Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice

Bradley W. Tonnessen; Ana M. Bossa-Castro; Ramil Mauleon; Nickolai Alexandrov; Jan E. Leach

doi:10.1038/s41598-018-38195-x

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Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice

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Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice

Bradley W. Tonnessen, Ana M. Bossa-Castro, Ramil Mauleon, Nickolai Alexandrov and Jan E. Leach

Scientific reports, Vol.9, 1536

07/02/2019

DOI: https://doi.org/10.1038/s41598-018-38195-x

PMCID: PMC6367480

PMID: 30733489

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Abstract

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

Biotic

Data mining

Plant disease resistance that is durable and effective against diverse pathogens (broad-spectrum) is essential to stabilize crop production. Such resistance is frequently controlled by Quantitative Trait Loci (QTL), and often involves differential regulation of Defense Response (DR) genes. In this study, we sought to understand how expression of DR genes is orchestrated, with the long-term goal of enabling genome-wide breeding for more effective and durable resistance. We identified short sequence motifs in rice promoters that are shared across Broad-Spectrum DR (BS-DR) genes co-expressed after challenge with three major rice pathogens (Magnaporthe oryzae, Rhizoctonia solani, and Xanthomonas oryzae pv. oryzae) and several chemical elicitors. Specific groupings of these BS-DR-associated motifs, called cis-Regulatory Modules (CRMs), are enriched in DR gene promoters, and the CRMs include cis-elements known to be involved in disease resistance. Polymorphisms in CRMs occur in promoters of genes in resistant relative to susceptible BS-DR haplotypes providing evidence that these CRMs have a predictive role in the contribution of other BS-DR genes to resistance. Therefore, we predict that a CRM signature within BS-DR gene promoters can be used as a marker for future breeding practices to enrich for the most responsive and effective BS-DR genes across the genome.

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Title: Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice
Creators: Bradley W. Tonnessen - Colorado State University
Ana M. Bossa-Castro - Colorado State University
Ramil Mauleon - International Rice Research Institute (Phillipines)
Nickolai Alexandrov - International Rice Research Institute (Phillipines)
Jan E. Leach - Colorado State University
Publication Details: Scientific reports, Vol.9, 1536
Publisher: Springer Nature
Number of pages: 13
Grant note: IOS-1444511 / U.S. National Science Foundation; National Science Foundation (NSF) National Institute of Food and Agriculture pre-doctoral fellowship Global Rice Science Partnership
Identifiers: 991013099201502368
Academic Unit: Faculty of Science and Engineering
Language: English
Resource Type: Journal article

Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice

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