Data from: Ploidy determination of buffel grass accessions in the USDA National Plant Germplasm System collection by flow cytometry

The DNA content of 568 accessions of buffel grass in the USDA National Plant Germplasm System was determined through flow cytometry to predict their ploidy levels. Based on DNA content, 308 accessions were determined as tetraploids with 36 chromosomes, 139 as pentaploids with 45 chromosomes, 20 as hexaploids with 54 chromosomes, two as septaploids with 63 chromosomes, and 99 as aneuploids. Chromosome counts of selected plants confirmed ploidy levels from DNA findings. Chromosome number of euploid plants could be predicted from the DNA data.

Plants and Crops

GOSSYM

GOSSYM is a dynamic, process-level simulation model of cotton growth and yield. GOSSYM essentially is a materials balance model which keeps track of carbon and nitrogen in the plant and water and nitrogen in the soil root zone. GOSSYM predicts the response of the field crop to variations in the environment and to cultural inputs. Specifically, the model responds to weather inputs of daily total solar radiation, maximum and minimum air temperatures, daily total wind run, and rainfall and/or irrigation amount. The model also responds to cultural inputs such as preplant and withinseason applications of nitrogen fertilizer, row spacing and within row plant density as they affect total plant population, and cultivation practices.

Plants and Crops

2DLEAF

A 2D mechanistic model of CO2 and water vapor movement in a leaf and photosynthesis.

Plants and Crops

GUICS Version 2.41

GUICS is built on the usability paradigm developed by software designers and has a user-centered design based on results of human–computer interaction interface development lies in human–computer interaction studies.

Plants and Crops

WinFlume 1.06.0006

WinFlume is a Windows-based computer program used to design and calibrate long-throated flume and broad-crested weir flow measurement structures. The software was developed through the cooperative efforts of the Bureau of Reclamation, the Agricultural Research Service, and the International Institute for Land Reclamation & Improvement . Primary funding for WinFlume's development has come from the Bureau of Reclamation's Water Conservation-Field Services Program.

Plants and Crops

GENOSIM

The genosim package simulates genotypes, breeding values, and phenotypes; simulates DNA sequence read depth (numbers of A and B alleles); and resolves SNP conflicts between parent and offspring genotypes.

Genomics and Genetics

FINDMAP

The findmap.f90 program aligns sequence reads to reference map, calls previous variants, and identifies new variants.

Genomics and Genetics

FINDHAP

The findhap.f90 program finds haplotypes and imputes genotypes using multiple chip sets and sequence data.

Genomics and Genetics

ConvertCufflinksToExcel

This program converts several Cufflinks output files into easily readable Microsoft Excel tables using Apache's POI library. Only the "cuffdiff" output format currently is supported, but future versions may include other output formats.

Maps and Multimedia

STARFM

The STARFM algorithm uses comparisons of one or more pairs of observed Landsat/MODIS maps, collected on the same day, to predict maps at Landsat-scale on other MODIS observation dates. STARFM was initially developed at the NASA Goddard Space Flight Center by Dr. Feng Gao. This version (v1.2) has been greatly improved in computing efficiency (e.g. one run for multiple dates and parallel computing) for large-area processing (Gao et al., 2015). Additional improvements (e.g. Landsat and MODIS images co-registration, daily MODIS nadir BRDF-adjusted reflectance) in the operational data fusion system (Wang et al., 2014) are beyond the STARFM program and are not included in this package. Improvement and continuous maintenance are being undertaken in the USDA-ARS Hydrology and Remote Sensing Laboratory (HRSL), Beltsville, MD by Dr. Feng Gao.

Agroecosystems & Environment

Small Watershed Hydrology (WinTR-55)

WinTR-55 is a single-event rainfall-runoff small watershed hydrologic model. The model generates hydrographs from both urban and agricultural areas and at selected points along the stream system. Hydrographs are routed downstream through channels and/or reservoirs. Multiple sub-areas can be modeled within the watershed.

Agroecosystems & Environment

Nearest Neighbor Soil Water Retention Estimator

The k-nearest neighbor (k-NN) technique is a non-parametric technique that can be used to make predictions of discrete (class-type) as well as continuous variables. The k-NN technique and many of its derivatives belong to the group of .lazy learning algorithms.. It is lazy, as it passively stores the development data set until the time of application; all calculations are performed only when estimations need to be generated.

Agroecosystems & Environment

AROP

The automated registration and orthorectification package (AROP) uses precisely registered and orthorectified Landsat data (e.g., GeoCover or recently released free Landsat Level 1T data from the USGS EROS data center) as the base image to co-register, orthorectify and reproject (if needs) the warp images from other data sources, and thus make geo-referenced time-series images consistent in the geographic extent, spatial resolution, and projection. The co-registration, orthorectification and reprojection processes were integrated and thus image is only resampled once. This package has been tested on the Landsat Multi-spectral Scanner (MSS), TM, Enhanced TM Plus (ETM+) and Operational Land Imager (OLI), Terra ASTER, CBERS CCD, IRS-P6 AWiFS, and Sentinel-2 Multispectral Instrument (MSI) data.

Agroecosystems & Environment

Updated Bottom Up Solution for Triacylglycerols

This Microsoft Excel workbook (2.712 Mb) contains spreadsheets that implement the Updated Bottom Up Solution for Triacylglycerols that allows Critical Ratios that provide structural information from mass spectrometry to be used to reconstitute the original mass spectra from which they came. It contains spreadsheets that use the non-nested equations (Critical Limits explicitly shown), as well as spreadsheets that used the nested equations (Case determinations made with Critical Limits not explicitly shown).

Ag Data Commons

Quantification of TAGs by LC-MS

This Microsoft Excel workbook contains spreadsheets for calculating response-factor normalized triacylglycerol (TAG) compositions from response factors derived from GC-FID of fatty acid methyl esters (FAME). This workbook (1.160 Mb) reads the output from a ThermoScientific XCalibur Quan Browser •Excel Short Report• (In XCalibur: File • Export data to Excel • Export Short Excel report), and requires input of the FA composition determined by GC-FID (manually entered or read from Excel spreadsheet [provided upon request]).

Ag Data Commons

Isotope-corrected Critical Ratio calculations

This Microsoft Excel workbook (168.259 Mb) calculates Critical Ratios for triacylglycerols based on manually entered mass spectra, with isotope correction by isotope patterns calculated at www.ChemCalc.org. Average mass spectra across integrated peaks are manually entered according to the instructions in the Supplementary Material to the publication 'The Updated Bottom Up Solution for Mass Spectrometry of Soybean Oil in a Dietary Supplement Gelcap".

Ag Data Commons

UPIC

Unique Pattern Informative Combinations (UPIC), a decision tool for the cost-effective design of DNA fingerprinting/genotyping experiments using simple-sequence/tandem repeat (SSR/STR) markers.

Genomics and Genetics

PECMAN Software

Peanut Curing Manager (PECMAN) is a decision support system that assists drying facility managers with inventory control. It schedules sampling and removal times, estimates time remaining on dryer and current moisture content. Cooperators have reported reduced drying costs and improved peanut quality.

