Plant Research Program Research Articles

Measuring change within next‐generation agricultural and natural resources professionals

AbstractA dynamic and diverse workforce of agricultural professionals and scientists is needed to develop sustainable and innovative solutions for the challenges of food production for a growing population under the threat of climate extremes. One path to developing workforce talent is through summer research and extension experiences. The Applied Plant Systems (APS) Research and Extension Experiences for Undergraduates (REEUs) program provided 23 undergraduates a pathway to work with agricultural science, technology, engineering, and mathematics through plant and soil sciences research and extension programs. To develop the professional skills of interns and guide self‐reflection, weekly Think Tank Sessions were organized to focus on teamwork, time management, decision‐making, and systems thinking. To assess variation in the students’ approach to their work, the Approaches and Study Skills Inventory for Students (ASSIST) was incorporated into program evaluation. Using a pre–post design, students’ agreement with statements reflecting a deep, strategic, or surface approach to their work was measured. T‐tests revealed significant increases in mean scores for subscales measuring Deep Approach, one subscale measuring Strategic Approach, and the subscale measuring fear of failure to reflect the Surface Approach. Increased fear of failure scores may be explained by new experiences working with research, peers, and mentors. Eight of 23 students who participated in a follow‐up survey after the conclusion of the program reported increased knowledge of agricultural careers. Results provided evidence that the APS experience increased student confidence in facing challenges that require deeper and strategic thinking and elevated their attention to monitoring the effectiveness of their decisions and skills.

Hordatines and Associated Precursors Dominate Metabolite Profiles of Barley (Hordeum vulgare L.) Seedlings: A Metabolomics Study of Five Cultivars

In the process of enhancing crop potential, metabolomics offers a unique opportunity to biochemically describe plant metabolism and to elucidate metabolite profiles that govern specific phenotypic characteristics. In this study we report an untargeted metabolomic profiling of shoots and roots of barley seedlings performed to reveal the chemical makeup therein at an early growth stage. The study was conducted on five cultivars of barley: ‘Overture’, ‘Cristalia’, ‘Deveron’, ‘LE7′ and ‘Genie’. Seedlings were grown for 16 days post germination under identical controlled conditions, and methanolic extracts were analysed on an ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC–HRMS) system. In addition, an unsupervised pattern identification technique, principal component analysis (PCA), was performed to process the generated multidimensional data. Following annotation of specific metabolites, several classes were revealed, among which phenolic acids represented the largest group in extracts from both shoot and root tissues. Interestingly, hordatines, barley-specific metabolites, were not found in the root tissue. In addition, metabolomic profiling revealed metabolites potentially associated with the plants’ natural protection system against potential pathogens. The study sheds light on the chemical composition of barley at a young developmental stage and the information gathered could be useful in plant research and biomarker-based breeding programs.

Intercross: An Android app for plant breeding and genetics cross management

AbstractPlant breeding is fundamentally comprised of three cyclic activities: (a) intermating lines to generate novel allelic combinations, (b) evaluating the newly created lines in diverse environments, and (c) selecting superior individuals to be used as parents in the next breeding cycle. While digital technologies and tools are commonly utilized for the latter two stages, many plant research programs still rely on manual annotation and paper tags to track the crosses that constitute the basis of a plant breeding program. This presence of analog data is a crack in the foundation of a digital breeding ecosystem and a significant occasion for errors to be introduced that will propagate through the entire breeding process. However, implementing digital cross tracking into breeding programs is difficult due to the nonstandardized workflows that different breeders have adopted. Intercross, an open‐source Android app, aims to provide scientists with a robust and simple solution for planning, tracking, and managing the crosses being made each season and aims to serve as the primary tool to digitize crossing data for breeding programs. The simplicity and flexibility of Intercross allows rapid and broad adoption by diverse breeding programs and will solidify the concepts of a digital breeding ecosystem.

Toxicity and phytochemistry of eight species used in the traditional medicine of sul-mato-grossense, Brazil.

