{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T18:03:17Z","timestamp":1789668197346,"version":"4.0.1"},"reference-count":50,"publisher":"American Dairy Science Association","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"vor","delay-in-days":7,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["journalofdairyscience.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Dairy Science"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.3168\/jds.2025-28064","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T17:20:33Z","timestamp":1789665633000},"update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic inbreeding coefficients and inbreeding depression of semen production traits at genome-wide and chromosomal levels in Japanese Holstein bulls"],"prefix":"10.3168","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-7082-6615","authenticated-orcid":false,"given":"Ryogo","family":"Inagaki","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6031-3557","authenticated-orcid":false,"given":"Che-Hsuan","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ikuko","family":"Fujimoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taro","family":"Oka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6637-2056","authenticated-orcid":false,"given":"Toshimi","family":"Baba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junpei","family":"Kawakami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yukima","family":"Watanabe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9869-9400","authenticated-orcid":false,"given":"Koichi","family":"Hagiya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1747","reference":[{"key":"10.3168\/jds.2025-28064_bib1","doi-asserted-by":"crossref","DOI":"10.1093\/jas\/skad382","article-title":"The role of inbreeding depression on productive performance in the Italian Holstein breed","volume":"101","author":"Ablondi","year":"2023","journal-title":"J. Anim. Sci."},{"key":"10.3168\/jds.2025-28064_bib2","author":"Aguilar"},{"key":"10.3168\/jds.2025-28064_bib3","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1021\/acs.jproteome.5b01080","article-title":"Testis-specific Y-centric protein-protein interaction network provides clues to the etiology of severe spermatogenic failure","volume":"15","author":"Ansari-Pour","year":"2016","journal-title":"J. Proteome Res."},{"key":"10.3168\/jds.2025-28064_bib4","doi-asserted-by":"crossref","first-page":"33647","DOI":"10.1038\/srep33647","article-title":"Autophagy-related proteins are functionally active in human spermatozoa and may be involved in the regulation of cell survival and motility","volume":"6","author":"Aparicio","year":"2016","journal-title":"Sci. Rep."},{"key":"10.3168\/jds.2025-28064_bib5","first-page":"1900","article-title":"Genetic analysis of semen production traits of Japanese Black and Holstein bulls: Genome-wide marker-based estimation of genetic parameters and environmental effect trends","volume":"95","author":"Atagi","year":"2017","journal-title":"J. Anim. Sci."},{"key":"10.3168\/jds.2025-28064_bib6","doi-asserted-by":"crossref","first-page":"2807","DOI":"10.3168\/jds.2018-15520","article-title":"Symposium review: The genomic architecture of inbreeding: How homozygosity affects health and performance","volume":"102","author":"Baes","year":"2019","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2025-28064_bib7","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1111\/2041-210X.13167","article-title":"RZooRoH: An R package to characterize individual genomic autozygosity and identify homozygous-by-descent segments","volume":"10","author":"Bertrand","year":"2019","journal-title":"Methods Ecol. Evol."},{"key":"10.3168\/jds.2025-28064_bib8","author":"Blaser"},{"key":"10.3168\/jds.2025-28064_bib9","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.ajhg.2018.07.015","article-title":"A One-Penny Imputed Genome from Next-Generation Reference Panels","volume":"103","author":"Browning","year":"2018","journal-title":"Am. J. Hum. Genet."},{"key":"10.3168\/jds.2025-28064_bib10","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: Rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"Gigascience"},{"key":"10.3168\/jds.2025-28064_bib11","doi-asserted-by":"crossref","first-page":"12373","DOI":"10.1073\/pnas.1221104110","article-title":"Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development","volume":"110","author":"Chang","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.3168\/jds.2025-28064_bib12","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/s12711-015-0174-9","article-title":"A simple strategy for managing many recessive disorders in a dairy cattle breeding program","volume":"47","author":"Cole","year":"2015","journal-title":"Genet. Sel. Evol."},{"key":"10.3168\/jds.2025-28064_bib13","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1086\/521314","article-title":"Homozygous mutation in SPATA16 is associated with male infertility in human globozoospermia","volume":"81","author":"Dam","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"10.3168\/jds.2025-28064_bib14","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/s12711-019-0497-z","article-title":"Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle","volume":"51","author":"Doekes","year":"2019","journal-title":"Genet. Sel. Evol."},{"key":"10.3168\/jds.2025-28064_bib15","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12711-018-0385-y","article-title":"Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015","volume":"50","author":"Doekes","year":"2018","journal-title":"Genet. Sel. Evol."