{"id":3320,"date":"2026-02-12T05:00:04","date_gmt":"2026-02-12T05:00:04","guid":{"rendered":"https:\/\/climatesmartagrifood.ca\/?p=3320"},"modified":"2026-02-11T18:37:40","modified_gmt":"2026-02-11T18:37:40","slug":"holstein-cattle-db-by-ndgp","status":"publish","type":"post","link":"https:\/\/climatesmartagrifood.ca\/fr\/holstein-cattle-db-by-ndgp\/","title":{"rendered":"[Research Roundup] Introducing a New Structural Variant Database for Holstein Cattle by NDGP"},"content":{"rendered":"<div data-elementor-type=\"wp-post\" data-elementor-id=\"3320\" class=\"elementor elementor-3320\" data-elementor-post-type=\"post\">\n\t\t\t\t<div data-particle_enable=\"false\" data-particle-mobile-disabled=\"false\" class=\"elementor-element elementor-element-22942196 e-flex e-con-boxed e-con e-parent\" data-id=\"22942196\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-13fe0680 elementor-widget elementor-widget-text-editor\" data-id=\"13fe0680\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t\t\t\t\t\t<p><span class=\"TextRun SCXW119921909 BCX0\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW119921909 BCX0\">This study by the <strong>Net-Zero Dairy Genome Project (NDGP)<\/strong> team used whole-genome sequencing of Holstein cattle to\u00a0<\/span><span class=\"NormalTextRun SCXW119921909 BCX0\">identify<\/span><span class=\"NormalTextRun SCXW119921909 BCX0\"> and characterize thousands of structural variants (SVs) across the genome. The researchers then developed an open, interactive <a href=\"https:\/\/svdb-dc.pslab.ca\/\" target=\"_blank\" rel=\"noopener\">database<\/a> linking these variants to genes and traits, for wider use amongst the dairy research community.\u00a0<\/span><\/span><\/p><h3>Keywords<\/h3><ul><li>Holstein cattle<\/li><li>Genotype<\/li><li>Phenotype<\/li><li>Structural variants (SVs)<\/li><\/ul>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7058c3c elementor-widget elementor-widget-image\" data-id=\"7058c3c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t\t\t\t\t\t\t\t\t<figure class=\"wp-caption\">\n\t\t\t\t\t\t\t\t\t\t\t<a href=\"https:\/\/drive.google.com\/file\/d\/1hqhngdjEY4ZN7WB_FUXZMCA80b3EejOD\/view?usp=sharing\" target=\"_blank\" rel=\"noopener\">\n\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"800\" height=\"450\" src=\"https:\/\/climatesmartagrifood.ca\/wp-content\/uploads\/2026\/01\/NDGP-Grant-et-al-2024-1024x576.png\" class=\"attachment-large size-large wp-image-3422\" alt=\"\" srcset=\"https:\/\/climatesmartagrifood.ca\/wp-content\/uploads\/2026\/01\/NDGP-Grant-et-al-2024-1024x576.png 1024w, https:\/\/climatesmartagrifood.ca\/wp-content\/uploads\/2026\/01\/NDGP-Grant-et-al-2024-300x169.png 300w, https:\/\/climatesmartagrifood.ca\/wp-content\/uploads\/2026\/01\/NDGP-Grant-et-al-2024-768x432.png 768w, https:\/\/climatesmartagrifood.ca\/wp-content\/uploads\/2026\/01\/NDGP-Grant-et-al-2024-1536x864.png 1536w, https:\/\/climatesmartagrifood.ca\/wp-content\/uploads\/2026\/01\/NDGP-Grant-et-al-2024-18x10.png 18w, https:\/\/climatesmartagrifood.ca\/wp-content\/uploads\/2026\/01\/NDGP-Grant-et-al-2024.png 1920w\" sizes=\"(max-width: 800px) 100vw, 800px\" \/>\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t<figcaption class=\"widget-image-caption wp-caption-text\">Click to view this visual abstract as a PDF<\/figcaption>\n\t\t\t\t\t\t\t\t\t\t<\/figure>\n\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-28552a4 elementor-widget elementor-widget-text-editor\" data-id=\"28552a4\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t\t\t\t\t\t<h3>Research Highlights<\/h3><ul><li>Structural Variants (SVs), or large DNA changes, play an important role in cattle traits but are hard to detect with standard genetic tools<\/li><li>Researchers identified thousands of SVs using whole-genome sequencing, advancing previous research<\/li><li>Their new interactive <a href=\"https:\/\/svdb-dc.pslab.ca\/\" target=\"_blank\" rel=\"noopener\">database<\/a> helps link variants to genes and traits, revealing that most SVs are missed by common genotyping approaches<\/li><\/ul><h3>Editorial Reflections<\/h3><p><span data-contrast=\"auto\">This study provides a fully interactive database that enables broad access to the results, supporting ongoing efforts to link specific DNA variants to phenotypic variation.