Gene function annotations for the maize NAM founder lines.

OBJECTIVES: We annotated the latest published sequences of the 26 Zea mays Nested Association Mapping (NAM) founder lines using GOMAP, the Gene Ontology Meta Annotator for Plants. The maize NAM panel enables researchers to understand and identify the genetic basis of complex traits. Annotations of predicted functions for genes can help researchers investigate gene-phenotype associations, prioritize candidate genes for phenotypes of interest, and formulate testable hypotheses about gene function/phenotype associations. The creation and release of high-confidence, high-coverage gene function annotation sets for the NAM founder lines is critical to accelerate the generation of knowledge in maize genetics research. GOMAP is a high-throughput computational pipeline that annotates gene functions genome-wide in plant genomes using Gene Ontology functional class terms. Here we report and share GOMAP-generated functional annotations for the NAM founder lines. DATA DESCRIPTION: Datasets include the protein sequences used as input, GOMAP-generated annotation files, scripts used to update obsolete terms, and GAF-formatted tab-delimited text files of gene function annotations along with README files that describe formatting, content, and how files relate to each other.

Wisconsin diversity panel phenotypes: spoken descriptions of plants and supporting data.

OBJECTIVES: Phenotyping plants in a field environment can involve a variety of methods including the use of automated instruments and labor-intensive manual measurement and scoring. Researchers also collect language-based phenotypic descriptions and use controlled vocabularies and structures such as ontologies to enable computation on descriptive phenotype data, including methods to determine phenotypic similarities. In this study, spoken descriptions of plants were collected and observers were instructed to use their own vocabulary to describe plant features that were present and visible. Further, these plants were measured and scored manually as part of a larger study to investigate whether spoken plant descriptions can be used to recover known biological phenomena. DATA DESCRIPTION: Data comprise phenotypic observations of 686 accessions of the maize Wisconsin Diversity panel, and 25 positive control accessions that carry visible, dramatic phenotypes. The data include the list of accessions planted, field layout, data collection procedures, student participants' (whose personal data are protected for ethical reasons) and volunteers' observation transcripts, volunteers' audio data files, terrestrial and aerial images of the plants, Amazon Web Services method selection experimental data, and manually collected phenotypes (e.g., plant height, ear and tassel features, etc.; measurements and scores). Data were collected during the summer of 2021 at Iowa State University's Agricultural Engineering and Agronomy Research Farms.

Assessing plant performance in the Enviratron.

BACKGROUND: Assessing the impact of the environment on plant performance requires growing plants under controlled environmental conditions. Plant phenotypes are a product of genotype × environment (G × E), and the Enviratron at Iowa State University is a facility for testing under controlled conditions the effects of the environment on plant growth and development. Crop plants (including maize) can be grown to maturity in the Enviratron, and the performance of plants under different environmental conditions can be monitored 24 h per day, 7 days per week throughout the growth cycle. RESULTS: The Enviratron is an array of custom-designed plant growth chambers that simulate different environmental conditions coupled with precise sensor-based phenotypic measurements carried out by a robotic rover. The rover has workflow instructions to periodically visit plants growing in the different chambers where it measures various growth and physiological parameters. The rover consists of an unmanned ground vehicle, an industrial robotic arm and an array of sensors including RGB, visible and near infrared (VNIR) hyperspectral, thermal, and time-of-flight (ToF) cameras, laser profilometer and pulse-amplitude modulated (PAM) fluorometer. The sensors are autonomously positioned for detecting leaves in the plant canopy, collecting various physiological measurements based on computer vision algorithms and planning motion via "eye-in-hand" movement control of the robotic arm. In particular, the automated leaf probing function that allows the precise placement of sensor probes on leaf surfaces presents a unique advantage of the Enviratron system over other types of plant phenotyping systems. CONCLUSIONS: The Enviratron offers a new level of control over plant growth parameters and optimizes positioning and timing of sensor-based phenotypic measurements. Plant phenotypes in the Enviratron are measured in situ-in that the rover takes sensors to the plants rather than moving plants to the sensors.

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning.

The accuracy of machine learning tasks critically depends on high quality ground truth data. Therefore, in many cases, producing good ground truth data typically involves trained professionals; however, this can be costly in time, effort, and money. Here we explore the use of crowdsourcing to generate a large number of training data of good quality. We explore an image analysis task involving the segmentation of corn tassels from images taken in a field setting. We investigate the accuracy, speed and other quality metrics when this task is performed by students for academic credit, Amazon MTurk workers, and Master Amazon MTurk workers. We conclude that the Amazon MTurk and Master Mturk workers perform significantly better than the for-credit students, but with no significant difference between the two MTurk worker types. Furthermore, the quality of the segmentation produced by Amazon MTurk workers rivals that of an expert worker. We provide best practices to assess the quality of ground truth data, and to compare data quality produced by different sources. We conclude that properly managed crowdsourcing can be used to establish large volumes of viable ground truth data at a low cost and high quality, especially in the context of high throughput plant phenotyping. We also provide several metrics for assessing the quality of the generated datasets.

Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets.

OBJECTIVES: Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F's genotype by environment project has released 2014 and 2015 datasets to the public, with 2016 and 2017 collected and soon to be made available. DATA DESCRIPTION: Datasets include DNA sequences; traditional phenotype descriptions, as well as detailed ear, cob, and kernel phenotypes quantified by image analysis; weather station measurements; and soil characterizations by site. Data are released as comma separated value spreadsheets accompanied by extensive README text descriptions. For genotypic and phenotypic data, both raw data and a version with outliers removed are reported. For weather data, two versions are reported: a full dataset calibrated against nearby National Weather Service sites and a second calibrated set with outliers and apparent artifacts removed.

