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The Plant Phenome Journal Author Instructions

Scope

The Plant Phenome Journal (TPPJ) is a transdisciplinary, open-access journal publishing original research, interpretations, and data sets investigating all aspects of plant phenomics. Broadly defined, the phenome includes all structural and physiological properties of plants, and phenomics is the study of the phenome. TPPJ is a forum to describe insights that result from transdisciplinary programs combining engineering, remote sensing, computer or data science with plant sciences, breeding, genetics, or agronomy. Specifically, TPPJ will publish reports on the development or novel methodological advancements of sensors, devices, vehicles, and/or advances in data collection, data management, algorithms, and data analysis that advance understanding of at least one domain in agronomy, genotype to phenotype linkage, physiology, pest management or plant breeding.

TPPJ’s editorial board believes that for articles to have the most impact and integrity for the scientific community and society, data must be made freely available and in an appropriate form for readers to perform reanalysis to reach the same conclusions. Furthermore, it is acknowledged that these data sets will probably be important to develop the next generation of analysis methods or algorithms and answer questions that were not initially planned. TPPJ recognizes that novel phenotyping technologies and phenomic data are rapidly evolving and emerging, and so too should the approaches and the standards to make these data publicly available. Editors and reviewers are charged with ensuring that such data follow best community practices at the time of submission. TPPJ seeks to be a leader and a forum for discussion on improving the practices of making phenotypic data both available and useful. Please see the Supplemental Material and Supplemental Data section for additional information.

Manuscript Types

Contributions to TPPJ may be Original Articles, Reviews, Technical Notes, Data Articles, Commentaries, Methods and Techniques, Protocol, and Letters to the Editor.

Original Article. Original Article papers report breakthrough research in applications domains and new technological advancements.
Review. Review articles are encouraged to synthesize across crops, disciplines and institutions.
Technical Note. Technical Notes are short articles (usually 4 printed pages or less) primarily concerned with specific methodological advancements that improve plant phenomics, and should at least describe the application domain. This is a good fit for describing new sensors, software, techniques, and other technologies that do not yet have substantial biological findings or impact from application.
Data Article. Data articles (limited to 2 pages or less) are papers that describe a large phenotypic data set submitted to the journal repository for community analysis. All data sets should adhere to the best metadata and curation practices at the time of submission, which we expect to evolve over time.
Commentary. Short papers on relevant issues related to science, policy, research trends, business trends, and exciting new discoveries (limited to 2500 words including figures and tables).
Methods and Techniques. A new methodological approach substantially advanced from previous approaches, that has been validated and remains of interest to, at a minimum, other researchers in a crop.
Protocol. Describes/documents the approach/steps needed to routinely apply an existing approach to make it repeatable among large numbers of independent laboratories. Expected to primarily be used by large collaborative projects, led by one or more laboratories having deep expertise in the protocol and an agreed upon standardized process to be deployed. Common pitfalls/imitations should be discussed as should be indications why this deserves peer review.
Invited Review. By invitation only. Review articles are encouraged to synthesize across crops, disciplines and institutions.
Letter to the Editor. Letters to the Editor are welcomed and are published subject to review and approval of the editor. When letters concern previous articles, the authors will be invited to reply; letter and reply are published together.
Book Review. Short description of a book related to the plant phenomics field.

Manuscript Submission

Templates

Download the TPPJ Submission Template and Pre-Submission Manuscript Formatting Checklist.

Submission

Submit manuscripts at the TPPJ Manuscript Submission Site. Submissions to TPPJ may not be previously published in their entirety or simultaneously submitted to any other scientific or technical journal. American Society of Agronomy (ASA), Crop Science Society of America (CSSA), and Soil Science Society of America (SSSA) journals follow the Publication Manual of the American Psychological Association (APA style) for references. Consult our Publications Handbook and Style Manual for specific questions about style.

Creating the Manuscript File

Microsoft Word or LaTeX files may be submitted for review. For your convenience, we encourage you to use our Word template. The manuscript should be double-spaced, using page and continuous line numbers. See our LaTex File Submission Guidelines for instructions on submitting LaTeX files.

Peer Review and Revisions

All manuscripts submitted undergo single blind peer review. Papers are assigned to a technical editor to solicit at least two reviews. After evaluating the completed reviews, the technical editor will recommend a decision to the editor. Authors will be prompted to provide a list of preferred and non-preferred reviewers. These reviewers cannot have a conflict of interest involving the authors or the study, and the editorial board has the right to not use any reviewers suggested by authors. See the ASA, CSSA, SSSA Editorial Policies information page for additional information on review policy, including the policy for appeal of manuscript review. . All revisions to the manuscript during the review process will be made by the author only, and revisions will be given the same manuscript number, with an R number on the end (e.g., TPPJ-2006-04-0017-ORA.R1). Each revision has the opportunity for another round of review—the manuscript status “awaiting reviewer selection” is automatic and does not indicate a resubmission. Authors have four weeks to review and return their manuscript following reviewer and technical editor comments. Manuscripts may be released if revisions are not received, and the paper will have to be submitted as a new manuscript. The average time from submission to final decision (including revisions) is about 60 days.

