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

Abstract

Sugarcane (Saccharum spp. hybrids) is a major source of sugar and renewable bioenergy crop worldwide and suffers serious yield losses due to many pathogen infections. Leaf scald caused by Xanthomonas albilineans is a major bacterial disease of sugarcane in most sugarcane-planting countries. The molecular mechanisms of resistance to leaf scald in this plant are, however, still unclear. We performed a comparative transcriptome analysis between resistant (LCP 85-384) and susceptible (ROC20) sugarcane cultivars infected by X. albilineans using the RNA-seq platform. 24 cDNA libraries were generated with RNA isolated at four time points (0, 24, 48, and 72 h post inoculation) from the two cultivars with three biological replicates. A total of 105,783 differentially expressed genes (DEGs) were identified in both cultivars and the most upregulated and downregulated DEGs were annotated for the processes of the metabolic and single-organism categories, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the 7612 DEGs showed that plant–pathogen interaction, spliceosome, glutathione metabolism, protein processing in endoplasmic reticulum, and plant hormone signal transduction contributed to sugarcane’s response to X. albilineans infection. Subsequently, relative expression levels of ten DEGs determined by quantitative reverse transcription-PCR (qRT-PCR), in addition to RNA-Seq data, indicated that different plant hormone (auxin and ethylene) signal transduction pathways play essential roles in sugarcane infected by X. albilineans. In conclusion, our results provide, for the first time, valuable information regarding the transcriptome changes in sugarcane in response to infection by X. albilineans, which contribute to the understanding of the molecular mechanisms underlying the interactions between sugarcane and this pathogen and provide important clues for further characterization of leaf scald resistance in sugarcane.

Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis

“…In the present study, the levels of gene transcripts encoding CTR1 were strongly increased, whereas those for genes encoding EIN2, EIN3, and ERF1 were decreased in both cultivars, suggesting that the ET signal transduction pathway plays negative roles in response to Aaa infection. Also, Ntambo et al revealed that this pathway was essential in sugarcane against X. albilineans [25] For auxin signal transduction pathways, we found that expression of genes for GH3 and a gene (Cluster-13677.452329) for SAUR was significantly upregulated in sugarcane, similar to a previous study upon sugarcane in response to X. albilineans infection [25]. Plants infected successfully by biotrophic pathogens show significant increases in IAA concentration and thereby upregulation of GH3 [60,61].…”

“…Induction of many genes involved in photosynthesis and carbon metabolism, plant-pathogen interaction, plant hormone signal transduction, and phenylpropanoid biosynthesis was also observed. These metabolic process and defense-responsive pathways were also previously reported to be involved in responses of sugarcane to infection by diverse pathogens, further suggesting that these responses are largely conserved in sugarcane exposed to biotic stress [25,26,35].…”

Genome‐wide analysis of mitogen‐activated protein (MAP) kinase gene family expression in response to biotic and abiotic stresses in sugarcane

“…To check the reliability of our identified MAP kinase gene families, the genes were further confirmed in the S. spontaneum AP85‐441 genome (http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/) and two publicly available published transcriptome datasets (PRJNA579959 and PRJNA549590) based on similarity >90% and high bit score (806–3578) with the R570 genome. The two transcriptome datasets originated from the sugarcane cultivars, ROC22 (resistant to red stipe) vs MT11‐610 (susceptible to red stipe) (Chu et al 2020) as well as LCP 85–384 (resistant to leaf scald) vs ROC20 (susceptible to leaf scald) (Ntambo et al 2019), which were inoculated with the pathogenic bacteria Aaa and Xa , respectively.…”

“…The two RNA‐seq datasets published by our group, which are available in the NBCI Short Read Archive (SRA) database under BioProject accession number PRJNA579959 and PRJNA549590, were used to investigate expression patterns of MAP kinase family genes in sugarcane cultivars (Ntambo et al 2019, Chu et al 2020). A value for fragments per kilobase of transcript per million fragments mapped (FPKM) was calculated for each gene, and the log 2 (Fold Change) transformed values for each MAP kinase family gene were used to generate a heatmap.…”

Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement

“…coeruleum or Ralstonia solanacearum in N. benthamiana [38]. More recently, most of WRKY33 alleles were significantly upregulated in sugarcane against the Xanthomonas albilineans attacks [54]. Collectively, WRKY TFs through self-regulation or hormones mediated signal transduction pathways proved to be effective for alleviating the infection stress caused by biotic or abiotic agents.…”