Plants and Crops

Irrigator Pro

Irrigator Pro is an expert system designed to provide irrigation scheduling recommendations based on scientific data resulting in conservation minded irrigation management. The success of Irrigator Pro for Peanuts created interest in other groups. A collaborative effort between the NPRL, Cotton Commission, University of Georgia, and the Peanut Foundation was established to create comparable models for cotton and corn.

Plants and Crops

Gas Flux from Band Application

Gas Flux from Band Application (GF-Band) is an MS Excel spreadsheet tool that calculates the effective gas flux from soil of a multiple-band area to which manure or fertilizer has been applied in bands. One spreadsheet is for circular gas flux chambers and another is for rectangular chambers.

Agroecosystems & Environment

PhotoSim

This program models the photosynthetic response of 13 floriculture crops to light, temperature, or carbon dioxide (CO2) and allows users to estimate the impact of adjusting their greenhouse environment. You can predict the impact on photosynthesis for different management changes (shading, supplemental high pressure sodium lighting, CO2 injection,or heating or cooling).

Plants and Crops

DRIFTSIM

DRIFTSIM can be used to determine the effects of major drift-causing factors on the mean drift distances up to 656 feet from the release point for individual water droplets or classes of droplets.

Agroecosystems & Environment

DepositScan

DepositScan is a scanning program that can quickly evaluate spray deposit distribution on water sensitive paper or Kromekote cards. The program consists of a set of custom plugins that are used by an image-processing program to produce a number of measurements useful for expressing spray deposit distribution. The DepositScan program offers a convenient solution for on-the-spot evaluation of spray quality even under field working conditions.

Agroecosystems & Environment

Yield Editor 2.0.7

Yield Editor is a tool which allows the user to select, apply and analyze a variety of automated filters and editing techniques used to process and clean yield data. The software imports either AgLeader advanced or Greenstar text file formats, and exports data in a delimited ASCII format.

Plants and Crops

Management Zone Analyst Version 1.0 Software

Management Zone Analyst (MZA) is a decision-aid for creating within-field management zones based on quantitative field information. It mathematically breaks up a field into natural clusters or zones based on the classification parameters and number of zones you specify.

Plants and Crops

CALMIM

The California Landfill Methane Inventory Model is a 1-dimensional soil gas transport and oxidation model that calculates annual landfill methane emissions based on the cover soil characteristics and annual climatic data for a given global location.

Agroecosystems & Environment

Nitrogen Decision Aid

The Nitrogen Decision Aid is a computerized program that predicts the amount of N mineralized from planting to side-dress or 5-leaf growth-stage. By applying just enough N-fertilizer to reach the critical soil nitrate concentration it is possible reduce this waste. This model is designed for Northern climates that will have some frost in the soil during the winter.

Agroecosystems & Environment

Sorption Isotherm Spreadsheet

Spreadsheet from the paper entitled: On the Use of Linearized Langmuir Equations by C.H. Bolster and G.M. Hornberger, Soil Science Society of America Journal, 2007, 71(6): 1796-1806.

Agroecosystems & Environment

Modified Langmuir Equation Spreadsheet

Spreadsheet from the paper entitled: Revisiting a Statistical Shortcoming when Fitting the Langmuir Model to Sorption Data by C.H. Bolster, Journal of Environmental Quality, 2008, 37:1986-1992. Spreadsheet has been modified to make a correction to the calculation of E for weighted data. (3/18/2010).

Agroecosystems & Environment

The Ogallala Agro-Climate Tool

The Ogallala Agro-Climate Tool is a Visual Basic application that estimates irrigation demand and crop water use over the Ogallala Aquifer region.

Agroecosystems & Environment

Cotton Irrigation Tool

A Web Application for Estimating Irrigated and Dryland Cotton Profitability using Modeled Yield Data.

Ag Data Commons

Bushland ET Calculator

The Bushland Reference ET calculator was developed at the USDA-ARS Conservation and Production Research Laboratory, Bushland, Texas. Although it was designed and developed for use mainly by producers and crop consultants to manage irrigation scheduling, it can also be used in educational training, research, and other practical application. It uses the ASCE Standardized Reference Evapotranspiration (ET) Equation for calculating grass and alfalfa reference ET at hourly and daily time steps. This program uses the more complex equation for estimating clear-sky solar radiation provided in Appendix D of the ASCE-EWRI ET Manual. Users have the option of using single set or time series weather data to calculate reference ET. Daily reference ET can be calculated either by summing the hourly ET values for a given day or by using averages of the climatic data.

Agroecosystems & Environment

Bushland Evapotranspiration and Agricultural Remote Sensing System (BEARS) Software

Evapotranspiration (ET) is a major component of the hydrologic cycle. ET data are used for a variety of water management and research purposes such as irrigation scheduling, water and crop modeling, streamflow, water availability, and many more. Remote sensing products have been widely used to create spatially representative ET data sets which provide important information from field to regional scales. As UAV capabilities increase, remote sensing use is likely to also increase. For that purpose, scientists at the USDA-ARS research laboratory in Bushland, TX developed the Bushland Evapotranspiration and Agricultural Remote Sensing System (BEARS) software. The BEARS software is a Java based software that allows users to process remote sensing data to generate ET outputs using predefined models, or enter custom equations and models. The capability to define new equations and build new models expands the applicability of the BEARS software beyond ET mapping to any remote sensing application. The software also includes an image viewing tool that allows users to visualize outputs, as well as draw an area of interest using various shapes.

Agroecosystems & Environment

WinDAM

Prioritization of dam rehabilitation, improved flood warning systems, development of emergency action plans, and inform policy makers on zoning regulations.

Agroecosystems & Environment

SITES

Prioritization of dam rehabilitation, improved flood warning systems, development of emergency action plans, and inform policy makers on zoning regulations.

Agroecosystems & Environment

Crop Sequence Calculator Version 3.1

The Crop Sequence Calculator software is an interactive program for viewing crop sequencing information. The Crop Sequence Calculator program is designed to assist agricultural managers determine workable cropping sequences for the northern Great Plains. Version (3.1) contains the previous version (3.0) and adds new information gathered from additional cropping sequence research, as well as supplemental information related to use of annual crops as cover crops.

Plants and Crops

AgroEcosystem Performance Assessment Tool

The AgroEcosystem Performance Assessment Tool is a computer program used to evaluate the agronomic and environmental performance of management practices in long-term agroecosystem experiments. The program employs a simple scoring method to quantify the performance of management practices using indicators grouped within agroecosystem functions. Management practices are evaluated on a relative basis using the method, thereby internalizing comparisons. Because of its specialized application to long-term experiments, the program is designed primarily for use by agricultural researchers.

Agroecosystems & Environment

SGA

Stored Grain Advisor (SGA) is a decision support system for managing insect pests of farm-stored wheat. The program predicts the likelihood of insect infestation, and recommends appropriate preventative actions . It also provides advice on how to sample and identify insect pests of stored wheat. SGA Pro was designed for use in commercial elevators as part of the Areawide IPM Project for stored grain. Grain samples are taken with a vacuum probe and processed over an inclined sieve. SGA Pro analyzes the insect data, grain temperatures and moistures, and determines which bins need to be fumigated.