\u00a0It is\u00a0an excellent example of research with an immediate, tangible outcome that we\u00a0anticipate\u00a0will be taken up by the cattle breeding research community in Canada and beyond.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;335559738&quot;:240,&quot;335559739&quot;:240}\">\u00a0<\/span><\/p><p><span data-contrast=\"auto\">Le <strong>Net-Zero Dairy Genome Project (NDGP)<\/strong>\u00a0aims to create a roadmap and toolbox to reduce GHG emissions in the Canadian dairy industry by 55%, focusing on improving efficiency and animal welfare in dairy production.\u00a0<\/span><span data-contrast=\"none\">Contributing authors from the team are (in alphabetical order):<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;335559738&quot;:240,&quot;335559739&quot;:240}\">\u00a0<\/span><\/p><ul><li><a href=\"https:\/\/www.linkedin.com\/in\/christine-baes-732b2bbb\/?originalSubdomain=ca\" target=\"_blank\" rel=\"noopener\"><span data-contrast=\"none\">Christine Baes<\/span><\/a><span data-contrast=\"auto\"> \u2013 Project Lead (Activity 2 Lead), University of Guelph <\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;335559738&quot;:240,&quot;335559739&quot;:240}\">\u00a0<\/span><\/li><li><a href=\"https:\/\/www.linkedin.com\/in\/filippomiglior\/?originalSubdomain=ca\" target=\"_blank\" rel=\"noopener\"><span data-contrast=\"none\">Filippo\u00a0Miglior<\/span><\/a><span data-contrast=\"auto\"> \u2013 Project Lead (Activity 6 Lead), Lactanet &amp; University of Guelph <\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;335559738&quot;:240,&quot;335559739&quot;:240}\">\u00a0<\/span><\/li><li><span data-contrast=\"auto\"><a href=\"https:\/\/apps.ualberta.ca\/directory\/person\/stothard\" target=\"_blank\" rel=\"noopener\">Paul\u00a0Sthothard<\/a> \u2013 Project Lead (Activity 4 Lead), University of Alberta<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;335559738&quot;:240,&quot;335559739&quot;:240}\">\u00a0<\/span><\/li><\/ul><p><span data-contrast=\"none\">Curious about Team <strong>Net-Zero Dairy Genome Project (NDGP)<\/strong>\u2019s ongoing work? Visit\u00a0<\/span><a href=\"https:\/\/www.ndgp.ca\/\" target=\"_blank\" rel=\"noopener\"><span data-contrast=\"none\">ndgp.ca<\/span><\/a><span data-contrast=\"auto\">\u00a0<\/span><span data-contrast=\"none\">\u00a0to learn more.\u00a0\u00a0<\/span><span data-contrast=\"auto\">\u00a0<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;335559685&quot;:0,&quot;335559738&quot;:240,&quot;335559739&quot;:240}\">\u00a0<\/span><\/p><p><b><span data-contrast=\"auto\">Food for Thought:<\/span><\/b><span data-contrast=\"auto\">\u00a0Read the\u00a0<\/span><a href=\"https:\/\/doi.org\/10.1186\/s12864-024-10812-2\" target=\"_blank\" rel=\"noopener\"><span data-contrast=\"none\">full article here<\/span><\/a><span data-contrast=\"auto\">.\u00a0What opportunities does this public database create for rethinking policy and cattle breeding guidelines in the Canadian context?<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;335559685&quot;:0,&quot;335559738&quot;:240,&quot;335559739&quot;:240}\">\u00a0<\/span><\/p><h3>References<\/h3><p><span class=\"TextRun SCXW263515936 BCX0\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW263515936 BCX0\">Grant, J. R., Herman, E. K., Barlow, L. D.,\u00a0<\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW263515936 BCX0\">Miglior<\/span><span class=\"NormalTextRun SCXW263515936 BCX0\">, F., Schenkel, F. S., Baes, C. F., &amp; Stothard, P. (2024). A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application. BMC Genomics, 25, 903.