Development of a Comprehensive GWAS Atlas for Chicken Breeds

Development of a Comprehensive GWAS Atlas for Chicken Breeds | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF database Development of a Comprehensive GWAS Atlas for Chicken Breeds Bader F. Al-Anzi, Nasser B. Alkhalifah, Hesham A. Almansouri, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7035180/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 21 Mar, 2026 Read the published version in BMC Bioinformatics → Version 1 posted 12 You are reading this latest preprint version Abstract Modern poultry breeding requires integrated genomic and phenotypic data to optimize production traits, yet comprehensive resources remain fragmented and often inaccessible. We developed a comprehensive electronic Genome-Wide Association Studies (GWAS) Atlas for chicken breeds that consolidates genomic data with phenotypic information from both commercial and heritage breeds. This web-based platform addresses critical gaps in existing databases through a unified, cross-referenced system linking more than 2,300 SNPs and other DNA alterations to 454 documented traits across diverse chicken breeds. The Atlas features four integrated portals: breed profiles with visual catalogs, trait-based breed searches using hierarchical classification, genomic information with DNA alterations and affected genes linked to specific traits, and advanced search functionality. A key innovation is the platform's ability to reveal previously hidden cross-source genetic associations, such as connecting the GJA5 gene's roles in both egg production and feather coloration. This publicly accessible resource provides breeders and researchers worldwide with comprehensive tools for informed decision-making in poultry breeding programs Figures Figure 1 Figure 2 Figure 3 Figure 4 Introduction The global poultry industry comprises a complex network of interconnected components, spanning feed production, hatcheries, breeding programs, and processing facilities[ 1 – 5 ]. A primary goal for sustainable intensification in this sector is the development of chicken lines that optimize production traits while maintaining commercial viability[ 4 , 6 – 9 ]. Key priorities include accelerating growth rates to enhance meat yield, improving feed conversion efficiency to manage costs, and bolstering disease resistance to safeguard flock health and productivity[ 4 , 6 – 8 ]. The extensive domestication history of chickens has given rise to a diverse array of heritage breeds, each adapted to its local environment[ 10 – 14 ]. This genetic diversity represents a valuable reservoir of adaptive traits with significant economic potential. For example, the Middle Eastern Fayoumi breed exhibits notable heat resistance[ 15 , 16 ], while Canadian breed called Chanticleer demonstrate superior cold tolerance[ 17 ]. These heritage breeds serve as living repositories of genetic variants that hold immense value for modern poultry breeding programs addressing climate resilience challenges. Over the past three decades, poultry breeding has undergone revolutionary transformation driven by Next-Generation Sequencing (NGS) technologies[ 18 ]. This has enabled the integration of NGS data with phenotypic observations through sophisticated database systems and facilitated Genome-Wide Association Studies (GWAS) for identifying DNA variants linked to desirable production traits[ 19 – 26 ]. However, current publicly available chicken genome resources present several critical limitations: Restricted access to many genomic databases Data fragmentation across multiple sources with inconsistent schemas Lack of cross-breed validation for trait-associated SNPs Absence of electronically curated data on heritage breed characteristics These limitations significantly hamper the practical application of existing genomic datasets in poultry research and breeding programs. To address these shortcomings, we developed a comprehensive electronic GWAS Atlas for chicken breeds that consolidates fragmented genomic data, incorporates diverse chicken breeds, provides cross-breed validation of genetic markers, and offers a unified platform for breed-specific characteristics with full traceability to primary sources. Materials and Methods Data Collection A comprehensive research effort was conducted to compile data on various chicken breeds from multiple sources, including reputable chicken encyclopedias, scholarly publications, and specialized databases. The University of Sydney's Online Mendelian Inheritance in Animals (OMIA) website served as a particularly valuable resource for systematic documentation of Mendelian traits[ 27 ]. Our data curation focused on four major areas: Mendelian Traits Catalog : We generated an extensive catalog of Mendelian traits observed across chicken breeds, systematically documenting phenotypic expression, associated breeds, and genetic abnormalities where possible[ 12 , 27 – 29 ]. Heritage Breed Characteristics : We curated datasets describing distinguishing characteristics of historical chicken breeds, including size, egg production capacity, temperament, and breed-specific features[ 11 – 13 , 30 ]. Genomic Data Integration : We integrated data from multiple online databases and peer-reviewed studies to build a cohesive resource for chicken genomics SNPs and other DNA alterations. This process involved linking phenotypes to GWAS-detected DNA anomalies and cataloging the breeds analyzed[ 29 , 31 – 38 ]. Close to 2,300 SNPs have been documented in our current dataset. Visual Documentation : We obtained images of chicken breeds from public domain and royalty-free sources, providing full attribution in accordance