Haplotypes affecting stillbirth and fertility in Icelandic Dairy Cattle

Haplotypes affecting stillbirth and fertility in Icelandic Dairy Cattle | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Haplotypes affecting stillbirth and fertility in Icelandic Dairy Cattle Egill Gautason, Þórdís Þórarinsdóttir, Goutam Sahana This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5491278/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 02 Jun, 2025 Read the published version in Journal of Applied Genetics → Version 1 posted 5 You are reading this latest preprint version Abstract In the last decades, the rate of stillbirths in the Icelandic Dairy Cattle population has increased. Some of these stillbirths may be caused by recessive lethal mutations segregating in the population. These alleles can be identified by detecting homozygous haplotype deficiency (HHD) in genotyped animals. The aim of this study was to find genomic regions affecting stillbirth and fertility in the Icelandic Dairy Cattle population. We analysed genotypes from 20,557 animals with 35,481 autosomal markers. We identified HHD segments and estimated their effects on stillbirths and insemination failure, measured as non-return rates. We conducted genome-wide association studies (GWAS) for stillbirth and five fertility traits: interval from first to last inseminations, conception rate, number of inseminations, calving interval and infertility. While no GWAS association reached the genome-wide significance threshold, some of the top signals co-located with HHD haplotypes. A total of 19 haplotypes significantly either decreased fertility, or increased incidence of stillbirths, or both. Two HHD regions on BTA13: 43,577,221 − 59,026,521 and BTA8: 83,276,598 − 84,472,391 were associated with both lower fertility and higher incidence of stillbirths. We found no evidence of large structural variations in or around the HHD regions, suggesting that these signals are likely due to single loss-of-function mutation or small structural variations. Further research should focus on exploring these regions using whole genome sequence data. Cattle stillbirth fertility homozygous haplotype deficiency recessive lethal Full Text Supplementary Files Supplemental1.xlsx Supplemental2Revision1542025.xlsx Supplemental3.xlsx Supplemental4.xlsx Supplemental5.docx Cite Share Download PDF Status: Published Journal Publication published 02 Jun, 2025 Read the published version in Journal of Applied Genetics → Version 1 posted Reviewers agreed at journal 29 Apr, 2025 Reviewers invited by journal 23 Apr, 2025 Editor assigned by journal 21 Apr, 2025 First submitted to journal 16 Apr, 2025 Editorial decision: Minor Revisions Needed 03 Mar, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Some of these stillbirths may be caused by recessive lethal mutations segregating in the population. These alleles can be identified by detecting homozygous haplotype deficiency (HHD) in genotyped animals. The aim of this study was to find genomic regions affecting stillbirth and fertility in the Icelandic Dairy Cattle population. We analysed genotypes from 20,557 animals with 35,481 autosomal markers. We identified HHD segments and estimated their effects on stillbirths and insemination failure, measured as non-return rates. We conducted genome-wide association studies (GWAS) for stillbirth and five fertility traits: interval from first to last inseminations, conception rate, number of inseminations, calving interval and infertility. While no GWAS association reached the genome-wide significance threshold, some of the top signals co-located with HHD haplotypes. A total of 19 haplotypes significantly either decreased fertility, or increased incidence of stillbirths, or both. 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