Transcriptomic Analysis of Partial Resistance Against Sclerotinia sclerotiorum in Soybeans.

Sclerotinia sclerotiorum is one of the most devastating and cosmopolitan plant pathogens and the causal agent of Sclerotinia stem rot (SSR) in soybean. No source of complete resistance has been described against this pathogen in soybean; however, a number of studies including identification of QTL for partial resistance, introduction of oxalic acid degrading enzymes into soybean germplasm and functional genomics analyses have offered insights into the quantitative nature of the resistance. Two soybean cultivars, susceptible OAC Shire and partially-resistant OAC Salem were studied for genome-wide gene expression using RNA-Sequencing at early to advanced and late stages of infection with S. sclerotiorum. Differentially expressed genes were classified into functional categories and pathways and analyzed for differences in the transcriptomic profiles of the two lines. A total of 2316 genes were found differentially expressed in at least one of the treatments use of which 712 were up-regulated whereas 1604 were down-regulated. Genes related to PAMP-triggered Immunity (PTI) were identified, including receptor-like kinases, respiratory burst oxidases and mitogen activated protein kinases. In addition, other genes related to such as peroxidases, PR proteins, PGIPs, lignin and jasmonic acid/ ethylene biosynthesis and regulation were differentially expressed as well. In general, we found several mechanisms related to defense responses that were activated in both cultivars at similar times during the experiment. However, for the susceptible line, a transient activation of defense mechanisms is observed only at 3 days post inoculation (dpi) with a shutdown of several processes at 5 dpi while the activation of those responses was stronger and remained steady in the partially-resistant line up to 5 dpi. These results obtained may contribute to the understanding of the plant defense mechanisms against necrotrophic pathogens and the development of strategies to incorporate partial resistance to SSR into commercial soybean cultivars and possibly other crops affected by this pathogen.