Abstract
BackgroundPlant–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.ResultsWe 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.ConclusionsOur 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 materialThe online version of this article (doi:10.1186/s12870-014-0300-9) contains supplementary material, which is available to authorized users.
Highlights
Plant–parasitic nematodes (PPNs) are obligate parasites that feed on the roots of living host plants
Illumina sequencing and read alignment cDNA libraries from soybean roots were generated after independently inoculating roots for both 6 and 8 dai in two soybean cyst nematode (SCN) populations, NH1-RHg and TN8
Using the BWA aligner [9], quality reads were mapped against the soybean transcriptome build version 1.1 [10]
Summary
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. 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. Obligate parasites, such as plant–parasitic nematodes (PPNs), are infamously known for their ability to suppress host defense mechanisms and cripple yield of many agricultural crops. Fueled by the economic impact of SCN infestations, numerous studies have utilized NGS assays to sequence and quantify the soybean transcriptome [5,6,7,8]
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