{"id":2249,"date":"2019-07-08T17:22:56","date_gmt":"2019-07-08T09:22:56","guid":{"rendered":"https:\/\/www.agrinoon.com\/agriculture\/?p=2249"},"modified":"2019-07-08T17:22:56","modified_gmt":"2019-07-08T09:22:56","slug":"genomic-project-discovers-new-tomato-genes","status":"publish","type":"post","link":"https:\/\/www.agrinoon.com\/agriculture\/2019\/07\/08\/genomic-project-discovers-new-tomato-genes\/","title":{"rendered":"Genomic project discovers new tomato genes"},"content":{"rendered":"<div><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter\" src=\"https:\/\/img.agropages.com\/UserFiles\/FCKFile\/zkc_2019-07-08_08-26-38_604.jpg\" alt=\"\" width=\"600\" height=\"314\" \/><\/div>\n<p><em>Molecular biologist James Giovannoni of the U.S. Department of Agriculture\u2019s Plant, Soil and Nutrition Research Laboratory in Ithaca, New York, studies how fruit ripening is controlled genetically in tomatoes. | USDA photo<br \/>\n<\/em><\/p>\n<div>Previously unknown genes, including some for flavour, were missing from the original genome map done in 2012<\/div>\n<div><\/div>\n<div>If you think that store-bought tomatoes lack flavor and sweetness, you\u2019re not alone. It\u2019s been a complaint of consumers for years.<\/div>\n<div><\/div>\n<div>But now, scientists at the U.S. Department of Agriculture\u2019s Agricultural Research Service may have found the solution by developing the tomato pan-genome.<\/div>\n<div><\/div>\n<div>\n<p>A genome is the reference map for an organism\u2019s genes and what those genes do. A genome profiles a single variety of a plant or a single species of animal. However, the tomato pan-genome includes all the genes from 725 different cultivated and closely related wild tomatoes.<\/p>\n<div>The study revealed 4,873 unknown genes \u2014 including genes for flavour \u2014 that were absent from the original genome reference.<\/div>\n<div><\/div>\n<div>Tomatoes originated in the Andean region of South America. They have undergone hundreds of years of domestication and the breeding of so many cultivars with physical and metabolic variations has enhanced yield, shelf life, disease resistance, and stress tolerance. But it has resulted in severe genetic bottlenecks with today\u2019s tomatoes having a narrow genetic base.<\/div>\n<div><\/div>\n<div>\u201cThe pan-genome effort was driven by a desire to capture what was missed in sequencing a single reference genome,\u201d said molecular biologist James Giovannoni with the ARS Plant, Soil and Nutrition Research Laboratory in Ithaca, New York.<\/div>\n<div><\/div>\n<div>The tomato genome was sequenced in 2012 by an international consortium. That identified a large number of genes, but it led to the loss of some of the genes\u2019 underlying important variations. Pan-genome, however, is a composite genome from sequencing more than 700 tomato varieties, including wild relatives, early domesticates, heirloom types and modern varieties.<\/div>\n<div><\/div>\n<div>\u201cWe are interested in fruit ripening; how it is controlled genetically and how it brings about desirable flavour and nutrient characteristics of the fruit,\u201d said Giovannoni. \u201cTomato is considered a \u2018model\u2019 system for fruit biology due to a number of features that make it easy to work with. We assumed that important genes associated with ripening and quality would be found as these characteristics vary so much among varieties and gene variation must underlie some of this. We did not specifically expect to identify flavour genes nor those that influence flavour via aroma, as was the case, but we did hope to find interesting fruit quality associated genes.\u201d<\/div>\n<div><\/div>\n<div>Giovannoni said the reference tomato genome revealed 35,000 genes. The tomato is highly inbred, so they anticipated finding less novelty. In addition, the domesticated tomato is somewhat narrow in terms of what germplasm has been used in breeding. Much of what has been bred until recently reflected the relatively small number of varieties brought back to Europe by the Spanish in the 1500s.<\/div>\n<div><\/div>\n<div>\u201cWe did not know what to expect but an increase of 15 percent (some 5,000 new genes for a 35,000 gene reference) was not surprising,\u201d he said.<\/div>\n<div><\/div>\n<div>He said the classes of genes that emerged would be valuable to breeders.<\/div>\n<div><\/div>\n<div>\u201cThe most prevalent class of novel genes are potentially related to disease resistance,\u201d he said.