{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T10:26:00Z","timestamp":1787135160066,"version":"build-2736575974"},"reference-count":77,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:00:00Z","timestamp":1787097600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100015103","name":"Japan Racing Association","doi-asserted-by":"publisher","award":["No. 2025-NK-P44"],"award-info":[{"award-number":["No. 2025-NK-P44"]}],"id":[{"id":"10.13039\/100015103","id-type":"DOI","asserted-by":"publisher"}]},{"award":["No. 2025-NK-P44"],"award-info":[{"award-number":["No. 2025-NK-P44"]}],"id":[{"id":"https:\/\/ror.org\/00v8w0b34","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Introduction: The Kumamoto sub-breed of Japanese Brown cattle is a small population facing increasing inbreeding and declining effective population size driven by the intensive use of a limited number of elite sires. Methods: We analyzed 811 Japanese Brown cows genotyped using a 30K SNP array, retaining 19,745 SNPs after quality control. We calculated and compared ten genomic inbreeding estimators, including SNP-by-SNP and segment-based measures. Population structure was first assessed by rearing region using principal component analysis (PCA) and was then evaluated using ADMIXTURE-based clustering and distance-based hierarchical clustering, from which representative subsets were retained under predefined filtering criteria and further examined using PCA and neighbor-joining (NJ) tree analyses. Finally, we calculated the contribution of each ADMIXTURE group to total gene and allelic diversity, and integrated these two measures into a final conservation index after Z-score standardization. Results: ROH- and HBD-based estimators showed high concordance, whereas allele-frequency-dependent SNP-by-SNP estimators exhibited distinct distributions. Rearing region did not explain the main genetic structure. Instead, four representative ADMIXTURE-based groups, supported by independently identified family groups, captured the major genetic structure associated with paternal backgrounds. ADMIXTURE group 2 made the largest contribution to both gene and allelic diversity, and showed lowest genomic inbreeding. Conclusions: These findings suggest that ROH- and HBD-based estimators may serve as valuable indicators of genomic inbreeding in the Kumamoto sub-breed of Japanese Brown cattle; paternal background has played an important role in shaping the current genomic structure; and ADMIXTURE group 2, mainly associated with the Haru-yama-to\/-sakae sire background, may provide a valuable breeding resource for limiting future inbreeding accumulation and maintaining genetic diversity.<\/jats:p>","DOI":"10.3390\/ani16162587","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T09:30:53Z","timestamp":1787131853000},"page":"2587","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Analysis of Inbreeding, Population Structure, and Genetic Diversity in the Kumamoto Sub-Breed of Japanese Brown Cattle"],"prefix":"10.3390","volume":"16","author":[{"given":"Tenghui","family":"Wang","sequence":"first","affiliation":[{"name":"Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China"},{"name":"Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keiichi","family":"Inoue","sequence":"additional","affiliation":[{"name":"Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kasumi","family":"Ichinoseki","sequence":"additional","affiliation":[{"name":"National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0363-9411","authenticated-orcid":false,"given":"Masayuki","family":"Takeda","sequence":"additional","affiliation":[{"name":"National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan"},{"name":"Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-3384-8323","authenticated-orcid":false,"given":"Yo","family":"Fukuzawa","sequence":"additional","affiliation":[{"name":"National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takatoshi","family":"Ozaki","sequence":"additional","affiliation":[{"name":"Nihon Akaushi Registration Association, Kumamoto 861-2101, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Peng","sequence":"additional","affiliation":[{"name":"Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7793-4181","authenticated-orcid":false,"given":"Guowen","family":"Wang","sequence":"additional","affiliation":[{"name":"Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takafumi","family":"Ishida","sequence":"additional","affiliation":[{"name":"Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e13770","DOI":"10.1111\/asj.13770","article-title":"Comprehensive Assessment of Genetic Diversity, Structure, and Relationship in Four Japanese Cattle Breeds by Illumina 50 K SNP Array Analysis","volume":"93","author":"Kawaguchi","year":"2022","journal-title":"Anim. 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