The Brazilian Cerrado has several botanical species for medicinal purposes used by traditional communities and many of these plants are not included in the list of Medicinal Plants Research Program of Central Medicines. The purpose of this study was the phytochemical screening and toxicology bioassay front of Brine shrimp L. of ethanolic extracts of eight species of plants used in folk medicine of Campo Grande, Mato Grosso do Sul, Brazil. The ethanolic extracts were submitted to phytochemical screening, determination of phenolic compounds and flavonoids. Toxicological assays were carried front of Brine shrimp according to standard methodology. The analysis TLC and HPLC-DAD confirmed the predominance of phenolic compounds and derivatives, specifically for the quercetin. The most toxic was the C. affinis DC. with death at all concentrations, the A. humile A. St. Hil. showed no mortality and the other species showed intermediate toxicity. The extracts of the investigated species are rich in phenolic compounds and derivatives, specifically quercetin, and feature toxicity between moderate to high, a fact that requires attention, since much of the traditional communities rely on herbal drugs in its raw form with preventive and curative purpose, meeting the basic health care.

Comparison of array‐ and sequencing‐based markers for genome‐wide association mapping and genomic prediction in spring wheat

AbstractNotwithstanding the rapid development of high‐throughput genotyping platforms in recent years, several plant research programs find themselves in a dilemma of which marker system to use while conducting genome‐wide association studies (GWAS) and genomic selection. To gain insight into this, we genotyped an elite spring wheat (Triticum aestivum L.) association mapping initiative (WAMI, 287 lines) panel with various array‐based platforms—(i) Diversity Arrays Technology (DArT), (ii) Illumina Infinium BeadChip wheat 9K iSelect (I9K), and (iii) wheat 90K iSelect (I90K)—and sequencing‐based platform DArTseq. The raw markers refined using a common set of protocols after the bioinformatics analysis were compared by performing a series of genetic analyses: estimates of genetic diversity through nucleotide diversity (π), population structure and familial relatedness, marker‐trait associations (MTAs), and genomic prediction. Results indicated that genetic data from DArTseq consisted of a high proportion of rare allele markers (1% < minor allele frequency < 5%). The nucleotide diversity statistic (π) was higher for the array‐based single nucleotide polymorphisms (SNPs) than sequencing‐based SNPs. The I9K detected population structure caused by the variety ‘Kauz’ and grouped the population into two subgroups, whereas I90K, DArT, and DArTseq detected five subgroups driven by key pedigrees. The I90K with the highest marker density identified a high number of significant MTAs. Genomic prediction accuracy varied among traits; DArTseq and I90K produced similar prediction accuracies. Among the marker platforms compared, I90K was the best genotyping platform for GWAS, and DArTseq—given the low cost per SNP—was the best platform for genomic prediction in spring wheat.

In Situ Cotton Leaf Area Index by Height Using Three‐Dimensional Point Clouds

Three‐dimensional (3‐D) high‐throughput crop phenotyping may benefit plant research and breeding programs by providing a rapid, nondestructive method of determining in‐season crop growth and development. In this study, a set of three inexpensive, structured, near‐infrared laser projectors mounted on a robotic platform were used to generate high‐density color point clouds (PCs) in cotton (Gossypium hirsutum L.) in 2016 and 2017. The PCs were calibrated based on destructive leaf area measurements, and the transformed PCs were analyzed to quantify leaf area by canopy height in 1‐cm intervals. We conducted weekly scans of 8‐m plots throughout the growing season for two cotton cultivars and two irrigation treatments during the 2 yr. The calibrated PCs were used to accurately measure leaf area index and leaf area index by canopy height. The analysis of leaf area distribution throughout the growing season indicated significant cultivar and irrigation effects by canopy height as well as significant interactions between cultivar and irrigation. Based on the results, it is possible to use a 3‐D sensor system to distinguish growth habits that are not easily measured using traditional growth measurements. The information obtained from 3‐D measurements may provide additional information about several canopy characteristics that are currently difficult to measure, including radiation capture parameters and biomass partitioning.Core Ideas Leaf area index (LAI) has not traditionally been separated in plants by height. Three‐dimensional sensing was used to accurately measure LAI by height in cotton. Cotton cultivar, irrigation, and growth stage measurably affected LAI by height. Three‐dimensional sensing may complement measures of radiation capture and other spatial factors.