Agricultural Products

SPUR2

SPUR2 DOS ver. 2.2 is a general grassland ecosystem simulation model designed to determine beef cattle performance and production by simultaneously simulating production of up to 15 plant species on 36 heterogeneous grassland sites. SPUR2 simulates grassland hydrology, nitrogen cycling, and soil organic matter on grazed ecosystems as well as rangeland production under different climatic regimes, environmental conditions, and management alternatives.

Agroecosystems & Environment

SHOOTGRO

SHOOTGRO emphasizes the development and growth of the shoot apex of small-grain cereals such as winter and spring wheat (Triticum aestivum L.) and spring barley (Hordeum vulgare L.). To better incorporate the variability typical in the field, up to six cohorts, or age classes, of plants are followed using a daily time step.

Plants and Crops

RZWQM2

Root Zone Water Quality Model 2 (RZWQM2) is a whole-system model for studying crop production and environmental quality under current and changing climate conditions. It emphasizes the effects of agricultural management practices on physical, chemical and biological processes. RZWQM2 is a one-dimensional model with a pseudo 2-dimensional drainage flow. Crop simulation options include the generic plant growth model, DSSAT-CSM 4.0 and HERMES SUCROS models. It also can simulate surface energy balance with components from the SHAW model and water erosion from the GLEAMS model. An automated parameter estimation algorithm (PEST) was added to RZWQM2 for objective model calibration and uncertainty analysis.

Plants and Crops

PhenologyMMS

PhenologyMMS is a simulation model that outlines and quantifies the developmental sequence of different crops under varying levels of water deficits, provides developmental information relevant to each crop, and is intended to be used either independently or inserted into existing crop growth models.

Plants and Crops

PAL

Profit and Loss (PAL) Farm Budgeting Economic Software for Colorado Agriculture is a windows desktop software for analyzing farm operations budgets. The software was developed in cooperation with Colorado State University.

Ag Data Commons

iFEAT

iFEAT (iFARM Economic Analysis Tool) is a spreadsheet based tool developed to allow the user to assess current and potential management options for economic sustainability. The user can evaluate lease arrangements, input costs, government programs, and insurance options to arrive at the best economic combination of these variables.

Ag Data Commons

iFarm Record Keeper

The easy to use iFARM Field Record Keeper spreadsheet-based tool was designed to help farmers keep track of field operational records. The tool is designed to be farm specific allowing the user inputs to be specific to their operation. Drop down menus are created from user input including field names, crops, tillages, fertilizer, chemicals, landlords, and storage locations. This information needs only to be entered once. After initial setup each field will be saved as a file with the completed information. Up to four spray operations can be entered per field with the spray reports satisfying current Colorado Department of Agriculture and EPA requirements for Restricted Use Pesticide (RUP). The one page field report meets the fundamental requirements for the current Conservation Security Program (CSP) requirements for record keeping.

Plants and Crops

HIRO2

HIRO2 (Hortonian Infiltration and Run-Off/On) is a spatially distributed rainfall-runoff model for event-based studies of space-time watershed processes. A grid-based routing hierarchy was defined over the watershed using the D-infinity contributing area algorithm. Computation of ponding time was included to handle variable run-on and rainfall intensity. The Green-Ampt model was adopted to calculate surface infiltration, and the kinematic wave model was used to route Hortonian runoff and channel flow. The model can handle input rainfall, soil parameters, surface roughness, and other properties that vary in space and time.

Agroecosystems & Environment

GPFARM

GPFARM (Great Plains Framework for Agricultural Resource Management) is a simulation model computer application. It incorporates state of the art knowledge in agronomy, animal science, economics, weed science and risk management into a user-friendly, decision support tool. Producers, agricultural consultants, action agencies and scientists can utilize GPFARM to test alternative management strategies that may in turn lead to sustainable agriculture, a reduction in pollution, or maximum economic return. GPFARM Express contains default projects to allow users to quickly set up their operations.

Plants and Crops

WISDEM

WISDEM simulates the variation in multi-species weed populations over time in response to crop rotation, tillage system, and specific weed management tactics and the consequent crop yield loss due to weed competition. Population dynamics of individual weed species are predicted from a limited number of parameters that can be derived from literature sources and expert opinion.

Plants and Crops

WeedSite

Software for learning about the benefits of site-specific weed management compared to a uniform herbicide application. No GIS software is needed. The benefits are predicted from weed maps drawn by the user.

Plants and Crops

OPUS

A hydrologic simulation model for studying the effects of management practices on movement of sediment and chemicals in response to rainfall or irrigation on small field areas. Includes models for plant growth and nutrient cycling, and operates on a continuous basis. Weather conditions and rainfall may be stochastically simulated.

Agroecosystems & Environment

OTUshuff

OTUshuff is a set of tools written in Perl to identify and correct for the presence of pseudo-diversity in contrasts between microbial communities. The variably weighted Odum dissimilarity (DwOdum) allows for down-weighting the influence of either abundant or rare taxa in calculating a measure of similarity between two communities. We show that down-weighting the influence of rare taxa can be used to minimize pseudo b-diversity arising from incomplete sampling. Down-weighting the influence of abundant taxa can increase the sensitivity of hypothesis testing. OTUshuff is an associated test for identifying the presence of pseudo-diversity in pairwise community contrasts.

Genomics and Genetics

NLEAP GIS 5.0

NLEAP GIS 5.0 can help users identify hot spots across the landscape and identify management practices that can increase nitrogen use efficiency. A Nitrogen Trading Tool (NTT) analysis can be conducted to determine the potential benefits of implementing best management practices and the quantity of nitrogen savings that could potentially be traded in future air or water quality markets.

Agroecosystems & Environment

CCE Nitrogen Index Tool

The Nitrogen Index is a tool written in the programming language Java that is used to calculate nitrogen uptake and leaching in farming techniques.

Agroecosystems & Environment

AgroAtlas

The Russian-English Agricultural Atlas is the world’s most comprehensive source of information on the geographic distribution of plant-based agriculture in Russia and neighboring countries. The Atlas contains 1500 maps that illustrate the distribution of 100 crops, 560 wild crop relatives, 640 diseases, pests and weeds, and 200 environmental parameters. Additionally, the Atlas provides detailed biological descriptions, illustrations, metadata and reference lists. Currently, individual maps can be downloaded and viewed using freely available AgroAtlas GIS Utility software, which can also be downloaded at this site.

Agroecosystems & Environment

Non-dominated Sorting Genetic Algorithm-II

This code is implements the nondominated sorting genetic algorithm (NSGA-II) in the R statistical programming language. The function is theoretically applicable to any number of objectives without modification. The function automatically detects the number of objectives from the population matrix used in the function call. NSGA-II has been applied in ARS research for automatic calibration of hydrolgic models (whittaker link) and economic optimization (whittaker link).

