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.
Highlights
Rice is among the most important staple foods, contributing 23% of total calories consumed globally
To study early defense mechanisms against M. oryzae in rice, RNA-Seq was performed on Pusa Basmati1 (PB1)+Pi9 near-isogenic line (NIL) and susceptible control PB1 24 hpi
Pi9 is a constitutively expressing gene regardless of pathogen infection; post-transcriptional reprogramming allows the R gene to activate downstream processes involved in biotic stress only after M. oryzae infection (Qu et al, 2006)
Summary
Rice is among the most important staple foods, contributing 23% of total calories consumed globally. Rice is the model system for monocotyledons because its genome has been fully sequenced (International Rice Genome Sequencing Project, 2005; 430 Mb), the availability of high-density genetic maps, genome-wide microarrays (Jung et al, 2007), and genetic transformation methods. Both biotic and abiotic stresses affect rice growth. Infection by Magnaporthe oryzae (a hemibiotrophic fungus) causes rice blast disease, resulting in a 20–100% global crop loss, an amount that can feed 60 million people (Sharma et al, 2012)
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