A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel.

Simple Sequence Repeat (SSR) is one of the most effective markers used in plant and animal genetic research and molecular breeding programs. Silver staining is a widely used method for the detection of SSR markers in a polyacrylamide gel. However, conventional protocols for silver staining are technically demanding and time-consuming. Like many other biological laboratory techniques, silver staining protocols have been steadily optimized to improve detection efficiency. Here, we report a simplified silver staining method that significantly reduces reagent costs and enhances the detection resolution and picture clarity. The new method requires two major steps (impregnation and development) and three reagents (silver nitrate, sodium hydroxide, and formaldehyde), and only 7 min of processing for a non-denaturing polyacrylamide gel. Compared to previously reported protocols, this new method is easier, quicker and uses fewer chemical reagents for SSR detection. Therefore, this simple, low-cost, and effective silver staining protocol will benefit genetic mapping and marker-assisted breeding by a quick generation of SSR marker data.

Multitemporal field-based plant height estimation using 3D point clouds generated from small unmanned aerial systems high-resolution imagery

Plant breeders and agronomists are increasingly interested in repeated plant height measurements over large experimental fields to study critical aspects of plant physiology, genetics and environmental conditions during plant growth. However, collecting such measurements using commonly used manual field measurements is inefficient. 3D point clouds generated from unmanned aerial systems (UAS) images using Structure from Motion (SfM) techniques offer a new option for efficiently deriving in-field crop height data. This study evaluated UAS/SfM for multitemporal 3D crop modelling and developed and assessed a methodology for estimating plant height data from point clouds generated using SfM. High-resolution images in visible spectrum were collected weekly across 12 dates from April (planting) to July (harvest) 2016 over 288 maize (Zea mays L.) and 460 sorghum (Sorghum bicolor L.) plots using a DJI Phantom 3 Professional UAS. The study compared SfM point clouds with terrestrial lidar (TLS) at two dates to evaluate the ability of SfM point clouds to accurately capture ground surfaces and crop canopies, both of which are critical for plant height estimation. Extended plant height comparisons were carried out between SfM plant height (the 90th, 95th, 99th percentiles and maximum height) per plot and field plant height measurements at six dates throughout the growing season to test the repeatability and consistency of SfM estimates. High correlations were observed between SfM and TLS data (R2=0.88–0.97, RMSE=0.01–0.02m and R2=0.60–0.77 RMSE=0.12–0.16m for the ground surface and canopy comparison, respectively). Extended height comparisons also showed strong correlations (R2=0.42–0.91, RMSE=0.11–0.19m for maize and R2=0.61–0.85, RMSE=0.12–0.24m for sorghum). In general, the 90th, 95th and 99th percentile height metrics had higher correlations to field measurements than the maximum metric though differences among them were not statistically significant. The accuracy of SfM plant height estimates fluctuated over the growing period, likely impacted by the changing reflectance regime due to plant development. Overall, these results show a potential path to reducing laborious manual height measurement and enhancing plant research programs through UAS and SfM.

GrainScan: a low cost, fast method for grain size and colour measurements.

BackgroundMeasuring grain characteristics is an integral component of cereal breeding and research into genetic control of seed development. Measures such as thousand grain weight are fast, but do not give an indication of variation within a sample. Other methods exist for detailed analysis of grain size, but are generally costly and very low throughput. Grain colour analysis is generally difficult to perform with accuracy, and existing methods are expensive and involved.ResultsWe have developed a software method to measure grain size and colour from images captured with consumer level flatbed scanners, in a robust, standardised way. The accuracy and precision of the method have been demonstrated through screening wheat and Brachypodium distachyon populations for variation in size and colour.ConclusionBy using GrainScan, cheap and fast measurement of grain colour and size will enable plant research programs to gain deeper understanding of material, where limited or no information is currently available.

