{"id":12412,"date":"2019-05-23T14:35:52","date_gmt":"2019-05-23T14:35:52","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/?p=12412"},"modified":"2019-06-17T16:55:04","modified_gmt":"2019-06-17T16:55:04","slug":"scientist-spotlight-farhad-ghavami","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/scientist-spotlight-farhad-ghavami\/","title":{"rendered":"Eurofins: Using AgriSeq Panels to Improve Sunflowers"},"content":{"rendered":"<p>Genomics information is at the center of more and more research in biology, whether in academia, government laboratories or private industry. Independent service providers are an increasingly\u00a0important part of this process, offering next-generation sequencing, genotyping and similar services to\u00a0all of these researchers for a fee. Able to provide services at enormous scales using the latest tools, service providers\u00a0such as <a href=\"https:\/\/www.eurofinsus.com\/agrigenomics\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"s1\">Eurofins <\/span><\/a>bring <a href=\"http:\/\/bit.ly\/2w6KR6q\"><span class=\"s1\">genotyping-by-sequencing <\/span><\/a>and similar capabilities to labs that cannot maintain\u00a0them on their own, making the power of genomics more accessible.<\/p>\n<p><iframe loading=\"lazy\" width=\"760\" height=\"428\" src=\"https:\/\/www.youtube.com\/embed\/GwMy7ycSGKc?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/p>\n<p>Starting with tools for testing wine authenticity, Eurofins has built a particularly strong presence in the\u00a0field of plant agrigenomics, offering genetic assays that can assess plant health, identity, authenticity and overall vigor. These tools help plant breeders make sure that plant varieties they create show the\u00a0attributes they desire, and track rare or valuable traits that are important for viable agriculture. Plant\u00a0genetics features complications, such as extraordinarily large genomes and allopolyploidy, that are rare\u00a0or nonexistent among animals, making plant agrigenomics an especially challenging field. Within that\u00a0challenge, single-nucleotide polymorphisms (SNPs) are an area of increasing interest, difficult to detect\u00a0with other methods because of their small size. Particularly when one is interested in numerous possible\u00a0SNPs at different loci, reading and understanding them all can be beyond many practitioners and tools.<\/p>\n<p>Eurofins achieves its presence here with the aid of Applied Biosystems genotyping solutions. For high-density\u00a0genotyping requests, Eurofins uses the Applied Biosystems GeneTitan and associated Axiom\u00a0array, but the <a href=\"http:\/\/bit.ly\/2w4Gn0n\"><span class=\"s1\">AgriSeq NGS <\/span><\/a>has proven ideal for smaller, medium-scale requests of 100 to 3,000 genes or\u00a0markers per run. The AgriSeq platform has proven particularly versatile, thanks to the option to use predesigned\u00a0panels or create custom panels using the Ion AmpliSeq Designer. This enables AgriSeq to serve\u00a0both common requests and rare ones, including species and varieties for which gene panels do not\u00a0already exist. Additionally, as <a href=\"https:\/\/youtu.be\/DOid6zZqJck\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"s1\">Eurofins chief scientific officer Dr. Farhad Ghavami <\/span><\/a>puts it, \u201cThe nice thing\u00a0about these AgriSeq panels and chemistry that we\u2019ve found is that you don\u2019t need that much DNA,\u201d\u00a0which saves time, effort and possibility all around. Eurofins collaborates with Thermo Fisher Scientific to\u00a0develop and implement custom gene panels, appreciating the fast turnaround time and comprehensive\u00a0validation that this approach offers. \u201cOur experience with AgriSeq has been excellent in different animal\u00a0and plant species,\u201d as Dr. Ghavami tells it, and Eurofins has made use of numerous pre-existing and\u00a0custom AgriSeq panels.<\/p>\n<p>Eurofins worked with Thermo Fisher to develop an AgriSeq genotyping-by-sequencing (GBS) panel for\u00a0sunflowers at this medium scale, filling a gap in current offerings in order to help sunflower breeders\u00a0make use of this modern technique as they develop and maintain new varieties as ornamental plants, for\u00a0food and for seed oil. This panel was based on 5,019 SNP markers taken from three distinct sunflower\u00a0varieties, providing a comprehensive overview of sunflower genetics suitable for breeding. The 700 best-performing\u00a0markers, distributed uniformly through the genome and across all chromosomes, were\u00a0selected for the GBS panel.<\/p>\n<p>In both the long process of developing and validating this new sunflower panel and their uses of existing\u00a0panels for maize, soy, canola, sunflower, pine trees, cattle, horses, sheep, dogs and swine, Dr. Farhad\u00a0Ghavami and Eurofins report excellent results from their use of and collaboration with Thermo Fisher\u00a0Scientific. \u201cWe chose AgriSeq because of Thermo Fisher\u2019s support and collaboration,\u201d Dr. Ghavami tells\u00a0us. \u201cThe process for making a custom panel was really easy and user-friendly\u2026it was a fast approach to\u00a0get the panel we wanted.\u201d<\/p>\n<p>Learn more about <a href=\"http:\/\/bit.ly\/2JnUQ05\">Thermo Fisher\u2019s AgriSeq genotyping-by-sequencing tools<\/a>.<\/p>\n<p><!-- BEGIN KAPOST ANALYTICS CODE --><\/p>\n<p><!-- var _kaq = _kaq || []; _kaq.push([2, \"5cdf144965c4be00500001cf\", \"5674227b963491538f00011d\"]); (function(){ var ka = document.createElement(\"script\"); ka.async=true; ka.id=\"ka_tracker\"; ka.src = (document.location.protocol == \"https:\" ? \"https\" : \"http\") + \":\/\/analytics.kapost.com\/ka.js\"; var s = document.getElementsByTagName(\"script\")[0]; s.parentNode.insertBefore(ka, s); })(); \/\/--><\/p>\n<p><!-- END KAPOST ANALYTICS CODE --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Genomics information is at the center of more and more research in biology, whether in academia, government laboratories or private industry. Independent service providers are an increasingly\u00a0important part of this process, offering next-generation sequencing, genotyping and similar services to\u00a0all of these researchers for a fee. Able to provide services at enormous scales using the latest<\/p>\n","protected":false},"author":120,"featured_media":12417,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[83],"tags":[262],"division":[],"class_list":{"0":"post-12412","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-animal-health-and-agrigenomics","8":"tag-agrigenomics","9":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v27.8 (Yoast SEO v27.8) - https:\/\/yoast.com\/product\/yoast-seo-premium-wordpress\/ -->\n<title>Scientist Spotlight: Eurofins Chief Scientific Officer Farhad Ghavami<\/title>\n<meta name=\"description\" content=\"Independent genomics service providers make genotyping and sequencing services more accessible to researchers. 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