with license requirements. All data were compiled with appropriate citations to original sources. Each trait included in the GWAS Atlas for Chicken Breeds platform is cross-referenced with either an external online database or a research paper. Given the extensive number of references used, the majority of these citations are included on the GWAS website rather than in this manuscript for brevity. Data Standardization and Integration The primary challenge in constructing the user-friendly online GWAS Atlas lay in reconciling information from heterogeneous data sources, each employing different schemas, nomenclature, and file formats. We developed a comprehensive preprocessing framework that normalizes raw data from CSV exports, XML feeds, and PDF tables into a unified representation. This involved creating source-specific parsers, automated transformation routines, and a manually curated synonym dictionary to resolve conflicting terminologies. Database Architecture and Technologies We designed a flexible relational schema using MySQL to accommodate current and future data additions. Core entities like Breeds, Traits, SNPs, and Genes are represented in dedicated tables, while intermediary join tables capture many-to-many relationships and synonym mappings. Referential integrity is enforced through foreign-key constraints, and performance is optimized via targeted indexing on frequently queried fields. The application employs a multi-tier architecture: Frontend : HTML5, CSS3, and JavaScript for responsive, mobile-friendly interfaces[ 39 ] Backend : PHP running under Apache web server for request routing and business logic[ 40 ] Database : MySQL for robust data storage, indexing, and retrieval[ 41 ] All curated data was organized into well-structured CSV files compatible with standard analysis tools, and cross-referenced with external databases or research papers to ensure scientific validity and traceability. Results Platform Architecture and Features The GWAS Atlas website incorporates four major portals serving distinct research purposes (see Fig. 1): 1. Breed Portal : Users can select breeds of interest to access detailed profiles including physical characteristics, behavioral traits, and historical information (Fig. 1, upper left panel). The portal features two functional windows: a clickable visual catalogue where users can scroll through pictures of different breeds (Fig. 2A), and a clickable name catalogue where breed names are listed alphabetically (Fig. 2B). Additional detailed information about breed genetics, including inherited traits and genomic data, is displayed in the lower panel (Fig. 2C). 2. Trait Portal : Users can select specific traits (e.g., comb type, feather pattern, egg production capacity) to view all chicken breeds exhibiting those characteristics (Fig. 1, middle upper panel). We documented 454 traits exhibited across all known chicken breeds, with each trait linked to references characterizing the associated genetic factors (Fig. 3A). To enhance clarity and facilitate efficient querying in the trait portal, we organized trait data into a four-level hierarchical schema: Main Category, Sub-Category-1, Sub-Category-2, and Value. Traits are first assigned to broad Main Categories (e.g., "Physical Features"), then progressively refined through Sub-Category-1 (e.g., "Comb Type") and Sub-Category-2 (e.g., "Shape") before specifying particular Values (e.g., "Single Comb"). By clicking the "view tarit details" icon, further information is provided including the name of genes, breeds, and refernces linked to trait (Fig. 3B)[42–69]. 3. Genomic and Gene Portal : Provides access to genomic information (Fig. 1, upper right panel). The DNA alterations linked to phenotypes section primarily contains GWAS-identified variants associated with specific phenotypes. The portal lists potentially affected genes, types of genomic alterations detected, and their associated traits (Fig. 4A). Clicking the "view DNA alteration" icon reveals additional details (Fig. 4B). The "Explore genes linked to phenotypes" portal contains a curated list of genes with high-confidence links to specific traits. The "view gene detail" icon provides comprehensive gene information (Fig. 4D). Finally, the portal includes a list of chicken breeds with fully sequenced genomes (Fig. 4E), featuring interactive links to references and the sequenced genomes." 4. Advanced Search Engine : Enables direct queries by breed name, gene, or specific genetic markers, facilitating rapid targeted searches across the entire database (Fig. 1, lower panel). Novel Cross-Source Associations One of the Atlas's most significant features is its ability to reveal cross-source associations previously unavailable in any single resource. For example, the GJA5 gene appears to be significantly associated with egg number[49], while the OMIA database implicates the same gene in feather-color variation[70]. By linking both observations to the canonical GJA5 record, our database uncovers relationships that would otherwise remain obscured across separate databases. Accessibility and User Features The platform includes advanced search functionality for complex queries combining traits, breeds, and genetic markers simultaneously. User login functionality enables registered researchers to contribute new data following verification processes, bookmark entries, and participate in expanding the knowledge base. The resource is publicly available through Amazon Web Services with a subdomain from the Kuwait Institute for Scientific Research (KISR) at http://cga.kisr.edu.kw/, broadening accessibility to scientists and researchers worldwide. Discussion We report