High-throughput developing novel microsatellite marker of faba bean via next generation sequencing
Background  Faba bean (Vicia faba L.) is an important food legume crop, grown for human  consumption globally including in China, Turkey, Egypt and Ethiopia. Although genetic  gain has been made through conventional selection and breeding efforts, this could be  substantially improved through the application of molecular methods. For this, a set of  reliable molecular markers representative of the entire genome is required.  Results  A library with 125,559 putative SSR sequences was constructed and characterized for  repeat type and length from a mixed genome of 247 spring and winter sown faba bean  genotypes using 454 sequencing. A suit of 28,503 primer pair sequences were designed  and 150 were randomly selected for validation. Of these, 94 produced reproducible  amplicons that were polymorphic among 32 faba bean genotypes selected from diverse  geographical locations. The number of alleles per locus ranged from 2 to 8, the expected  heterozygocities ranged from 0.0000 to 1.0000, and the observed heterozygosities ranged  from 0.0908 to 0.8410. The validation by UPGMA cluster analysis of 32 genotypes based  on Nei's genetic distance, showed high quality and effectiveness of those novel SSR  markers developed via next generation sequencing technology.  Conclusions  Large scale SSR marker development was successfully achieved using next generation  sequencing of the V. faba genome. These novel markers are valuable for constructing  genetic linkage maps, future QTL mapping, and marker-assisted trait selection in faba  bean breeding efforts.