A dynamic degradome landscape on miRNAs and their predicted targets in sugarcane caused by Sporisorium scitamineum stress

Yachun Su,Khushi Muhammad,Hui Ling,Weihua Su,Liping Xu,Xinhuan Xiao,Feng Liu,Yuye Zhang,Ning Huang,Youxiong Que

doi:10.1186/s12864-018-5400-8

Yachun Su, Khushi Muhammad + Show 8 more

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https://doi.org/10.1186/s12864-018-5400-8

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Abstract

BackgroundSugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. scitamineum is a complex network system. However, to date, there is no report on the identification of microRNA (miRNA) target genes of sugarcane in response to smut pathogen infection by degradome technology.ResultsTaqMan qRT-PCR detection and enzyme activity determination showed that S. scitamineum rapidly proliferated and incurred significant enzyme activity changes in the reactive oxygen species metabolic pathway and phenylpropanoid metabolic pathway at 2 d and 5 d after inoculation, which was the best time points to study target gene degradation during sugarcane and S. scitamineum interaction. A total of 122.33 Mb of raw data was obtained from degradome sequencing analysis of YC05–179 (smut-resistant) and ROC22 (smut-susceptible) after inoculation. The Q30 of each sample was > 93%, and the sequence used for degradation site analysis exactly matched the sugarcane reference sequence. A total of 309 target genes were predicted in sugarcane, corresponding to 97 known miRNAs and 112 novel miRNAs, and 337 degradation sites, suggesting that miRNAs can efficiently direct cleavage at multiple sites in the predicted target mRNAs. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the predicted target genes were involved in various regulatory processes, such as signal transduction mechanisms, inorganic ion transport and metabolism, defense mechanisms, translation, posttranslational modifications, energy production and conversion, and glycerolipid metabolism. qRT-PCR analysis of the expression level of 13 predicted target genes and their corresponding miRNAs revealed that there was no obvious negative regulatory relationship between miRNAs and their target genes. In addition, a number of putative resistance-related target genes regulated by miRNA-mediated cleavage were accumulated in sugarcane during S. scitamineum infection, suggesting that feedback regulation of miRNAs may be involved in the response of sugarcane to S. scitamineum infection.ConclusionsThis study elucidates the underlying response of sugarcane to S. scitamineum infection, and also provides a resource for miRNAs and their predicted target genes for smut resistance improvement in sugarcane.

Highlights

Sugarcane smut is a fungal disease caused by Sporisorium scitamineum
The main stems of plants infected by S. scitamineum are small, the cane leaves are slender and light green in color, and tillers usually grow black whips that lead to a sharp decline in sugarcane production [3]
Smut pathogen proliferation and changes in the activity of key enzymes involved in reactive oxygen species metabolic and phenylpropanoid metabolic pathways during the early stage of infection The results of TaqMan qRT-PCR (Fig. 1) showed that the Ct values of smut-resistant genotype (YC05–179) and -susceptible genotype (ROC22) inoculated with sterile water, negative control, and blank control were all higher than 37, indicating the absence of S. scitamineum, whereas the Ct value of samples inoculated with S. scitamineum was between 27 and 33

Summary

Introduction

Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. Sugarcane smut, caused by Sporisorium scitamineum, is a worldwide airborne fungal disease that affects sugarcane production [1]. A typical symptom of sugarcane smut involves cane tips of infected plants growing a black whip that points downwards and curls inwards around 120 d of planting. The main stems of plants infected by S. scitamineum are small, the cane leaves are slender and light green in color, and tillers usually grow black whips that lead to a sharp decline in sugarcane production [3]. Cultivating sugarcane varieties with excellent smut-resistance is the most economical and effective way to control the disease [4]

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