Abstract

Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

中文翻译：

---

VfODB：蚕豆中EST，EST-SSR，mtSSR，microRNA靶标和遗传图谱的综合数据库

摘要

蚕豆（Vicia faba）由于其蛋白质和纤维含量高，是全世界必不可少的食品和饲料豆类作物。分子标记工具代表着蚕豆育种者快速改善作物的宝贵工具。尽管历史上很少有蚕豆基因组资源，但是已经发布了一些转录组和线粒体基因组序列数据。这些数据以及以前开发的遗传连锁图谱为开发可加速蚕豆育种计划的功能标记和图谱提供了重要资源。在这里，我们介绍了蚕豆蚕豆Omics数据库（VfODB）作为整合种质信息，蚕豆中表达序列标签（EST），表达序列标签-简单序列重复（EST-SSR）和线粒体-简单序列重复（mtSSR），microRNA靶标和遗传图谱的综合数据库。此外，基于KEGG途径的标记和功能图已集成为一类新的基于注释的标记/图。总的来说，我们开发了31个536 EST标记，9071 EST-SSR标记和3023的microRNA靶标记基于蚕豆RefTrans V2挖掘。通过将7940 EST和2282 EST-SSR标记与KEGG通路数据库作图，我们成功开发了107个功能图。此外，基于线粒体基因组挖掘，开发了40个mtSSR标记。在数据管理水平上，我们检索了3461个标记，它们代表12种类型的标记（CAPS，EST，EST-SSR，基因标记，INDEL，同工酶，ISSR，RAPD，SCAR，RGA，SNP和SSR），它们映射在18 V上。蚕豆遗传连锁图谱。Vf ODB提供了两个用户友好的工具来识别，分类SSR主题和计算机模拟扩增其目标。Vf ODB可以作为蚕豆研究社区以及对基因组辅助育种感兴趣的育种者的强大数据库和有用平台。