Broad-spectrum resistance to bacterial blight in rice using genome editing

Abstract

anthomonas oryzae pv. oryzae (Xoo) is the etiological agent of bacterial blight disease in rice. The disease is most severe in southeast Asia but is increasingly damaging in west African countries, and results in substantial yield loss 1. TALes from Xoo are injected by a type III secretion system into plant cells and recognize effector-binding elements (EBEs) in cognate SWEET host gene promoters, which results in induction of SWEET genes and production of sugars that enable disease susceptibility in rice 2,3. An array of central repeats, which are 34-35 amino acids long, are present in each TALe and interact with EBEs via two repeat variable di-residues (RVDs) at the 12th and 13th position of each repeat 4,5. Aberrant repeats, longer than 35 amino acids, are hypothesized to allow looping out of the repeat to accommodate alternate sequence binding for a particular TALe 6. Bacterial blight depends on TALe-mediated induction of at least one member of a family of sugar-transporter genes. Although rice has more than 20 SWEET genes, only those of clade III are reported to be induced by Xoo 7-10. Although all five of the known clade III SWEET genes in rice can function as susceptibility genes for bacterial blight, only three are known to be targeted in nature 10. More specifically, SWEET11 expression is induced by strains encoding the TALe PthXo1, SWEET13 by PthXo2 and SWEET14 by any one of several TALes, namely AvrXa7, PthXo3, TalC and TalF (originally Tal5) 7,9-15 (Table 1). Effectors of Xoo that target clade III SWEET genes are referred to as major TALes owing to their strong virulence effect. Naturally occurring resistance has arisen as the result of nucleotide polymorphisms in EBEs of SWEET promoters. EBE alleles of SWEET11 that are not recognized by PthXo1 are collectively referred to as the recessive resistance gene xa13. Rice varieties containing xa13 are resistant to strains that solely depend on PthXo1 for SWEET induction. Most indica rice varieties carry a SWEET13 allele that contains four adenines in the EBE for PthXo2, and rice lines carrying this allele are susceptible to PthXo2-dependent strains 12. A rare exception is the recessive resistance allele xa25, which contains three adenines in the EBE for SWEET13 in the indica cultivar Minghui 63, conferring resistance to strains that depend solely on PthXo2 16. A similar recessive resistance allele in japonica rice varieties is equally effective against strains relying on PthXo2 (ref. 12). Additional naturally occurring recessive EBE polymorphisms that confer resistance to strains carrying PthXo2, and the overlapping EBEs for PthXo3, TalF and AvrXa7 have subsequently been identified in the promoters of SWEET13 and SWEET14, respectively, in germplasm collections 17,18. Rice susceptibility genes are good targets for genome editing for disease resistance. TALe-mediated susceptibility is particularly modifiable. For instance, transcription-activator-like effector nuclease (TALEN)-directed mutations in SWEET14 created lines resistant to strains carrying PthXo3/Avr...

Genome-Wide Profiling and Phylogenetic Analysis of the SWEET Sugar Transporter Gene Family in Walnut and Their Lack of Responsiveness to Xanthomonas arboricola pv. juglandis Infection

“…Considering that this particular pathogen strain has a functional type III secretion system that in other Xanthomonas pathogens is able to secrete TALEs into the plant cell and influence SWEET genes expression [59], a logical hypothesis was that Xaj417 would adopt this strategy. If this was the case, a disease control strategy could encompass the inactivation of a particular responsive SWEET member in walnut to deprive the pathogen from this sugar source, as recently shown for the rice blight pathosystem [60,61]. Since we observed no induction of specific SWEET genes in response to Xaj417 infection, we investigated the pathogen's genome in search of any known TALEs.…”

Beyond Seek and Destroy: how to Generate Allelic Series Using Genome Editing Tools

“…This feature could theoretically allow us to study the effects of one or more amino acid deletions on protein function and represents a comparative advantage of LbCPF1 over SpCAS9. Generating mainly small deletions proved also an advantage for abolishing the recognition of promoter sequences by TALE effectors of bacterial blight thereby conferring partial or complete resistance to different strains (Oliva et al 2019).…”

A SWEET solution to rice blight

“…Activation of target SWEET genes elevates sugar transport to where the pathogen needs it, enhancing its virulence and leading to disease susceptibility. Oliva et al 1 undertook an extensive survey of Xoo TALE diversity in 33 Asian and 30 African isolates, sequencing 856 distinct TALEs. They found more copies of TALEs in Asian isolates (18-21 per genome) than in African isolates (9 per genome).…”

“…Oliva et al 1 chose to target specific EBE polymorphisms based on their sequencelevel characterization of TALEs in 63 Xoo strains from diverse areas, and the mutations they discovered in the EBEs in promoters of SWEET11, SWEET13 and SWEET14 in rice. First, they engineered a rapidly cycling japonica line, Kitaake.…”

“…In this issue, an international team of researchers describes the use of CRISPR editing to generate rice plants that are broadly resistant to the main pathogen that causes rice blight, Xanthomonas oryzae pv. oryzae (Xoo) 1 . To enhance the durability and management of resistance, the team has also developed a kit to trace the disease, and its virulence and resistance alleles 2 .…”