A Statistical Analysis of Medicinal Plants: A Case Study of Plant Families in Kansas and the Great Plains

We analyzed ethnobotanical data on Kansas plants to evaluate differences among families for medicinal uses by Native Americans. We compared three different statistical methods used in previous ethnobotanical studies for use in our Native Medicinal Plant Research Program, which seeks to determine which plant families are more likely to contain species with medicinal compounds. The three approaches were linear regression, binomial approach, and Bayesian analysis. All were useful for determining medicinal plant use differences among plant families, although regression analysis was most useful for our purposes. Asteraceae and Fabaceae are abundant in the open sun environments of Great Plains grasslands and contain high numbers of medicinal plants. In contrast, although grasses (Poaceae) and sedges (Cyperaceae) also are species-rich and ecologically abundant, each is underrepresented as being used by Native Americans as medicine, which can be explained at least partially by their paucity of secondary compounds.

Technological development of Cecropia glaziovi extract pellets by extrusion-spheronization

Cecropia glaziovi Snethl., Urticaceae, is commonly used in South America and is one of the species included in the Brazilian Medicinal Plants Research Program. Pharmacological studies have led to reports of the potential of C. glaziovi as a hypotensive, antiasthmatic and anxiolytic agent. The strict requirements regarding the quality, safety and effectiveness of phytopharmaceutical products represent an enormous challenge in the search for products with a high level of uniformity, reproducibility and stability. The incorporation of dry extracts into multiparticulate dosage forms, such as pellets produced by extrusion/spheronization technology, is a suitable alternative to overcome the lack of technological properties of dry extracts, since they are associated with low fowability and high hygroscopicity. In this study, an optimized dry extract (ODE) of C. glaziovi was incorporated into pellets seeking to decrease the moisture sorption and increase the stability, safety and percentage of the extract in the i nal product. Pellets containing around 50% of ODE were considered the most technologically viable, offering a narrow particle size distribution, signii cant improvement in the l owability and compressibility properties, and decrease in the moisture compared with the ODE. In conclusion, pellets containing a high dose of the C. glaviovi extract were successfully prepared, achieving degrees of quality, physical stability and feasibility compatible with the desirable characteristics of a phytopharmaceutical.

La Etnobotánica y Etnofarmacología de los Tomatillos Silvestres, Physalis longifolia Nutt., y Especies Afines a Physalis: Una Revisión

The Ethnobotany and Ethnopharmacology of Wild Tomatillos, Physalis longifolia Nutt., and Related Physalis Species: A Review. The wild tomatillo, Physalis longifolia Nutt., and related species have been important wild-harvested foods and medicinal plants. This paper reviews their traditional use as food and medicine; it also discusses taxonomic difficulties and provides information on recent medicinal chemistry discoveries within this and related species. Subtle morphological differences recognized by taxonomists to distinguish this species from closely related taxa can be confusing to botanists and ethnobotanists, and many of these differences are not considered to be important by indigenous people. Therefore, the food and medicinal uses reported here include information for P. longifolia, as well as uses for several related taxa found north of Mexico. The importance of wild Physalis species as food is reported by many tribes, and its long history of use is evidenced by frequent discovery in archaeological sites. These plants may have been cultivated, or “tended,” by Pueblo farmers and other tribes. The importance of this plant as medicine is made evident through its historical ethnobotanical use, information in recent literature on Physalis species pharmacology, and our Native Medicinal Plant Research Program’s recent discovery of 14 new natural products, some of which have potent anti-cancer activity.

Advantages for the Use of Standardized Phenotyping in Databases

Genomic sequence data are becoming prevalent in databases; however, associated phenotypic data are much more expensive and difficult to obtain. Standardized ontologies for trait classification provide a mechanism by which searches can be efficiently performed. Through standardization efforts, results can be compared across years, researchers, and locations. Examples of databases that have developed standardized ontologies within medical, animal, and plant research programs demonstrate that standardization is both possible and desirable. With standardization, genotypic and phenotypic data can be analyzed to materials for improved yield, quality, and stress tolerance.

