_California Agriculture_ is an open access journal publishing peer-reviewed research on California's agricultural, natural and human resources. We welcome submissions for peer-reviewed research and review articles (see "Article types" below). While most of our authors are affiliated with UC Agriculture and Natural Resources (UC ANR), authors from other institutions are encouraged to submit manuscripts, and author affiliation is not considered in our review process. The journal welcomes out-of-state or international submissions. However, all research published in _California Agriculture_ must be relevant to California's agricultural, natural or human resources. If you conducted your research outside of California, please state in the manuscript how that research is relevant and useful to California. - Article types - Writing for the _California Agriculture_ audience - Sections of the article - Matters of style - Submitting the manuscript online - Other information for authors ___ # Article types All published research and review papers are peer-reviewed. Research must be relevant to California's agricultural, natural or human resources. We recognize that evidence can be qualitative as well as quantitative, but it must adhere to accepted standards of research methodology and statistical significance in the relevant discipline. **Research** articles are up to 4,000 words in length, including tables, figures and references. Articles are expected to contain original research representing a significant advance in one field; they may synthesize results from related experiments, presenting them in terms meaningful to both an interdisciplinary audience and educated lay readers. We encourage authors with previously published technical data to analyze it with a focus on policy or management questions in California. Such articles must make an original contribution to research; submissions should be made within 6 months of publication in a disciplinary journal. **Reviews** are up to 4,500 words in length, including tables, figures and references. They synthesize and evaluate a body of original research that is significant to agricultural, natural or human resources in California. Reviews must make an original contribution to the research discourse. Readers should be able to learn what has been firmly established and what are unresolved questions or future directions for research. **Special collections and focus issues** typically include both reviews and research articles on subjects that have stimulated significant interdisciplinary research and/or extension efforts at UC, and that have interest for a wide cross-section of the audience. **News** articles are developed by editorial staff and typically cover research or extension projects conducted by UC ANR-affiliated researchers. Faculty sources review these items for accuracy and balance of presentation. However, they are not peer-reviewed for original research content, or as a review of the same. **Outlook** articles are 1,000- to 2,000-word, non-peer-reviewed, op-ed style pieces that analyze recent developments in research and policy. They are typically authored by a researcher or a group of researchers. An Outlook may include citations, but it should follow a more conversational style than a research manuscript. Please contact us at calag@ucanr.edu for more information. **Editorials** synthesize or analyze recent developments in research and public policy and express opinions regarding the impacts on California's agricultural, natural and human resources. An editorial is typically authored by a leader in academia, government, agriculture or business who is invited by the UC ANR vice president or the executive editor. Editorials range from 600 to 1,500 words. ___ # Writing for the _California Agriculture_ audience _California Agriculture_ targets a broader audience than most academic journals. Outreach to this broad audience is a key mission of its publisher, UC ANR. As such, published articles must be clear to non-specialist readers while also meeting disciplinary standards for scientific rigor. It is not necessary to write in a style dramatically different from what you would use when preparing a paper for a disciplinary journal in your field. Rather, write a well-organized scientific article using plain, direct language. It should address the following questions: * What is the problem your research addresses, and how does the problem affect agricultural, natural or human resources in California? * What did you do, where, when and how did you do it, and what did you find? * What are the practical implications of the findings in the California context? ___ # Sections of the article Please follow the guidelines for the sections of the manuscript below. Paragraphs should have clear topic sentences and should be short, no more than 150 words. **Title.** The title presents the key finding of the article. It indicates the article content directly, using an active verb, in 100 characters at most. For example, from the July-September 2015 issue: > Thinning treatments had minimal effect on soil compaction in mixed-conifer plantations **Abstract.** The abstract is about 170 words and has three components: 1\. One sentence or two on the context of the study, so the reader knows immediately what's at stake. For example (from same article): > If using biomass results in soil compaction and reduced forest productivity, the potential benefits may be considered to be not worth the long-term impacts. 2\. A couple of sentences describing the research: > We analyzed soil strength, . . . 3\. Two or three sentences that present the key findings of the research: > Neither the commercial thins nor the mastication treatments resulted in . . . Most of the compaction came from . . . This study suggests that managers should not expect large impacts . . . **Introductory paragraphs.** The first two or three paragraphs of the main article text state the reasons for conducting the research and any background necessary for understanding the research. For example, if the research were on methods of controlling a particular pest, the reader would like to know how extensive is the damage to crops, what current controls exist, why the researchers undertook this particular approach to controlling the pest. The focus of each of these paragraphs is immediately recognizable as important to the article topic. Please only include material that is directly relevant to the topic of your article. **Research study design and methods.