<\/div>\n<div><\/div>\n<div>More research is necessary to be sure but this group of genes could become very helpful in reducing crop loss, cost of pesticides and other disease issues, he said.<\/div>\n<div><\/div>\n<div>He said at least 12 wild tomato species are interfertile and the modern tomato (Solanum lycopersicum) resulted from the domestication of one of them (Solanum pimpinellifolium), which was the only red-fruited wild species. They served as the basis for much tomato breeding until, in the mid 1900s, breeders revisited the wild species in search of genetic resistance to tomato diseases.<\/div>\n<div><\/div>\n<div>\u201c(Now) breeders can use the pan-genome as a resource in determining what additional varieties to test for certain traits and the genes that underlie them, which could be easily selected using modern molecular breeding,\u201d he said.<\/div>\n<div><\/div>\n<div>The researchers focused on finding genes absent from the reference genome but prevalent in the additional genes analyzed. One that is relatively rare in modern tomatoes is a variant version of TomLOXc. This gene breaks down fats into compounds that are volatile (gaseous) with aromas influencing flavours.<\/div>\n<div><\/div>\n<div>\u201cWe showed that the presence of this gene variant also results in the conversion of carotenoids into aroma compounds that influence flavour,\u201d he said. \u201cThe enzyme encoded by this gene likely does not metabolize carotenoids directly. Rather, we suspect the intermediates of lipid (fat) metabolism act on the carotenoids to convert them to the volatile apocarotenoids. Interestingly, this gene is prevalent in wild tomatoes but nearly absent in older varieties and likely unintentionally lost during breeding when focusing on other traits like yield, disease resistance and shelf life. But it seems to be making a resurgence in more modern varieties roughly in parallel with the timing of more interest in flavour by consumers.\u201d<\/div>\n<div><\/div>\n<div>He said that knowing the gene that underlies a trait makes it easier to breed for because breeders can use molecular diagnostics to select for the gene.<\/div>\n<div><\/div>\n<div>Why the desired qualities of sweetness and flavour were lost in the first place was more by accident than design in breeders\u2019 pursuit of shelf life and firmness to meet supply chain demands. In addition, that desirable gene may have been linked to others with undesirable effects related to plant performance, yield or characteristics.<\/div>\n<div>\n<div class=\"tl clearfix mt10\">\n<h4 class=\"p-source c-999 cb pt5\"><span style=\"color: #000000;\"><strong>Source<\/strong>:\u00a0<a class=\"c-orange fs16\" style=\"color: #000000;\" href=\"http:\/\/news.agropages.com\/Media\/MediaIndex-1262.htm\" target=\"_blank\" rel=\"noopener noreferrer\">THE WESTERN PRODUCER<\/a><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Molecular biologist James Giovannoni of the U.S. Department of Agriculture\u2019s Plant, Soil and Nutrition Research Laboratory in Ithaca, New York, studies how fruit ripening is controlled genetically in tomatoes. | USDA photo Previously unknown genes, including some for flavour, were missing from the original genome map done in 2012 If you think that store-bought tomatoes&hellip; <a class=\"more-link\" href=\"https:\/\/www.agrinoon.com\/agriculture\/2019\/07\/08\/genomic-project-discovers-new-tomato-genes\/\">Continue reading <span class=\"screen-reader-text\">Genomic project discovers new tomato genes<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[17],"tags":[],"class_list":["post-2249","post","type-post","status-publish","format-standard","hentry","category-industry-news","entry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Genomic project discovers new tomato genes - agrinoon<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.agrinoon.com\/agriculture\/2019\/07\/08\/genomic-project-discovers-new-tomato-genes\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Genomic project discovers new tomato genes - agrinoon\" \/>\n<meta property=\"og:description\" content=\"Molecular biologist James Giovannoni of the U.S. Department of Agriculture\u2019s Plant, Soil and Nutrition Research Laboratory in Ithaca, New York, studies how fruit ripening is controlled genetically in tomatoes. | USDA photo Previously unknown genes, including some for flavour, were missing from the original genome map done in 2012 If you think that store-bought tomatoes&hellip; 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