Transcriptomic Analysis through RNA Sequencing of Soybean Roots and Leaves in Response to Fusarium virguliforme Infection and its Toxins

Sudden death syndrome (SDS) is caused by Fusarium virguliforme (Fv), a soil-borne fungus that colonizes soybean roots causing root rot, and also produces toxins leading to leaf scorching symptoms and defoliation. The objectives of our study were to i) characterize the defense mechanisms of soybean roots and leaves in response to Fv infection and its toxins, and ii)  determine the role of fungal toxins during the programmed cell death (PCD) that is triggered in roots and leaves upon infection by Fv. Total RNA was extracted from roots and leaves collected from same plants either at 7 day post infection (dpi) on plants infected by the pathogen or at 12 hour post treatment (hpt) on plants treated by fungal culture filtrates. A total of 48 cDNA libraries were sequenced via Illumina HiSeq2500 sequencing using a paired-end read 2x100 bp long. Data from the susceptible genotype (Essex) was compared with those from the partial resistant genotype (PI 567.374) to identify differentially expressed genes.  Comparison between transcripts induced in roots either infected by FV or treated by the fungal toxins revealed that many genes are induced by both, reflecting a potential role of the fungal toxins during the infection initiation and the development of root symptoms. Cross comparison between roots and leaves showed that genes involved in toxin induction pathways are induced in leaves, while genes involved in signaling transduction are induced in roots, suggesting different mechanisms employed by roots and leaves to fight the pathogen infection and the toxin damage. Functional annotations of unique genes from resistant genotype suggested that these genes likely encode proteins involved in cell-wall modification, detoxification, primary metabolism, scavenging the oxidative stress and membrane transport, thus suggesting multiple mechanisms might be employed by resistant leaves to reduce damage caused by Fv toxins. On the other hand, it appears that the fungal toxins manipulate the HR and SA pathway in susceptible leaves to induce host cell death in the absence of the pathogen. Genes identified in this study can be further used to develop molecular markers that would be integrated into soybean breeding programs to accelerate breeding for resistance to both root rot and Fv toxins.