Genomics and Genetics

SWAGMAN-Whatif

An interactive computer program was developed to simulate the interactions among the above factors. It shows how changing one factor impacts the outcome of the other factors for a single growing season. The user selects a climate, a crop, and soil characteristics from menu lists, and then sets the water table depth and quality, irrigation (river or well) water quality and then develops an irrigation schedule. On execution, the relative yield reductions due to over irrigation, under irrigation, and salinity, water table rise or fall and surface runoff are shown numerically for the growing season. Soil water content, soil salinity, water table depth changes and rain and irrigation events during the season are also shown graphically.

Agroecosystems & Environment

PIVNOZ-PIPELOSS

These two software programs have been developed to aid in the design and analysis of center pivot and traveling lateral sprinkler irrigation systems.

Agroecosystems & Environment

Imperfect SSR Finder

The Imperfect SSR Finder is an interactive website to help you find imperfect (and perfect) SSRs. You can test small snippets or upload large files, change the lengths and types of the SSRs your are looking for, and create output with SSRs in inverted case and/or color highlights. A tabular information file is also created in .CSV format, for easy import into any spreadsheet program.

Genomics and Genetics

WATSUIT

Predicts the salinity, sodicity, and toxic-solute concentration of the soil-water within a simulated crop root zone resulting from the use of a particular irrigation water of given composition and at a specified leaching fraction. It can be used to evaluate the effect of a given salinity level (or solute concentration) on crop yield and of a given sodicity level on soil permeability.

Agroecosystems & Environment

UNSATCHEM

Simulates water, heat, carbon dioxide and solute movement in one-dimensional variably saturated media.

Agroecosystems & Environment

SWMS-3D

Simulates water and solute movement in three-dimensional variably saturated media.

Agroecosystems & Environment

SWMS-2D

Simulates water and solute movement in two-dimensional variably saturated media.

Agroecosystems & Environment

STANMOD

Computer Software for Evaluating Solute Transport in Porous Media Using Analytical Solutions of the Convection-Dispersion Equation.

Agroecosystems & Environment

ROSETTA

Estimates water retention, saturated and unsaturated hydraulic conductivity from basic soil data (requires 32-bit Windows).

Agroecosystems & Environment

RETC

Analyzes the hydraulic properties of unsaturated soils.

Agroecosystems & Environment

N3DADE

Evaluates analytical solutions for two- and three-dimensional non-equilibrium solute transport.

Agroecosystems & Environment

HYDRUS-1D

HYDRUS-1D is a Microsoft Windows-based modeling environment for analysis of water flow and solute transport in variably saturated porous media. The software package includes the one-dimensional finite element model HYDRUS (version 7.0) for simulating the movement of water, heat, and multiple solutes in variably saturated media. The model is supported by an interactive graphics-based interface for data-preprocessing, discretization of the soil profile, and graphic presentation of the results.

Agroecosystems & Environment

HYDRUS

Simulates water, heat, and solute movement in one-dimensional variably-saturated porous medium.

Agroecosystems & Environment

GEOPACK

Geopack is a comprehensive, user-friendly software package containing several computer programs for carrying out geostatistical analyses of spatially correlated data. The programs were written so that they can be used by scientists, engineers or regulators with little experience in geostatistical techniques and still satisfy the requirements of more advanced users. Using the programs, and spending a little time becoming familiar with geostatistics, the end-user should be able to include the geostatistical techniques in their work and research environment.

Agroecosystems & Environment

FilmPC

Estimates the film permeability (i.e., mass transfer coefficient) from the analysis of permeability cell concentration data.

Agroecosystems & Environment

ExtractChem

Numerical software package for estimating changes in solution composition due to changes in soil water content.

Agroecosystems & Environment

ESAP

Statistical software package for estimating field scale spatial salinity patterns from electromagnetic induction signal data (for Windows XP)

Agroecosystems & Environment

CXTFIT

Estimates parameters in several equilibrium and non-equilibrium transport models from laboratory or field tracer experiments.

Agroecosystems & Environment

3DADE

Model evaluates analytical solutions for two- and three-dimensional solute transport.

Agroecosystems & Environment

Varroa Pop

Varroa Pop simulates the growth of Varroa mite population in honey bee colonies. The program demonstratres how Varroa mites influence colony population growth throughout the year. You can change many factors through the menus in the model such as the initial population size, queen egg laying potential, and mite reproduction rates, so you can see how these factors influence both colony and mite population growth. We hope that the model will help you understand the interactions between the honey bee and mite populations and provide insights on how best to control Varroa in colonies.

Agroecosystems & Environment

Redapol

A computer-based model simulating the interactions of weather, bloom and honey bee foraging activity that culminate in 'Delicious' apple fruit-set. The model predicts the percentage of blossoms setting fruit based upon weather conditions, orchard design, tree characteistics, and honey bee colonies per hectare.

Agroecosystems & Environment

BK-Economics

BK-Economics is a software package that was developed by a team of scientists at the Carl Hayden Bee Research Center in Tucson, Arizona to assist commercial beekeepers in streamling their business practices. This software allows beekeepers to simulate years of business, taking into account factors like equipment purchases, labor force, transportation, marketing strategies, loans, honey flow, and other hive products without taking the usual risks. This software, when used in combination with the marketing strategy information in publication, can help beekeepers formulate a successful business plan when making financial decisions, expanding an operation or just starting out.

Ag Data Commons

Bio-Control Parasite

A model that simulates host and parasitoid population interactions, parasitism rates, and plant damage is described. BIOCONTROL-PARASITE can simulate many different species of phytophagus insects, parasitoids, and plants because specifics of the insect and plant biology are entered though menus at the beginning of a simulation.

Agroecosystems & Environment

WinSRFR

WinSRFR is a hydraulic analysis tool for surface irrigation systems. The software combines simulation, evaluation, operational analysis, and design functionalities. Intended users are irrigation specialists, extension agents, researchers, consultants, students, and farmers with moderate to advanced knowledge of surface irrigation hydraulics. WinSRFR 4.1 is the fourth major release of the software. The new version offers a reprogrammed simulation engine, an application programming interface, batch simulation capabilities, and enhancements to the user interface.

Plants and Crops

Resampling Validation of Sample Plans (RVSP)

Sets of tools for sample plan evaluation originally released in 1997, these Monte Carlo simulations can be used to evaluate sampling models during the developmental phase; however, they may not be adequate for testing model validity and performance under field conditions. This is primarily due to the assumption of an underlying statistical distribution (e.g., negative-binomial, normal) which may not adequately represent the actual distributions of insects in all instances. Here we present a method in which actual field data is resampled to evaluate sample plan performance. We originally developed DOS-based computer software for this purpose.

Agroecosystems & Environment

CPM - Cotton Production Model

A new process-based cotton model, CPM, has been developed to simulate the growth and development of upland cotton (Gossypium hirsutum L.) throughout the growing season with minimal data input. CPM predicts final cotton yield for any combination of soil, weather, cultivar and sequence of management actions.