Agrobacterium-mediated transformation of plants: Basic principles and influencing factors

Transformation is an important topic in plant biology and transgenic plants have become a major focus in plant research and breeding programs. Agrobacterium-mediated transformation as a practical and common method for introducing specific DNA fragments into plant genomes is well established and the number of transgenic plants produced using this method is increasing. Despite the popularity of the method, low efficiency of transformation is a major challenge for scientists. Modification of different genetic and environmental aspects of transformation method may lead to better understanding of the system and result in high efficiency transformation. In this review, we deal with recent genetic findings as well as different environmental factors which potentially influence Agrobacterium-mediated transformation.

Status and Prospects of Association Mapping in Plants

There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and development of robust statistical analysis methods make association mapping appealing and affordable to plant research programs. Association mapping identifies quantitative trait loci (QTLs) by examining the marker‐trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. General understanding of association mapping has increased significantly since its debut in plants. We have seen a more concerted effort in assembling various association‐mapping populations and initiating experiments through either candidate‐gene or genome‐wide approaches in different plant species. In this review, we describe the current status of association mapping in plants and outline opportunities and challenges in complex trait dissection and genomics‐assisted crop improvement.

Historical overview of the efficacy of two decades of power plant fisheries impact assessment activities in Chesapeake Bay

Abstract The Chesapeake Bay is world renowned as an estuary that historically yielded large harvests of a wide variety of fish and shellfish species. Thirteen power plants are located on the mainstem of the Bay and its tributaries in Maryland, drawing out of and discharging into the Bay eight billion gallons per day of the Bay’s waters for cooling purposes. Maryland DNR’s Power Plant Research Program (PPRP) has, since 1974, funded a wide variety of fisheries assessment, entrainment and impingement studies. PPRP’s Potomac River Fisheries Program (PRFP) encompassed multi-year, statistically rigorous, quantitative studies of all life stages of striped bass, from egg to adult, together with estuarine hydrodynamics modeling and water quality assessments, all yielding data integrated to project potential entrainment impacts from a proposed nuclear power plant. PPRP and utility-sponsored monitoring programs at BGE’s Calvert Cliffs NPP, PEPCO’s Chalk Point SES and DP&L’s Vienna SES, as well as other generating facilities throughout the state have provided comprehensive data on impingement, entrainment and receiving water populations of all life stages of potentially impacted resource species. These studies have resulted in unusually complete and long term data sets being available for impact assessment applications, and provide a basis for confirming and validating impact assessment findings and conclusions based on much shorter time series. The state/federal Chesapeake Bay Program has extensively characterized the status and trends of all important resource species in the Bay. We compare and contrast impact conclusions and projections from studies conducted in the 1970s and 1980s with current data and information on the status of and trends in affected fish stocks in Chesapeake Bay. We use that comparison to establish the role that power plant impacts play as factors driving changes in species abundance over time. These comparisons and contrasts between historical and current data and information also illustrate and confirm the methodologies that have proven to be most and least useful for assessing entrainment and impingement impacts.

