{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T10:37:53Z","timestamp":1768559873252,"version":"3.49.0"},"reference-count":86,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2022,10,13]],"date-time":"2022-10-13T00:00:00Z","timestamp":1665619200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100001250","name":"Morris Animal Foundation","doi-asserted-by":"publisher","award":["2018-06521"],"award-info":[{"award-number":["2018-06521"]}],"id":[{"id":"10.13039\/100001250","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and\/or infertility, 5 Przewalski\u2019s horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2\u20133 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski\u2019s horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P &amp;lt;\u20090.05). No significant copy number variations were observed in subfertile\/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.<\/jats:p>","DOI":"10.1093\/g3journal\/jkac278","type":"journal-article","created":{"date-parts":[[2022,10,13]],"date-time":"2022-10-13T15:43:08Z","timestamp":1665675788000},"source":"Crossref","is-referenced-by-count":6,"title":["Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5910-9666","authenticated-orcid":false,"given":"Caitlin","family":"Castaneda","sequence":"first","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University , College Station, TX 7784-4458, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4621-3856","authenticated-orcid":false,"given":"Lara","family":"Radovi\u0107","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna , Vienna 1210, Austria"},{"name":"Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna , Vienna 1210, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8935-8305","authenticated-orcid":false,"given":"Sabine","family":"Felkel","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna , Vienna 1210, Austria"},{"name":"Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna , Vienna 1210, Austria"},{"name":"Department of Biotechnology, Institute of Computational Biology, BOKU University of Life Sciences and Natural Resources , Vienna 1190, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7385-0618","authenticated-orcid":false,"given":"Rytis","family":"Juras","sequence":"additional","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University , College Station, TX 7784-4458, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6121-135X","authenticated-orcid":false,"given":"Brian W","family":"Davis","sequence":"additional","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University , College Station, TX 7784-4458, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2791-4331","authenticated-orcid":false,"given":"Ernest Gus","family":"Cothran","sequence":"additional","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University , College Station, TX 7784-4458, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4159-0695","authenticated-orcid":false,"given":"Barbara","family":"Wallner","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna , Vienna 1210, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2276-475X","authenticated-orcid":false,"given":"Terje","family":"Raudsepp","sequence":"additional","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University , College Station, TX 7784-4458, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,13]]},"reference":[{"issue":"11","key":"2022120108073468600_jkac278-B1","doi-asserted-by":"crossref","first-page":"5051","DOI":"10.1093\/molbev\/msab230","article-title":"Human-mediated admixture and selection shape the diversity on the modern swine (Sus scrofa) Y chromosomes","volume":"38","author":"Ai","year":"2021","journal-title":"Mol Biol 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