Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.

Hydrogen peroxide (H₂O₂) is a ubiquitous signal regulating many biological processes, including innate immunity, in all eukaryotes. However, it remains largely unknown that how transcription factors directly sense H₂O₂ in eukaryotes. Here, we report that rice basic/helix-loop-helix transcription factor bHLH25 directly senses H₂O₂ to confer resistance to multiple diseases caused by fungi or bacteria. Upon pathogen attack, rice plants increase the production of H₂O₂, which directly oxidizes bHLH25 at methionine 256 in the nucleus. Oxidized bHLH25 represses miR397b expression to activate lignin biosynthesis for plant cell wall reinforcement, preventing pathogens from penetrating plant cells. Lignin biosynthesis consumes H₂O₂ causing accumulation of non-oxidized bHLH25. Non-oxidized bHLH25 switches to promote the expression of Copalyl Diphosphate Synthase 2 (CPS2), which increases phytoalexin biosynthesis to inhibit expansion of pathogens that escape into plants. This oxidization/non-oxidation status change of bHLH25 allows plants to maintain H₂O₂, lignin and phytoalexin at optimized levels to effectively fight against pathogens and prevents these three molecules from over-accumulation that harms plants. Thus, our discovery reveals a novel mechanism by which a single protein promotes two independent defense pathways against pathogens. Importantly, the bHLH25 orthologues from available plant genomes all contain a conserved M256-like methionine suggesting the broad existence of this mechanism in the plant kingdom. Moreover, this Met-oxidation mechanism may also be employed by other eukaryotic transcription factors to sense H₂O₂ to change functions.

Background: Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent a large class of proteins in regulating plant development and immunity. The LRR-RLK XA21 confers resistance to the bacterial disease caused by the pathogen ofXanthomonas oryzae pv. oryzae(Xoo). Several XA21 binding proteins have been characterized, however the early events governing XA21 signaling have not been fully elucidated.Results: Here we report the identification of one LRR-RLK gene (XIK1) whose expression is induced rapidly upon the infection with the pathogen ofXoo. Expression pattern analysis reveals thatXIK1is preferentially expressed in reproductive leaves and panicles, and that expression is associated with plant development. By using RNA interference (RNAi), we silenced the expression ofXIK1in rice withXa21and found that reduced expression ofXIK1compromised disease resistance mediated by XA21. In addition, we found that the expression of the downstream marker genes of pathogen associated molecular pattern (PAMP) triggered immunity (PTI) in rice was compromised inXa21plants silenced forXIK1.Conclusion: Our study reveals that the LRR-RLK geneXIK1isXoo-responsive and positively regulatesXa21-mediated disease resistance.

Global warming impacts crop production and increases crop disease. It is commonly known that heat stress (HS) caused by extreme high temperature induces HS responses but suppresses disease resistance in plants. However, the molecular basis of this trade-off remains largely unknown. Here, we report that OsHsfA4d shows strongest induction upon HS and pathogen infection among Heat Shock Factors (HSFs) in rice. The transcription factor OsHSFA4d enhances thermotolerance by binding to the heat shock element (HSE) in the promoter of HSP101 to activate its expression. OsHSFA4d also binds to the HSE in the first intron of Cellulose synthase-like F6 (CslF6) to promote its expression for suppressing PAMP-triggered ROS bursts and pathogenesis-related gene expression, inhibiting disease resistance. OsCDPK24 and OsCDPK28 interact with OsHSFA4d to form a complex that phosphorylates serine 146 (S146) of OsHSFA4d, thereby enhancing its DNA binding ability. HS induces the kinase activity of OsCDPK24/28 to increase the phosphorylation level of OsHSFA4d. Importantly, residues similar to S146 are conserved in OsHSFA4d orthologues across plant species, suggesting that such phosphorylation modules are widely employed to regulate abiotic and biotic stress responses in the plant kingdom.

Fungal pathogens typically use secreted effector proteins to suppress host immune activators to facilitate invasion. However, there is rarely evidence supporting the idea that fungal secretory proteins contribute to pathogenesis by transactivating host genes that suppress defense. We previously found that pathogen Magnaporthe oryzae induces rice Bsr-d1 to facilitate infection and hypothesized that a fungal effector mediates this induction. Here, we report that MoSPAB1 secreted by M. oryzae directly binds to the Bsr-d1 promoter to induce its expression, facilitating pathogenesis. Amino acids 103-123 of MoSPAB1 are required for its binding to the Bsr-d1 promoter. Both MoSPAB1 and rice MYBS1 compete for binding to the Bsr-d1 promoter to regulate Bsr-d1 expression. Furthermore, MoSPAB1 homologues are highly conserved among fungi. In particular, Colletotrichum fructicola CfSPAB1 and Colletotrichum sublineola CsSPAB1 activate kiwifruit AcBsr-d1 and sorghum SbBsr-d1 respectively, to facilitate pathogenesis. Taken together, our findings reveal a conserved module that may be widely utilized by fungi to enhance pathogenesis.