},{"key":"10.3168\/jds.2025-28064_bib16","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1111\/j.1439-0388.2008.00788.x","article-title":"Estimation of genetic parameters and genome scan for 15 semen characteristics traits of Holstein bulls","volume":"126","author":"Druet","year":"2009","journal-title":"J. Anim. Breed. Genet."},{"key":"10.3168\/jds.2025-28064_bib17","doi-asserted-by":"crossref","first-page":"5820","DOI":"10.1111\/mec.14324","article-title":"A model-based approach to characterize individual inbreeding at both global and local genomic scales","volume":"26","author":"Druet","year":"2017","journal-title":"Mol. Ecol."},{"key":"10.3168\/jds.2025-28064_bib18","doi-asserted-by":"crossref","first-page":"4721","DOI":"10.3168\/jds.2016-12164","article-title":"Genome-wide mapping and estimation of inbreeding depression of semen quality traits in a cattle population","volume":"100","author":"Feren\u010dakovi\u0107","year":"2017","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2025-28064_bib19","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1038\/hdy.1954.17","article-title":"A fuller theory of \u201cjunctions\u201d in inbreeding","volume":"8","author":"Fisher","year":"1954","journal-title":"Heredity"},{"key":"10.3168\/jds.2025-28064_bib20","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s12711-020-00563-5","article-title":"X chromosome variants are associated with male fertility traits in two bovine populations","volume":"52","author":"Fortes","year":"2020","journal-title":"Genet. Sel. Evol."},{"key":"10.3168\/jds.2025-28064_bib21","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1186\/s12864-018-4453-z","article-title":"Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle","volume":"19","author":"Forutan","year":"2018","journal-title":"BMC Genomics"},{"key":"10.3168\/jds.2025-28064_bib22","doi-asserted-by":"crossref","DOI":"10.1111\/asj.13739","article-title":"Longitudinal genetic analysis of semen production traits in Holstein bulls according to a random regression animal models on age","volume":"93","author":"Fujimoto","year":"2022","journal-title":"Anim. Sci. J."},{"key":"10.3168\/jds.2025-28064_bib23","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1186\/1297-9686-41-55","article-title":"Deregressing estimated breeding values and weighting information for genomic regression analyses","volume":"41","author":"Garrick","year":"2009","journal-title":"Genet. Sel. Evol."},{"key":"10.3168\/jds.2025-28064_bib24","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1186\/s12864-023-09298-1","article-title":"Genome-wide assessment and mapping of inbreeding depression identifies candidate genes associated with semen traits in Holstein bulls","volume":"24","author":"Ghoreishifar","year":"2023","journal-title":"BMC Genomics"},{"key":"10.3168\/jds.2025-28064_bib25","doi-asserted-by":"crossref","first-page":"11807","DOI":"10.3168\/jds.2020-20006","article-title":"Use of insemination data for joint evaluation of male and female fertility in predominantly seasonal-calving dairy herds","volume":"104","author":"Haile-Mariam","year":"2021","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2025-28064_bib26","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1017\/S0016672310000480","article-title":"Variation in actual relationship as a consequence of Mendelian sampling and linkage","volume":"93","author":"Hill","year":"2011","journal-title":"Genet. Res."},{"key":"10.3168\/jds.2025-28064_bib27","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1186\/s12864-021-07523-3","article-title":"Autosomal recessive loci contribute significantly to quantitative variation of male fertility in a dairy cattle population","volume":"22","author":"Hiltpold","year":"2021","journal-title":"BMC Genomics"},{"key":"10.3168\/jds.2025-28064_bib28","doi-asserted-by":"crossref","first-page":"6009","DOI":"10.3168\/jds.2017-12787","article-title":"Invited review: Inbreeding in the genomics era: Inbreeding, inbreeding depression, and management of genomic variability","volume":"100","author":"Howard","year":"2017","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2025-28064_bib29","doi-asserted-by":"crossref","first-page":"101","DOI":"10.2508\/chikusan.87.101","article-title":"Estimates of heritability and repeatability of semen characteristics in Holstein bulls","volume":"87","author":"Kawakami","year":"2016","journal-title":"Nihon Chikusan Gakkaiho."},{"key":"10.3168\/jds.2025-28064_bib30","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1534\/genetics.111.130922","article-title":"Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data","volume":"189","author":"Keller","year":"2011","journal-title":"Genetics"},{"key":"10.3168\/jds.2025-28064_bib31","doi-asserted-by":"crossref","first-page":"8956","DOI":"10.3168\/jds.2022-22116","article-title":"Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle","volume":"105","author":"Lozada-Soto","year":"2022","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2025-28064_bib32","doi-asserted-by":"crossref","first-page":"5183","DOI":"10.3168\/jds.2019-18013","article-title":"Effect of genomic selection on rate of inbreeding and coancestry and effective population size of Holstein and Jersey cattle populations","volume":"103","author":"Makanjuola","year":"2020","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2025-28064_bib33","first-page":"307","article-title":"Application of Genomic Information in Livestock Breeding and Future Perspectives","volume":"91","author":"Masuda","year":"2020","journal-title":"Nihon Chikusan Gakkaiho."