Scope and Aims of the Section
AJB Primer Notes & Protocols in the Plant Sciences is an online-only section of the American Journal of Botany (AJB) intended to promote rapid dissemination of protocols used in genetic analyses of plants. Subjects appropriate for this section include: (1) marker notes providing primer sequences for microsatellite or other markers in particular taxa, and (2) protocol notes describing new methods for isolating, visualizing, or scoring genetic markers. Protocol notes are expected to provide evidence that the new protocol increases the accuracy or reproducibility of marker scoring, decreases the time or expense of marker scoring, or provides the ability to score new classes of markers.

For primer notes, the intent is to demonstrate the usefulness of newly developed primers for subsequent, more detailed studies.  Sampling distribution and numbers will depend on the life history characteristics of the organism under study, but sample sizes should be adequate to support the genetic parameters presented.  For example, sample sizes are expected to be greater for abundant and widely distributed species than for rare species.  Whenever possible, the use of data from multiple populations is encouraged to capture a wider range of potential variation.  Although most primers are expected to exhibit polymorphism, monomorphic primers are also acceptable because they may be useful in other populations or related taxa.  Given the limited sampling and biological characteristics of some species (small population sizes, recent colonization, admixture, clonality, etc.), tests of linkage disequilibrium and Hardy-Weinberg equilibrium are not required for primer notes articles but are instead reserved for later in-depth population surveys. 

Review Procedure and Policy
Contributions to Primer Notes & Protocols in the Plant Sciences will be published online when production-ready copy is received from the author. Each note will receive a unique digital object identifier (doi), and the date of publication will be the date on which the note is posted to the AJBwebsite.

To facilitate automated publication, all papers must conform to strict word limits and the publication template (Author_PNP_template). Papers submitted to Primer Notes & Protocols will be reviewed by a section editor for content, suitability to the section, conformity to the guidelines, and assurance that protocols are described with sufficient detail to allow other investigators to use them. Review will generally be completed within 2 weeks. Authors of accepted notes will be expected to return revised manuscripts within 1 week of an editorial decision. Revisions will be evaluated for satisfactory response to editorial comments, and checked for conformity to word limits and the publication template, but they will not be copy edited. Authors will be solely responsible for any errors that appear in the published version.

Copyrighted material—If copyrighted material is reproduced in the manuscript, full attribution must be provided in the text; proof of permission must be sent to the Editorial Office. If suspicion is raised about the originality of the material (unattributed to source) the Editorial Office may check the manuscript for plagiarism.

Data—When using unpublished data owned or created by a researcher who is not the author or a co-author, a formal statement from the owner of the data must be sent to the Editorial Office acknowledging the use of the data and granting formal permission.

Nomenclature—AJB requires that nomenclature for all extant and extinct species conform to the current International Code of Botanical Nomenclature. Taxonomic authorities are given at first mention in the text (not in the manuscript title).

Use conventions adopted by the scientific community for genetic symbols and nomenclature.

Genetic Analyses—AJB requires supporting genetic information, such as DNA, RNA, or protein sequences, be submitted to an appropriate data bank, such as GenBank/EMBL. Alignments used to produce phylogenies must be submitted to TreeBase or to AJB to be published as an online supplement with the paper. The data matrices must be in an editable format (i.e., text files) for reanalysis by anyone interested..

Vouchers—At the time of submission, AJB requires supporting genetic and voucher specimen information to be provided (see Appendices). In discussions of morphological character states, access to the data must be provided.

Include GPS coordinates for each of the populations sampled, if available, unless the species is federally listed as threatened or endangered. Provide accuracy to the nearest second, or the fifth decimal place if using decimal degrees. If vouchers or GPS coordinates are unavailable, an explanation must be provided in the cover letter, as well as within the article itself. Exceptions to the voucher requirement will be assessed by the section editors.

General Instructions and Requirements
Before submitting, please review all instructions and the publication template.

To take advantage of the free-page-charge policy, at least one author must be a member of the Botanical Society of America (BSA) when the manuscript is submitted for review as well as during the year of publication.  Authors who are not members of the BSA may also submit manuscripts for consideration; however, a mandatory page charge of $130 per published page (based on the pdf version) must be paid prior to a manuscript going into production.

Note that papers published in the AJB Primer Notes & Protocols section do not count against an author's yearly allotment of free pages in AJB when he/she is a BSA member. For detailed information, see the overall AJB instructions for authors (http://www.amjbot.org/misc/ifora.shtml).

AJB requires that at least one colleague whose first language is English critically read and edit the manuscript before submission. Manuscripts may be returned without review if the English needs significant improvement.

