{"id":11427,"date":"2018-07-10T15:01:04","date_gmt":"2018-07-10T15:01:04","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/?p=11427"},"modified":"2022-08-18T20:29:09","modified_gmt":"2022-08-18T20:29:09","slug":"big-catch-genomics-matters-in-aquaculture-research","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/big-catch-genomics-matters-in-aquaculture-research\/","title":{"rendered":"Big Catch: Genomics Matters in Aquaculture Research"},"content":{"rendered":"<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.thermofisher.com\/blog\/wp-content\/uploads\/sites\/9\/2018\/07\/natural20world20istock20000003853042xlarge-1.jpg\" alt=\"A group of fish swim in a circle. Image: \" width=\"422\" height=\"284\" style=\"float: left\" class=\"alignleft\" \/>Worldwide, consumer preference for and consumption of aquatic species is increasing. <a href=\"http:\/\/circ.ahajournals.org\/content\/early\/2018\/05\/16\/CIR.0000000000000574\" target=\"_blank\" rel=\"noopener\">New guidelines from the American Heart Association<\/a> cement the importance of eating fish to help protect heart health, and around <a target=\"_blank\" rel=\"noopener\">16% of animal protein eaten globally in 2009<\/a> came from fish and shellfish.&nbsp;This increase puts pressure on the aquaculture industry to meet the market&#8217;s demands. Application of genomics in this market helps drive growth in the field by helping to improve fish production, decrease loss from disease and pests, increase traceability, and optimize feed formula for healthy, profitable and sustainable fish farms.<\/p>\n<p>Thermo Fisher Scientific has several tools that enable the advancement of genomics in the aquaculture market. Some of these tools include microarrays for various species such as oyster, tilapia, <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/550571%20\" target=\"_blank\" rel=\"noopener\">trout<\/a>&nbsp;and <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/550540\" target=\"_blank\" rel=\"noopener\">salmon<\/a>.&nbsp;&nbsp;<\/p>\n<p><a target=\"_blank\" rel=\"noopener\">A review published in February 2017<\/a>&nbsp;summarizes the current status of genomics and aquaculture species breeding in the United States, as reported to a US Department of Agriculture (USDA) workshop held in March 2016.<sup>1<\/sup> The report focuses on major aquaculture species farmed in the United States, including catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters and shrimp.<\/p>\n<p>The authors note the following:<\/p>\n<ul>\n<li>Research into genomic variations with identification of polymorphic markers, DNA markers, s<span>ingle nucleotide polymorphisms (<\/span>SNPs) and microsatellite markers is underway. Linkage maps have been constructed for most major species.<\/li>\n<li>Whole-genome sequences are available for several major aquaculture species, with higher-quality reads for fish compared to shellfish.<\/li>\n<li>Large RNA-Seq datasets have been generated for important species to characterize production traits of interest. Some include proteomic assessments in tandem.<\/li>\n<li>Non-coding regions and epigenetic regulation are less well understood.<\/li>\n<\/ul>\n<p> One reason for aquaculture lagging behind livestock and crop genomic breeding programs is the relatively short period for aquaculture species domestication. Humans have been tinkering with plants and food animal pedigrees for hundreds and thousands of years to refine them for agriculture; aquaculture has appeared on the radar only in the last few decades. Species such as catfish, oysters and trout therefore show considerable genetic variation among farmed varieties.<\/p>\n<p>Although a major goal for any breeding program is to leverage the genomic data to maximize yields through phenotype selection, without molecular data it is difficult to develop high-efficiency molecular screening tools. With research and development, it&rsquo;s possible these could positively impact several aspects of aquaculture:<\/p>\n<ul>\n<li>Growth rate and sex selection: all-female populations grow faster for some species, whereas identifying traits associated with faster maturation decrease time to harvest.<\/li>\n<li>Husbandry conditions: selecting traits for tolerance to heat stress, salinity and food conversion boosts yields under specific farming methods.<\/li>\n<li>Disease resistance: selecting stock lines according to health indicators can increase stocking density without adding drugs or chemicals to the system.