the development and release of the GWAS Atlas for Chicken Breeds, a comprehensive genomic resource addressing significant gaps in poultry genetics research and breeding. By consolidating fragmented data, integrating diverse breed information, and providing an intuitive interface, this resource facilitates more efficient and targeted breeding programs. The integration of heritage breed information alongside commercial varieties represents a particular strength of our platform. While commercial breeds have been extensively studied for production traits, heritage breeds often harbor unique genetic adaptations that remain largely undocumented electronically. By capturing adaptations such as heat resistance in Fayoumi chickens or cold tolerance in Canadian breeds, our Atlas provides valuable genetic resources for climate-resilient breeding programs. The comprehensive cross-referencing system addresses common limitations in existing databases by ensuring every entry links to peer-reviewed publications or established external databases. This enhances reliability and enables critical evaluation of underlying evidence before incorporating genetic associations into breeding programs. Our hierarchical trait organization system and flexible database architecture enable sophisticated comparative analyses while maintaining user accessibility. Unlike specialized repositories focusing primarily on genetic variants or QTLs, our platform provides holistic integration of phenotypic, genetic, and visual information accessible to diverse user groups from genomics specialists to small-scale breeders. The public availability of this resource represents our commitment to open science and global collaboration. As climate change and food security challenges intensify, the need for resilient, productive chicken breeds becomes increasingly critical. The GWAS Atlas for Chicken Breeds contributes to addressing these global challenges by providing comprehensive, accessible genomic information that enhances poultry breeding capabilities worldwide. By enabling unprecedented cross-source genetic associations and maintaining rigorous scientific traceability, this platform represents a significant advancement in poultry genomics research and practical breeding applications. Declarations Acknowledgments The authors express their gratitude to the Kuwait Institute for Scientific Research (KISR) for their support of this project. Ethics approval and consent to participate Not applicable. This study involved the compilation and curation of publicly available genomic and phenotypic data from existing databases and published literature. No human subjects, animal experiments, or collection of primary biological samples were involved in this research. Consent for publication Not applicable. This manuscript does not contain any individual person's data in any form (including individual details, images, or videos). Availability of data and materials The GWAS Atlas for Chicken Breeds is publicly accessible at http://cga.kisr.edu.kw/. All curated datasets, including breed profiles, trait classifications, genomic variants, and associated metadata, are freely available through the web interface without registration requirements. The underlying database structure, data processing scripts, and comprehensive documentation are available upon reasonable request from the corresponding author. All original data sources are properly cited and linked within the database, ensuring full traceability to primary publications and external databases. References (FAO), F.a.A.O.o.t.U.N., Poultry Development Review. 2013. A. Mottet, G.T., Global poultry production: current state and future outlook and challenges. World’s Poultry Science Journal 73(2):1-12, 2017. 73 (2): p. 1-12. 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Cite Share Download PDF Status: Published Journal Publication published 21 Mar, 2026 Read the published version in BMC Bioinformatics → Version 1 posted Editorial decision: Revision requested 28 Oct, 2025 Reviews received at journal 13 Oct, 2025 Reviewers agreed at journal 24 Sep, 2025 Reviewers agreed at journal 23 Sep, 2025 Reviews received at journal 04 Sep, 2025 Reviewers agreed at journal 11 Aug, 2025 Reviewers agreed at journal 11 Aug, 2025 Reviewers invited by journal 11 Aug, 2025 Editor assigned by journal 09 Aug, 2025 Editor invited by journal 08 Aug, 2025 Submission checks completed at journal 07 Aug, 2025 First submitted to journal 07 Aug, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7035180","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"database","associatedPublications":[],"authors":[{"id":498800917,"identity":"697bfa15-0224-41d8-bf21-4c23078a64ab","order_by":0,"name":"Bader F. 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Almansouri","email":"","orcid":"","institution":"Kuwait Institute for Scientific Research","correspondingAuthor":false,"prefix":"","firstName":"Hesham","middleName":"A.","lastName":"Almansouri","suffix":""},{"id":498800920,"identity":"6bcaaccf-c81c-4049-8a2f-389c4f86a68f","order_by":3,"name":"Arwa AlSirhan","email":"","orcid":"","institution":"Kuwait Institute for Scientific Research","correspondingAuthor":false,"prefix":"","firstName":"Arwa","middleName":"","lastName":"AlSirhan","suffix":""}],"badges":[],"createdAt":"2025-07-03 07:08:27","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7035180/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7035180/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12859-026-06427-x","type":"published","date":"2026-03-21T15:59:12+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":89327965,"identity":"f6c5553a-1369-4a41-91eb-515907d12873","added_by":"auto","created_at":"2025-08-18 21:34:06","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":871759,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eApplication search features of the GWAS Atlas website.