Plants and Crops

Cligen

Cligen is a stochastic weather generator which produces daily estimates of precipitation, temperature, dewpoint, wind, and solar radiation for a single geographic point, using monthly parameters (means, SD's, skewness, etc.) derived from the historic measurements. Unlike other climate generators, it produces individual storm parameter estimates, including time to peak, peak intensity, and storm duration, which are required to run the WEPP and the WEPS soil erosion models.

Agroecosystems & Environment

WEPPCAT

WEPPCAT is a web-based erosion simulation tool that allows for the assessment of changes in erosion rates as a consequence of user-defined climate change scenarios. This tool is based on the USDA-ARS Water Erosion Prediction Project (WEPP) erosion model.

Agroecosystems & Environment

KINEROS - The kinematic runoff and erosion model

The kinematic runoff and erosion model KINEROS is an event oriented, physically based model describing the processes of interception, infiltration, surface runoff and erosion from small agricultural and urban watersheds. The watershed is represented by a cascade of planes and channels; the partial differential equations describing overland flow, channel flow, erosion and sediment transport are solved by finite difference techniques. The spatial variation of rainfall, infiltration, runoff, and erosion parameters can be accomodated. KINEROS may be used to determine the effects of various artificial features such as urban developments, small detention reservoirs, or lined channels on flood hydrographs and sediment yield.

Agroecosystems & Environment

AGWA - Automated Geospatial Watershed Assessment Tool

The Automated Geospatial Watershed Assessment (AGWA) tool is a GIS-based hydrologic modeling tool that uses commonly available GIS data layers to fully parameterize, execute, and spatially visualize results for the RHEM, KINEROS2, KINEROS-OPUS, SWAT2000, and SWAT2005 watershed runoff and erosion models. Accommodating novice to expert GIS users, it is designed to be used by watershed, water resource, land use, and resource managers and scientists investigating the hydrologic impacts of land-cover/land-use change in small watershed to basin-scale studies.

Agroecosystems & Environment

The RHEM Web Tool

RHEM is designed to provide sound, science-based technology to model and predict runoff and erosion rates on rangelands and to assist in assessing rangeland conservation practice effects. RHEM is a newly conceptualized, process-based erosion prediction tool specific for rangeland application, based on fundamentals of infiltration, hydrology, plant science, hydraulics and erosion mechanics.

Long-term Agro-ecosystem Research Initiative

Data from: Quality controlled research weather data – USDA-ARS, Bushland, Texas

The dataset contains 15-minute mean weather data from the USDA-ARS Conservation and Production Laboratory (CPRL), Soil and Water Management Research Unit (SWMRU) research weather station, Bushland, Texas (Lat. 35.186714°, Long. -102.094189°, elevation 1170 m above MSL) for all days in 2016. The data are from sensors deployed at standard heights over grass that is irrigated and mowed during the growing season to reference evapotranspiration standards.

Agroecosystems & Environment

Data from: Genome-Wide Association Mapping of Loci Associated with Plant Growth and Forage Production under Salt Stress in Alfalfa (Medicago sativa L.)

Salinity tolerance is highly desirable to sustain alfalfa production in marginal lands that have been rendered saline. In this study, we used a diverse panel of 198 alfalfa accessions for mapping loci associated with plant growth and forage production under salt stress using genome-wide association studies (GWAS). The plants were genotyped using genotyping-by-sequencing (GBS). A greenhouse procedure was used for phenotyping four agronomic and physiological traits affected by salt stress, including dry weight (DW), plant height (PH), leaf chlorophyll content (LCC), and stomatal conductance (SC). For each trait, a stress susceptibility index (SSI) was used to evaluate plant performance under stressed and non-stressed conditions. Marker-trait association identified a total of 42 markers significantly associated with salt tolerance. They were located on all chromosomes except chromosome 2 based on the alignment of their flanking sequences to the reference genome (Medicago truncatula). Of those identified, 13 were associated with multiple traits. Several loci identified in the present study were also identified in previous reports. BLAST search revealed that 19 putative candidate genes linked to 24 significant markers. Among them, B3 DNA-binding protein, Thiaminepyrophosphokinase and IQ calmodulin-binding motif protein were identified among multiple traits in the present and previous studies. With further investigation, these markers and candidates would be useful for developing markers for marker-assisted selection in breeding programs to improve alfalfa cultivars with enhanced tolerance to salt stress.

Genomics and Genetics

Data from: Identification of Single-Nucleotide Polymorphic Loci Associated with Biomass Yield under Water Deficit in Alfalfa (Medicago sativa L.) Using Genome-Wide Sequencing and Association Mapping

Alfalfa is a worldwide grown forage crop and is important due to its high biomass production and nutritional value. However, the production of alfalfa is challenged by adverse environmental factors such as drought and other stresses. Developing drought resistance alfalfa is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. In the present study, we used genotyping-by-sequencing and genome-wide association to identify marker loci associated with biomass yield under drought in the field in a panel of diverse germplasm of alfalfa.

Genomics and Genetics

Data from: Proteomics analysis reveals novel host molecular mechanisms associated with thermotherapy of 'Ca. Liberibacter asiaticus'-infected citrus plants

The goal of this study is to identify potential Las resistance/tolerance-related genes in citrus plants for application in breeding or genetic engineering programs, and apply comparative proteomics analysis via 2-DE and mass spectrometry to elucidate the molecular processes associated with heat-induced mitigation of HLB in citrus plants.

Genomics and Genetics

Data from: Key molecular processes of the diapause to post‐diapause quiescence transition in the alfalfa leafcutting bee Megachile rotundata identified by comparative transcriptome analysis

Insect diapause (dormancy) synchronizes an insect's life cycle to seasonal changes in the abiotic and biotic resources required for development and reproduction. Transcription analysis of diapause to post‐diapause quiescent transition in the alfalfa leafcutting bee Megachile rotundata Fabricius identifies 643 post‐diapause up‐regulated gene transcripts and 242 post‐diapause down‐regulated transcripts. The log2 fold change in gene expression levels ranges from −5 to 7. Transcripts from several pivotal diapause‐related processes, including chromatin remodelling, cellular signalling pathways, microRNA processing, anaerobic glycolysis, cell cycle arrest and neuroendocrine control, are identified as being differentially expressed during the diapause to post‐diapause transition. In conjunction with studies from other insect species, the data indicate that there are several common mechanisms of diapause control and maintenance.

Genomics and Genetics

Data from: The Majority of Genotypes of the Virulence Gene inlA Are Intact among Natural Watershed Isolates of Listeria monocytogenes from the Central California Coast

Internalin A is an essential virulence gene involved in the uptake of the foodborne pathogen Listeria monocytogenes into host cells. It is intact in clinical strains and often truncated due to Premature Stop Codons (PMSCs) in isolates from processed foods and processing facilities. Less information is known about environmental isolates. We sequenced the inlA alleles and did Multi Locus Variable Number Tandem Repeat Analysis (MLVA) on 112 L. monocytogenes isolates from a 3-year period from naturally contaminated watersheds near a leafy green growing area in Central California.