ORCID iD

Corresponding authors are required to use an ORCID iD when submitting a manuscript. More information on ORCID can be found on their website. We encourage all authors to list their ORCID iD in the manuscript.

Plagiarism Screening

Papers submitted to ASA, CSSA, SSSA journals are screened for plagiarism before being sent for review. If there appears to be major repetition from other sources, the editor will evaluate the duplication and take appropriate action as warranted.

Article Requirements

Authors should follow the Publications Handbook and Style Manual when formatting manuscripts for submission. Please submit the manuscript file containing the title, abstract, text, references, and tables. Please submit figures in separate files as well as embedded in the main text.

The submission should contain the following elements:

Title
Authors
Affiliations
Core Ideas
Abstract
Plain Language Summary (optional)
Abbreviations
Text
Tables*
Figure captions
Figures*
Supplemental Material statement
Data Availability statement (optional)
Author Contributions
Conflict of Interest statement (mandatory as of 2022)
Acknowledgments (optional)
References list

*Tables and figures (review quality) with captions should be placed into the text document at first mention. Figures of accepted papers must also be submitted separately for production as high-resolution image files in the following acceptable formats: EPS, TIF, PDF, or JPEG.

Paper Structure

On the first page, give the title, a byline with the names of all authors, an author–paper documentation, a list of all nonstandard abbreviations used in the paper (standard abbreviations available in the Publications Handbook and Style Manual), and any other necessary footnotes. An abstract is required and is normally the second manuscript page. After the title page and abstract, the usual order of sections is an untitled introduction (which includes the literature review), Materials and Methods, Results, Discussion, Conclusions (optional), Acknowledgments (optional), and References, followed by any figure captions and the tables. Results and Discussion may be combined and conclusions can be given at the close of the Discussion section.

Title and Byline. A title gives the reader a clear idea of what the article is about; it should be brief and informative. Use common names for crops and avoid abbreviations. The usual limit for titles is 10 to 12 words (not counting “and,” “of,” and similar conjunctions and prepositions). Titles in a numbered series of articles may be longer. Below the title, list the names of all authors. Place an asterisk after the name of the corresponding author (i.e., the person from whom reprints are to be requested).

Authorship. Authors should meet four conditions to be listed as authors as recommended by the International Committee of Medical Journal Editors (ICMJE):

Substantial contributions to the conception or design; or the acquisition, analysis, or interpretation of data; AND
Drafting the work or revising it critically for important intellectual content; AND
Final approval of the version to be published; AND
Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

All other contributors should be listed in the acknowledgments section. The corresponding author will speak on behalf of all authors both before and after publication, including promptly addressing any concerns. The corresponding author is also responsible for ensuring that the entire submission conforms to TPPJ guidelines.

Affiliations. The author–paper documentation is a single paragraph. The first sentence lists the authors (without professional titles) and their complete, current addresses. If a paper has only one author, or if all authors are from the same department and institution, omit the names (i.e., give the address only). The second sentence lists institutional sponsors, with the institutional article number of similar contribution acknowledgment. Add such an acknowledgment if an author has moved and using the current address leaves no other mention of the involvement of the former institution. Other information such as granting, funding, or dissertation status may follow here or in a separate acknowledgment section at the end of the paper. End the author–paper documentation paragraph with contact information for the corresponding author.

Core Ideas. Include 3 to 5 summary statements that convey the core findings of the article. The purpose of these short, bullet-pointed statements is to identify the most relevant outcomes of the paper and to provide a synopsis encapsulating the significance of the research and its implications for readers. Each statement must be 115 characters or less (spaces included). If the article is accepted, the core ideas may also be used for promoting and publicizing the research.

Abstract. Abstracts are a single self-contained paragraph of no more than 1500 characters—including word spaces—for papers or 750 characters for Technical Notes and Data Articles. Abstracts should contain the rationale, objectives, methods, results, and their meaning or scope of application. Be specific. The abstract needs to stand alone--do not use phrases such as “is discussed” and do not cite references.

Plain Language Summary. You may include a plain language summary (limit 1000 characters). The summary should be clear, concise, and free from jargon. See guidelines for writing plain language summaries here.