\u003c/strong\u003e Screenshot of the website page displaying the search features, showing all four major portals (Breed, Traits, Genome and Gene, and Advanced Search Engine).\u003c/p\u003e","description":"","filename":"Figure1.png","url":"https://assets-eu.researchsquare.com/files/rs-7035180/v1/8a4673fb8237b7cf03877438.png"},{"id":89328353,"identity":"bd49d848-713a-4936-b668-6f9580877bb5","added_by":"auto","created_at":"2025-08-18 21:42:06","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":5160641,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eBreed Profile Website Interface\u003c/strong\u003e. Screenshot showing the results of clicking the GWAS Atlas breed window (Figure 1, upper left), which opens two exploration options: (A) visual breed selection through images, and (B) text-based breed search by name. Both interfaces have clickable icons (arrows) that provide comprehensive breed information including phenotypic traits, country of origin, and available genomic data.\u003c/p\u003e","description":"","filename":"Figure2chickencopy.png","url":"https://assets-eu.researchsquare.com/files/rs-7035180/v1/ebbea85f71787da122c2dfa8.png"},{"id":89327967,"identity":"1389a291-d14f-4580-9d1a-a42ba78f5b99","added_by":"auto","created_at":"2025-08-18 21:34:06","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":2426488,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eTrait Profile Website Interface\u003c/strong\u003e. Screenshot showing the results of clicking the GWAS Atlas trait window (Figure 1, middle upper panel). This section of the GWAS Atlas website provides detailed descriptions of 454 traits documented across all known chicken breeds (A). Each trait entry includes a clickable reference icon (arrows) that links directly to the literature characterizing the associated genetic factors. By clicking the \"view tarit details\" icon, further information is provided including the name of genes, breeds, and refernces linked to trait (B).\u003c/p\u003e","description":"","filename":"Figure3chickencopy.png","url":"https://assets-eu.researchsquare.com/files/rs-7035180/v1/3def70a040fb45d18f3157a0.png"},{"id":89328539,"identity":"706cd946-bf45-41d2-a430-2afcf151f982","added_by":"auto","created_at":"2025-08-18 21:50:06","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":2347610,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGenome and Gene Profile Website Interface\u003c/strong\u003e. Screenshot displaying results from the GWAS Atlas genome window (Figure 1, upper right panel), which provides comprehensive access to genomic information. The interface contains three main sections: A) The DNA alteration section features GWAS-identified genetic variants linked to specific phenotypes, containing approximately 2,500 entries that catalog genes, associated DNA alterations, potentially affected genes, and linked traits. Clicking the \"view DNA alteration\" icon (arrows) reveals additional detailed information (B). C) The \"Explore gene linked to phenotype\" portal presents a curated collection of nearly 600 entries displaying genes with high-confidence associations to specific traits. Additional details are accessible by clicking the \"view gene detail\" icon (arrows) (D). E) The interface also includes a comprehensive list of chicken breeds with fully sequenced genomes, featuring clickable references and direct links to the sequenced genome data.\u003c/p\u003e","description":"","filename":"Figure4chickencopy.png","url":"https://assets-eu.researchsquare.com/files/rs-7035180/v1/5b8f2aa96464577bdc71ba8e.png"},{"id":105223751,"identity":"19cf616a-1911-435f-8178-5947109947d9","added_by":"auto","created_at":"2026-03-23 16:09:55","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":10465837,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7035180/v1/6e9bcbc6-44da-450a-a593-877b894ef4f5.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Development of a Comprehensive GWAS Atlas for Chicken Breeds","fulltext":[{"header":"Introduction","content":"\u003cp\u003eThe global poultry industry comprises a complex network of interconnected components, spanning feed production, hatcheries, breeding programs, and processing facilities[\u003cspan additionalcitationids=\"CR2 CR3 CR4\" citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. A primary goal for sustainable intensification in this sector is the development of chicken lines that optimize production traits while maintaining commercial viability[\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e, \u003cspan additionalcitationids=\"CR7 CR8\" citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. Key priorities include accelerating growth rates to enhance meat yield, improving feed conversion efficiency to manage costs, and bolstering disease resistance to safeguard flock health and productivity[\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e, \u003cspan additionalcitationids=\"CR7\" citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eThe extensive domestication history of chickens has given rise to a diverse array of heritage breeds, each adapted to its local environment[\u003cspan additionalcitationids=\"CR11 CR12 CR13\" citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. This genetic diversity represents a valuable reservoir of adaptive traits with significant economic potential. For example, the Middle Eastern Fayoumi breed exhibits notable heat resistance[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e, \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e], while Canadian breed called Chanticleer demonstrate superior cold tolerance[\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. These heritage breeds serve as living repositories of genetic variants that hold immense value for modern poultry breeding programs addressing climate resilience challenges.