Response Of Rice NLR Genes To Low Temperature Stress And Mining Potential Disease Resistance Related Genes

Utilizing rice’s inherent disease resistance is one of the most economical and effective means of disease prevention,which requires a comprehensive and in-depth understanding of the mechanisms behind rice’s disease resistance.Most plant disease resistance genes belong to the nucleotide-binding leucine-rich repeat receptors(NLRs)protein family,which is an essential component of effector-triggered immunity(ETI)in plants.It is known that plant NLR genes can be induced by pathogens,but some studies have shown that they can also be induced by environmental factors.The transcriptional expression of genes is closely related to DNA methylation,posttranscriptional processing,and modification.Plant NLR genes are the main executors of plant-specific immune responses,but other genes also play a crucial role.Genomewide association analysis(GWAS)has been proven to be a useful tool for discovering new functional genes.By utilizing GWAS to deeply mine rice disease resistance-related data in public databases,more disease-resistant genes can be discovered.This study was conducted from the three aspects mentioned above,and the main results are as follows:1.The effect of low-temperature stress on the DNA methylation and transcriptional activity of rice NLR genesThis study analyzed the cytosine methylation levels and transcriptome data of all NLR genes in two rice varieties,9311(cold-sensitive japonica rice)and P427(coldtolerant indica rice),under low-temperature stress to reveal the effects of low temperature on DNA methylation modifications and transcriptional activity of rice NLR genes.The results showed that low-temperature stress altered the methylation status of some NLR genes,with more NLR genes exhibiting methylation level changes in P427 than in 9311.After low-temperature stress,significant CG methylation changes were observed in some NLR genes’ promoter regions and transcribed regions.Interestingly,the changes in DNA methylation levels in the 500 bp promoter region were usually more severe than those in the transcribed region,indicating that the promoter region of NLR genes is often the target of low-temperature-induced methylation or demethylation.On the other hand,the methylation changes of many NLR genes showed varietyspecificity in 9311 and P427.Compared with 9311,more NLR genes’ DNA methylation levels were affected by low-temperature stress in P427,indicating a close relationship between DNA methylation of rice NLR genes and their tolerance to low temperatures.This study found that most rice NLR genes had relatively low expression levels after 24 and 72 hours of low temperature stress,but there were also some cases where the opposite was true.In addition,the expression levels of some rice NLR genes depended on the duration of low temperature stress.After 72 hours of cold stress,139 differentially expressed NLR genes were found in both 9311 and P427,accounting for more than 73%of the differentially expressed NLR genes in both varieties.This study also observed that differentially expressed NLR genes in 9311 and P427 were significantly enriched in genes responding to low temperature stress,further indicating that NLR genes can indeed be induced by low temperature.After low temperature stress,a group of differentially expressed NLR genes with the same change trend were found in both 9311 and P427,but their methylation change trends were often inconsistent,suggesting that low temperature stress has different effects on DNA methylation and transcriptional activity of some NLR genes in rice.2.Molecular evolution of the PGDH gene and its impact on plant disease resistanceIn this study,the molecular evolution of the PGDH(PhosphoGlycerate DeHydrogenase)gene and its impact on plant disease resistance were investigated.In previous studies in our laboratory,analysis of microarray data from 51 sets of Xanthomonas oryzae pv.oryzae(Xoo)infected rice and 18 sets of Magnaporthe oryzae(Mor)infected rice revealed that the PGDH gene responded to the infection of both pathogens.This study further analyzed 27 sets of second-generation transcriptome sequencing data of Arabidopsis thaliana infected with Pseudomonas syringae pv.tomato DC3000(Pst DC3000),a pathogenic variant of Pseudomonas syringae,and found that the PGDH gene in Arabidopsis also responded to Pst DC3000 infection.A total of 369 PGDH genes were identified in 110 different plant species in this study.Analysis revealed that PGDH genes are present in two categories,PGDH-Ⅰ and PGDHⅡ,with monocotyledonous plants mainly possessing PGDH-Ⅰ and dicotyledonous plants mainly possessing PGDH-Ⅱ.Through analysis of gene structure and intron phase,this study hypothesized that there were intron loss events during the evolution of the PGDH gene.3.Identification of Potential Disease-Resistant Genes through Genome-Wide Association AnalysisIn order to discover more rice genes related to disease resistance,this study conducted a genome-wide association analysis(GWAS)on the phenotypic data of 662 sets of lesion length of rice bacterial blight in a public database and the corresponding genomic data of rice materials.At the same time,combining the phenotype data of 391 sets of lesion size of rice blast and the SNPs data of relevant rice materials,some new significant association loci related to disease resistance were identified in rice.This study found that there were responsive pathogen-induced genes between QTLs for resistance to bacterial blight and QTLs for resistance to blast disease.Based on the transcriptome data,this study identified 12 potential disease resistance genes,among which LOC_Os02g41680,LOC_Os04g33390,LOC_Os02g17390 and LOC_Os08g29570 were supported by more transcriptome data.4.Constructing the PlantFamily DatabaseMany coding genes in plants exist in the form of families,such as typical diseaseresistant proteins with NBS and LRR domains.Through the protein domains,we can understand the gene function and its corresponding family.In order to facilitate researchers in studying gene families,this study constructed the PlantFamily database,which contains annotation information on the complete proteomes of 110 plant species...