Genome editing of a rice CDP-DAG synthase confers multipathogen resistance

Abstract

The discovery and application of genome editing introduce a new era of plant breeding, giving researchers efficient tools for the precise engineering of crop genomes 1 . Here, we demonstrate the power of genome editing for engineering broad-spectrum disease resistance in rice (Oryza sativa). We first isolated a lesion mimic mutant (LMM) from a mutagenized rice population, demonstrated that a 29-bp deletion in a gene we named RESISTANCE TO BLAST1 (RBL1) caused this phenotype and showed that this mutation caused a ca. 20-fold reduction in yield. RBL1encodes a cytidine diphosphate diacylglycerol (CDP-DAG) synthase required for phospholipid biosynthesis 2 . Mutation of RBL1 results in reduced levels of phosphatidylinositol (PI) and its derivative PI(4,5)P2. Rice PI(4,5)P2 is enriched in cellular structures specifically associated with effector secretion and fungal infection, suggesting a role as a disease susceptibility factor 3 . Using targeted mutagenesis, we obtained an allele of RBL1, named RBL12, which confers broad-spectrum resistance but does not decrease yield in a model rice variety as assessed in small-scale field trials. Our study has demonstrated the usefulness of editing of an LMM gene, a strategy relevant to diverse LMM genes and crops. Main textGenome editing has been widely used in functional studies of genes but its potential for crop improvement has not yet been broadly utilized 4 . Plant diseases cause severe losses in agriculture, threatening global food security 5 . Rice blast alone, caused by the fungal pathogen Magnaporthe oryzae, results in annual yield losses that are sufficient to feed more than 60 million people worldwide 6 . Given this cost, cultivating crops with resistance to diseases, particularly broad-spectrum resistance, is highly desirable 7 . Despite the importance of this goal, only a limited number of broad-spectrum resistance genes have been cloned and used in the field, such as rice Xa21 (ref. 8 ), bsr-d1 (ref. 9 ), Pigm 10 , IPA1 (ref. 11 ), ROD1 (ref. 12 ), UMP1 (ref. 13 ), wheat Lr34 (ref. 14 ) and PsIPK1 (ref. 15 ), and barley mlo 16,17 .LMMs form hypersensitive response-like lesions (a form of programmed cell death) in the absence of pathogens 18 . LMMs often confer durable and broad-spectrum resistance, representing a potential source for breeding resistance to diseases. However, LMMs are usually associated with reduced yield, and therefore the use of the genes conferring LMM phenotypes (hereafter referred to as LMM genes) has not been fully exploited in plant breeding due to the lack of useful alleles.Phospholipids are essential components of biological membranes and are involved in various biological processes, including development and response to biotic and abiotic stress 19 . In phospholipid biosynthesis (Extended Data Fig. 1), phosphatidic acid (PA) and cytidine triphosphate (CTP) are converted to CDP-DAG by CDP-DAG synthases (CDSs). CDP-DAG and Myo-inositol are used to produce PI by phosphatidylinositol synthases (PISs) 20 . PI is added to by a varied number of p...

Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance

“…Rice blast leads to significant yield losses and adversely impacts rice quality (Sha et al, 2023). NLR proteins, including Pi genes, play a key role in activating rice immune responses to rice blast.…”

Effector‐triggered susceptibility by the rice blast fungus Magnaporthe oryzae

“…Elucidation of the mechanism by which the Bas83 effector binds to the EIHM, for instance, could provide new insight into BIC function and CME‐dependent effector uptake. A gene editing approach to identify rice mutants conferring blast resistance and, significantly, recently identified a cytidine diphosphate diacylglycerol (CDP‐DAG) synthase, that is required for phospholipid biosynthesis at the BIC, perhaps impairing effector delivery as a means of conferring disease resistance (Sha et al ., 2023). This demonstrates the utility of developing an understanding of effector delivery at the BIC and also in adopting large‐scale genetic screens to look for novel mechanisms leading to disease resistance, distinct from NLR deployment.…”

CRISPR‐Cas9 and beyond: identifying target genes for developing disease‐resistant plants

“…In addition, LOF mutations in genes, such as Arabidopsis EDR1 (ENHANCED DISEASE RESISTANCE 1) encoding a MAP kinase kinase kinase (Frye et al 2001), DND1 (DEFENCE NO DEATH 1) (Clough et al 2000) and DND2 (Jurkowski et al 2004), AGD2 (ABERRANT GROWTH AND DEATH 2) (Rate & Greenberg 2001), and rice RBL1 (RESISTANCE TO BLAST 1) (Sha et al 2023), are also engaged in plant autoimmunity; group IV involves genes essential for signal transduction of plant growth and immunity. These studies strongly indicate that many genes associated with autoimmunity can be putative targets to breed genome-edited disease-resistant plants.…”

“…2004), AGD2 ( ABERRANT GROWTH AND DEATH 2 ) (Rate & Greenberg 2001), and rice RBL1 ( RESISTANCE TO BLAST 1 ) (Sha et al . 2023), are also engaged in plant autoimmunity; group IV involves genes essential for signal transduction of plant growth and immunity. These studies strongly indicate that many genes associated with autoimmunity can be putative targets to breed genome‐edited disease‐resistant plants.…”