Submit your manuscript via the online submission and review system, Editorial Manager, at http://ajb.edmgr.com. First-time users need to register for an account at this URL using their active e-mail addresses. The same Username and Password are used to log in as an author or as a reviewer. All reviews, revisions, and proofs are handled electronically. If you are unable to access the Internet, please contact the Editorial Office (contact information given at end).

Authors are encouraged to submit figures in color, if doing so enhances the presentation of the scientific information.  Color plates are free for all BSA members, regardless of length of membership.

Article Type
Please choose "AJB Primer Notes & Protocols" as the Article Type when submitting your article within Editorial Manager.

Manuscript Preparation
A cover letter, an author agreement form, a manuscript file, and separate files for figures should be uploaded at http://ajb.edmgr.com. The manuscript file includes in the following order:

• Short Title [running head—AJB Primer Notes & Protocols-+ 2 or 3 descriptive words, e.g., "Ziziphus microsatellites"]
• Title [up to 125 characters]
• Footnotes [authors' addresses, contact info for corresponding author, Manuscript received.___; revision accepted___.
• Abstract [in structured format, no more than 150 words]
• Keywords [3-6]
• Text [See below for format]
• Literature Cited [limited to 10 references]
• Tables [2 maximum], Appendices, and Figure Legends
• For manuscript files MS Word (.doc) or Rich Text Format (.rtf) format is requested

Double-space and left justify the margin of the entire manuscript, including Literature Cited, Tables, Appendices, and Figure Legends, using continuous pagination. Leave at least a 2.5-cm margin on all sides. Place a header with last name(s) of author(s) and page number in upper right corner.

Number figures and tables in the order discussed in the text.

Cover/Response Letter
A cover letter should accompany the manuscript and should include a statement that this is the authors' own work and that all co-authors have contributed to the work.  Any potential conflicts of interest or declarations of competing interests must be mentioned. List any papers on related topics by any of the authors that have been published within the past year or that are in review or in press. For a revision, include a letter detailing your response to all the review comments.

Author Agreement Form
Upon initial submission of a manuscript, the corresponding author must fill out an author agreement form and either upload an electronic version at the online submission site or mail or fax a hard copy to the Editorial Office in St. Louis, Missouri (American Journal of Botany, P.O. Box 299, St. Louis, MO 63166-0299, USA; 1-314-577-9515). The author agreement form is available online at http://www.botany.org/ajb/AJB_Author_Agreement_Form.dot; on the Editorial Manager website at the “Attach Files” screen; and from the Editorial Office.

Manuscript Contents
Follow the Publication Template for preparing your manuscript.  Additional information is provided below.

1. Title and Footnotes
Place a running head 2.5 cm below top of page with AJB Primer Notes & Protocols-+ 2 or 3 descriptive words, e.g., "Ziziphus microsatellites".

Center boldfaced title of no more than 125 characters written with sentence-style capitalization, and after a species name, include the family name in parentheses.  The title should be followed by superscript 1 (for footnote 1). Include the following footnote:
1Manuscript received _______; revision accepted _______.

Below the title, list authors: each author’s first name, middle initial, surname. On the next line, give affiliation and unabbreviated address. If authors have different affiliations and addresses, add a superscript number after each author’s name to indicate the footnoted address. Include another footnote superscript number to indicate the author for correspondence.

In the submission process, please include an email for all authors in case we need to contact a co-author during the publication process; this is important due to the quick turnaround, especially at the e-Galley stage.

2. Abstract
The abstract is 150 words or less, written in a structured format:

• Premise of the study (why the work was done)
• Methods and Results
• Conclusions (In the case of primer development, briefly mention other related species in which the markers also amplify.)

Avoid references; if essential, cite parenthetically with journal name, volume number, pages, and year.

Provide a list of 3 to 6 “Key words” that will be used for the volume index. Capitalize proper nouns, place in alphabetical order, and separate by semicolons.

3. Text
The overall text is limited to 1200 words.  Follow the publication template for details on the following sections to be included in the paper.
Introduction: no more than two paragraphs outlining the reasons behind the study, a brief explanation of its importance, and any information regarding the species or the protocol that would be of interest to the general botanical community.  Of particular appeal is the potential for widespread applicability of the markers or techniques to other species or systems.
Center main headings and capitalize all letters: ABSTRACT, INTRODUCTION, METHODS AND RESULTS, CONCLUSIONS, and LITERATURE CITED.
In METHODS AND RESULTS, add name, city, spelled-out state (if in USA), and country of manufacturers/suppliers after brand names.

