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Background  Many previous studies have shown that soybean WRKY transcription factors are involved in the plant response to biotic and abiotic stresses.  Phakopsora pachyrhizi  is the causal agent of Asian Soybean Rust, one of the most important soybean diseases. There are evidences that WRKYs are involved in the resistance of some soybean genotypes against that fungus. The number of  WRKY  genes already annotated in soybean genome was underrepresented. In the present study, a genome-wide annotation of the soybean WRKY family was carried out and members involved in the response to  P. pachyrhizi  were identified.    Results  As a result of a soybean genomic databases search, 182  WRKY -encoding genes were annotated and 33 putative pseudogenes identified. Genes involved in the response to  P. pachyrhizi  infection were identified  using  superSAGE, RNA-Seq of microdissected lesions and microarray experiments. Seventy-five genes were differentially expressed during fungal infection. The expression of eight  WRKY  genes was validated by RT-qPCR. The expression of these genes in a resistant genotype was earlier and / or stronger compared with a susceptible genotype in response to  P. pachyrhizi  infection. Soybean somatic embryos were transformed in order to overexpress or silence  WRKY  genes. Embryos overexpressing a  WRKY  gene were obtained, but they were unable to convert into plants. When infected with  P. pachyrhizi , the leaves of the silenced transgenic line showed a higher number of lesions than the wild-type plants .Conclusions  The present study reports a genome-wide annotation of soybean WRKY family. The participation of some members in response to  P. pachyrhizi  infection was demonstrated. The results contribute to the elucidation of gene function and suggest the manipulation of WRKYs as a strategy to increase fungal resistance in soybean plants.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-014-0236-0) contains supplementary material, which is available to authorized users.

Genome-wide annotation of the soybean WRKY family and functional characterization of genes involved in response to Phakopsora pachyrhiziinfection