Genomics and Genetics

Data from: Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects

Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs).

Genomics and Genetics

pySnobal

Spatial Modeling for Resources Framework (SMRF) was developed at the USDA Agricultural Research Service (ARS) in Boise, ID, and was designed to increase the flexibility of taking measured weather data and distributing the point measurements across a watershed.

Agroecosystems & Environment

Automated Water Supply Model (AWSM)

Automated Water Supply Model (AWSM) was developed at the USDA Agricultural Research Service in Boise, ID, to streamline the workflow used to forecast the water supply of multiple water basins.

Spatial Modeling for Resources Framework (SMRF)

Spatial Modeling for Resources Framework (SMRF) was developed at the USDA Agricultural Research Service (ARS) in Boise, ID, and was designed to increase the flexibility of taking measured weather data and distributing the point measurements across a watershed.

Agroecosystems & Environment

Data from: The assembled transcriptome of the adult horn fly, Haematobia irritans

To better understand the adult horn fly, Haematobia irritans irritans, and the development of resistance in natural populations, an Illumina paired-end read HiSeq and GAII approach was used to determine the transcriptomes of untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males from a Louisiana population of horn flies with a moderate level of pyrethroid resistance.

Genomics and Genetics

USDA-ARS Colorado Maize Water Productivity Dataset 2012-2013

The USDA-Agricultural Research Service carried out an experiment on water productivity in response to seasonal timing of irrigation of maize (Zea mays L.) at the Limited Irrigation Research Farm (LIRF) facility in northeastern Colorado (40°26’ N, 104°38’ W) starting in 2012. Twelve treatments involved different water availability targeted at specific growth-stages. This dataset includes data from the first two years, which were complete years with intact treatments. Data includes canopy growth and development (canopy height, canopy cover and LAI), irrigation, precipitation, and soil water storage measured periodically through the season; daily estimates of crop evapotranspiration; and seasonal measurement of crop water use, harvest index and crop yield. Hourly and daily weather data are also provided from the CoAgMET, Colorado’s network of meteorological information.

Maize field

Data from: Population structure and genetic diversity within the endangered species Pityopsis ruthii (Asteraceae)

Pityopsis ruthii (Ruth’s golden aster) is a federally endangered herbaceous perennial endemic to the Hiwassee and Ocoee Rivers in southeastern Tennessee, USA. Comprehensive genetic studies providing novel information to conservationists for preservation of the species are lacking. Genetic variation and gene flow were evaluated for 814 individuals from 33 discrete locations using polymorphic microsatellites: seven chloroplast and twelve nuclear. A total of 198 alleles were detected with the nuclear loci and 79 alleles with the chloroplast loci.

Genomics and Genetics

Data from: Dataset on characterization of recombinant interleukin-23α, IL-12p40 and IL-23 complex protein, which activates JAK-STAT signaling pathway in chicken cell lines using immunocytochemical staining

The data herein is related to the research article entitled "Functional analyses of the interaction of chicken interleukin 23 subunit p19 with IL-12 subunit p40 to form the IL-23 complex", where it is demonstrated that the chicken interleukin (IL)-23α, IL-12p40, and IL-23 complex regulates Th1, Th17, and Treg cytokine production through heterodimer receptors as well as a homodimer receptor consisting of IL-12Rβ1 and IL-23R, and activates the JAK/STAT signaling pathways.

Animals and Livestock

Data from: Bran data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity, and profiles of proanthocyanidins and whole grain physical traits of 32 red and purple rice varieties

The description of the origin and physical traits of the whole grain (color, length, width, thickness and 100-kernel weight) of this red and purple bran rice germplasm collection are provided along with data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity and total proanthocyanidin contents.

Plants and Crops

Data from: Shoot transcriptome of the giant reed, Arundo donax

The giant reed, Arundo donax, is a perennial grass species that has become an invasive plant in many countries. To establish a foundational molecular dataset, an llumina Hi-Seq protocol was used to sequence the transcriptome of actively growing shoots from an invasive genotype collected along the Rio Grande River, bordering Texas and Mexico. The assembly of 27,491 high confidence transcripts (≥200 bp) are reported with at least 70% coverage of known genes in other Poaceae species.

Plants and Crops

Data from: Datasets for transcriptomic analyses of maize leaves in response to Asian corn borer feeding and/or jasmonic acid

Corn's (Zea mays) response to initial insect damage involves a variety of changes to the levels of defensive enzymes, toxins, and communicative volatiles. Such a dramatic change secondary metabolism necessitates the regulation of gene expression at the transcript level. This Data In Brief paper summarizes the datasets of the transcriptome of corn plants in response to corn stalk borers (Ostrinia furnacalis) and/or methyl jasmonate (MeJA). Altogether, 39,636 genes were found to be differentially expressed.

Genomics and Genetics

Integrated Farm System Model (IFSM)

The Integrated Farm System Model (IFSM) is a process-based simulation of dairy, beef, and crop farming systems. This whole farm model provides a tool for evaluating the long term performance, economics, and environmental impacts of production systems over many years of weather.

Agroecosystems & Environment

Dairy Gas Emissions Model (DairyGEM)

The Dairy Gas Emissions Model (DairyGEM) uses process level simulation and process related emission factors to predict ammonia, hydrogen sulfide, VOC and greenhouse gas emissions along with the carbon, energy and water footprints of dairy production systems.

Agroecosystems & Environment

USLE Project

The USLE_1981-4 project data (Universal Soil Loss Equation) was collected from of (9) sites at (4) locations. A Swanson rotating boom simulator with (30) V-Jet 80100 nozzles applied rainfall at two different intensities, 60 or 130 mm/hour depending on how many nozzles were turned on. Specially designed flumes used with the FW-1 automatic water level recorder were used to obtain continuous runoff flow measurements. The sites in this data set followed a standardized rainfall simulator protocol which future studies by multiple investigators would continue to use. The data set contains rainfall simulator hydrologic and erosion data as well as vegetation and ground data collected in spring and fall from 1981 to 1984.

Agroecosystems & Environment

Data from: Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers

Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also…

Genomics and Genetics

Data from: Effects of conifer treatments on soil nutrient availability and plant composition in sagebrush steppe

Conifer control in sagebrush steppe of the western United States causes various levels of site disturbance influencing vegetation recovery and resource availability. The data set presented in this article include growing season availability of soil micronutrients and levels of total soil carbon, organic matter, and N spanning a six year period following western juniper (Juniperus occidentalis spp. occidentalis) reduction by mechanical cutting and prescribed fire of western juniper woodlands in southeast Oregon. These data can be useful to further evaluate the impacts of conifer woodland reduction to soil resources in sagebrush steppe plant communities.

Agroecosystems & Environment

USDA Plant Hardiness Zone Map (PHZM)

The 2012 USDA Plant Hardiness Zone Map (PHZM) is the standard by which gardeners and growers can determine which plants are most likely to thrive at a location. The map is based on the average annual minimum winter temperature, divided into 10-degree F zones. For the first time, the map is available as an interactive GIS-based map, for which a broadband Internet connection is recommended, and as static images for those with slower Internet access. Users may also simply type in a ZIP Code and find the hardiness zone for that area. No posters of the USDA Plant Hardiness Zone Map have been printed. But state, regional, and national images of the map can be downloaded and printed in a variety of sizes and resolutions.

