Comparative transcriptomics of rice reveals an ancient pattern of response to microbial colonization

Abstract

Glomalean fungi induce and colonize symbiotic tissue called arbuscular mycorrhiza on the roots of most land plants. Other fungi also colonize plants but cause disease not symbiosis. Wholetranscriptome analysis using a custom-designed Affymetrix GeneChip and confirmation with real-time RT-PCR revealed 224 genes affected during arbuscular mycorrhizal symbiosis. We compared these transcription profiles with those from rice roots that were colonized by pathogens (Magnaporthe grisea and Fusarium moniliforme). Over 40% of genes showed differential regulation caused by both the symbiotic and at least one of the pathogenic interactions. A set of genes was similarly expressed in all three associations, revealing a conserved response to fungal colonization. The responses that were shared between pathogen and symbiont infection may play a role in compatibility. Likewise, the responses that are different may cause disease. Some of the genes that respond to mycorrhizal colonization may be involved in the uptake of phosphate. Indeed, phosphate addition mimicked the effect of mycorrhiza on 8% of the tested genes. We found that 34% of the mycorrhiza-associated rice genes were also associated with mycorrhiza in dicots, revealing a conserved pattern of response between the two angiosperm classes.expression profiling ͉ Glomus ͉ Oryza sativa ͉ pathogenesis ͉ phosphate

Identification of arbuscular mycorrhiza-inducible Nitrate Transporter 1/Peptide Transporter Family (NPF) genes in rice

“…To evaluate the success of mycorrhization of the R. irregularis-inoculated rice roots at the molecular level, we determined the expression of six genes that previously were shown to be specifically induced in rice roots during AM symbiosis: OsAM1, OsAM10, OsAM20 and OsAM25 (Güimil et al 2005), the mycorrhiza-specific phosphate transporter OsPT11 (Paszkowski et al 2002) and the ammonium transporter OsAMT3;1 (Perez-Tienda et al 2014;Koegel et al 2017). In all nutrient solutions of both experiments, OsAM1, OsAM10, OsAM20, OsAM25 and OsPT11 were significantly, greatly upregulated in AM roots compared to nonmycorrhizal roots (Supplementary Table S2), thus confirming a well-established rice-mycorrhiza under all five nutritional regimes.…”

“…In the AMF Rhizophagus intraradices (formerly called Glomus intraradices), that is found in rice roots in paddy fields and is used in most AM-rice studies (e.g. Paszkowski et al 2002;Güimil et al 2005;Glassop et al 2007;Gutjahr et al 2008), the ammonium transporters AMT1, AMT2 and AMT3 are expressed in the intraradical mycelium (Lopez-Pedrosa et al 2006;Perez-Tienda et al 2011;Calabrese et al 2016), suggesting a participation in retrieval of NH 4 + leaking from the fungus during fungal metabolism at the symbiotic interface. Alternatively, ammonium released by the AM at this interface may be taken up by the plant.…”

Plant immune responses triggered by beneficial microbes

“…For instance, defenserelated compounds like chitinases and glucanases have been shown to accumulate locally in mycorrhizal roots of tomato [9]. In rice, 40% of the mycorrhiza-responsive genes were also responsive to infection by fungal pathogens, indicating that the responses to beneficial and pathogenic fungi partly overlap [45]. Interestingly, some of the initial responses of Medicago truncatula to the mycorrhizal fungus Glomus mosseae and to the beneficial rhizobacterium P. fluorescens C7R12 have been shown to be overlapping as well [46].…”

A DELLA protein complex controls the arbuscular mycorrhizal symbiosis in plants

“…It has previously been shown by whole genome transcriptomic analysis that GA biosynthetic genes are induced during mycorrhizal colonization in rice [1]. Furthermore, GA has been shown to inhibit mycorrhizal colonization in Pisum sativum [2].…”