Abbreviations. Prepare a list in alphabetical order of abbreviations used in your article. Do not include SI units, chemical abbreviations, or abbreviations listed in the style manual as not needing definition.

Text. The main text of the manuscript typically includes an Introduction, Materials and Methods, Results, Discussion, and a conclusion. The Results and Discussion sections may be combined into one section. The author(s) can either (i) include a separate Conclusion, which will appear as a subheading under the Discussion section, or (ii) provide the conclusion (with no heading) at the end of the Discussion section. In either case, the conclusions should be no longer than 200 words. Within the 200 words, the conclusions and implications of the work should be provided. In some instances, no conclusions may have been drawn from the study. In this case, the implications of the study should be provided. In other words, if the author(s) decides to forego the inclusion of a Conclusion subheading within the Discussion section, then the final paragraph of the Discussion section should provide the conclusions (if any) and the implications of the study.

Supplemental Material. Most TPPJ manuscripts are expected to have supplemental material or data, and this will occasionally be large. Data essential to arrive at manuscript conclusions are expected to be included. While raw data are desirable for reanalysis, such data sets can be too large for long-term storage and challenging to use to ensure rigor and reproducibility. In contrast, providing only data sets that are too polished may have limited value for confirming conclusions or for additional future novel analyses. Given the emergence of technologies and community research goals, the standards for the data to be included is expected to also emerge. TPPJ seeks to be a forum for discussions on these standards and at the forefront of these issues. Therefore, supplemental material and supplemental data will be reviewed for appropriateness and usability (including metadata) according to these emerging standards at the time of submission.
A section with captions for each uploaded item of supplemental material should be included at the end of the main text. Captions should both give an overview of what the supplemental item is and include all information not present in the headers or legend, but not be overly complex or long because these descriptions will be published. A “readme” file is an appropriate way to include metadata and additional information when the data are complex or if there are multiple items to describe. Supplemental tables and figures should be cited in order in the main manuscript. Supplemental material should be formatted with a cover sheet listing authors and manuscript title and the number of pages, figures, and tables. Tables, figures, and data should be numbered Supplemental Table S1, S2; Supplemental Fig. S1, S2; Supplemental Data S1, S2, etc. Label the file as “Supplemental File” when you upload.

In place of supplemental material, our journals encourage the use of data repositories that assign DOIs or other persistent unique identifier (PID) to the data.

Data Availability Statement. Authors are encouraged to include a data availability statement. A data availability statement is required for dataset papers.

Conflicts of Interest Statement. Conflicts of interest must be described and will be published with the article. Conflicts of interest are anything that would interfere with, or a reasonable person could perceive to interfere with, the fully transparent and objective presentation of the paper. Potential conflicts could concern intellectual property, relationships with other entities, or financial gain but are not limited to these issues.

Author Contributions. The contributions of each author must now be indicated at submission. The submitting author is required to assign specific author contribution roles for each coauthor, using the CRediT taxonomy to indicate their respective roles. The 14 roles are Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, and Writing – review & editing. Author Contributions will be published with the accepted article (mandatory as of July 2021) and cannot be edited after article acceptance. Therefore, you must ensure the Author Contribution information you provide is accurate prior to final acceptance.

A final acknowledgments paragraph may be included.

References. ASA, CSSA, SSSA journals follow the APA style for citations and references. The author-year system for citations is required; do not use numbered references. Refer to chapter 1 of the Publications Handbook and Style Manual for examples of our reference and citation style, in addition to following these guidelines:

Arrange the list alphabetically by the surnames of the first authors and then by the second and third authors.
Single-authored articles should precede multiple-authored articles for which the individual is first author.
Two or more articles by the same author(s) are listed chronologically; two or more in the same year are indicated by a, b, c, etc.
Only literature that is available through libraries or other readily accessible public media can be cited. Material that does not meet this standard should be cited as personal communication or unpublished data.

Tables. Each entry should appear in a new table cell. Do not use tabs, spaces, or graphics. Cite each table in the text in numerical order; do not use table parts (1a, 1b). Each table must be cited in the text. Table heads should be brief but complete and self-contained. Define all variables and spell out all abbreviations. Table notes can include “Notes” for general notes that apply to the entire table, superscript lowercase letters for specific notes, and asterisks and other symbols as needed for significance notes.

Figures. At submission, review-quality figures with captions should be placed into the main text document at first mention. Authors may also submit figures as separate files. If the manuscript is accepted for publication, color figures must adhere to our color-figure policy. Figures must also be submitted separately as high-resolution image files (300 dpi preferred) in the following acceptable formats: PDF, EPS, TIFF, or JPEG. PPT files are acceptable if the figure was created in PowerPoint. Width of figures should approximate desired print size, i.e., 80 mm for a one-column figure, 180 mm for a two-column figure. All figure parts should be labeled. Multi-panel figures should be submitted as one image. Biplots should have equally scaled axes with tick marks.

