Details

Autor(en) / Beteiligte

• Mokhtar, Morad M
• Hussein, Ebtissam H A
• El-Assal, Salah El-Din S
• Atia, Mohamed A M
• Buckley, Tom

Titel

Vf ODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

Ist Teil von

• AoB plants, 2020-12, Vol.12 (6), p.plaa064

Ort / Verlag

England

Erscheinungsjahr

2020

Link zum Volltext

Quelle

Free E-Journal (出版社公開部分のみ）

Beschreibungen/Notizen

• 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.