** Only enough of methods should be described in the main text so that a non-specialist reader can understand and evaluate the results and conclusions. Additional technical information on methods and analysis may be provided in a technical appendix (see below). **Results.** The results section should analyze the data, not simply state data that is present in tables or figures. **Subheadings.** Please use subheadings to orient the reader to the main parts of your article. As you write your article, it may help to follow the standard structure for scientific papers: Introduction, Methods, Results, Discussion, Conclusions. Before submitting your article, change those headings to brief descriptive clauses of no more than 32 characters. Add more subheadings as needed to guide the reader through the article. In the article mentioned above, for example, the subheads read: * _Experimental treatments_ * _No statistical differences_ * _Soil compaction in perspective_ **Conclusion paragraphs.** The last paragraph or two should interpret your research results in terms of their practical value for practitioners or clients and mention the implications for future research. It's appropriate to mention each key finding of the research as you explain its value and the implications, but do not simply restate all the results. Readers need to be able to assess what your study results mean, why they are important and what sort of research needs to happen next. **Technical appendix.** Technical information on methods or analysis that does not fit neatly in the main body text but that may be useful for reviewers evaluating the manuscript may be submitted as a technical appendix. Text in the technical appendix does not count against the word limits specified under "Article types". ___ # Matters of style As you prepare your manuscript, please ensure that the elements below are formatted according to _California Agriculture_ style. **Author names.** Full names are used --- "John D. Doe" --- unless the author is known by initials only. **Author identification and acknowledgments.** Author identification should include the name, title, department or other affiliation and location of all authors (see the journal for style). After the author identification, you may thank collaborators who do not qualify for authorship; please also identify pertinent sources of research funding. For the purposes of anonymous peer review, include the author identification and acknowledgments only in your final, approved, post-review manuscript. **Figures and tables.** Figures and tables present the pertinent research data. Table headings are very short (e.g., "Average annual height growth in study of natural regeneration of blue oaks"). Figure captions can be longer; they should explain what the data shows. All tables and figures should be cited in numerical order. **Abbreviations, symbols and acronyms.** All abbreviations should be spelled out, in parentheses, the first time they are used: huanglongbing (HLB). **Chemical names.** We prefer the common name, with the trade name the first time in parentheses (no trademark symbol necessary). **Terms.** Technical terms should be defined on first reference. Maintain consistent use of terms. **Units/measurements.** We publish results in standard English measurements followed by metric equivalents in parentheses. If this is too cumbersome, a box listing metric equivalents may be published in the text of the article. Very small units that are difficult to convert to English measurements can remain in metric (i.e., milligrams, milliliters, etc.). **References.** _California Agriculture_ uses the "name-year system," in which references are cited parenthetically in the text by author name and date of publication and listed at the end of the article in alphabetical order. - DOIs (digital object identifiers): include DOIs for journal articles; see below for an example. - Unpublished work and personal communications should be cited in the text and should not be included in the References list. - Multiple references cited in a parenthetical should be alphabetized: (Brown 1987; Dawson et al. 1990; USDA 2000). - **NOTE**: _California Agriculture_ does not use footnotes. 1\. _Personal communications and unpublished data_ - If not author: (Richard Breitmeyer, affiliation, personal communication) - If author: (J. Nunez, unpublished data) or (J. Nunez, personal observation) 2\. _Journal articles_ O'Geen A, Saal M, Dahlke H, et al. 2015. Soil suitability index identifies potential areas for groundwater banking on agricultural lands. Calif Agr 69(2):75-84. 3\. _Books_ Shuford WD, Gardali T (eds.). 2008. _California Bird Species of Special Concern: A Ranked Assessment of Species, Subspecies, and Distinct Populations of Birds of Immediate Conservation Concern in California._ Sacramento, CA: Western Field Ornithologists and California Department of Fish and Game. 450 p. 4\. _Parts of books_ Katibah EF. 1984. A brief history of riparian forests in the Central Valley of California. In: Warner RE, Hendrix KM (eds.). _California Riparian Systems: Ecology, Conservation, and Productive Management._ Berkeley, CA: UC Press. p 23-9. 5\. _Electronic resources_ R Development Core Team. 2008. R: A language and environment for statistical computing. Vienna, Austria: Foundation for Statistical Computing. www.r-project.org **Style manuals.** If you would like more information about style, _California Agriculture_ uses the following manuals in this order: - AP Stylebook (current edition) - Merriam-Webster's Collegiate Dictionary (11th ed.) - Chicago Manual of Style (16th ed.) ___ # Submitting the manuscript online Please use the checklist below to properly format and submit your manuscript before submission to Scholastica. If you have any questions about online submission, contact Managing Editor Debbie Thompson at . **1. Cover letter** All manuscripts must be accompanied by a cover letter. The cover letter should include: - The names, addresses, e-mail addresses, telephone numbers and affiliations of all authors. - The title of the paper and a statement of its main point. - The total number of words (including text, references, and figure and table legends) in the manuscript. - A disclosure stating either: **(a)** That the material has not been published and is not under consideration for publication elsewhere, or **(b)** that the manuscript includes findings that have been published in whole or in part elsewhere, but are being presented in a substantially different form with a focus on policy or management questions in California. We encourage such submissions, but note that the manuscript must represent, in the judgment of the associate editor and peer reviewers, an original contribution to the research literature. Submissions should be made within 6 months of publication in another journal. In such cases, please provide details about where and when the material has been submitted or published. - A statement specifying when data was collected. If the final data was collected more than 3 years before submission, please state why it is timely and relevant. - A statement that you permit the electronic transfer of your manuscript to peer reviewers and associate editors. - A list of photographic illustrations, either available or suggested. - If relevant, a statement describing the approvals obtained for human subjects research, specifying the institutional review board or ethics committee that issued the approval. - If relevant, a statement affirming that care of experimental animals was in accordance with institutional guidelines. - A list of preferred reviewers (see below). **2. Manuscript text** In preparing the manuscript: - Double-space the whole manuscript, and place all tables, figures and captions at the end. - Use a 12-point font, such as Palatino or Times New Roman. - Leave margins that are a minimum of 1 inch. - Include continuous line numbering and page numbers. - For the purposes of double-blind peer review, remove all identifying information regarding all authors and co-authors. **3. Preferred reviewers** Authors are strongly encouraged to recommend five reviewers for the submitted paper. They should be experts with whom the authors have not collaborated in the past 3 years, and who are not currently affiliated with any author's institution. The associate editor may invite reviewers from the submitted list, or may choose to invite other experts. Authors should provide the names and email addresses of recommended reviewers as part of their cover letter. Authors affiliated with one of the 10 University California campuses or with UC Agriculture and Natural Resources are encouraged to recommend qualified reviewers who are not affiliated with a UC campus or UC ANR. If it is not possible to identify qualified non-UC reviewers for a paper with one or more UC-affiliated authors, the journal will consider reviewers from a different UC campus than any of the authors, with UC ANR to be considered a "campus" for these purposes. Campus-based UC ANR Specialists are considered to be affiliated with both UC ANR and their campus. A similar standard applies to an author associated with a California State University campus. For example: For a paper authored by a UC Berkeley Specialist, reviewers could not be affiliated with either UC Berkeley or UC ANR, but a reviewer from UC Davis or UCLA would be acceptable. A paper authored by a county-based advisor could not be reviewed by a UC ANR Specialist or Advisor, but reviewers from any of the 10 UC campuses would be acceptable. Note that this standard applies to all co-authors, so reviewers for a paper co-authored by a UC Berkeley postdoc, a UC ANR advisor, and a UC Davis-based specialist could not be affiliated with UC ANR, UC Berkeley or UC Davis. A similar standard applies to an author associated with a California State University campus or other multi-campus university systems. Authors associated with government agencies should recommend reviewers not affiliated with their agency. **4. Illustrative and supporting material** **Figures (charts, graphs, drawings).** As a rule, *California Agriculture* does not directly reproduce color charts and graphs. Our art director will reformat them, and you will have the opportunity to approve and/or revise them. Separate figures from the text and place them at the end of the manuscript. Number each figure and provide a numbered caption. On each graph, indicate units of measure and make interval marks along both the horizontal and vertical axes (see Council of Science Editors style manual). Where curves or bars need to be differentiated, include the legend to identify them in the graph itself rather than in the caption. Our practice is to number only charts, graphs and drawings (fig. 1, fig. 2, etc.), and refer to them in text. We do not number photographs or refer to them as figures. Also submit each of the charts, graphs and drawings in one of the following formats via email: - Charts and graphs created in Excel can be provided in an Excel worksheet with the data. - Charts, graphs and drawings created in other applications should be provided in a vector format such as .EPS, .AI, vector PDF, or SVG. If you have any questions regarding the formats, please contact Sandi Osterman at . **Captions.** Include simple descriptive captions for all graphs, drawings and photos, including as many relevant details as you can. For drawings and photos, please list the artist or photographer's name at the end of the caption. We generally rewrite captions at the final production stage to fit the space available in the layout; you will have the opportunity to approve or revise them. **Tables.** Separate tables from the text and place them at the end of the manuscript. Your reformatted, edited tables will be included with the edited proofs for your approval. **Survey instrument.** If the research involved a survey, please provide an electronic copy of the survey instrument. If the manuscript is accepted, we will publish the survey online as supplementary material, unless the author prefers not to. **Color images.** We generally run four to six images per article. Submit high-resolution digital images via e-mail, or CD. You may also submit 35-mm color slides, preferably originals. We will return your slides after publication. As a last resort, we can scan your good-quality color prints. Please be sure all art is identified and keyed to captions provided. Digitized images, whether captured with a digital camera or scanned from prints/slides, must provide the resolution needed for our purposes. - The minimum size for digital images is approximately 1400 × 2100 pixels. Larger files up to 3500 × 5200 pixels or larger are preferred. - Do not supply your images embedded in Word or PowerPoint documents - Do not submit composite images (multiple images brought together in one file for use as a figure). Submit each image as a separate file. - Provide the images as separate files in TIFF, JPEG, or any RAW camera format. Original camera files are preferred. - JPEGs should be original camera files or saved using the \"maximum quality\" setting. - Avoid converting the image to CMYK; we prefer RGB. If you are unsure of the capabilities of your camera or have questions about content, format or transport of your artwork, please contact Sandi Osterman at . **Tips:** - Sharp focus and correct exposure are necessities, as the reproduction process does not improve slide quality but, rather, tends to exaggerate fuzziness and incorrect exposures. Be sure that the subject of the photograph stands out clearly against the background, and avoid confusing light patterns. - A slightly "flat" tonal range is preferred. Avoid high contrasts and deep shadows; the printing process exaggerates lights and darks, so much detail will be lost in highlight and shadow areas. - Take several exposures of each desired subject and select the most successful ones (or feel free to let us do the selecting). - Give us as much to choose from as possible. Try to submit both horizontal and vertical format pictures to help with layout flexibility. From our point of view, the more images we have to choose from, the better. - As you conduct your research, try to anticipate your photo needs, especially if you are dealing with seasonal material. We encourage you to use professional photographers on the campuses. - When submitting illustrative material, please review its content and consider seeking advice on safety issues, including the depictions of equipment use, pesticide use and food safety. **Conditions of acceptance** When a paper is accepted for publication in _California Agriculture_, it is understood that: - Photos depict situations that conform to relevant regulatory code, if any. - Authors agree to grant to *California Agriculture* (UC Regents) a nonexclusive license to publish the paper in print and online. Material published in _California Agriculture_, excluding photographs, is licensed under the [Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International license (CC BY-NC-ND 4.0)](http://creativecommons.org/licenses/by-nc-nd/4.0/#). In general, photos may be reprinted for non-commercial purposes; photo reprint requests are processed using the [UC ANR Permissions Request Form](http://ucanr.edu/survey/survey.cfm?surveynumber=5147). - Authors agree to disclose all affiliations, funding sources, and financial or management relationships that could be perceived as potential sources of bias. - The paper will not be released to the press or the public before publication. ___ # Other information for authors **Submission fees and article processing charges (APCs)** _California Agriculture_ charges authors a fee of $10 per submission. The journal does not charge APCs. **Authorship** Authors must have made a substantial professional contribution to the paper, such as formulating the problem and hypothesis, structuring the experimental design, organizing and conducting the statistical analysis, or writing a major portion of the paper. "Authorship" means that all authors listed contributed a substantial portion of the total effort required to produce the manuscript. **Online and print publication** If you have an article that is time-sensitive, please notify Managing Editor Debbie Thompson (). _California Agriculture_ publishes research articles online as "Early View" as soon as the PDF layout process is complete. A permanent [DOI number](http://www.doi.org/) is assigned to each article when it is published online. The print edition of the journal includes research articles recently published online, along with news and opinion articles. Research articles are often grouped into thematic collections for an issue, meaning that print publication may occur several months after online publication. **Permissions** _California Agriculture_ is an open access journal and allows users to read, download, copy, distribute, print, search or link to the full text of all articles, subject to the following terms: * _Photographs_ To request permission to reprint a photograph published in California Agriculture in print or online, please complete the [UC ANR Permissions Request Form](http://ucanr.edu/survey/survey.cfm?surveynumber=5147). Permissions requests are considered on a case-by-case basis. In most instances, UC ANR will grant a reprint permission request if the photo is copyright UC Regents and the request is for a non-commercial purpose. * _All other material_ Material published in _California Agriculture_, excluding photographs, is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International license [CC BY-NC-ND 4.0](http://creativecommons.org/licenses/by-nc-nd/4.0/). Material may be copied and redistributed freely under the following terms: * Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. * NonCommercial — You may not use the material for commercial purposes. * NoDerivatives — If you remix, transform, or build upon the material, you may not distribute the modified material. * No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. * When attributing, please credit California Agriculture, University of California, citing volume and number, or complete date of issue, followed by page numbers. Indicate ©[year] The Regents of the University of California.

3. Plant genes: Understanding mechanisms of gene expression