Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated with pear petal defense responses against Monilinia laxa infection

Abstract

Pear brown rot and blossom blight caused by Monilinia laxa seriously affect pear production worldwide. Here, we compared the transcriptomic profiles of petals after inoculation with M. laxa using two pear cultivars with different levels of sensitivity to disease (Sissy, a relatively tolerant cultivar, and Kristalli, a highly susceptible cultivar). Physiological indexes were also monitored in the petals of both cultivars at 2 h and 48 h after infection (2 HAI and 48 HAI). RNA-seq data and weighted gene co-expression network analysis (WGCNA) allowed the identification of key genes and pathways involved in immune- and defense-related responses that were specific for each cultivar in a time-dependent manner. In particular, in the Kristalli cultivar, a significant transcriptome reprogramming occurred early at 2 HAI and was accompanied either by suppression of key differentially expressed genes (DEGs) involved in the modulation of any defense responses or by activation of DEGs acting as sensitivity factors promoting susceptibility. In contrast to the considerably high number of DEGs induced early in the Kristalli cultivar, upregulation of specific DEGs involved in pathogen perception and signal transduction, biosynthesis of secondary and primary metabolism, and other defense-related responses was delayed in the Sissy cultivar, occurring at 48 HAI. The WGCNA highlighted one module that was significantly and highly correlated to the relatively tolerant cultivar. Six hub genes were identified within this module, including three WRKY transcription factor-encoding genes: WRKY 65 (pycom05g27470), WRKY 71 (pycom10g22220), and WRKY28 (pycom17g13130), which may play a crucial role in enhancing the tolerance of pear petals to M. laxa. Our results will provide insights into the interplay of the molecular mechanisms underlying immune responses of petals at the pear–M. laxa pathosystem.

Deciphering the Interaction between Coniella granati and Pomegranate Fruit Employing Transcriptomics

“…A large repertoire of RLKs and RLPs-encoding genes involved in plant–microbe interaction, pathogen recognition, and signaling were upregulated mainly at 2 and 3 dai. Previously, RLK s, G- type LecRK s, and WAK s genes were reported to be involved in defense responses to pathogens [ 12 , 18 , 20 , 25 , 33 , 34 , 35 ]. Furthermore, CRK s, PERK s, and CDPK s genes are related to immune signaling pathways, acting as plant defense regulators [ 36 ].…”

“…TFs such as those of ERF, WRKY, MYB, bHLH, and ZFP families play a key role in the regulation of defense mechanisms [ 12 , 18 , 20 , 37 ]. Regarding C. granati infection, a large set of TFs were induced over the inoculation period.…”

“…Furthermore, MMPs, belonging to the PR-10 family and considered as multifunctional effector components involved in pivotal regulatory roles in defense homeostasis [ 12 , 45 ], were constitutively upregulated at 2 and 3 dai. It is known that an MMP protein is required for resistance against B. cinerea in tomato [ 46 ], whereas activation of members of the PR-10 family suggest a further enhancement of the JA-mediated transduction of defense signaling and activation of flavonoid biosynthesis [ 20 , 44 ]. However, at these time points, BAP genes were upregulated; these are negative regulators of immune reactions [ 47 ], indicating suppression of defense responses and promoting susceptibility as a result of pathogen expansion.…”

“…Notably, a cytokinin dehydrogenase (CKX)-encoding gene was found to be upregulated at 3 dai. These genes are related with resistance to pathogens [ 51 ], whereas a CKX gene has been assigned as the main hub gene related to the induced tolerance of pear petals against Monilinia laxa [ 20 ]. This finding further suggests that indeed pomegranate defense responses are induced in delay.…”

“…Nowadays, by employing state of the art next generation sequencing (NGS) platforms, such as Illumina and Single-molecule real-time (SMRT), sequencing, costs are declining and RNA-seq technology is becoming more practical [ 16 , 17 ]. However, although such approaches were recently employed on fruits and petals of other deciduous trees in order to decipher the defense responses against fungal infections [ 18 , 19 , 20 ], there is still a research gap in transcriptional profiles of pomegranate fruits upon their challenge with C. granati .…”