\u00a0<\/span><\/span><a class=\"Hyperlink SCXW263515936 BCX0\" href=\"https:\/\/doi.org\/10.1186\/s12864-024-10812-2\" target=\"_blank\" rel=\"noreferrer noopener\"><span class=\"TextRun Underlined SCXW263515936 BCX0\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW263515936 BCX0\" data-ccp-charstyle=\"Hyperlink\">https:\/\/doi.org\/10.1186\/s12864-024-10812-2<\/span><\/span><\/a><span class=\"EOP SCXW263515936 BCX0\" data-ccp-props=\"{}\">\u00a0<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6a20d3e elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"6a20d3e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9b2ea45 elementor-widget elementor-widget-text-editor\" data-id=\"9b2ea45\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t\t\t\t\t\t<h3 aria-level=\"1\"><span data-contrast=\"none\">About the Climate-Smart Agri-Food Network<\/span><span data-ccp-props=\"{&quot;134245418&quot;:true,&quot;134245529&quot;:true,&quot;335559738&quot;:360,&quot;335559739&quot;:80}\">\u00a0<\/span><\/h3><p><span data-contrast=\"none\">Funded by Genome Canada through the\u00a0<\/span><a href=\"https:\/\/genomecanada.ca\/challenge-areas\/climate-smart-agriculture-and-food-systems\/\" target=\"_blank\" rel=\"noopener\"><span data-contrast=\"none\">Climate\u2011Smart Agriculture and Food Systems<\/span><\/a><span data-contrast=\"none\">\u00a0portfolio, the Network brings together nine Interdisciplinary Challenge Teams (ICTs) and two hubs \u2014 the\u00a0<\/span><a href=\"https:\/\/climatesmartagrifood.ca\/fr\/ag-act-agricultural-genomics-action-centre\/\"><span data-contrast=\"none\">Agricultural Genomics Action Centre (AG\u2011ACt)<\/span><\/a><span data-contrast=\"none\">\u00a0and the\u00a0<\/span><a href=\"https:\/\/climatesmartagrifood.ca\/fr\/cs-dcc-climate-smart-data-collaboration-centre\/\"><span data-contrast=\"none\">Climate\u2011Smart Data Collaboration Centre (CS\u2011DCC)<\/span><\/a><span data-contrast=\"none\">\u00a0\u2014 to advance climate\u2011smart agriculture through genomic innovations.<\/span><span data-ccp-props=\"{}\">\u00a0<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>","protected":false},"excerpt":{"rendered":"<p>This study by the Net-Zero Dairy Genome Project (NDGP) team used whole-genome sequencing of Holstein cattle to\u00a0identify and characterize thousands of structural variants (SVs) across the genome. The researchers then developed an open, interactive database linking these variants to genes and traits, for wider use amongst the dairy research community. Keywords Holstein cattle Genotype Phenotype [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":3418,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[27,8],"tags":[],"class_list":["post-3320","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-homepage-news","category-news"],"_links":{"self":[{"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/posts\/3320","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/comments?post=3320"}],"version-history":[{"count":13,"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/posts\/3320\/revisions"}],"predecessor-version":[{"id":3432,"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/posts\/3320\/revisions\/3432"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/media\/3418"}],"wp:attachment":[{"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/media?parent=3320"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/categories?post=3320"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/climatesmartagrifood.ca\/fr\/wp-json\/wp\/v2\/tags?post=3320"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}