Understanding Host-Pathogen Interactions with Expression Profiling of NILs Carrying Rice-Blast Resistance Pi9 Gene

Abstract

Magnaporthe oryzae infection causes rice blast, a destructive disease that is responsible for considerable decrease in rice yield. Development of resistant varieties via introgressing resistance genes with marker-assisted breeding can eliminate pesticide use and minimize crop losses. Here, resistant near-isogenic line (NIL) of Pusa Basmati-1(PB1) carrying broad spectrum rice blast resistance gene Pi9 was used to investigate Pi9-mediated resistance response. Infected and uninfected resistant NIL and susceptible control line were subjected to RNA-Seq. With the exception of one gene (Pi9), transcriptional signatures between the two lines were alike, reflecting basal similarities in their profiles. Resistant and susceptible lines possessed 1043 (727 up-regulated and 316 down-regulated) and 568 (341 up-regulated and 227 down-regulated) unique and significant differentially expressed loci (SDEL), respectively. Pathway analysis revealed higher transcriptional activation of kinases, WRKY, MYB, and ERF transcription factors, JA-ET hormones, chitinases, glycosyl hydrolases, lipid biosynthesis, pathogenesis and secondary metabolism related genes in resistant NIL than susceptible line. Singular enrichment analysis demonstrated that blast resistant NIL is significantly enriched with genes for primary and secondary metabolism, response to biotic stimulus and transcriptional regulation. The co-expression network showed proteins of genes in response to biotic stimulus interacted in a manner unique to resistant NIL upon M. oryzae infection. These data suggest that Pi9 modulates genome-wide transcriptional regulation in resistant NIL but not in susceptible PB1. We successfully used transcriptome profiling to understand the molecular basis of Pi9-mediated resistance mechanisms, identified potential candidate genes involved in early pathogen response and revealed the sophisticated transcriptional reprogramming during rice-M. oryzae interactions.

Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice

“…WRKY transcription factors were again and again observed to be implicated in the rice resistance to Mor [8,68,69]. In our analysis, WRKY proteins (IPR003657) were the most frequently activated transcription factors by Mor (Table S26).…”

“…A number of researches reported the expression profiles of rice defense response genes [9,67]. For example, chitinase activities were detected to play roles in rice resistance to Mor [68,69]. Our results show that the expected defense enzymes were the most frequent products of the regulated genes by Xoo and Mor (Fig.…”

“…5). Two pathways mediated by jasmonic acid and ethylene were demonstrated to be activated by Xoo and Mor infections [11,68,69]. Our results show that the processes relative to jasmonic acid were frequently activated in the Xooand Mor-infected rice (GO: 2000022~regulation of jasmonic acid mediated signaling pathway; GO:0009695~jasmonic acid biosynthetic process; GO:0009753~response to jasmonic acid) ( Fig.…”

Integrated mRNA and microRNA transcriptome analysis reveals miRNA regulation in response to PVA in potato

“…9E ). The induction of chitinase can help to strengthen the cell wall by providing resistance 36 . Overexpression of chitinase in transgenic rice contributed to increased fungal resistance 37 .…”

Transcriptome analysis of rice leaves in response to Rhizoctonia solani infection

“…A set of time-scale transcriptome analysis revealed that functional ETI (effector triggered immunity) responses rely on an appropriate time point for transcriptional reprogramming, which is mediated by jasmonate, ethylene, salicylic acid, and PAD4 signaling (19). Transcriptome analysis provided useful information for understanding the resistance mechanism of Brassica napus to clubroot disease (20) and was performed to investigate the regulatory mechanism of Pi9 and Pi21, two R (resistance genes) that control blast fungus (21,22).…”