Spell out abbreviations on first mention in figure captions, even if they have already been defined in the main text. Define symbols used either in the caption or in a legend within the figure. For more information on figures, see Chapter 5 of the style manual.

Math. Use keyboard formatting where possible (i.e., bold, super-/subscripts, simple variables, Greek font, etc.); if needed, use MathType (preferred) or Word Equation Editor (only if MathType is not available).

Units of Measure. The International System of Units (SI) must be used. Other units may be indicated in parentheses after the SI unit if this helps understanding or is needed for replication of the work.

Citing Genetic Material

Authors of CSSA publications must cite plant introductions, as well as registered cultivars, germplasm, parental lines, and genetic stocks when they are mentioned in the text of the Introduction, Discussion, or Characteristics section of research papers. Such genetic materials must also be cited when they are used to develop unreleased genetic populations that are the focus of the research paper, unless the development of the population can be cited more directly. Authors are encouraged to cite the Journal of Plant Registrations if possible. Other sources for citation information include the Genetic Resource Information Network (GRIN) maintained by the USDA. Registrations published in Crop Science and the Journal of Plant Registrations are indexed on the GRIN website. A general search in GRIN is available here. Plant patents and plant variety protection (PVP) certificates are also appropriate to cite.

Nomenclature

Both the accepted common name and the chemical name of pesticides must be given upon first mention in the manuscript. Use chemical symbols for elements, ions, and simple compounds except at the beginning of a sentence or in a title or heading. The Latin binomial or trinomial (and authority for plants) must be included with the common name for all plants, insects, pathogens, and animals at first mention. When referring to soils, give at least the subgroup in accord with the U.S. system of soil taxonomy. Ideally, both the series and complete family name should be given.

Consent and Permissions

Before submitting the paper, the corresponding author should send each living coauthor a draft copy of the manuscript and obtain the coauthors’ assent to coauthorship. Authors are responsible for obtaining all permissions for use of figures or other material from other publishers and should supply these permissions when the manuscript is accepted. Authors are also responsible for obtaining permission from individuals whose images are included in photographs. Note that ASA, CSSA, and SSSA reserve the right to publish and republish any images you submit with a manuscript.

Changes to Author Byline

From time to time, authors' names are either added or removed from a given manuscript between the time of submission and publication. In situations such as this, the ethical and responsible manner of handling this type of change is for the lead author to advise the author being added or removed of the change and to notify, in writing, the journal editor and journal program manager for approval. In addition, all coauthors should notify the program manager that they are aware of and approve of the change.

Errata

Errata may be used by the authors of a paper to correct errors and omissions that affect the integrity of the version of record that are identified after publication. All additions and corrections are subject to editorial approval and must be approved by all coauthors before submission; corrections of minor errors or omissions will not be published. Send all errata requests to the journal’s program manager.

Publication Fees

Mandatory Open Access Fees

Authors are assessed a mandatory open access licensing fee of $2,800 to apply an open access license at the time of publication to make the article freely available without a subscription.

Journal articles in are published open access under the CC BY-NC-ND (attribution, noncommercial, no derivatives) license. Learn more

Authors may request that their article be published under the CC BY (attribution) license. Learn more

No licensing fees are charged for invited reviews, comments, book reviews, or letters to the editor.

For authors publishing in this open access journal, fee waivers and discounts may be available to qualifying corresponding authors based in low- and lower middle-income countries. Visit the waivers and discounts web page to learn more.

Institutional Funding and Transformational Agreements

Your institution or funder may be able to help with open access licensing fees through a transformational agreement. For qualified authors, fees may be covered in full or part when publishing in the journal. Visit the institutional funder payments web page to learn if you qualify and for more information.

Authors Funded by cOAlition S

If you or one of your co-authors received funding from a member of cOAlition S, there may be restrictions on where you can publish. Please check your agreement with your funder for specific details. The information and author compliance tool on this web page can help you make an informed decision about where to publish in alignment with funder and journal requirements.

Official Sources

Spelling: Merriam-Webster’s New Collegiate Dictionary
Plant scientific names: USDA–ARS GRIN database
Chemical names: PubChem
Soil series descriptions: USDA–NRCS Official Soil Series Descriptions
Fungal nomenclature: Fungi on Plants and Plant Products in the United States (APS Press)
ASA, CSSA, SSSA journal style: Publications Handbook and Style Manual

For questions about the format of submissions, the process of submitting a manuscript, or about the status of manuscripts that have been submitted and assigned a manuscript number, please contact the TPPJ program manager.

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