{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:56:41Z","timestamp":1760144201220,"version":"build-2065373602"},"reference-count":87,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2024,3,29]],"date-time":"2024-03-29T00:00:00Z","timestamp":1711670400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Shandong Province Special Economic Animal Innovation Team","award":["SDAIT-21-02","2021LZGC002","32102526"],"award-info":[{"award-number":["SDAIT-21-02","2021LZGC002","32102526"]}]},{"name":"Agricultural Improved Seed Project of Shandong Province","award":["SDAIT-21-02","2021LZGC002","32102526"],"award-info":[{"award-number":["SDAIT-21-02","2021LZGC002","32102526"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["SDAIT-21-02","2021LZGC002","32102526"],"award-info":[{"award-number":["SDAIT-21-02","2021LZGC002","32102526"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Domestication has shaped the diverse characteristics of rabbits, including coat color, fur structure, body size, and various physiological traits. Utilizing whole-genome resequencing (DNBSEQ-T7), we analyzed the genetic diversity, population structure, and genomic selection across 180 rabbits from 17 distinct breeds to uncover the genetic basis of these traits. We conducted whole-genome sequencing on 17 rabbit breeds, identifying 17,430,184 high-quality SNPs and analyzing genomic diversity, patterns of genomic variation, population structure, and selection signatures related to coat color, coat structure, long hair, body size, reproductive capacity, and disease resistance. Through PCA and NJ tree analyses, distinct clusters emerged among Chinese indigenous rabbits, suggesting varied origins and domestication histories. Selective sweep testing pinpointed regions and genes linked to domestication and key morphological and economic traits, including those affecting coat color (TYR, ASIP), structure (LIPH), body size (INSIG2, GLI3), fertility (EDNRA, SRD5A2), heat stress adaptation (PLCB1), and immune response (SEC31A, CD86, LAP3). Our study identified key genomic signatures of selection related to traits such as coat color, fur structure, body size, and fertility; these findings highlight the genetic basis underlying phenotypic diversification in rabbits and have implications for breeding programs aiming to improve productive, reproductive, and adaptive traits. The detected genomic signatures of selection also provide insights into rabbit domestication and can aid conservation efforts for indigenous breeds.<\/jats:p>","DOI":"10.3390\/genes15040433","type":"journal-article","created":{"date-parts":[[2024,3,29]],"date-time":"2024-03-29T06:33:16Z","timestamp":1711693996000},"page":"433","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Resequencing Analyses Revealed Genetic Diversity and Selection Signatures during Rabbit Breeding and Improvement"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5934-5025","authenticated-orcid":false,"given":"Kerui","family":"Xie","sequence":"first","affiliation":[{"name":"College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chao","family":"Ning","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai\u2019an 271018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aiguo","family":"Yang","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai\u2019an 271018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai\u2019an 271018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dan","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinzhong","family":"Fan","sequence":"additional","affiliation":[{"name":"College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,3,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"S167","DOI":"10.1186\/1297-9686-26-S1-S167","article-title":"Rabbit and man: Genetic and historic approach","volume":"26","author":"Monnerot","year":"1994","journal-title":"Genet. 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