{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T01:21:22Z","timestamp":1783560082421,"version":"3.55.0"},"reference-count":156,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T00:00:00Z","timestamp":1740700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Domestication of wild boars into local and intensive pig breeds has driven adaptive genomic changes, resulting in significant phenotypic differences in intestinal immune function. The intestine relies on diverse immune cells, but their evolutionary changes during domestication remain poorly understood at single-cell resolution.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We performed single-cell RNA sequencing (scRNA-seq) and marker gene analysis on jejunal tissues from wild boars, a Chinese local breed (Jinhua), and an intensive breed (Duroc). Then, we developed an immune cell evaluation system that includes immune scoring, gene identification, and cell communication analysis. Additionally, we mapped domestication-related clustering relationships, highlighting changes in gene expression and immune function.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We generated a single-cell atlas of jejunal tissues, analyzing 26,246 cells and identifying 11 distinct cell lineages, including epithelial and plasma cells, and discovered shared and unique patterns in intestinal nutrition and immunity across breeds. Immune cell evaluation analysis confirmed the conservation and heterogeneity of immune cells, manifested by highly conserved functions of immune cell subgroups, but wild boars possess stronger immune capabilities than domesticated breeds. We also discovered four patterns of domestication-related breed-specific genes related to metabolism, immune surveillance, and cytotoxic functions. Lastly, we identified a unique population of plasma cells with distinctive antibody production in Jinhua pig population.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our findings provide valuable single-cell insights into the cellular heterogeneity and immune function evolution in the jejunum during pig at various domestication stages. The single-cell atlas also serves as a resource for comparative studies and supports breeding programs aimed at enhancing immune traits in pigs.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fimmu.2025.1530214","type":"journal-article","created":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T07:04:22Z","timestamp":1740726262000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Pig jejunal single-cell RNA landscapes revealing breed-specific immunology differentiation at various domestication stages"],"prefix":"10.3389","volume":"16","author":[{"given":"Wenyu","family":"Fu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinqin","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengfei","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingyao","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaowei","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qishan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuchun","family":"Pan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhe","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,2,28]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1901169116","article-title":"Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe","volume":"116","author":"Frantz","year":"2019","journal-title":"Proc Natl Acad Sci U.S.A"},{"key":"B2","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s12711-022-00754-2","article-title":"Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs","volume":"54","author":"Liu","year":"2022","journal-title":"Genet Sel Evol"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0912264107","article-title":"Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA","volume":"107","author":"Larson","year":"2010","journal-title":"Proc Natl Acad Sci U.S.A"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evx186","article-title":"Signatures of selection and interspecies introgression in the genome of chinese domestic pigs","volume":"9","author":"Zhu","year":"2017","journal-title":"Genome Biol Evol"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1217149109","article-title":"Strong signatures of selection in the domestic pig genome","volume":"109","author":"Rubin","year":"2012","journal-title":"Proc Natl Acad Sci U.S.A"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1095740","article-title":"The interaction between dietary fiber and gut microbiota, and its effect on pig intestinal health","volume":"14","author":"Hu","year":"2023","journal-title":"Front Immunol"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2019.1690363","article-title":"Interactions between host and gut microbiota in domestic pigs: a review","volume":"11","author":"Patil","year":"2020","journal-title":"Gut Microbes"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1058346","article-title":"Genetic architecture of innate and adaptive immune cells in pigs","volume":"14","author":"Ballester","year":"2023","journal-title":"Front Immunol"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-020-0225-0","article-title":"Animal domestication in the era\u00a0of\u00a0ancient genomics","volume":"21","author":"Frantz","year":"2020","journal-title":"Nat Rev Genet"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-animal-022516-022747","article-title":"Taming the past: ancient DNA and the study of animal domestication","volume":"5","author":"MacHugh","year":"2017","journal-title":"Annu Rev Anim Biosci"},{"key":"B11","first-page":"77","article-title":"The intestinal tract and the Peyer\u2019s patch dimensions of wild boars (Sus scrofa L., 1758) and domestic pigs (Sus scrofa f. domestica). 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