Cloned
Abstract
Rice (Oryza sativa L.) is a valuable resource for understanding the complex processes controlling yield and value-added traits. Bacterial blight (BB) is a vascular disease of rice, caused by strains of Xanthomonas oryzae pv. oryzae (Xoo) and provides insight, both practical and basic, into the concepts of susceptibility and resistance. Basic knowledge has been empirically and, more recently, intentionally exploited for broad and durable resistance to the disease. Bacterial blight involves representatives of most classes of resistance genes (R genes) and pathways for basal plant immunity. The study of BB also revealed novelties not observed in other models, possibly due to the long history of rice cultivation and the constant disease pressure. Conspicuous are the recessive R genes that target the notorious type III Transcription Activator-like effectors (TALes) of Xoo. Results indicate that pathogen and host are currently in a battle over a small patch of ground involving TALes function. At the same time, analyses of rice disease physiology are adding to a growing body of knowledge for plant disease processes and to how these processes are intertwined with disease susceptibility. The basic processes of BB present rich targets for the rapid advances in genome editing.
Keywords
- Xanthomonas oryzae pv. oryzae
- rice
- recessive resistance
- TAL effector
- genome editing
- CRISPR
1. Introduction
World population is expected to rise beyond 9 billion by 2050 [1]. Rice (
2. Post genomic era and rice grain protection
Advancements in genomics, referring here to DNA and RNA analyses, is as beneficial to crop protection as is to other discipline of biology. Rice MetaSysB, an open source which provides detailed information about BB-responsive genes, is based on the global expression analysis. The database provided 7475 unique genes and 5375 simple sequence repeats, which were responsive to
Multiple rice and
3. The genetic context of rice-Xoo interaction
Many BB-resistance genes in modern rice germplasm were selected long before the concepts of modern plant breeding were established, and a rich assortment of major dominant and recessive
Gene | Class | Comments | Cognate elicitor/effector | Ref |
---|---|---|---|---|
RLK1 | extracellular, membrane and intracellular domains; kinase; broad resistance | RaxX | [25, 27] | |
RLK | similar to |
Unknown | [26] | |
NBS-LRR2 | cytoplasm; narrow resistance | Multiple TALes | [31, 32, 33] | |
WAK3 | narrow | unknown | [40] | |
TAL effector inducible | membrane and cell wall; novel protein; broad resistance | AvrXa27, AvrXa23, AvrXa10 | [37, 38, 39] | |
Missense mutant of |
nuclear; broad resistance | TALe interference | [51, 53, 54] | |
promoter mutants of |
membrane; unresponsive to PthXo1 | PthXo1 | [42, 47] | |
promoter mutant of OsSWEET13, nodulin 3 family | TATA box polymorphisms; unresponsive to PthXo2 | PthXo2 | [44, 52] |
Perhaps the best known of these genes,
RLKs play a central role in disease immunity pathways in plants, largely via the characterization of the bacterial flagellin receptor FLS2 and the related receptor EFR in
The nucleotide binding site-LRR (NBS-LRR) is another large class of
Specific TALe-dependent
3.1 SWEET genes and recessive resistance
A class of major TALe-dependent susceptibility (
Mutated
The gene
The gene
Perhaps not all
4. Implication of interactions between TALes and the corresponding host genes
Due to the large reservoir of TALes in each strain of
In the case of
Type III effectors, in general, are hypothesized to interfere with host defense and defense signaling mechanisms. Strains of
Sequencing of
Not all TALE genes of
4.1 Executor R genes and super promoters
4.2 Targeted genome regulation and editing
Central to TALe function is the discovery of the DNA recognition cipher of TALEs [71, 72]. The central domain of a TALe, also known as binding domain, consists of variable number of tandem repeats, each consisting 33–35 amino acid residues. The 12th and 13th amino acid residues (known as repeat variable di-residues, RVDs) of each repeat preferentially binds to the respective nucleotides in the EBEs of target gene, such that HD, NG, NI and NN bind to C, T, A, and G, respectively in the effector binding elements (EBEs) of the promoter of a target gene [71, 72, 73]. The TALe recognition code allowed custom-engineer of DNA binding domains, also called designer TALes (dTALes), with novel specificity to the user-chosen DNA sequences [74, 75, 76]. dTALes provide a useful tool box to transiently activate host genes of interest for their functional analysis and assess the associated effect on host phenotype and physiology during rice-
5. Prospects for engineered broad and durable resistance in rice to BB
Traditional resistance breeding has identified many useful
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