{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T06:48:41Z","timestamp":1785739721336,"version":"3.56.0"},"reference-count":39,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key Research and Development Program of the Xinjiang Uygur Autonomous Region","award":["2023B02036"],"award-info":[{"award-number":["2023B02036"]}]},{"name":"Key Research and Development Program of the Xinjiang Uygur Autonomous Region","award":["2023B02036-1"],"award-info":[{"award-number":["2023B02036-1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The Tumbler pigeon, a genetic resource of pigeons, exhibits diverse feather colors and distinct flight characteristics compared with other pigeon species, but the genetic basis of these traits remains unclear. Using whole-genome resequencing technology with Illumina NovaSeq X Plus paired-end sequencing (PE150, read length 150 bp) at an average genome coverage of 14.5\u00d7, this study analyzed the genetic structure, genetic diversity, and genetic differentiation of 80 individual Tumbler pigeons, Tarim pigeons and homing pigeons, collected from different regions of Xinjiang. In principal component analysis, the Tarim pigeon (TP) and the homing pigeon (XY) each formed relatively independent clusters, and there is a detectable genetic distance between them and the Tumbler pigeon (FC, FY) from the two regions. Moreover, there is an individual overlap phenomenon between the two Tumbler pigeon populations. In the analysis of genetic diversity, Na ranged from 1.93 to 1.97 and Ne from 1.55 to 1.56 across populations, with the TP population exhibiting the highest Na. PIC values ranged between 0.251 and 0.256, and HE values were lower than HO values in all four pigeon populations, indicating that moderate levels of genetic polymorphism were retained. In phylogenetic tree and population structure analyses, TP and XY formed relatively independent clusters. At the same time, individuals from the two Tumbler pigeon regions showed intermixing, resulting in the most distinct clustering pattern. Based on these findings, detectable genetic differentiation exists among the Tumbler pigeon, Tarim pigeon, and homing pigeon, suggesting that Tumbler pigeons may represent a locally differentiated genetic resource. The findings of this study will enhance our understanding of the population genetic structure of Tumbler pigeon resources, which is of great significance for promoting the conservation of Tumbler pigeon genetic resources and facilitating breed innovation and genetic improvement.<\/jats:p>","DOI":"10.3390\/ani16152343","type":"journal-article","created":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T06:17:40Z","timestamp":1785737860000},"page":"2343","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Population Structure and Genetic Diversity of Tumbler Pigeon Based on Whole-Genome Resequencing"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-2634-7617","authenticated-orcid":false,"given":"Xiaomei","family":"Ma","sequence":"first","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830091, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiying","family":"Li","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830091, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangxi","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830091, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaobin","family":"Li","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830091, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Nutrition and Feed, Yili Vocational and Technical College, Yining 835000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingping","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830091, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8194-7129","authenticated-orcid":false,"given":"Xiaoyu","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830091, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.ydbio.2016.11.008","article-title":"Pigeonetics Takes Flight: Evolution, Development, and Genetics of Intraspecific Variation","volume":"427","author":"Domyan","year":"2017","journal-title":"Dev. Biol."},{"key":"ref_2","unstructured":"Shu, D.G. (2005). The Origin of Species, Peking University Press."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"R302","DOI":"10.1016\/j.cub.2013.01.063","article-title":"Domestic pigeons","volume":"23","author":"Shapiro","year":"2013","journal-title":"Curr. Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1038\/252706a0","article-title":"Tumbling in pigeons","volume":"252","author":"Entrikin","year":"1974","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Zhang, R., Mu, C., Chang, L., Shen, X., Bu, Z., Yang, M., Fu, S., Tang, Q., Liu, P., and Yang, X. (2024). Whole-Genome Sequencing for Identifying Candidate Genes Related to the Special Phenotypes of the Taihu Dianzi Pigeon. Animals, 14.","DOI":"10.3390\/ani14071047"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Nature Genetics Editorial Team (2005). Touching Base: Tumbler pigeons. Nat. Genet., 37, 667.","DOI":"10.1038\/ng0705-667"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Lab Animal Editorial Team (2013). The Internal Compass of the pigeon. Lab. Anim., 42, 47.","DOI":"10.1038\/laban.210"},{"key":"ref_8","first-page":"554","article-title":"Genetic Diversity and Population Structure of Chinese Indigenous Chicken Breeds Based on Genome-Wide SNP Markers","volume":"54","author":"Gao","year":"2023","journal-title":"Acta Vet. Zootech. Sin."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"740559","DOI":"10.1016\/j.aquaculture.2024.740559","article-title":"Identification of Sex Locus and a Male-Specific Marker in Blunt-Snout Bream (Megalobrama amblycephala) Using a Whole Genome Resequencing Method","volume":"582","author":"Wen","year":"2024","journal-title":"Aquaculture"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Shi, H., Li, T., and Su, M. (2023). Whole Genome Sequencing Revealed Genetic Diversity, Population Structure, and Selective Signature of Panou Tibetan Sheep. BMC Genet., 24.","DOI":"10.1186\/s12864-023-09146-2"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1126\/science.1230422","article-title":"Genomic Diversity and Evolution of the Head Crest in the Rock pigeon","volume":"339","author":"Shapiro","year":"2013","journal-title":"Science"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.cub.2011.12.045","article-title":"Divergence, Convergence, and the Ancestry of Feral Populations in the Domestic Rock pigeon","volume":"22","author":"Stringham","year":"2012","journal-title":"Curr. