First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification
First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification
复制标题
DOI：
10.1186/1471-2229-13-197
复制
发表时间：
2013-12-04
影响因子：
5.3
通讯作者：
Kumar D
中科院分区：
文献类型：
--
作者：
Iquebal MA; S;Arora V;Verma N;Rai A;Kumar D
栽培番茄是世界上消费量第二大的蔬菜，并且是多样化和均衡饮食的重要组成部分，作为具有抗癌特性的维生素、矿物质、酚类抗氧化剂和抗氧化剂番茄红素的丰富来源。为使国产番茄基因组学研究取得更大的效益，由番茄基因组联盟（The Tomato Genome Consortium）（The Tomato Genome Consortium，2012）揭示的，其标记的整体批量挖掘是必要的并且是关键需要的。茄基因组学研究中发现的茄科微卫星DNA标记数量有限（2867个）。由于这些标记属于具有相对距离的连锁图谱，因此缺少基于物理图谱的绝对距离选择标记。微卫星标记在品种鉴定中的应用有限，存在一定的局限性，需要更多的微卫星标记作为DUS检测的补充，同时也需要对全球市场的产品进行溯源。我们在这里介绍了第一个基于全基因组的番茄微卫星DNA标记数据库，TomSatDB（番茄微卫星数据库）与超过140万个标记，在硅片上挖掘，使用微卫星（MISA）工具。为了满足湿实验室的定制需求，添加了自动引物设计工具的新奇。TomSatDB（http：//cabindb.iasri.res.in/tomsatdb）是一种用户友好且可免费访问的工具，提供引物的染色体和位置搜索。它是一个基于“三层结构”的在线关系数据库，在MySQL中编目微卫星信息，并使用PHP（超文本预处理器）开发用户友好的界面。除非生物胁迫外，番茄还具有生物胁迫，这是由于其对由病原真菌、细菌、病毒和线虫引起的200多种疾病的敏感性。这些标记有望为非生物和生物胁迫下的种质管理以及通过分子育种进行改良铺平道路，从而提高印度和世界其他地区的番茄产量。在知识产权时代，可以根据品种间的等位变异来鉴定新品种，补充DUS检测和产品溯源。
The cultivated tomato is second most consumed vegetable of the world and is an important part of a diverse and balanced diet as a rich source of vitamins, minerals, phenolic antioxidants and antioxidant lycopene having anti-cancer properties. To reap benefit of genomics of the domestic tomato (Solanum lycopersicum L.) unravelled by Tomato Genome Consortium (The Tomato Genome Consortium, 2012), the bulk mining of its markers in totality is imperative and critically required. The solgenomics has limited number of microsatellite DNA markers (2867) pertaining to solanaceae family. As these markers are of linkage map having relative distance, the choice of selected markers based on absolute distance as of physical map is missing. Only limited microsatellite markers with limitations are reported for variety identification thus there is a need for more markers supplementing DUS test and also for traceability of product in global market. We present here the first whole genome based microsatellite DNA marker database of tomato, TomSatDB (Tomato MicroSatellite Database) with more than 1.4 million markers mined in-silico, using MIcroSAtellite (MISA) tool. To cater the customized needs of wet lab, features with a novelty of an automated primer designing tool is added. TomSatDB (http://cabindb.iasri.res.in/tomsatdb), a user-friendly and freely accessible tool offers chromosome wise as well as location wise search of primers. It is an online relational database based on “three-tier architecture” that catalogues information of microsatellites in MySQL and user-friendly interface developed using PHP (Hypertext Pre Processor). Besides abiotic stress, tomato is known to have biotic stress due to its susceptibility over 200 diseases caused by pathogenic fungi, bacteria, viruses and nematodes. These markers are expected to pave the way of germplasm management over abiotic and biotic stress as well as improvement through molecular breeding, leading to increased tomato productivity in India as well as other parts of the world. In era of IPR the new variety can be identified based on allelic variation among varieties supplementing DUS test and product traceability.
登录
查看更多内容
影响因子：
2.3
作者：
Kolmer, J. A.;Anderson, J. A.;Flor, J. M.
通讯作者：
Flor, J. M.
影响因子：
2.9
作者：
Archak, Sunil;Lakshminarayanareddy, V.;Nagaraju, Javaregowda
通讯作者：
Nagaraju, Javaregowda
影响因子：
12.3
作者：
Ranjan, Aashish;Ichihashi, Yasunori;Sinha, Neelima R.
通讯作者：
Sinha, Neelima R.
影响因子：
--
作者：
Karakousis, A;Barr, AR;Langridge, P
通讯作者：
Langridge, P
影响因子：
5.4
作者：
Seyfarth, R;Feuillet, C;Keller, B
通讯作者：
Keller, B