments for enhanced environmental protection. Profit was only lower with PAS in a drainage channel where no-till sometimes hindered soybean stands and wet soils caused wheat (Triticum aestivum L.) disease. Although profit gains were not realized after 11 years of PA and conservation practices, this system sustained profits. These results should help growers gain confidence that PA and conservation practices will be successful

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.journal articl

Reconstructing Native American Population History

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1–5. One contentious issue is whether the settlement occurred via a single6–8 or multiple streams of migration from Siberia9–15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. We show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call “First American”. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan-speakers on both sides of the Panama Isthmus, who have ancestry from both North and South America

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships

Comparative analysis of the transcriptome across distant species

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters