Abstract
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.
Highlights
Rice (Oryza sativa L.) is a staple food for more than 60% of humanity[1]
Each Quantitative Trait Loci (QTL) imparts a partial contribution to resistance, and pyramiding multiple QTL to include many functional defense response (DR) genes has proven a useful predictor of durable resistance in wheat and rice[6,12,23,24,25]
Given the pivotal role of broad-spectrum defense response (BS-DR) genes in modulating the pathways involved in resistance, a well-orchestrated transcriptional response is necessary[11]
Summary
Rice (Oryza sativa L.) is a staple food for more than 60% of humanity[1]. The growing human demand, together with losses caused by pathogens worldwide, require novel strategies and agricultural practices to increase global production of rice. An 856 bp promoter insertion that contains known defense-responsive cis-elements is present in the resistant haplotype of OsGLP8-6, and the gene shows faster and higher expression relative to the susceptible haplotype[26]. To identify shared regulatory signatures of BS-DR co-expression cluster genes, we first detected overrepresented short sequence motifs in their respective promoters relative to the rest of the promoterome using the program Gimmemotifs[34].
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