Morpho-Pathological and Global Transcriptomic Analysis Reveals the Robust Nonhost Resistance Responses in Chickpea Interaction with Alternaria brassicae

Abstract

Alternaria blight, caused by Alternaria brassicae, causes considerable yield loss in Brassica crops. While several blight-resistant varieties have been developed using resistance sources from host germplasm, none of them are entirely successful in imparting durable resistance. This has prompted the exploration of novel gene pools of nonhost plant species. Nonhost resistance (NHR) is a durable form of resistance, comprising pre- and postinvasion layers of defense. We aimed to identify the molecular basis of NHR to A. brassicae and identify the layers of NHR operating in a nonhost, chickpea (Cicer arietinum). To elucidate the layers of NHR operating against A. brassicae, we compared the histopathology and infection patterns of A. brassicae in C. arietinum and Brassica juncea. Delayed conidial germination, impeded hyphal growth, suppressed appressorium formation, and limited hyphal penetration occurred in the nonhost plant compared with the host plant, implying the involvement of the preinvasion layer of NHR in C. arietinum. Next, we investigated the molecular basis of robust NHR, in C. arietinum challenged with A. brassicae, by microarray-based global transcriptome profiling. Genes involved in stomatal closure, cuticular wax biosynthesis, cell-wall modification, and secondary metabolite production (contributing to preinvasion NHR) as well as reactive oxygen species (ROS) and cell death (contributing to postinvasion NHR) were found to be upregulated. Consistent with transcriptomic analysis, the morpho-pathological analysis revealed stomatal closure, ROS accumulation, and localized cell death in C. arietinum as the defense strategies against A. brassicae. Thus, we identified NHR-contributing genes with potential applications in blight resistance gene transfer to B. juncea.

Transcriptome Analysis of the Necrotrophic Pathogen Alternaria brassicae Reveals Insights into Its Pathogenesis in Brassica juncea

“…The processed reads were stored in FASTQ format. The processed reads were mapped to the reference genome obtained from a previous report ( 16 , 22 ) using HISAT2 ( 45 ). The resulting bam files were then used as inputs to stringtie2 ( 46 ) to assemble the alignments into transcripts.…”

“…The processed reads were mapped to the reference genome ( 16 ) using HISAT2, and the resulting bam files were used to assemble and quantify the transcripts using stringtie2 default parameters. The FPKM (fragments per kilobase per million) values from stringtie gff output were converted to raw count values using the prepDE.py script supplied along with the stringtie2 software.…”

“…While this has accelerated the study of pathogen biology and the identification of various effectors and pathogenicity factors, functional evidence for most identified genes in the form of transcriptomic data is lacking. Transcriptome analysis of Alternaria leaf spot infections has primarily focused on the plant responses to infection ( 13 – 16 ). Additionally, these transcriptome studies were performed with cDNA microarrays; hence, retrieving fungal reads/transcripts from the raw data is not feasible.…”

Transcriptome analysis of the necrotrophic pathogen Alternaria brassicae reveals a biphasic mode of pathogenesis in Brassica juncea

“…Transcriptome analysis of Alternaria leaf spot infections has primarily focused on the plant responses to infection (9)(10)(11)(12). Additionally, these transcriptome studies were performed with cDNA microarrays; hence, retrieving fungal reads/transcripts from the raw data is not feasible.…”

“…While this has accelerated the study of pathogen biology and the identification of various effectors and pathogenicity factors, functional evidence for most identified genes in the form of transcriptomic data is lacking. Transcriptome analysis of Alternaria leaf spot infections has primarily focused on the plant responses to infection (9-12). Additionally, these transcriptome studies were performed with cDNA microarrays; hence, retrieving fungal reads/transcripts from the raw data is not feasible.…”