About VfODB

Faba bean (Vicia faba L.) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibers. 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. Besides, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps.

Collectively, we developed 31536 EST markers, 9071 EST-SSR markers and 3023 microRNA-targets 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 101 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, RGA, SCAR, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. Also, VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets.

     We expect that VfODB will serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

Transcriptome-based markers

Vicia faba RefTrans V2 (37,378 sequences) was subjected to Primer3 software in order to develop transcriptome-wide EST markers and were combined with their annotation information and classified into one of the following classes: 1) EST primers with general annotation, 2) EST primers with gene-ontology, and 3) EST primers assigned to certain enzymes.

Also, for EST-SSR markers development, the Vicia faba RefTrans V2 was analyzed using the MISA tool to identify the sequences containing SSR motifs, which were consequently extracted and subjected to Primer3 software to develop EST-SSR markers. These markers were subsequently combined with their annotation information and also classified into three classes: 1) EST-SSR primers with general annotation, 2) EST-SSR primers with gene-ontology, and 3) EST-SSR primers assigned to certain enzymes.

Mitochondrial-based markers


Vicia faba mitochondrial genome was analyzed in terms of microsatellites identification, classification and marker development. The workflow of analysis was done in five main steps, as follows: (a) detection of SSR motifs on the genome-scale; (b) classifying identified SSR motifs into non-genic or genic according to their location within the genome; (c) designing SSR primers and developing markers; (e) organizing and integrating developed SSR markers as well as their associated information into the VfODB database; and (f) implementing all generated datasets into the VfODB web interface

Genetic maps-based markers


We downloaded all previously developed and published genetic linkage maps of Vicia faba. All available information of mapped markers on these maps were manually curated and categorized according to their type. In case that markers sequence was available such as SNP markers sequence, these sequences were further curated and aligned against the NCBI GenBank database by using blastx tool to determine its corresponding protein

KEGG pathway-based markers


The developed EST and EST-SSR markers (assigned to enzymes) were further mapped against the KEGG pathways database to build Vicia faba functional maps. Each map contains; Pathway ID, Pathway image, mapped enzymes ID (highlighted), mapped enzymes associated primer/marker, marker annotation information and all other information related to this primer (Tm, GC%, Length, …etc.). All generated maps were finalized in a user-friendly attractive form.


Vicia faba mitochondria available in NCBI GenBank database (Accession number: KC189947)


Vicia fabatranscriptome version 2 was downloaded from Pulse Crop Database


Previously published Genetic Maps available in PubMed and Google Scholar till 2020


Our developed markers were further mapped against the KEGG pathways to build V. faba functional maps


We provide users with preliminary information about most of the faba bean germplasm available worldwide and listed in IPK Genebank and Genesys databases