\u003c/p\u003e\u003cp\u003eOver the past three decades, poultry breeding has undergone revolutionary transformation driven by Next-Generation Sequencing (NGS) technologies[\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. This has enabled the integration of NGS data with phenotypic observations through sophisticated database systems and facilitated Genome-Wide Association Studies (GWAS) for identifying DNA variants linked to desirable production traits[\u003cspan additionalcitationids=\"CR20 CR21 CR22 CR23 CR24 CR25\" citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. However, current publicly available chicken genome resources present several critical limitations:\u003c/p\u003e\u003cp\u003e\u003col\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003eRestricted access to many genomic databases\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003eData fragmentation across multiple sources with inconsistent schemas\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003eLack of cross-breed validation for trait-associated SNPs\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003eAbsence of electronically curated data on heritage breed characteristics\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003c/ol\u003e\u003c/p\u003e\u003cp\u003eThese limitations significantly hamper the practical application of existing genomic datasets in poultry research and breeding programs. To address these shortcomings, we developed a comprehensive electronic GWAS Atlas for chicken breeds that consolidates fragmented genomic data, incorporates diverse chicken breeds, provides cross-breed validation of genetic markers, and offers a unified platform for breed-specific characteristics with full traceability to primary sources.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003eData Collection\u003c/h2\u003e\u003cp\u003eA comprehensive research effort was conducted to compile data on various chicken breeds from multiple sources, including reputable chicken encyclopedias, scholarly publications, and specialized databases. The University of Sydney's Online Mendelian Inheritance in Animals (OMIA) website served as a particularly valuable resource for systematic documentation of Mendelian traits[\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eOur data curation focused on four major areas:\u003c/p\u003e\u003cp\u003e\u003col\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003e\u003cb\u003eMendelian Traits Catalog\u003c/b\u003e: We generated an extensive catalog of Mendelian traits observed across chicken breeds, systematically documenting phenotypic expression, associated breeds, and genetic abnormalities where possible[\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e, \u003cspan additionalcitationids=\"CR28\" citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e].\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003e\u003cb\u003eHeritage Breed Characteristics\u003c/b\u003e: We curated datasets describing distinguishing characteristics of historical chicken breeds, including size, egg production capacity, temperament, and breed-specific features[\u003cspan additionalcitationids=\"CR12\" citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e, \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e].\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003e\u003cb\u003eGenomic Data Integration\u003c/b\u003e: We integrated data from multiple online databases and peer-reviewed studies to build a cohesive resource for chicken genomics SNPs and other DNA alterations. This process involved linking phenotypes to GWAS-detected DNA anomalies and cataloging the breeds analyzed[\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e, \u003cspan additionalcitationids=\"CR32 CR33 CR34 CR35 CR36 CR37\" citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. Close to 2,300 SNPs have been documented in our current dataset.\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003e\u003cb\u003eVisual Documentation\u003c/b\u003e: We obtained images of chicken breeds from public domain and royalty-free sources, providing full attribution in accordance with license requirements.\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003c/ol\u003e\u003c/p\u003e\u003cp\u003eAll data were compiled with appropriate citations to original sources. Each trait included in the GWAS Atlas for Chicken Breeds platform is cross-referenced with either an external online database or a research paper. Given the extensive number of references used, the majority of these citations are included on the GWAS website rather than in this manuscript for brevity.\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003eData Standardization and Integration\u003c/h3\u003e\n\u003cp\u003eThe primary challenge in constructing the user-friendly online GWAS Atlas lay in reconciling information from heterogeneous data sources, each employing different schemas, nomenclature, and file formats. We developed a comprehensive preprocessing framework that normalizes raw data from CSV exports, XML feeds, and PDF tables into a unified representation.\u003c/p\u003e\u003cp\u003eThis involved creating source-specific parsers, automated transformation routines, and a manually curated synonym dictionary to resolve conflicting terminologies.