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.cub.2014.01.020","article-title":"Epistatic and Combinatorial Effects of Pigmentary Gene Mutations in the Domestic pigeon","volume":"24","author":"Domyan","year":"2014","journal-title":"Curr. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map Format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: Functional Annotation of Genetic Variants from High-Throughput Sequencing Data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.ajhg.2010.11.011","article-title":"GCTA: A Tool for Genome-Wide Complex Trait Analysis","volume":"88","author":"Yang","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast Model-Based Estimation of Ancestry in Unrelated Individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"144874","DOI":"10.1016\/j.gene.2020.144874","article-title":"Apolipoprotein D","volume":"756","author":"Rassart","year":"2020","journal-title":"Gene"},{"key":"ref_20","first-page":"25","article-title":"Genetic Diversity Protection Grade Analysis of Chinese Domestic Duck Breeds","volume":"42","author":"Zou","year":"2011","journal-title":"Acta Vet. Zootech. Sin."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Hou, H., Liu, X., Wang, X., Cai, X., Lv, W., Tu, Y., Shen, X., Yao, J., and Yang, C. (2025). Genetic Structure and Diversity of Different pigeon Breeds Based on a 5 K Single-Nucleotide Polymorphism Chip. Animals, 15.","DOI":"10.3390\/ani15192864"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1111\/eva.13284","article-title":"Whole-Genome Sequencing Reveals the Artificial Selection and Local Environmental Adaptability of pigeons (Columba livia)","volume":"15","author":"Hou","year":"2022","journal-title":"Evol. Appl."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"105731","DOI":"10.1016\/j.psj.2025.105731","article-title":"The Genetic Structure and Selective Sweep Analysis of Meat pigeon Breeds Raised in Hainan Using Whole Genome Resequencing Technology","volume":"104","author":"Xu","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Esmailizadeh, A., Kharrati-Koopaee, H., and Nanaei, H.A. (2021). Whole genome resequencing data for rock pigeon (Columba livia). BMC Res. Notes, 14.","DOI":"10.1186\/s13104-021-05718-1"},{"key":"ref_25","first-page":"1939","article-title":"Genetic Diversity Analysis of Yongdeng Qishan Sheep Based on Specific-Locus Amplified Fragment Sequencing","volume":"54","author":"Ma","year":"2023","journal-title":"Acta Vet. Zootech. Sin."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e14863","DOI":"10.1016\/j.heliyon.2023.e14863","article-title":"Genetic Diversity and Within-Breed Variation in Three Indigenous Ethiopian Sheep Based on Whole Genome Analysis","volume":"9","author":"Asmare","year":"2023","journal-title":"Heliyon"},{"key":"ref_27","first-page":"30","article-title":"Genetic Diversity and Population Structure Analysis of Changdu Black Goat Based on Resequencing Data","volume":"43","author":"Awangcuoji","year":"2022","journal-title":"Acta Ecol. Anim. Domast."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Rahmatalla, S.A., Arends, D., Reissmann, M., Said Ahmed, A., Wimmers, K., Reyer, H., and Brockmann, G.A. (2017). Whole Genome Population Genetics Analysis of Sudanese Goats Identifies Regions Harboring Genes Associated with Major Traits. BMC Genet., 18.","DOI":"10.1186\/s12863-017-0553-z"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1038\/217624a0","article-title":"Evolutionary Rate at the Molecular Level","volume":"217","author":"Kimura","year":"1968","journal-title":"Nature"},{"key":"ref_30","first-page":"4","article-title":"Overview of Genetic Diversity","volume":"18","author":"Shen","year":"2001","journal-title":"J. Biol."},{"key":"ref_31","unstructured":"Ladd, M., and Bordoni, B. (2023). Genetics, Transposons. StatPearls [Internet], StatPearls Publishing."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"104310","DOI":"10.1016\/j.psj.2024.104310","article-title":"MtDNA Genetic Diversity and Phylogeographic Insights into Giant Domestic pigeon (Columba livia domestica) Breeds: Connections between Central Europe and the Middle East","volume":"103","author":"Balog","year":"2024","journal-title":"Poult. Sci."},{"key":"ref_33","first-page":"143","article-title":"Identification of Some Local Egg Duck Breeds in China","volume":"42","author":"Wang","year":"2020","journal-title":"Acta Agric. Univ. Jiangxiensis"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Podbielska, A., and Radko, A. (2022). Genetic Structure of racing pigeons (Columba livia) Kept in Poland Based on Microsatellite Markers. Genes, 13.","DOI":"10.3390\/genes13071175"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1093\/molbev\/msx322","article-title":"Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing","volume":"35","author":"Mei","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2298406","DOI":"10.1080\/10495398.2023.2298406","article-title":"Whole Genome Resequencing-Based Analysis of Plateau Adaptation in Meiren Yak (Bos grunniens)","volume":"35","author":"Wang","year":"2024","journal-title":"Anim. Biotechnol."},{"key":"ref_37","first-page":"624","article-title":"Analysis of Population Genetic Structure and Litter Size Candidate Genes of Pishan Red Sheep Based on Whole Genome Resequencing","volume":"51","author":"Shi","year":"2024","journal-title":"China Anim. Husb. Vet. Med."},{"key":"ref_38","first-page":"143","article-title":"Genetic Analysis of Genetic Relationship Between Two Populations of Guangxi Ma Chicken Using Gene Chip","volume":"57","author":"Tu","year":"2021","journal-title":"Chin. J. Anim. Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"104620","DOI":"10.1016\/j.isci.2022.104620","article-title":"Limited Domestic Introgression in a Final Refuge of the Wild pigeon","volume":"25","author":"Smith","year":"2022","journal-title":"iScience"}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/15\/2343\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T06:38:45Z","timestamp":1785739125000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/15\/2343"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,1]]},"references-count":39,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["ani16152343"],"URL":"https:\/\/doi.org\/10.3390\/ani16152343","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,1]]}}}