Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopy

Abstract

Smut caused by biotrophic fungus Sporisorium scitamineum is a major disease of cultivated sugarcane that can cause considerable yield losses. It has been suggested in literature that there are at least two types of resistance mechanisms in sugarcane plants: an external resistance, due to chemical or physical barriers in the sugarcane bud, and an internal resistance governed by the interaction of plant and fungus within the plant tissue. Detailed molecular studies interrogating these two different resistance mechanisms in sugarcane are scarce. Here, we use light microscopy and global expression profiling with RNA-seq to investigate these mechanisms in sugarcane cultivar CP74-2005, a cultivar that possibly possesses both internal and external defence mechanisms. A total of 861 differentially expressed genes (DEGs) were identified in a comparison between infected and non-infected buds at 48 hours post-inoculation (hpi), with 457 (53%) genes successfully annotated using BLAST2GO software. This includes genes involved in the phenylpropanoid pathway, cell wall biosynthesis, plant hormone signal transduction and disease resistance genes. Finally, the expression of 13 DEGs with putative roles in S. scitamineum resistance were confirmed by quantitative real-time reverse transcription PCR (qRT-PCR) analysis, and the results were consistent with the RNA-seq data. These results highlight that the early sugarcane response to S. scitamineum infection is complex and many of the disease response genes are attenuated in sugarcane cultivar CP74-2005, while others, like genes involved in the phenylpropanoid pathway, are induced. This may point to the role of the different disease resistance mechanisms that operate in cultivars such as CP74-2005, whereby the early response is dominated by external mechanisms and then as the infection progresses, the internal mechanisms are switched on. Identification of genes underlying resistance in sugarcane will increase our knowledge of the sugarcane-S. scitamineum interaction and facilitate the introgression of new resistance genes into commercial sugarcane cultivars.

Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans

“…Recently, this technology has been used to identify the molecular mechanisms triggering the response of sugarcane to infection by various pathogens. For example, the transcriptome analysis of susceptible sugarcane cultivars in response to Sugarcane streak mosaic virus and Sorghum mosaic virus have been investigated by Dong et al (2017) [16] and Ling et al (2018) [17], respectively; major genes and pathways that were triggered in sugarcane infected by pathogenic fungi, such as Colletotrichum falcatu causing red rot [18], Sporisorium scitamineum causing smut [19,20], and Fusarium verticillioides associated with pokkah boeng [21], have also been identified. Additionally, transcriptome analysis studies depicted the sugarcane response to infection by bacterial pathogens such as Acidovorax avenae subsp.…”

Time-series expression profiling of sugarcane leaves infected withPuccinia kuehniireveals an ineffective defense system leading to susceptibility

“…Furthermore, this kind 462 of response can be delayed in compatible interactions [107]. Hence, high expression of 463 PAL-encoding genes is a common attribute of resistant cultivars [31,34], including 464 those of sugarcane [39,40,42]. In the P. kuehnii pathosystem the five DEGs annotated 465 as PAL were repressed at 12 hai, but three of them were upregulated in the next hours, 466 returning to the basal level at 5 dai (Fig 2-C).…”

“…Stress-related genes quickly 655 showed changes in expression, manifested as a general downregulation pattern of an Hsp 656 at 6 hai [103]. McNeil and coworkers [39] detected sugarcane response against S. 657 scitamineum at 48 hai in an incompatible interaction. However, they did not exclude 658 the possibility of it occurring earlier, in a not sampled time point.…”

“…364 We also investigated the DEGs that composed the hypersensitive and defense 365 response terms, where transcripts with homology to resistance genes were present. upregulation [39].…”

“…To achieve an overview of the showed temporary activation at 36 hai of genes encoding these last two enzymes [103]. 445 Several authors noted that genes encoding enzymes of the phenylpropanoid pathway are 446 differentially expressed in the first hours or many days after infection [33,38,39,42]. 447 Other authors observed that upregulation of these genes can be associated with 448 resistance [40,90].…”