Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum

Abstract

Background Anthracnose is a damaging disease of sorghum caused by the fungal pathogen Colletotrichum sublineolum. Genome-wide mRNA and microRNA (miRNA) profiles of resistant and susceptible sorghum genotypes were studied to understand components of immune responses, and fungal induced miRNA and target gene networks. Results A total of 18 mRNA and 12 miRNA libraries from resistant and susceptible sorghum lines were sequenced prior to and after inoculation with C. sublineolum. Significant differences in transcriptomes of the susceptible and resistant genotypes were observed with dispersion distance and hierarchical cluster tree analyses. Of the total 33,032 genes predicted in the sorghum genome, 19,593 were induced by C. sublineolum, and 15,512 were differentially expressed (DEGs) between the two genotypes. The resistant line was marked by significant reprogramming of the transcriptome at 24 h post inoculation (hpi), and a decrease at 48 hpi, whereas the susceptible line displayed continued changes in gene expression concordant with elevated fungal growth in the susceptible genotype. DEGs encode proteins implicated in diverse functions including photosynthesis, synthesis of tetrapyrrole, carbohydrate and secondary metabolism, immune signaling, and chitin binding. Genes encoding immune receptors, MAPKs, pentatricopeptide repeat proteins, and WRKY transcription factors were induced in the resistant genotype. In a parallel miRNA profiling, the susceptible line displayed greater number of differentially expressed miRNAs than the resistant line indicative of a widespread suppression of gene expression. Interestingly, we found 75 miRNAs, including 36 novel miRNAs, which were differentially expressed in response to fungal inoculation. The expression of 50 miRNAs was significantly different between resistant and susceptible lines. Subsequently, for 35 differentially expressed miRNAs, the corresponding 149 target genes were identified. Expression of 56 target genes were significantly altered after inoculation, showing inverse expression with the corresponding miRNAs. Conclusions We provide insights into genome wide dynamics of mRNA and miRNA profiles, biological and cellular processes underlying host responses to fungal infection in sorghum. Resistance is correlated with early transcriptional reprogramming of genes in various pathways. Fungal induced genes, miRNAs and their targets with a potential function in host responses to anthracnose were identified, opening avenues for genetic dissection of resistance mechanisms.

Transcriptome analysis of early stages of sorghum grain mold disease reveals defense regulators and metabolic pathways associated with resistance

“…RNA was extracted from the developing grain before and after the genotypes were challenged by a mixture of spore suspension of five Fusarium and an Alternaria species. The sampling time points 0, 24 and 48 h after inoculation were based on our previous study on grain [ 46 ] and leaf [ 47 ] that defense related genes are induced within 24 to 48 h after inoculation. RNA samples from two of the time points (0 and 24 h) were used for sequencing as preliminary studies indicated that defense genes were already induced at 24 h after infection while the 48 h samples were used for validation studies.…”

“…Sorghum defensins have not been studied as they are mostly grain specific and pathogen inducible whereas most previous studies focus on foliar tissues. It is notable that defensins were not prominently described in recent RNA-seq experiments conducted in leaf tissues of sorghum consistent with their grain specific expression [ 47 , 64 ].…”

The inheritance of anthracnose (Colletotrichum sublineola) resistance in sorghum differential lines QL3 and IS18760

“…Both genomic regions explained only a limited portion of the variance for anthracnose resistance, suggesting their effects are determined by the parallel additive effects of other, yet to be detected loci. A gene expression atlas derived from anthracnose-differential line SC283 identified genes encoding immune receptors, MAPKs, pentatricopeptide repeat proteins, and WRKY transcription factors as the most highly expressed genes in response to infection 35 . Increasing the mapping population size or fine mapping these loci are not affordable approaches to detect minor additive effect genes.…”

RNA-Sequencing in Resistant (QL3) and Susceptible (Theis) Sorghum Cultivars Inoculated With Johnsongrass Isolates of Colletotrichum sublineola

“…Basic blue proteins in plants are copper-containing plantacyanins that are regulated via conserved microRNA408 (miR408), which is present in sorghum ( Zhang et al, 2011 ). Although, miR408 was not identified among the upregulated miRNAs detected by RNAseq in anthracnose-resistant sorghum cultivar SC383 following inoculation with C. sublineolum ( Fu et al, 2020 ), a miR408 induced basic blue protein in wheat has been demonstrated to have a role in resistance to stripe rust ( Puccinia striiformis f. sp. tritici ; Feng et al, 2013 ).…”

“…In this study, we have used RNASeq to investigate differences in gene expression in early defense responses of two sorghum cultivars that differ significantly in anthracnose sensitivity to try to pinpoint genes and pathways that may contribute to that difference, and to compare results with another very recent publication that did similar experiments but with emphasis on microRNAs with a different pair of anthracnose resistant and susceptible cultivars ( Fu et al, 2020 ). Here, a mix of two C. sublineola isolates from Johnsongrass that had previously been shown lead to different visible responses on QL3 and Theis were used to examine gene expression changes in the two cultivars 24 h post-inoculation.…”