Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction

BACKGROUND: Plant–parasitic nematodes (PPNs) are obligate parasites that feed on the roots of living host plants. Often, these nematodes can lay hundreds of eggs, each capable of surviving without a host for as long as 12 years. When it comes to wreaking havoc on agricultural yield, few nematodes can compare to the soybean cyst nematode (SCN). Quantifying soybean (Glycine max) transcription factor binding sites (TFBSs) during a late–stage SCN resistant and susceptible reaction can shed light onto the systematic interplay between host and pathogen, thereby elucidating underlying cis–regulatory mechanisms. RESULTS: We sequenced the soybean root transcriptome at 6 and 8 days upon independent inoculation with a virulent and avirulent SCN population. Genes such as β–1,4 glucanase, chalcone synthase, superoxide dismutase and various heat shock proteins (HSPs) exhibited reaction–specific expression profiles. Several likely defense–response genes candidates were also identified which are believed to confer SCN resistance. To explore magnitude of TFBS representation during SCN pathogenesis, a multivariate statistical software identified 46 over–represented TFBSs which capture soybean regulatory dynamics across both reactions. CONCLUSIONS: Our results reveal a set of soybean TFBSs which are over–represented solely throughout a resistant and susceptible SCN reaction. This set furthers our understanding of soybean cis–regulatory dynamics by providing reaction–specific levels of over–representation at 6 and 8 days after inoculation (dai) with SCN. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-014-0300-9) contains supplementary material, which is available to authorized users.