The effect of artificial selection on phenotypic plasticity in maize.

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0-5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements.

MaizeGDB update: new tools, data and interface for the maize model organism database.

MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays. Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, the original maize genetics database MaizeDB was created. In 2003, the combined contents of MaizeDB and the sequence data from ZmDB were made accessible as a single resource named MaizeGDB. Over the next decade, MaizeGDB became more sequence driven while still maintaining traditional maize genetics datasets. This enabled the project to meet the continued growing and evolving needs of the maize research community, yet the interface and underlying infrastructure remained unchanged. In 2015, the MaizeGDB team completed a multi-year effort to update the MaizeGDB resource by reorganizing existing data, upgrading hardware and infrastructure, creating new tools, incorporating new data types (including diversity data, expression data, gene models, and metabolic pathways), and developing and deploying a modern interface. In addition to coordinating a data resource, the MaizeGDB team coordinates activities and provides technical support to the maize research community. MaizeGDB is accessible online at http://www.maizegdb.org.

MaizeGDB: curation and outreach go hand-in-hand.

First released in 1991 with the name MaizeDB, the Maize Genetics and Genomics Database, now MaizeGDB, celebrates its 20th anniversary this year. MaizeGDB has transitioned from a focus on comprehensive curation of the literature, genetic maps and stocks to a paradigm that accommodates the recent release of a reference maize genome sequence, multiple diverse maize genomes and sequence-based gene expression data sets. The MaizeGDB Team is relatively small, and relies heavily on the research community to provide data, nomenclature standards and most importantly, to recommend future directions, priorities and strategies. Key aspects of MaizeGDB's intimate interaction with the community are the co-location of curators with maize research groups in multiple locations across the USA as well as coordination with MaizeGDB's close partner, the Maize Genetics Cooperation--Stock Center. In this report, we describe how the MaizeGDB Team currently interacts with the maize research community and our plan for future interactions that will support updates to the functional and structural annotation of the B73 reference genome.

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.

Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popular video currently available is 'Using the MaizeGDB Genome Browser', which describes how the maize genome was sequenced and assembled as well as how the sequence can be visualized and interacted with via the MaizeGDB Genome Browser. Database

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data.

The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time-sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn's utility are provided herein.

Choosing a genome browser for a Model Organism Database: surveying the maize community.

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers' needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers' needs. Here, we document the survey's outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/

The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps.

SUMMARY: Methods to automatically integrate sequence information with physical and genetic maps are scarce. The Locus Lookup tool enables researchers to define windows of genomic sequence likely to contain loci of interest where only genetic or physical mapping associations are reported. Using the Locus Lookup tool, researchers will be able to locate specific genes more efficiently that will ultimately help them develop a better maize plant. With the availability of the well-documented source code, the tool can be easily adapted to other biological systems. AVAILABILITY: The Locus Lookup tool is available on the web at http://maizegdb.org/cgi-bin/locus_lookup.cgi. It is implemented in PHP, Oracle and Apache, with all major browsers supported. Source code is freely available for download at http://ftp.maizegdb.org/open_source/locus_lookup/.

MaizeGDB becomes 'sequence-centric'.

MaizeGDB is the maize research community's central repository for genetic and genomic information about the crop plant and research model Zea mays ssp. mays. The MaizeGDB team endeavors to meet research needs as they evolve based on researcher feedback and guidance. Recent work has focused on better integrating existing data with sequence information as it becomes available for the B73, Mo17 and Palomero Toluqueño genomes. Major endeavors along these lines include the implementation of a genome browser to graphically represent genome sequences; implementation of POPcorn, a portal ancillary to MaizeGDB that offers access to independent maize projects and will allow BLAST similarity searches of participating projects' data sets from a single point; and a joint MaizeGDB/PlantGDB project to involve the maize community in genome annotation. In addition to summarizing recent achievements and future plans, this article also discusses specific examples of community involvement in setting priorities and design aspects of MaizeGDB, which should be of interest to other database and resource providers seeking to better engage their users. MaizeGDB is accessible online at http://www.maizegdb.org.Database URL:http://www.maizegdb.org.

MaizeGDB: The maize model organism database for basic, translational, and applied research.

In 2001 maize became the number one production crop in the world with the Food and Agriculture Organization of the United Nations reporting over 614 million tonnes produced. Its success is due to the high productivity per acre in tandem with a wide variety of commercial uses. Not only is maize an excellent source of food, feed, and fuel, but also its by-products are used in the production of various commercial products. Maize's unparalleled success in agriculture stems from basic research, the outcomes of which drive breeding and product development. In order for basic, translational, and applied researchers to benefit from others' investigations, newly generated data must be made freely and easily accessible. MaizeGDB is the maize research community's central repository for genetics and genomics information. The overall goals of MaizeGDB are to facilitate access to the outcomes of maize research by integrating new maize data into the database and to support the maize research community by coordinating group activities.

MaizeGDB's new data types, resources and activities.

MaizeGDB is the Maize Genetics and Genomics Database. Available at MaizeGDB are diverse data that support maize research including maps, gene product information, loci and their various alleles, phenotypes (both naturally occurring and as a result of directed mutagenesis), stocks, sequences, molecular markers, references and contact information for maize researchers worldwide. Also available through MaizeGDB are various community support service bulletin boards including the Editorial Board's list of high-impact papers, information about the Annual Maize Genetics Conference and the Jobs board where employment opportunities are posted. Reported here are data updates, improvements to interfaces and changes to standard operating procedures that have been made during the past 2 years. MaizeGDB is freely available and can be accessed online at http://www.maizegdb.org.