\u003c/p\u003e\n\u003ch3\u003eDatabase Architecture and Technologies\u003c/h3\u003e\n\u003cp\u003eWe designed a flexible relational schema using MySQL to accommodate current and future data additions. Core entities like Breeds, Traits, SNPs, and Genes are represented in dedicated tables, while intermediary join tables capture many-to-many relationships and synonym mappings. Referential integrity is enforced through foreign-key constraints, and performance is optimized via targeted indexing on frequently queried fields.\u003c/p\u003e\u003cp\u003eThe application employs a multi-tier architecture:\u003c/p\u003e\u003cp\u003e\u003cul\u003e\u003cli\u003e\u003cp\u003e\u003cb\u003eFrontend\u003c/b\u003e: HTML5, CSS3, and JavaScript for responsive, mobile-friendly interfaces[\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e]\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003e\u003cb\u003eBackend\u003c/b\u003e: PHP running under Apache web server for request routing and business logic[\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003e\u003cb\u003eDatabase\u003c/b\u003e: MySQL for robust data storage, indexing, and retrieval[\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]\u003c/p\u003e\u003c/li\u003e\u003c/ul\u003e\u003c/p\u003e\u003cp\u003eAll curated data was organized into well-structured CSV files compatible with standard analysis tools, and cross-referenced with external databases or research papers to ensure scientific validity and traceability.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec7\"\u003e\n \u003ch2\u003ePlatform Architecture and Features\u003c/h2\u003e\n \u003cp\u003eThe GWAS Atlas website incorporates four major portals serving distinct research purposes (see Fig. 1):\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003e1. Breed Portal\u003c/strong\u003e: Users can select breeds of interest to access detailed profiles including physical characteristics, behavioral traits, and historical information (Fig. 1, upper left panel). The portal features two functional windows: a clickable visual catalogue where users can scroll through pictures of different breeds (Fig. 2A), and a clickable name catalogue where breed names are listed alphabetically (Fig. 2B). Additional detailed information about breed genetics, including inherited traits and genomic data, is displayed in the lower panel (Fig. 2C).\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003e2. Trait Portal\u003c/strong\u003e: Users can select specific traits (e.g., comb type, feather pattern, egg production capacity) to view all chicken breeds exhibiting those characteristics (Fig. 1, middle upper panel). We documented 454 traits exhibited across all known chicken breeds, with each trait linked to references characterizing the associated genetic factors (Fig. 3A). To enhance clarity and facilitate efficient querying in the trait portal, we organized trait data into a four-level hierarchical schema: Main Category, Sub-Category-1, Sub-Category-2, and Value. Traits are first assigned to broad Main Categories (e.g., \u0026quot;Physical Features\u0026quot;), then progressively refined through Sub-Category-1 (e.g., \u0026quot;Comb Type\u0026quot;) and Sub-Category-2 (e.g., \u0026quot;Shape\u0026quot;) before specifying particular Values (e.g., \u0026quot;Single Comb\u0026quot;). By clicking the \u0026quot;view tarit details\u0026quot; icon, further information is provided including the name of genes, breeds, and refernces linked to trait (Fig. 3B)[42\u0026ndash;69].\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003e3. Genomic and Gene Portal\u003c/strong\u003e: Provides access to genomic information (Fig. 1, upper right panel). The DNA alterations linked to phenotypes section primarily contains GWAS-identified variants associated with specific phenotypes. The portal lists potentially affected genes, types of genomic alterations detected, and their associated traits (Fig. 4A). Clicking the \u0026quot;view DNA alteration\u0026quot; icon reveals additional details (Fig. 4B). The \u0026quot;Explore genes linked to phenotypes\u0026quot; portal contains a curated list of genes with high-confidence links to specific traits. The \u0026quot;view gene detail\u0026quot; icon provides comprehensive gene information (Fig. 4D). Finally, the portal includes a list of chicken breeds with fully sequenced genomes (Fig. 4E), featuring interactive links to references and the sequenced genomes.\u0026quot;\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003e4. Advanced Search Engine\u003c/strong\u003e: Enables direct queries by breed name, gene, or specific genetic markers, facilitating rapid targeted searches across the entire database (Fig. 1, lower panel).\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec8\"\u003e\n \u003ch2\u003eNovel Cross-Source Associations\u003c/h2\u003e\n \u003cp\u003eOne of the Atlas\u0026apos;s most significant features is its ability to reveal cross-source associations previously unavailable in any single resource. For example, the GJA5 gene appears to be significantly associated with egg number[49], while the OMIA database implicates the same gene in feather-color variation[70]. By linking both observations to the canonical GJA5 record, our database uncovers relationships that would otherwise remain obscured across separate databases.\u003c/p\u003e\n\u003c/div\u003e\n\u003ch3\u003eAccessibility and User Features\u003c/h3\u003e\n\u003cp\u003eThe platform includes advanced search functionality for complex queries combining traits, breeds, and genetic markers simultaneously. User login functionality enables registered researchers to contribute new data following verification processes, bookmark entries, and participate in expanding the knowledge base.