Maryland, the Power Plant Research Program, and the Chesapeake Bay watershed

Chesapeake Bay has long been recognized as a biologically rich ecosystem, one whose wide expanse of shallow estuarine waters is unique in the world. When the biological bounty of the Bay declined dramatically, federal, state, and local governments began restoration efforts on a mammoth scale. While the successes have been many, the lesson of the last few decades has been that this great estuary cannot be restored without addressing the multitude of human activities in the watershed that cumulatively distort its ecological processes and degrade its resources. Today governments, industry, and the public are focusing on three major restoration efforts: reducing nutrient inputs, reducing toxic pollutant loads, and restoring living resources. Recognizing that power generation is an important component of the activities affecting the Bay, the Maryland Department of Natural Resources (DNR) Power Plant Research Program (PPRP) is working in partnership with electric utilities to avoid, minimize, and mitigate adverse impacts on both local and regional scales. Historically, PPRP has participated in cooperative state and industry efforts at Conowingo Dam and other upstream dams on the Susquehanna River (the Bay’s largest freshwater tributary) that have helped quantify impacts to migratory fish, resulting in modifications to dam operations and installation of fish lifts to restore populations of American shad and other anadromous fish. Other restoration projects include mitigation of acid mine drainage in the upper reaches of the watershed, installation of lime dosers in affected streams, investigation of the beneficial uses of coal combustion products for mine reclamation, and operation of a successful hatchery and release program. Currently, PPRP recognizes that its research efforts need to look up the watershed at cumulative effects on a regional scale. Recent research on the regional level undertaken by DNR includes a statewide biological stream survey to provide comprehensive baseline information on the health of freshwater systems in Maryland, and development of reference-based ecological indicators. These indicators are critical for assessing the effects of different degrading activities and measuring progress towards environmental goals. A related cumulative impact model, currently under development, will couple indicators of biological integrity with spatial data on land uses, power-related impacts, and other anthropogenic stressors to evaluate watershed impacts on aquatic systems. As part of model development, the role of vegetated riparian corridors is being evaluated to support watershed-wide initiatives to restore riparian forest buffers on Chesapeake Bay tributaries. These biological survey data and other information are being used to identify biodiversity hotspots in the State and construct maps of ecologically sensitive areas for the evaluation of cumulative effects and targeting of conservation and restoration priorities.

Plant-module for autonomous space support (P-MASS)

A wide variety of technical and science questions arise when attempting to envision the long-term support of plants, algae and bacteria in space. Currently, spaceflight data remain elusive since there are no U.S. carriers for investigating either the germane technical or scientific issues. The first flight of the Commercial Experiment Transporter (COMET) will provide a nominal 30 day orbital opportunity to evaluate such issues. The P-MASS is a small payload that is designed to meet the mass (40 lbs.), volume (1.5 cu.ft.), and power (120 W) constraints of one of several COMET payloads while enabling flight evaluations of plants, algae and bacteria. Various P-MASS subsystems have been subjected to extensive ground tests as well as KC135 tests. Various biological sub-systems have been similarly evaluated. Through a variety of sensors coupled with color video, the P-MASS performance and the supported biological systems will be compared for terrestrial controls versus spaceflight materials. This small, low cost payload should return valuable information regarding the requirements for hardware and biological systems needed to move toward bioregenerative life support systems in space. In addition, it should be possible to accurately identify major unresolved difficulties that may arise in the long-term, spaceflight support of various biological systems. Finally, this generic spaceflight capability should enable a variety of plant research programs focused on the use of microgravity to modulate and exploit plant products for commercial applications ranging from new agricultural products to pharmacological feedstocks and new controlled agricultural strategies.

Activated carbon injection in spray dryer/ESP/FF for mercury and toxics control

In the last decade, dry scrubbing by spray dryer absorption (SDA) has been applied to more than 17 000 MW of coal-fired boilers, and several hundred municipal solid waste (MSW) and hazardous waste plants. In the MSW application, process development for air toxic control has advanced to a point where a spray dryer absorber, followed by a fabric filter, has been determined to be the best available control technology (BACT) in several countries throughout the world. Extremely high removal of dioxins and furans, as well as mercury and other trace toxics, is now state of the art in this application. The paper describes the recent development in the air toxics removal capability of dry scrubbing for coal-fired utility plants. Results of a study characterizing the inherent mercury removal efficiency of full-scale dry scrubbers in Europe and the United States are presented, as well as results of activated carbon injection tests performed at one full-scale installation. The paper further reports results of two pilot plant research programs. One pilot plant was equipped with an electrostatic precipitator, the other pilot plant with a baghouse. The paper reports results of activated carbon injection and identifies the parameters and conditions important for achieving high mercury removal in a dry FGD system. Options for control of mercury on eastern and western US coals are suggested. Results of mercury speciation are also given. Removal results of other vapor phase toxic trace metals, such as boron and selenium, are presented. Finally, the paper makes reference to the results of two mercury revolatilization studies.