},{"key":"10.3168\/jds.2025-28064_bib34","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.ajhg.2008.08.007","article-title":"Runs of Homozygosity in European Populations","volume":"83","author":"McQuillan","year":"2008","journal-title":"Am. J. Hum. Genet."},{"key":"10.3168\/jds.2025-28064_bib35","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1186\/1297-9686-24-4-305","article-title":"Computing inbreeding coefficients in large populations","volume":"24","author":"Meuwissen","year":"1992","journal-title":"Genet. Sel. Evol."},{"key":"10.3168\/jds.2025-28064_bib36","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/s12864-020-6463-x","article-title":"How to study runs of homozygosity using plink? a guide for analyzing medium density SNP data in livestock and pet species","volume":"21","author":"Meyermans","year":"2020","journal-title":"BMC Genomics"},{"key":"10.3168\/jds.2025-28064_bib37","series-title":"Manual for BLUPF90 family of programs","author":"Misztal","year":"2014"},{"key":"10.3168\/jds.2025-28064_bib38","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1186\/s12864-020-6758-y","article-title":"Whole-genome homozygosity mapping reveals candidate regions affecting bull fertility in US Holstein cattle","volume":"21","author":"Nani","year":"2020","journal-title":"BMC Genomics"},{"key":"10.3168\/jds.2025-28064_bib39","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1186\/s12864-023-09480-5","article-title":"Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle","volume":"24","author":"Nishio","year":"2023","journal-title":"BMC Genomics"},{"key":"10.3168\/jds.2025-28064_bib40","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1002\/jcp.25330","article-title":"First evidence of DAAM1 localization during the post-natal development of rat testis and in mammalian sperm","volume":"231","author":"Pariante","year":"2016","journal-title":"J. Cell. Physiol."},{"key":"10.3168\/jds.2025-28064_bib41","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s12711-014-0071-7","article-title":"Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle","volume":"46","author":"Pryce","year":"2014","journal-title":"Genet. Sel. Evol."},{"key":"10.3168\/jds.2025-28064_bib42","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: A tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"10.3168\/jds.2025-28064_bib43","doi-asserted-by":"crossref","first-page":"11832","DOI":"10.3168\/jds.2021-20326","article-title":"How genomic selection has increased rates of genetic gain and inbreeding in the Australian national herd, genomic information nucleus, and bulls","volume":"104","author":"Scott","year":"2021","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2025-28064_bib44","doi-asserted-by":"crossref","first-page":"5369","DOI":"10.1093\/nar\/gkf696","article-title":"Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes","volume":"30","author":"Uechi","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"10.3168\/jds.2025-28064_bib45","doi-asserted-by":"crossref","first-page":"4414","DOI":"10.3168\/jds.2007-0980","article-title":"Efficient methods to compute genomic predictions","volume":"91","author":"VanRaden","year":"2008","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2025-28064_bib46","doi-asserted-by":"crossref","first-page":"2771","DOI":"10.3168\/jds.S0022-0302(99)75534-7","article-title":"Selection and mating considering expected inbreeding of future progeny","volume":"82","author":"VanRaden","year":"1999","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2025-28064_bib47","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1086\/279872","article-title":"Coefficients of Inbreeding and Relationship","volume":"56","author":"Wright","year":"1922","journal-title":"Am. Nat."},{"key":"10.3168\/jds.2025-28064_bib48","doi-asserted-by":"crossref","first-page":"4616","DOI":"10.1073\/pnas.1218318110","article-title":"ARID4A and ARID4B regulate male fertility, a functional link to the AR and RB pathways","volume":"110","author":"Wu","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.3168\/jds.2025-28064_bib49","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.anireprosci.2018.08.038","article-title":"Functional haplotypes of ARID4A affect promoter activity and semen quality of bulls","volume":"197","author":"Yang","year":"2018","journal-title":"Anim. Reprod. Sci."},{"key":"10.3168\/jds.2025-28064_bib50","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s12863-019-0752-x","article-title":"Estimation of the genetic parameters for semen traits in Chinese Holstein bulls","volume":"20","author":"Yin","year":"2019","journal-title":"BMC Genet."}],"container-title":["Journal of Dairy Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022030226032637?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022030226032637?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T17:20:39Z","timestamp":1789665639000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0022030226032637"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":50,"alternative-id":["S0022030226032637"],"URL":"https:\/\/doi.org\/10.3168\/jds.2025-28064","relation":{},"ISSN":["0022-0302"],"issn-type":[{"value":"0022-0302","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Genomic inbreeding coefficients and inbreeding depression of semen production traits at genome-wide and chromosomal levels in Japanese Holstein bulls","name":"articletitle","label":"Article Title"},{"value":"Journal of Dairy Science","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.3168\/jds.2025-28064","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s).","name":"copyright","label":"Copyright"}]}}