Common Latin words (e.g., in vivo, sensu lato) are not italicized.
Footnotes are not used in the text.

4. Literature Cited
No more than 10 references should be listed in this section.  Verify all entries against original sources. Double check that all references in the manuscript text are in the Literature Cited and vice-versa and that they agree in spelling and year. For more information on formatting for the Literature Cited section, refer to the general AJB instructions. For formatting examples (note spacing, italics, etc.), go to http://www.botany.org/ajb/ajb_Lit_Cited_Instructions.pdf.

5. Tables – include in manuscript file
For marker development papers, two tables should be presented. One should contain the names of the forward and reverse primers, their DNA sequences, repeat, fragment size range, annealing temperatures, and GenBank ID. The second should report the number of alleles and observed heterozygosity in each population surveyed. In species expected to be primarily outcrossing, results of tests for departures from single-locus Hardy-Weinberg expectations and for departures from gametic equilibrium may be included. Voucher accession numbers for each population must be provided, if available. List the name of the herbarium in the table caption. See Author_PNP_template for an example.

Tables need to be formatted using the Table feature in Word (preferred) or in a spreadsheet such as Excel. For additional information on formatting tables, see http://www.amjbot.org/misc/ifora.shtml#tables.

6. Appendices – include in manuscript file
Voucher and gene accession information supporting the study is listed in Appendix 1. (If vouchers are unavailable, an explanation must be provided in the cover letter, as well as within the article itself.) Provide an appendix title and a sentence-style row of headings for the data. For each taxon sampled, include specimen voucher information and/or gene accession numbers, separated by commas. To save space, the taxa can be listed consecutively in a paragraph. See http://www.amjbot.org/cgi/content/full/97/1/e1 for an example.

Additional appendices may be included (see Online Supplemental Materials).

7. Figure/Illustration – upload as a separate file (limited to one) (do not include in the manuscript file)
For details and illustrated examples, see www.amjbot.org/misc/ifora.shtml and http://www.botany.org/ajb/AJB_Digital_Art_Guidellines.pdf. A figure checklist is also available at http://www.botany.org/ajb/AJB_Figure_Checklist.pdf.

TIFF or EPS formats are preferred for color and black and white photographs, drawings, and graphs. Prepare figure at the final size desired: 1 column (8.9 cm [3.5 in]), 1.5 column (12.7-15.24 cm [5-6 in]), or 2 columns (18.4 cm [7.5 in]) wide and less than the length of the page (23 cm [9 in]).

Color plates are free for all BSA members, regardless of length of membership.

Figure Manipulations: Certain types of electronic manipulations of micrographs and other digital images may not be ethically acceptable. See the AJB instructions for authors for the journal's policy regarding image manipulation [www.amjbot.org/misc/ifora.shtml].

8. Figure Legend – include in manuscript file
The figure legend must be complete and informative so that reference to the text is not necessary to understand the content of the figure. For detailed instructions, see the AJB instructions for authors at www.amjbot.org/misc/ifora.shtml.

9. Online Supplemental Materials
Authors may wish to augment their manuscripts with online supplemental materials (e.g., large data sets). Upload these appendices as separate files with the initial manuscript submission. Include a header on each file using this format: Smith et al.—American Journal of Botany 97(#): ###-###. 2010. – Data Supplement S1 – Page 1”. Name online supplements Appendix S1, Appendix S2, etc, in the order in which they appear in the text, regardless of whether they are tables, figures, text, other media, or a combination thereof. In the manuscript, after the mention of an online appendix, include the following: “(see Supplemental Data with the online version of this article)”.

Abbreviations, Units, and Symbols
See a recent Table of Contents page for commonly used abbreviations (Sample_TOC); these are also available at www.amjbot.org/misc/ifora.shtml.

Copyright and Color Agreement Forms
Once your manuscript has been accepted for publication, return signed copyright forms for the article to the Editorial Office in St. Louis, Missouri. All authors must sign off on the copyright form or contact the Editorial Office to confirm their participation in the work.
Copyright Assignment - http://www.botany.org/ajb/AJBcopyright.pdf
If you have reproduced copyrighted material in your manuscript, send proof of permission to the Editorial Office.
If you would like to reproduce copyrighted material previously published in the American Journal of Botany, return the completed permission request form available online at http://www.botany.org/ajb/BSAPermission.pdf.

Questions? Contact the Editorial Office
American Journal of Botany
Amy McPherson, Managing Editor
Editorial Office
P.O. Box 299
St. Louis, MO 63166-0299
phone: 314-577-5112; fax: 314-577-9515
E-mail: ajb{at}botany.org
[Last updated 21 April 2010]