<\/li>\n<\/ul>\n<p>With a more concise overview of aquaculture species genomics, the industry can look forward to benefits arising from more accurate breeding programs. In addition to breeding for disease resistance, better food conversion and meat quality, producers can also expect advances in other areas:<\/p>\n<ul>\n<li>Vaccine development and therapeutic diet formulation<\/li>\n<li>Sustainability, with farmed fish relieving pressure on wild stocks<\/li>\n<li>Gene editing strategies such as CRISPR\/Cas9 to enhance phenotypes without introducing foreign DNA for consumer acceptance<\/li>\n<li>Husbandry and welfare, breeding species that perform well in captive conditions<\/li>\n<li>Traceability as a tool to manage overfishing and illegal catch and to preserve wild stocks<\/li>\n<\/ul>\n<p>In order for genomics to meet aquaculture breeding program needs, technology must deliver accurate data with fast turnaround and at low cost. Next-generation sequencing (NGS) approaches are already increasing throughput and reducing costs to accelerate crop and food animal breeding programs. Solutions such as <a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/agricultural-biotechnology\/agrigenomics.html\" target=\"_blank\" rel=\"noopener\">Axiom, from the Thermo Fisher Scientific agrigenomics portfolio<\/a>,&nbsp;offer <a href=\"https:\/\/www.thermofisher.com\/ca\/en\/home\/life-science\/microarray-analysis\/agrigenomics-solutions-microarrays-gbs\/axiom-genotyping-solution-agrigenomics.html\" target=\"_blank\" rel=\"noopener\">expert-designed arrays<\/a> for specific aquaculture species to accelerate genomic discovery and breeding programs.&nbsp;<\/p>\n<p>High- and mid-density genotyping arrays exist for <a href=\"https:\/\/assets.thermofisher.com\/TFS-Assets\/LSG\/brochures\/axiom_trout_genotyping_array_datasheet.pdf\" target=\"_blank\" rel=\"noopener\">rainbow trout<\/a> &nbsp;and for&nbsp;<span><a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/550540\" target=\"_blank\" rel=\"noopener\">Atlantic salmon<\/a><\/span> in addition to several other aquatic species.&nbsp;Developed in collaboration with aquaculture experts, these arrays offer fast, cost-effective solutions to high-resolution genetics research.<\/p>\n<p>If you&#8217;d like to find out more about how Thermo Fisher Scientific agrigenomics solutions can help your breeding program,&nbsp;<a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/global\/forms\/agbio-contact-form.html%20\" target=\"_blank\" rel=\"noopener\">contact us for a free consultation with one of our experts<\/a>. Visit our website to&nbsp;<a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/agricultural-biotechnology\/agrigenomics.html\" target=\"_blank\" rel=\"noopener\">learn more about our agrigenomics solutions<\/a>.<\/p>\n<p>&nbsp;<\/p>\n<p><strong>References<\/strong><\/p>\n<p>1. Abdelrahman, H., et al. (2017) &#8220;Aquaculture genomics, genetics and breeding in the United States: Current status, challenges, and priorities for future research,&#8221; BMC Genomics 18(191).&nbsp;<a href=\"https:\/\/doi.org\/10.1186\/s12864-017-3557-1\">https:\/\/doi.org\/10.1186\/s12864-017-3557-1<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><em>&nbsp;For research use only. Not for use in diagnostic&nbsp;procedures.<\/em><\/p>\n<p><!-- BEGIN KAPOST ANALYTICS CODE --><\/p>\n<p><!--\nvar _kaq = _kaq || [];\n_kaq.push([2, \"5b27e25fc7b1010077000234\", \"5674227b963491538f00011d\"]);\n(function(){\nvar ka = document.createElement(\"script\"); ka.async=true; ka.id=\"ka_tracker\";\nka.src = (document.location.protocol == \"https:\" ? \"https\" : \"http\") + \":\/\/analytics.kapost.com\/ka.js\";\nvar s = document.getElementsByTagName(\"script\")[0]; s.parentNode.insertBefore(ka, s);\n})();\n\/\/--><\/p>\n<p><!-- END KAPOST ANALYTICS CODE --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Worldwide, consumer preference for and consumption of aquatic species is increasing. New guidelines from the American Heart Association cement the importance of eating fish to help protect heart health, and around 16% of animal protein eaten globally in 2009 came from fish and shellfish.&nbsp;This increase puts pressure on the aquaculture industry to meet the market&#8217;s<\/p>\n","protected":false},"author":120,"featured_media":11426,"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":[74],"division":[],"class_list":{"0":"post-11427","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-animal-health-and-agrigenomics","8":"tag-sequencing","9":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- 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