{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T04:46:45Z","timestamp":1782535605813,"version":"3.54.5"},"reference-count":140,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T00:00:00Z","timestamp":1782172800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Natural Science Foundation Project of Inner Mongolia Autonomous Region","award":["2026LHQC0197"],"award-info":[{"award-number":["2026LHQC0197"]}]},{"name":"Science and Technology Breakthrough & Open Competition Project","award":["BR251004"],"award-info":[{"award-number":["BR251004"]}]},{"name":"Science and Technology Breakthrough & Open Competition Project","award":["BR261013"],"award-info":[{"award-number":["BR261013"]}]},{"name":"Science and Technology Breakthrough & Open Competition Project","award":["2025KJTW002201"],"award-info":[{"award-number":["2025KJTW002201"]}]},{"name":"Conservation and Innovative Utilization of Sheep & Goat Genetic Resources","award":["BR261201"],"award-info":[{"award-number":["BR261201"]}]},{"name":"Ministry of Finance","award":["CARS-38"],"award-info":[{"award-number":["CARS-38"]}]},{"name":"Ministry of Finance","award":["CARS-39"],"award-info":[{"award-number":["CARS-39"]}]},{"name":"Joint Research Project for Breeding in Inner Mongolia Autonomous Region: Germplasm Resource Innovation and Breeding System Construction of Sheep","award":["YZ2023011"],"award-info":[{"award-number":["YZ2023011"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Single-cell omics technologies have transformed the study of cellular heterogeneity, enabling high-resolution analysis of tissue development and complex traits. In sheep and goats, these approaches have been applied to skin, hair follicles, reproductive organs, metabolic tissues, and adipose tissue, revealing cell type-specific regulatory programs underlying traits such as wool quality, fertility, growth, and fat deposition. However, most studies rely on single-cell RNA sequencing (scRNA-seq) and are limited by incomplete genome annotation, insufficient coverage of production traits, and weak integration with population genetics, restricting their application in molecular breeding. This review summarizes advances in single-cell omics in sheep and goats, focusing on tissue development and trait formation. We further discuss emerging strategies that integrate single-cell multi-omics, spatial transcriptomics, and population genetics to resolve regulatory mechanisms in a cell type-specific and spatially informed context. Finally, we discuss CRISPR\/Cas9-based validation to link genotype and phenotype, accelerating gene discovery and precision breeding in small ruminants.<\/jats:p>","DOI":"10.3390\/ani16131948","type":"journal-article","created":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T17:11:49Z","timestamp":1782234709000},"page":"1948","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Single-Cell Omics Advances in Understanding Tissue Development and Complex Trait Formation in Sheep and Goats"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5763-8983","authenticated-orcid":false,"given":"Jianfang","family":"Wang","sequence":"first","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haobin","family":"Ma","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-9508-770X","authenticated-orcid":false,"given":"Diba Dedacha","family":"Jilo","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"},{"name":"Department of Animal Science, Bule Hora University, Bule Hora P.O. Box 144, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5144-3475","authenticated-orcid":false,"given":"Abebe Belete","family":"Kuraz","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"},{"name":"Department of Animal Science, Werabe University, Werabe P.O. Box 46, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juntao","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yajuan","family":"Li","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaogao","family":"Diao","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6808-1765","authenticated-orcid":false,"given":"Bouabid","family":"Badaoui","sequence":"additional","affiliation":[{"name":"Laboratory of Biodiversity, Ecology and Genome, Department of Biology, Faculty of Sciences Rabat, Mohammed V University, Rabat 10106, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8386-7408","authenticated-orcid":false,"given":"Rui","family":"Su","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region, Hohhot 010018, China"},{"name":"Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Inner Mongolia Autonomous Region, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongbin","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region, Hohhot 010018, China"},{"name":"Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot 010018, China"},{"name":"China-Mongolia Biomacromolecule Application \u201cBelt and Road\u201d Joint Laboratory, Inner Mongolia Autonomous Region, Hohhot 010018, China"},{"name":"Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Inner Mongolia Autonomous Region, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"108362","DOI":"10.1016\/j.compbiolchem.2025.108362","article-title":"A systematic review of single-cell RNA sequencing applications and innovations","volume":"115","author":"Rafi","year":"2025","journal-title":"Comput. 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