{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:34:49Z","timestamp":1767918889382,"version":"3.49.0"},"reference-count":50,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T00:00:00Z","timestamp":1747785600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012659","name":"Foundation for Innovative Research Groups of the National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Vet. Sci."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Polydactyly\u2014the presence of extra digits\u2014is a heritable limb anomaly observed in several chicken breeds. The Puan Panjiang black-bone chicken uniquely exhibits both four- and five-toed phenotypes, yet the genetic and transcriptional bases of this trait remain unclear. This study aimed to elucidate the genomic variants and gene expression changes underlying polydactyly in this breed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We performed whole-genome resequencing (WGS) on 43 Puan Panjiang chickens (22 four-toed, 21 five-toed) and integrated publicly available data from 17 red junglefowl (RJF). After stringent quality filtering, we aligned reads to GRCg7b, identified high-confidence SNPs and InDels, and conducted sliding-window analyses of nucleotide diversity (\u03b8\u03c0) and genetic differentiation (F &amp;lt;sub&amp;gt;ST&amp;lt;\/sub&amp;gt;) to detect selective sweeps. Concurrently, we carried out RNA-seq on embryonic foot tissues at days 6\u20139 (24 four-toed, 24 five-toed samples), quantified transcript levels (TPM), and identified differentially expressed genes (DEGs) with DESeq2 (adjusted <jats:italic>P<\/jats:italic> &amp;lt; 0.01, |log<jats:sub>2<\/jats:sub>FC|&amp;gt; 2). Fuzzy c-means clustering delineated temporal expression patterns, and enrichment analyses (KEGG, GO) characterized candidate pathways.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Genomic scans revealed 1,339 and 1,035 positively selected genes in five-toed and four-toed chickens, respectively, with 335 shared loci relative to RJF. Top candidates in polydactylous birds included AUH, SEMA4D, and ROR2, while four-toed birds showed strong signals at RYR2, KITLG, and PGR. KEGG enrichment highlighted the MAPK signaling pathway in both groups, and uniquely in five-toed birds, lipid metabolism and vascular signaling pathways (e.g., sphingolipid and apelin signaling). Transcriptome profiling demonstrated that the greatest transcriptional divergence between phenotypes occurred at embryonic Days 8\u20139, pinpointing a critical window for extra-digit differentiation. Clustering analyses indicated coordinated regulation of genes involved in ribosome biogenesis, extracellular matrix organization, and muscle development across stages.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>Our integrated analyses pinpoint MAPK pathway genes and lipid-vascular interactions as central to extra-toe formation, with the Days 8\u20139 embryonic window being pivotal. These findings offer clear targets for functional validation and may guide selective breeding for limb traits in poultry.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fvets.2025.1592068","type":"journal-article","created":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T08:57:25Z","timestamp":1747817845000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Integrated genomic and transcriptomic analysis of polydactyly in chickens"],"prefix":"10.3389","volume":"12","author":[{"given":"Zhiying","family":"Huang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaomeng","family":"Miao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Diyan","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jia","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haolin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuan","family":"Su","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,5,21]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1086\/690841","article-title":"Polydactyly in development, inheritance, and evolution","volume":"92","author":"Lange","year":"2017","journal-title":"Q Rev Biol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1111\/cge.12276","article-title":"Polydactyly: phenotypes, genetics and classification","volume":"85","author":"Malik","year":"2014","journal-title":"Clin Genet."},{"key":"B3","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1006\/geno.2000.6225","article-title":"A novel candidate gene for mouse and human preaxial polydactyly with altered expression in limbs of hemimelic extra-toes mutant mice","volume":"67","author":"Clark","year":"2000","journal-title":"Genomics."},{"key":"B4","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1002\/dvdy.22609","article-title":"Polydactyly: how many disorders and how many genes?","volume":"240","author":"Biesecker","year":"2011","journal-title":"Dev Dyn."},{"key":"B5","doi-asserted-by":"publisher","first-page":"e18","DOI":"10.1017\/erm.2015.18","article-title":"Advances in the molecular genetics of non-syndromic polydactyly","volume":"17","author":"Deng","year":"2015","journal-title":"Expert Rev Mol Med."},{"key":"B6","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1093\/genetics\/29.3.217","article-title":"Inheritance of polydactylism in the fowl","volume":"29","author":"Warren","year":"1944","journal-title":"Genetics."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1297-9686-32-1-73","article-title":"Mapping the Naked Neck (Na) and Polydactyly (Po) mutants of the chicken with microsatellite molecular markers","volume":"32","author":"Pitel","year":"2000","journal-title":"Genet. 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