\u003c/p\u003e\n\u003cp\u003eThe resource is publicly available through Amazon Web Services with a subdomain from the Kuwait Institute for Scientific Research (KISR) at http://cga.kisr.edu.kw/, broadening accessibility to scientists and researchers worldwide.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eWe report the development and release of the GWAS Atlas for Chicken Breeds, a comprehensive genomic resource addressing significant gaps in poultry genetics research and breeding. By consolidating fragmented data, integrating diverse breed information, and providing an intuitive interface, this resource facilitates more efficient and targeted breeding programs.\u003c/p\u003e\u003cp\u003eThe integration of heritage breed information alongside commercial varieties represents a particular strength of our platform. While commercial breeds have been extensively studied for production traits, heritage breeds often harbor unique genetic adaptations that remain largely undocumented electronically. By capturing adaptations such as heat resistance in Fayoumi chickens or cold tolerance in Canadian breeds, our Atlas provides valuable genetic resources for climate-resilient breeding programs.\u003c/p\u003e\u003cp\u003eThe comprehensive cross-referencing system addresses common limitations in existing databases by ensuring every entry links to peer-reviewed publications or established external databases. This enhances reliability and enables critical evaluation of underlying evidence before incorporating genetic associations into breeding programs.\u003c/p\u003e\u003cp\u003eOur hierarchical trait organization system and flexible database architecture enable sophisticated comparative analyses while maintaining user accessibility. Unlike specialized repositories focusing primarily on genetic variants or QTLs, our platform provides holistic integration of phenotypic, genetic, and visual information accessible to diverse user groups from genomics specialists to small-scale breeders.\u003c/p\u003e\u003cp\u003eThe public availability of this resource represents our commitment to open science and global collaboration. As climate change and food security challenges intensify, the need for resilient, productive chicken breeds becomes increasingly critical. The GWAS Atlas for Chicken Breeds contributes to addressing these global challenges by providing comprehensive, accessible genomic information that enhances poultry breeding capabilities worldwide.\u003c/p\u003e\u003cp\u003eBy enabling unprecedented cross-source genetic associations and maintaining rigorous scientific traceability, this platform represents a significant advancement in poultry genomics research and practical breeding applications.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors express their gratitude to the Kuwait Institute for Scientific Research (KISR) for their support of this project.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable. This study involved the compilation and curation of publicly available genomic and phenotypic data from existing databases and published literature. No human subjects, animal experiments, or collection of primary biological samples were involved in this research.\u003c/p\u003e\n\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable. This manuscript does not contain any individual person\u0026apos;s data in any form (including individual details, images, or videos).\u003c/p\u003e\n\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe GWAS Atlas for Chicken Breeds is publicly accessible at http://cga.kisr.edu.kw/. All curated datasets, including breed profiles, trait classifications, genomic variants, and associated metadata, are freely available through the web interface without registration requirements. The underlying database structure, data processing scripts, and comprehensive documentation are available upon reasonable request from the corresponding author. All original data sources are properly cited and linked within the database, ensuring full traceability to primary publications and external databases.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003e(FAO), F.a.A.O.o.t.U.N., \u003cem\u003ePoultry Development Review.\u003c/em\u003e 2013.\u003c/li\u003e\n\u003cli\u003eA. Mottet, G.T., \u003cem\u003eGlobal poultry production: current state and future outlook and challenges.\u003c/em\u003e World\u0026rsquo;s Poultry Science Journal 73(2):1-12, 2017. \u003cstrong\u003e73\u003c/strong\u003e(2): p. 1-12.\u003c/li\u003e\n\u003cli\u003eAgriculture-United-States, \u003cem\u003ePoultry- Production and Value 2020 Summary \u003c/em\u003e2021, United States Department of Agriculture.\u003c/li\u003e\n\u003cli\u003eGowd, R.N.S., \u003cem\u003eModern innovations in Poultry Farming.\u003c/em\u003e SR Publications, 2023.\u003c/li\u003e\n\u003cli\u003eShahbandeh, M., \u003cem\u003eChicken meat production worldwide by country.\u003c/em\u003e 2021.\u003c/li\u003e\n\u003cli\u003eCraig W. 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18.\u003c/li\u003e\n\u003cli\u003eXie, L., et al., \u003cem\u003eGenome-wide association study identified a narrow chromosome 1 region associated with chicken growth traits.\u003c/em\u003e PLoS One, 2012. \u003cstrong\u003e7\u003c/strong\u003e(2): p. e30910.\u003c/li\u003e\n\u003cli\u003eWang, W.H., et al., \u003cem\u003eGenome-wide association study of growth traits in Jinghai Yellow chicken hens using SLAF-seq technology.\u003c/em\u003e Anim Genet, 2019. \u003cstrong\u003e50\u003c/strong\u003e(2): p. 175-176.\u003c/li\u003e\n\u003cli\u003eZhang, G.X., et al., \u003cem\u003eGenome-wide association study of growth traits in the Jinghai Yellow chicken.