Mokhtar Morad M, Hussein Ebtissam H A, El-Assal Salah El-Din S, Atia Mohamed A M
Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt.
Genetics Department, Faculty of Agriculture, Cairo University, Giza, Egypt.
AoB Plants. 2020 Nov 29;12(6):plaa064. doi: 10.1093/aobpla/plaa064. eCollection 2020 Dec.
Faba bean () 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 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 Omics database (ODB) 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 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 genetic linkage maps. ODB provides two user-friendly tools to identify, classify SSR motifs and amplify their targets. ODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.
蚕豆（）因其高蛋白和纤维含量，是全球重要的食用和饲料豆类作物。分子标记工具是蚕豆育种者实现作物快速改良的宝贵工具。尽管历史上可用的基因组资源很少，但已发布了一些转录组和线粒体基因组序列数据。这些数据以及先前开发的遗传连锁图谱是开发功能标记和图谱的重要资源，可加速蚕豆育种计划。在此，我们展示了蚕豆组学数据库（ODB），这是一个综合数据库，整合了种质信息、表达序列标签（EST）、表达序列标签-简单序列重复（EST-SSR）、线粒体简单序列重复（mtSSR）、微小RNA靶标标记和遗传图谱。此外，基于KEGG通路的标记和功能图谱作为一类新型的基于注释的标记/图谱被整合进来。我们基于RefTrans V2挖掘共开发了31536个EST标记、9071个EST-SSR标记和3023个微小RNA靶标标记。通过将7940个EST和2282个EST-SSR标记映射到KEGG通路数据库，我们成功开发了107个功能图谱。同时，基于线粒体基因组挖掘开发了40个mtSSR标记。在数据整理层面，我们检索到3461个代表12种标记类型（CAPS、EST、EST-SSR、基因标记、插入缺失、同工酶、ISSR、RAPD、SCAR、RGA、SNP和SSR）的标记，这些标记分布在18个遗传连锁图谱上。ODB提供了两个用户友好的工具来识别、分类SSR基序并扩增其靶标。ODB可以作为一个强大的数据库和有用的平台，为蚕豆研究群体以及对基因组辅助育种感兴趣的育种者提供帮助。
