Comparative transcriptome of soybean interactions with pathogenic and non-pathogenic isolates of Fusarium oxysporum.

Fusarium oxysporum is one of the most common species causing soybean root rot and\r\nseedling blight in the U.S. In a recent study, significant variation in aggressiveness was observed\r\namong isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to\r\nweakly or non-pathogenic isolates. In the present work, a RNA-seq-based analysis was used for the\r\nfirst time to investigate the molecular aspect of the interaction of a partially resistant soybean\r\ngenotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 hours post\r\ninoculation (hpi). Markedly different gene expression profiles were observed in compatible and\r\nincompatible host-pathogen combinations. A peak of differentially expressed genes (DEGs) was\r\nobserved at 72 hpi in soybean roots in response to both isolates, although the number of DEGs was\r\nabout eight times higher for the pathogenic isolate compared to the non-pathogenic one (1,659 vs.\r\n203 DEGs, respectively). Furthermore, not only the number of genes, but also the magnitude of\r\ninduction was much greater in response to the pathogenic isolate. This response included a stronger\r\nactivation of many well-known defense-related genes, and several genes involved in ethylene\r\nbiosynthesis and signalling, transcription factors, secondary and sugar metabolism. In addition,\r\n1130 fungal genes were differentially expressed between the F. oxysporum isolates in planta during\r\nthe infection process. Interestingly, 10% of these genes encode plant cell-wall degrading enzymes,\r\nreactive oxygen species-related enzymes and fungal proteins involved in primary metabolic\r\npathways. These results may be useful to understand the molecular basis of soybean-F. oxysporum\r\ninteractions, and also in the development of new resistance mechanisms in soybean against F.\r\noxysporum, including the silencing of important fungal genes.