Maps and Multimedia

iSnobal

iSnobal is a physically-based distributed snowmelt model. A coupled energy and mass-balance model iSnobal is used to simulate the development and melting of the seasonal snowcover.

Agroecosystems & Environment

Water Erosion Prediction Project (WEPP)

The Water Erosion Prediction Project (WEPP) model is a process-based, distributed parameter, continuous simulation, erosion prediction model for use on personal computers running Windows 95/98/NT/2000/XP/Vista/Windows7. The current model version (v2012.8) available for download is applicable to hillslope erosion processes (sheet and rill erosion), as well as simulation of the hydrologic and erosion processes on small watersheds. Included in the download package is the WEPP model (version 2012.8), WEPP Windows interface (August 2012), CLIGEN climate generators (versions 4.3 and 5.3), documentation and example data.

Agroecosystems & Environment

Hymenoptera Holotypes of the Smithsonian Institution

This website and on-line searchable database is a collaborative effort among several individuals. The arrangement of the specimen labels in the images on this site reflect their top to bottom positioning on the pin as viewed from upper left to lower right.

Maps and Multimedia

Plant Expression Database

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.

Genomics and Genetics

Eddy Covariance Data from Office of Naval Research Biofuel project on Maui

These data come from three eddy covariance (EC) towers that were installed as part of a project to assess the productivity of sugarcane agricultural systems for biofuel production. These towers were operated from 2011-2013 in Maui, USA. Major observational parameters include net carbon exchange, evapotranspiration, and energy fluxes.

Eddy Covariance tower establishment in Maui

Measured Annual Nutrient loads from AGricultural Environments (MANAGE) database

The MANAGE (Measured Annual Nutrient loads from AGricultural Environments) database was developed to be a readily-accessible, easily-queried database of site characteristic and field-scale nutrient export data. Initial funding for MANAGE was provided by USDA-ARS to support the USDA Conservation Effects Assessment Project (CEAP) and the Texas State Soil and Water Conservation Board as part of their mission to understand and mitigate agricultural impacts on water quality. MANAGE contains data from a vast majority of published peer-reviewed N and P export studies on homogeneous cultivated, pasture/range, and forested land uses in the US under natural rainfall-runoff conditions, as well as artificially drained agricultural land. Thus MANAGE facilitates expanded spatial analyses and improved understanding of regional differences, management practice effectiveness, and impacts of land use conversions and management techniques, and it provides valuable data for modeling and decision-making related to agricultural runoff.

Agroecosystems & Environment

Data from: Eleven years of mountain weather, snow, soil moisture and stream flow data from the rain-snow transition zone - the Johnston Draw catchment, Reynolds Creek Experimental Watershed and Critical Zone Observatory, USA. v1.1

Detailed hydrometeorological data from the mountain rain-to-snow transition zone are present for water years 2004 through 2014. The Johnston Draw watershed (1.8 km2), ranging from 1497 – 1869 m in elevation, is a sub-watershed of the Reynolds Creek Experimental Watershed (RCEW) in southwestern Idaho. The dataset includes continuous hourly hydrometeorological variables across a 372 m elevation gradient, on north- and south-facing slopes, including air temperature, relative humidity and snow depth from 11 sites in the watershed. Hourly measurements of solar radiation, precipitation, wind speed and direction, and soil moisture and temperature are available at selected stations. The dataset includes hourly stream discharge measured at the watershed outlet. These data provide the scientific community with a unique dataset useful for forcing and validating models in interdisciplinary studies and will allow for better representation and understanding of the complex processes that occur in the rain-to-snow transition zone.

Agroecosystems & Environment

Data from: A field-scale sensor network data set for monitoring and modeling the spatial and temporal variation of soil moisture in a dryland agricultural field

Automated in situ soil sensor network - the data set includes hourly and daily measurements of volumetric water content, soil temperature, and bulk electrical conductivity, collected at 42 monitoring locations and 5 depths (30, 60, 90, 120, and 150 cm) across Cook Agronomy Farm. Data collection was initiated in April 2007 and is ongoing.

Long-term Agro-ecosystem Research Initiative

Data from: Integrating classical genetics with chromosome-scale genome assembly to characterize a genetic sexing system in Bactrocera cucurbitae (Diptera: Tephritidae)

This data supports the manuscript "Integrating classical genetics with chromosome-scale genome assembly to characterize a genetic sexing system in Bactrocera cucurbitae (Diptera: Tephritidae)". The melon fly, Bactrocera cucurbitae, is a destructive agricultural pest and is the subject of strict quarantines that are enforced to prevent its establishment outside of its current geographic range. In addition to quarantine efforts, additional control measures are necessary for its eradication in the case of invasion to agriculturally rich areas. The sterile insect technique (SIT) has been effective in the control of several invertebrate pest species, and is part of a management strategy that regulatory agencies would like to expand to other important pests such as the melon fly.

insects 5000 program

Feed the Future Grain Legumes Project Database

Data from this project focuses on the evaluation of breeding lines. These breeding lines, derived from 109 PIC populations specifically developed to combine abiotic and biotic stress tolerance, showed superior agronomic potential compared with checks and local landraces. The diversity, scale, and potential of the material in the PIC breeding pipeline is invaluable and requires continued support to ensure the release of varieties that promise to increase the productivity of common bean in the E. African region. Data available includes databases, spreadsheets, and images related to the project.

Agricultural Products

Unit process data for field operations: work processes and farm implements version 1

This document describes the preparation of datasets for the LCA Commons that represent unit process/ gate-to-gate operations for field operations (a.k.a. work processes e.g., soil preparation and planting for conventional tillage, applying fertilizer with incorporation) and farm implements (e.g., operation of moldboard plows, broadcast sprayers) used in the production of field crops. The data cover 49 types of field operations and 104 types of farm implements for 9 crops in 36 U.S. states, resulting in the development of almost 19,000 unit process datasets. The field operation and farm implement datasets described herein fall between the field crop production and the aggregated fleet equipment datasets already in the Commons.

Life Cycle Assessment program

Unit process data for agricultural self-propelled equipment version 1

This document describes the preparation of datasets for the LCA Digital Commons that represent unit process/ gate-to-gate operations for the production of work (in MJ) by agricultural self-propelled equipment and fleets of agricultural self-propelled equipment. The data cover 19 types of fleets and over 200 types of self-propelled equipment datasets, representing the potential to prepare thousands of unit-process datasets by varying the operating and model years, applicable power ranges, and operating temperatures.

Life Cycle Assessment program

Unit process data for field crop production version 2

The goals for the release of Version 2 of the field crop data are to rework the data to link up with the tier 2 field operations/ work process datasets, eliminate the use of service processes, and rework balance parameters using a simpler formula. Models represent states that produced field crops in the ARMS survey years included.

