Faba bean (Vicia faba L.) is an important temperate legume, grown for human consumption and animal feed due to its high protein and fibre content [1, 2]. The crop also replaces available nitrogen in the soil when used in rotation with cereals and oilseeds, and thus is expected to be a highly beneficial component in future temperate Low Carbon Agricultural systems. China is the largest faba bean producer (40.36%) with an average dry grain production (2005–2009) of 1,720,000 metric tonnes (mt) from 945,400 hectares; followed by Ethiopia (476,026 mt), France (331,122 mt), Egypt (274,040 mt) and Australia (196,800 mt) .
However, faba bean suffers from several major biotic and abiotic factors that constrain productivity. Although significant genetic gain to overcome these has been made through traditional breeding practices , progress through the use of genomics and associated biotechnologies is limited. This is due mainly to the large genome size (13GB; ), which is approximately 25 times larger than that of the model legume Medicago truncatula, and 2.5 times larger than Pisum sativum, together with a lack of financial investment in this crop species.
Recent advances in next generation sequencing (NGS) technologies enable the generation of large volumes of sequence efficiently and cost-effectively [5, 6]. This has led to a revolution in biological and agricultural applications including identification of genes correlated with key breeding traits through high-density SNP marker and genome-wide association analysis studies (GWAS) [7, 8]. Another outcome is the ability to accurately identify sequences flanking simple sequence repeat (SSR) regions for use as locus-specific markers for downstream genotyping. Otherwise known as microsatellites, SSRs are tandemly repeated motifs of 1 to 6 nucleotides found in both coding and non-coding regions [9, 10]. These have become a marker of choice in many genotyping applications due to their relatively high abundance, high level of allelic variation, co-dominant inheritance, analytical simplicity and transferability of results across laboratories .
A limited number of characterized SSR loci (<120) which have been validated over relatively few genetic backgrounds are available for faba bean. Initially, Pozarkova et al. developed primers to 25 SSR loci detected in chromosome 1 DNA libraries . Subsequently, Zeid et al. developed primers to 54 SSR loci  and Gong et al. developed 11 EST-SSR loci primers . Most recently, EST sequences within the public domain databases were screened and an additional 21 novel SSR loci were characterized and validated among 32 faba bean accessions .
Besides providing a cost-effective valuable source for molecular marker generation, the identification of SSR within ESTs is an effective approach for gene discovery and transcript pattern characterization, particularly if through mapping an EST-SSR or EST marker is significantly associated with a QTL [16–18]. This may be achieved by searching for SSR associated sequences within EST of a well characterised crop or model plant species. Together with the advantage of in silico analysis, this approach has the potential to substantially broaden the field of comparative studies to species where limited or no sequence information is available.
The present study identified high-quality putative SSR loci and flanking primer sequences cheaply and efficiently using the Roche 454 GS FLX Titanium platform. The resultant SSR sequences were characterized and validated through successful amplification of randomly selected target loci across a selection of faba bean genotypes from diverse geographic origin.