Intergenic spaces: a new frontier to improving plant health

Abstract

To more sustainably mitigate the impact of crop diseases on plant health and productivity, there is a need for broader spectrum, long-lasting resistance traits. Defense Response (DR) genes, located throughout the genome, participate in cellular and system-wide defense mechanisms to stave off infection by diverse pathogens. This multigenic resistance avoids rapid evolution of a pathogen to overcome host resistance. DR genes reside within resistance-associated Quantitative Trait Loci (QTL), and alleles of DR genes in resistant varieties are more active during pathogen attack relative to susceptible haplotypes. Differential expression of DR genes results from polymorphisms in their regulatory regions, which include cis-regulatory elements such as transcription factor binding sites as well as features that influence epigenetic structural changes to modulate chromatin accessibility during infection. Many of these elements are found in clusters, known as cis-Regulatory Modules (CRMs), which are distributed throughout the host genome. Regulatory regions involved in plantpathogen interactions may also contain pathogen effector binding elements that regulate DR gene expression, and that, when mutated, result in a change in the plants' response. We posit that CRMs Accepted ArticleThis article is protected by copyright. All rights reserved and the multiple regulatory elements that comprise them are potential targets for marker-assisted breeding for broad-spectrum, durable disease resistance.

Identification of a Unique Genomic Region in Sweet Chestnut (Castanea sativa Mill.) That Controls Resistance to Asian Chestnut Gall Wasp Dryocosmus kuriphilus Yasumatsu

“…In plants, CREs could be located kilobases to megabases away from their target genes. However, promoters are defined as being one or two kbp upstream of the transcription start site [48]. In this study, the analysis of the putative promoter region of candidate genes (2000 bp upstream ATG) revealed the presence of several CREs involved in the response to different environmental stresses.…”

“…Forward genetics is widely applied to detect non-coding regions, putative cis-regulatory modules (CRMs) associated with phenotypic variation [27]. In fact, a recent GWAS for plant resistance to biotic and abiotic stress has shown that more than 70% of significant functional hits are localized in intergenic regions [48]. In plants, CREs could be located kilobases to megabases away from their target genes.…”

“…In this study, the analysis of the putative promoter region of candidate genes (2000 bp upstream ATG) revealed the presence of several CREs involved in the response to different environmental stresses. Polymorphisms in regulatory regions can change the phenotype from susceptible to resistant with, for example, the loss of binding sites for pathogen effector proteins [48]. Some of the CREs identified in C. sativa could be involved in the response to ACGW attack.…”

Plant Synthetic Promoters: Advancement and Prospective

“…Other protein factors bind to the downstream of a gene, such as Inr and regulate gene expressions [10] (Table 1, Figure 1). Several studies have shown that the proximal promoters (~1-2 kb upstream from the transcription start site) contain various important Cis-elements that strongly influence gene expression by recruiting TFs under specific cellular or environmental conditions [45][46][47]. For instance, the proximal sequence of the DREB2C promoter is sufficient for the tissue-specific spatiotemporal gene expression by heat stress in Arabidopsis [47].…”

Cacao pod transcriptome profiling of seven genotypes identifies features associated with post-penetration resistance to Phytophthora palmivora

“…While identifying differentially regulated genes is of interest to understanding how plants respond to disease stress, there is also a need to understand how non-coding regions of plant genomes act to direct gene expression 30 . Understanding how plant promoters are organized and how regulatory DNA elements interact will allow rapid advancement of crops via both conventional breeding and the design and deployment of synthetic promoters 31 , 32 .…”