Gene co-expression analysis reveals conserved and distinct gene networks between resistant and susceptible Lens ervoides challenged by hemibiotrophic and necrotrophic pathogens

As field crops are likely to be challenged by multiple pathogens during their development, the investigation of broad-spectrum resistance in the host is of great interest for crop genetic enhancement. In this study, we attempted to address this question by adopting a weighed gene co-expression approach to study the temporal transcriptome dynamics of resistant and susceptible recombinant inbred lines (RILs) derived from an intraspecific Len ervoides cross during the infection process with either the necrotrophic pathogens Ascochyta lentis or Stemphylium botryosum, or the hemibiotrophic pathogen Colletotrichum lentis. By comparing networks of resistant and susceptible RILs, seven network module pairs were found to possess high correlation coefficients (R > 0.70) and large number of overlapping genes (n > 100). The conserved co-regulation of genes in these network module pairs were involved in plant cell wall synthesis, cell division, cytoskeleton organization, and protein ubiquitin related processes and appeared to be common disease responses against these pathogens. On the other hand, we also identified eight modules with low correlation between resistance and susceptibility networks. Among those, a stronger gene co-expression in R-genes and small RNA processes in the resistant hosts may be enhancing L. ervoides resistance against A. lentis, C. lentis, and S. botryosum, whereas the higher level of synergistic regulation in the synthesis of arginine and glutamine and phospholipid and glycerophospholipids in the susceptible hosts may contribute to increased susceptibility in L. ervoides.