\u003c/em\u003e Genet Mol Res, 2015. \u003cstrong\u003e14\u003c/strong\u003e(4): p. 15331-8.\u003c/li\u003e\n\u003cli\u003eGu, X., et al., \u003cem\u003eGenome-wide association study of body weight in chicken F2 resource population.\u003c/em\u003e PLoS One, 2011. \u003cstrong\u003e6\u003c/strong\u003e(7): p. e21872.\u003c/li\u003e\n\u003cli\u003eGrams, V., et al., \u003cem\u003eGenetic parameters and signatures of selection in two divergent laying hen lines selected for feather pecking behaviour.\u003c/em\u003e Genet Sel Evol, 2015. \u003cstrong\u003e47\u003c/strong\u003e: p. 77.\u003c/li\u003e\n\u003cli\u003eSun, Y., et al., \u003cem\u003eGenomewide association study of immune traits in chicken F2 resource population.\u003c/em\u003e J Anim Breed Genet, 2016. \u003cstrong\u003e133\u003c/strong\u003e(3): p. 197-206.\u003c/li\u003e\n\u003cli\u003eLien, C.Y., et al., \u003cem\u003eDetection of QTL for traits related to adaptation to sub-optimal climatic conditions in chickens.\u003c/em\u003e Genet Sel Evol, 2017. \u003cstrong\u003e49\u003c/strong\u003e(1): p. 39.\u003c/li\u003e\n\u003cli\u003eJingyi Li, M.-O.L., Junfeng Chen, Brian W Davis, Benjamin J Dorshorst, Paul B Siegel, Masafumi Inaba, Ting-Xin Jiang, Cheng-Ming Chuong, Leif Andersson \u003cem\u003eCis-acting mutation affecting GJA5 transcription is underlying the Melanotic within feather pigmentation pattern in chickens.\u003c/em\u003e Proc Natl Acad Sci U S A, 2021. \u003cstrong\u003e12\u003c/strong\u003e(118): p. e2109363118.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-bioinformatics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"binf","sideBox":"Learn more about [BMC Bioinformatics](http://bmcbioinformatics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/binf","title":"BMC Bioinformatics","twitterHandle":"@BMC_Bioinformatics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-7035180/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7035180/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eModern poultry breeding requires integrated genomic and phenotypic data to optimize production traits, yet comprehensive resources remain fragmented and often inaccessible. We developed a comprehensive electronic Genome-Wide Association Studies (GWAS) Atlas for chicken breeds that consolidates genomic data with phenotypic information from both commercial and heritage breeds. This web-based platform addresses critical gaps in existing databases through a unified, cross-referenced system linking more than 2,300 SNPs and other DNA alterations to 454 documented traits across diverse chicken breeds. The Atlas features four integrated portals: breed profiles with visual catalogs, trait-based breed searches using hierarchical classification, genomic information with DNA alterations and affected genes linked to specific traits, and advanced search functionality. A key innovation is the platform's ability to reveal previously hidden cross-source genetic associations, such as connecting the GJA5 gene's roles in both egg production and feather coloration. This publicly accessible resource provides breeders and researchers worldwide with comprehensive tools for informed decision-making in poultry breeding programs\u003c/p\u003e","manuscriptTitle":"Development of a Comprehensive GWAS Atlas for Chicken Breeds","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-08-18 21:34:01","doi":"10.21203/rs.3.rs-7035180/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-28T14:37:28+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-14T00:14:11+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"269247181099104411303187309655247051795","date":"2025-09-24T12:29:17+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"15319563178159692365710203946605829746","date":"2025-09-23T06:02:59+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-04T11:15:19+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"317843034470074948272619299433225798942","date":"2025-08-11T12:45:45+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"68333052470068634829075194710994633612","date":"2025-08-11T09:17:57+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-08-11T06:43:24+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-08-09T07:42:18+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-08-08T08:11:44+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-08-07T12:46:07+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Bioinformatics","date":"2025-08-07T12:40:26+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-bioinformatics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"binf","sideBox":"Learn more about [BMC Bioinformatics](http://bmcbioinformatics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/binf","title":"BMC Bioinformatics","twitterHandle":"@BMC_Bioinformatics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"6a21469a-2a2f-43ff-bf4f-4f6118b92b23","owner":[],"postedDate":"August 18th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2026-03-23T16:06:57+00:00","versionOfRecord":{"articleIdentity":"rs-7035180","link":"https://doi.org/10.1186/s12859-026-06427-x","journal":{"identity":"bmc-bioinformatics","isVorOnly":false,"title":"BMC Bioinformatics"},"publishedOn":"2026-03-21 15:59:12","publishedOnDateReadable":"March 21st, 2026"},"versionCreatedAt":"2025-08-18 21:34:01","video":"","vorDoi":"10.1186/s12859-026-06427-x","vorDoiUrl":"https://doi.org/10.1186/s12859-026-06427-x","workflowStages":[]},"version":"v1","identity":"rs-7035180","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7035180","identity":"rs-7035180","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}