{ "abstract": "This study used mitochondrial DNA (mtDNA) D-loop region sequence polymorphisms as molecular markers to investigate the genetic structure and maternal origin of six cattle breeds in the Ili River Valley region of Xinjiang, China. Blood samples were collected from six cattle breeds in the region, including Xinjiang Brown cattle (n = 30), Kazakh cattle (n = 33), Altay White-headed cattle (n = 33), Chinese Simmental cattle (n = 34), Chinese Holstein cattle (n = 31), and Angus cattle (n = 22), for DNA extraction. Complete mtDNA D-loop region sequences were obtained from 183 individuals. Sequence alignment, correction and SNP screening were implemented to characterize sequence variation and base composition. Genetic diversity parameters and pairwise genetic distances were estimated, and a neighbor-joining (NJ) phylogenetic tree was constructed. The complete sequences of the mtDNA D-loop region in the six cattle breed populations were 910–911 bp. The average contents of A, G, T, and C were 32.76%, 13.83%, 28.79%, and 24.62%, respectively, and the overall AT content was higher than GC content. A total of 147 SNPs were detected, accounting for 16.10% of the total sequence length. In total, 107 haplotypes were identified, of which 92 were classified as Bos taurus and 15 as Bos indicus. The k, Hd, and Pi values were 14.24, 0.99, and 0.02, respectively. The constructed NJ phylogenetic tree revealed two major maternal origins—Bos taurus and Bos indicus—among the six cattle breeds. The six cattle breeds in the Ili River Valley region exhibit rich genetic diversity and two maternal origins, predominantly influenced by Bos taurus. These findings provide a theoretical basis for the conservation and rational use of cattle genetic resources in the region.", "abstract_shown": true, "affiliations": [ "Xinjiang Key Laboratory of Feed Biotechnology, Urumqi, China.", "Institute of Feed Research, Xinjiang Academy of Animal Science, Urumqi, China.", "College of Life Science, Xinjiang Agricultural University, Urumqi, China.", "Institute of Animal Sciences, Xinjiang Academy of Animal Sciences, Urumqi, China." ], "article_type": "Research Article", "arxiv": null, "author_total": 11, "authors": [ { "affs": [ 0, 1 ], "name": "Guzalnur Amat" }, { "affs": [ 2 ], "name": "Adiljan Kader" }, { "affs": [ 0, 1 ], "name": "Zhenghong Zhan" }, { "affs": [ 0, 1 ], "name": "Yong Tuo" }, { "affs": [ 0, 1 ], "name": "Ziting Wang" }, { "affs": [ 0, 1 ], "name": "Zhijun Zhang" }, { "affs": [ 0, 1 ], "name": "Xiaoyan Wen" }, { "affs": [ 0, 1 ], "name": "Ziyi Ren" }, { "affs": [ 0, 1 ], "name": "Akida Tursun" }, { "affs": [ 3 ], "name": "Ablat Sulayman", "orcid": "0000-0002-3404-1121" }, { "affs": [ 0 ], "name": "Tongjun Guo" } ], "bibtex": "https://research.draconitic.com/paper/2kcsef6m4r6hg.bib", "cited_by": 0, "doi": "10.1371/journal.pone.0359629", "fulltext_url": "https://europepmc.org/articles/PMC13693866", "id": "2kcsef6m4r6hg", "issns": [ "1932-6203" ], "landing_url": "https://doi.org/10.1371/journal.pone.0359629", "language": "eng", "licence": "CC-BY", "licence_label": "CC BY", "licence_source": "article", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1311|Genetic and phenotypic traits in livestock" ], [ "plos", "/Biology and life sciences/Agriculture/Animal management/Animal husbandry" ], [ "plos", "/Biology and life sciences/Agriculture/Animal management/Livestock" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/Forms of DNA/Mitochondrial DNA" ], [ "plos", "/Biology and life sciences/Conservation biology/Conservation genetics" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Population genetics" ], [ "plos", "/Biology and life sciences/Genetics/Conservation genetics" ], [ "plos", "/Biology and life sciences/Genetics/DNA/Forms of DNA/Mitochondrial DNA" ], [ "plos", "/Biology and life sciences/Genetics/Heredity/Genetic mapping/Haplotypes" ], [ "plos", "/Biology and life sciences/Genetics/Population genetics" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Animals/Vertebrates/Amniotes/Mammals/Bovines/Cattle" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Animals/Vertebrates/Amniotes/Mammals/Ruminants/Cattle" ], [ "plos", "/Biology and life sciences/Population biology/Population genetics" ], [ "plos", "/Biology and life sciences/Zoology/Animals/Vertebrates/Amniotes/Mammals/Bovines/Cattle" ], [ "plos", "/Biology and life sciences/Zoology/Animals/Vertebrates/Amniotes/Mammals/Ruminants/Cattle" ], [ "plos", "/Earth sciences/Geomorphology/Topography/Landforms/Valleys" ], [ "plos", "/Ecology and environmental sciences/Conservation science/Conservation biology/Conservation genetics" ] ], "openalex": "W7223417369", "pdf_url": "https://europepmc.org/articles/PMC13693866?pdf=render", "pmcid": "PMC13693866", "pmid": "42912699", "published": "2026-10-23", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/2kcsef6m4r6hg.ris", "sources": [ { "first_seen": "2026-10-30T12:17:17Z", "native_id": "10.1371/journal.pone.0359629", "source": "plos", "url": "https://doi.org/10.1371/journal.pone.0359629" }, { "first_seen": "2026-10-30T12:20:03Z", "native_id": "MED:42912699", "source": "europepmc", "url": "https://europepmc.org/article/MED/42912699" } ], "subjects": [ { "field": "biology", "origin": "plos:conservation biology", "subfield": "ecology" }, { "field": "biology", "origin": "plos:genetics", "subfield": "genetics-genomics" }, { "field": "biology", "origin": "plos:zoology", "subfield": "zoology-behaviour" } ], "title": "Analysis of genetic diversity and phylogenetic evolution of cattle population in the Ili River Valley region, Xinjiang, based on mtDNA D-loop sequence", "title_text": "Analysis of genetic diversity and phylogenetic evolution of cattle population in the Ili River Valley region, Xinjiang, based on mtDNA D-loop sequence", "type": "peer-reviewed", "updated_at": "2026-10-30T12:20:03Z", "url": "https://research.draconitic.com/paper/2kcsef6m4r6hg", "venue": "PLOS One", "versions": [] }