TriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae
TriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae
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DOI：
10.1186/1471-2229-8-72
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发表时间：
2008-06-30
影响因子：
5.3
通讯作者：
Shinozaki, Kazuo
中科院分区：
文献类型：
--
作者：
Mochida, Keiichi;Saisho, Daisuke;Shinozaki, Kazuo
背景资料：近年来，各种作物物种序列资源的快速积累，保证了遗传学方法的改进，包括数量性状基因座（QTL）分析以及整体群体分析和自然变异的关联作图。由于部落小麦族包括重要的谷物，如小麦和大麦，在这些作物的遗传标记信息的整合应有效地加速基于图的遗传研究小麦族物种，并导致发现关键基因座参与植物生产力，这可以有助于可持续的粮食生产。因此，需要信息学应用和全基因组标记的语义知识库来整合小麦和大麦遗传标记的信息和进一步开发，以推进小麦族物种的常规标记辅助遗传分析和群体基因组学。小麦族映射表达序列标签（EST）数据库（TriMEDB）提供信息，沿着各种注释，关于与大麦及其小麦同源物相关的定位cDNA标记。TriMEDB的最新版本提供了大麦和小麦EST的定位数据，这些数据来自3个已发表的大麦连锁图谱（苏格兰作物研究所的大麦单核苷酸多态性数据库、莱布尼茨植物遗传学和作物研究所的大麦转录图谱和HarvEST大麦版本）。1.63）和1张小麦二倍体图谱。这些数据被导入到CMap中，以使EST的图谱位置以及这些EST与公共基因模型和代表性cDNA序列的相互关系可视化。将检索到的每个EST标记对应的cDNA序列分配到水稻基因组中，以预测外显子-内含子结构。此外，为了在小麦族植物的公共域中产生一组独特的EST标记，将3472个标记组装成2737个独特的标记群作为重叠群。这些重叠群应用于从不同EST图谱资源获得的连锁图谱之间的成对比较。结论：TriMEDB提供了关于转录遗传标记的信息，并作为语义知识库的功能，为加速QTL分析和小麦族群体遗传学研究提供了信息学工具。
Background: The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach, including quantitative trait loci (QTL) analysis as well as the holistic population analysis and association mapping of natural variations. Because the tribe Triticeae includes important cereals such as wheat and barley, integration of information on the genetic markers in these crops should effectively accelerate map-based genetic studies on Triticeae species and lead to the discovery of key loci involved in plant productivity, which can contribute to sustainable food production. Therefore, informatics applications and a semantic knowledgebase of genome-wide markers are required for the integration of information on and further development of genetic markers in wheat and barley in order to advance conventional marker-assisted genetic analyses and population genomics of Triticeae species.Description: The Triticeae mapped expressed sequence tag (EST) database (TriMEDB) provides information, along with various annotations, regarding mapped cDNA markers that are related to barley and their homologues in wheat. The current version of TriMEDB provides map-location data for barley and wheat ESTs that were retrieved from 3 published barley linkage maps (the barley single nucleotide polymorphism database of the Scottish Crop Research Institute, the barley transcript map of Leibniz Institute of Plant Genetics and Crop Plant Research, and HarvEST barley ver. 1.63) and 1 diploid wheat map. These data were imported to CMap to allow the visualization of the map positions of the ESTs and interrelationships of these ESTs with public gene models and representative cDNA sequences. The retrieved cDNA sequences corresponding to each EST marker were assigned to the rice genome to predict an exon-intron structure. Furthermore, to generate a unique set of EST markers in Triticeae plants among the public domain, 3472 markers were assembled to form 2737 unique marker groups as contigs. These contigs were applied for pairwise comparison among linkage maps obtained from different EST map resources.Conclusion: TriMEDB provides information regarding transcribed genetic markers and functions as a semantic knowledgebase offering an informatics facility for the acceleration of QTL analysis and for population genetics studies of Triticeae.