Life Cycle Assessment program

Unit process data for field crop production version 1

These unit process models represent crop production in US states in multiple years. The main data source used for the development of the field crop data described here is the annual USDA Agricultural Resource Management Survey (ARMS). ARMS data are from an annual national survey of field-level farm practices sponsored jointly by USDA Economic Research Service (ERS) and the USDA National Agricultural Statistics Service (NASS). These datasets were released in ecospold version 1 in June 2012.

Life Cycle Assessment program

Expressed Sequence Tags from the Ciliate Protozoan Parasite Ichthyophthirius Multifiliis

Researchers sequenced 10,368 expressed sequence tags (EST) clones using a normalized cDNA library made from pooled samples of the trophont, tomont, and theront life-cycle stages, and generated 9,769 sequences (94.2% success rate). Post-sequencing processing led to 8,432 high quality sequences. Clustering analysis of these ESTs allowed identification of 4,706 unique sequences containing 976 contigs and 3,730 singletons.

Genomics and Genetics

Agricultural Conservation Planning Framework (ACPF) Database

Spatial data on soils, land use, and topography, combined with knowledge of conservation effectiveness can be used to identify alternatives to reduce nutrient discharge from small watersheds. This database was developed to be used in conjunction with the Agricultural Conservation Planning Framework Toolkit. Data comprise soil survey information and land use.

Agroecosystems & Environment

Agricultural Conservation Planning Framework (ACPF) Toolbox

The Agricultural Conservation Planning Framework (ACPF) Toolbox software includes tools to process the LiDAR-based digital elevation models for hydrologic analysis, which then allows a series of prioritization, riparian classification, and conservation-practice placement tools to be used. These toolsets identify agricultural fields most prone to deliver runoff directly to streams, map and classify riparian zones to inform whole-watershed riparian corridor management, and estimate the extent of tile drainage in the watershed. The software maps out suites of locations appropriate to install each of several types of conservation practices. These practice-placement opportunities are mapped for practices including controlled drainage, grassed waterways, water and sediment control basins, and nutrient removal wetlands. Rather than making any recommendations, ACPF provides an inventory of watershed assessment data and conservation placement opportunities across a watershed, in order to inform local watershed planning.

Agroecosystems & Environment

Oncopeltus fasciatus genome assembly 1.0

The Baylor College of Medicine recently sequenced and annotated the Oncopeltus fasciatus genome as part of the i5k pilot project.
The O. fasciatus research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.1. This dataset presents the Oncopeltus fasciatus genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the National Center for Biotechnology Information's GenBank resource.

Milkweed bug

Oncopeltus fasciatus genome annotations v0.5.3

The Oncopeltus fasciatus genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine.
The O. fasciatus research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.1. This dataset presents the Oncopeltus fasciatus gene set BCM_v_0.5.3, which was generated computationally. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Oncopeltus fasciatus genome assembly 1.0.

insects 5000 program

Oncopeltus fasciatus Official Gene set v1.1

Oncopeltus fasciatus genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine.
The O. fasciatus research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.1. This dataset presents the Oncopeltus fasciatus Official Gene Set (OGS) v1.1. The OGS is an integration of automatic gene predictions from Maker (done by Dan Hughes at Baylor) with manual annotations by the research community (done via Web Apollo).

insects 5000 program

USDA ARS Image Gallery

This Image Gallery is provided as a complimentary source of high-quality digital photographs available from the Agricultural Research Service information staff. Photos, (over 2,000 .jpegs) in the Image Gallery are copyright-free, public domain images unless otherwise indicated.

Maps and Multimedia

Sample of Mandan, North Dakota Aerial Image Dataset

Originally produced by the Farm Security Administration, these are georeferenced aerial images from Morton County, North Dakota. Historic print images housed at the Mandan, North Dakota ARS Long-Term Agricultural Research facility were digitized, georeferenced, and processed for use in both professional and consumer level GIS applications, or in photo-editing applications. The original images were produced by the Farm Security Administration to monitor government compliance for farm land agreements. Current applications include assessing land use change over time with regard to erosion, land cover, and natural and man-made structures. Not for use in high precision applications.

Long-term Agro-ecosystem Research Initiative

PIECE: Plant Intron Exon Comparison and Evolution Database

PIECE is a plant gene structure comparison and evolution database with 25 species. Annotated genes extracted from the species are classified based on the Pfam motif and phylogenetic trees are reconstructed for each gene category integrating exon-intron and protein motif information.

Ag Data Commons

USDA Potato Small RNA Database

This is a public resource highlighting efforts at ARS in developing small RNA genome information for the potato genome. Updates and progress are reported here.

Ag Data Commons

USDA Public Citrus Genome Database

This is a public resource highlighting efforts at ARS in developing genome information for the Citrus Carrizo Genome. Updates and progress are reported here.

Ag Data Commons

Transformative Research for Large Genome Physical Maps

The main goal of the project is to construct and utilize high-resolution genome-wide RH-based physical maps of the wheat D-genome chromosomes to facilitate the construction of sequence-ready physical maps. This research provides an unprecedented view into the evolution of cereal genomes. Importantly, the methodology is…

Ag Data Commons

Cooperative Oat Research Enterprise

This is part of the CORE project efforts to further develop tools for oat research through the development of oat SNP panels and Identification of loci affecting key traits in North American germplasm. Project activities are reported here.

Ag Data Commons

Stuttgart local weather data archive

Weather data from two weather stations at Stuttgart Rice Research and Extension center are archived. Current air temperature, relative humidity, wind speed, solar radiation and soil temperature data are provided by station and are displayed and archived either hourly or daily. Historical weather data goes…

Ag Data Commons

Brachypodium Resources

The Brachypodium Resource site focuses on research efforts located at the ARS GGD research site toward developing the plant Brachypodium distachyon as a model system to study plant genes for cereals species.

Ag Data Commons

Copy (2) Southwest Watershed Research Center Online Data Access

Hydrologic data, primarily precipitation and runoff, have been collected on experimental watersheds operated by the U.S. Department of Agriculture Agricultural Research Service (USDA-ARS) and on other lands in southeastern Arizona since the 1950s. These data are of national and international importance and make up one…

Ag Data Commons

Copy (3) Southwest Watershed Research Center Online Data Access

Hydrologic data, primarily precipitation and runoff, have been collected on experimental watersheds operated by the U.S. Department of Agriculture Agricultural Research Service (USDA-ARS) and on other lands in southeastern Arizona since the 1950s. These data are of national and international importance and make up one…

Ag Data Commons

The Wheat and Barley Scab Initiative

The goal of the U.S. Wheat and Barley Scab Initiative (USWBSI) is to develop effective control measures that minimize the threat of Fusarium head blight (scab), including the reduction of mycotoxins, to the producers, processors, and consumers of wheat and barley. Community activities are reported…

Ag Data Commons

National Cotton Variety Test

The National Cotton Variety Test is an on-going standardized cotton research database originating in 1960 and covers the entire US Cotton Belt.

Ag Data Commons