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Semen from individual bulls is used for thousands of artificial inseminations for which the fertilization success is monitored. Results from the breeding soundness examination and repeated observations of semen quality complement the fertility evaluation for each bull.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      In a cohort of 3881 Brown Swiss bulls that had genotypes at 683,609 SNPs, we reveal four novel recessive QTL for male fertility on BTA1, 18, 25, and 26 using haplotype-based association testing. A QTL for bull fertility on BTA1 is also associated with sperm head shape anomalies. All other QTL are not associated with any of the semen quality traits investigated. We perform complementary fine-mapping approaches using publicly available transcriptomes as well as whole-genome sequencing data of 125 Brown Swiss bulls to reveal candidate causal variants. We show that missense or nonsense variants in\n                      <jats:italic>SPATA16<\/jats:italic>\n                      ,\n                      <jats:italic>VWA3A, ENSBTAG00000006717<\/jats:italic>\n                      and\n                      <jats:italic>ENSBTAG00000019919<\/jats:italic>\n                      are in linkage disequilibrium with the QTL. Using whole-genome sequence data, we detect strong association (\n                      <jats:italic>P<\/jats:italic>\n                      \u00a0=\u20094.83\u2009\u00d7\u200910\n                      <jats:sup>\u2212\u200912<\/jats:sup>\n                      ) of a missense variant (p.Ile193Met) in\n                      <jats:italic>SPATA16<\/jats:italic>\n                      with male fertility. However, non-coding variants exhibit stronger association at all QTL suggesting that variants in regulatory regions contribute to variation in bull fertility.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Our findings in a dairy cattle population provide evidence that recessive variants may contribute substantially to quantitative variation in male fertility in mammals. Detecting causal variants that underpin variation in male fertility remains difficult because the most strongly associated variants reside in poorly annotated non-coding regions.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-021-07523-3","type":"journal-article","created":{"date-parts":[[2021,3,30]],"date-time":"2021-03-30T13:03:01Z","timestamp":1617109381000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Autosomal recessive loci contribute significantly to quantitative variation of male fertility in a dairy cattle population"],"prefix":"10.1186","volume":"22","author":[{"given":"Maya","family":"Hiltpold","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naveen Kumar","family":"Kadri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fredi","family":"Janett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulrich","family":"Witschi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fritz","family":"Schmitz-Hsu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hubert","family":"Pausch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,3,30]]},"reference":[{"issue":"2","key":"7523_CR1","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/S0301-6226(01)00291-3","volume":"74","author":"M Thibier","year":"2002","unstructured":"Thibier M, Wagner H-G. 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Semen samples of bulls were provided from an artificial insemination center after regular collection as part of their insemination straw production. Semen quality, sperm morphology, and insemination success were recorded at the Swiss artificial insemination center Swissgenetics to monitor bull fertility. Fertility records and genotypes were provided by breeding organizations and had been collected as part of normal breeding procedures. No samples were collected specifically for the present study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"HP is a member of the editorial board of BMC Genomics. UW and FSH are employees of Swissgenetics. 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