Screening of rice (Oryza sativa L.) OsPR1b-interacting factors and their roles in resisting bacterial blight

Luan, Zhihui; Zhou, Dangwei

doi:10.4238/2015.march.13.15

Cited by 8 publications

(5 citation statements)

References 11 publications

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“…One biological process, namely, to respond to biotic stimuli (marked by the red dots in Figure 3 A), was enriched with eighteen genes ( Table S2 ), including pathogenesis-related protein 1b ( OsPR1b ) ( Figure 3 B, red dots). OsPR1b is a rice defense-related gene specifically triggered by JA/SA or blast fungus infection [ 40 , 41 ]. We further confirmed the results using a qRT-PCR assay and found that without M. oryzae invasion, the transcription level of OsPR1b was higher in ossnrk1a − 1 than in the wild type, whereas at 24 and 48 hpi with Guy11, OsPR1b was upregulated in ZH11 but not in the ossnrk1a mutant, resulting in a significantly lower OsPR1b transcription in ossnrk1a − 1 compared to that in ZH11 ( Figure 3 C).…”

Section: Resultsmentioning

confidence: 99%

Identification of Ossnrk1a−1 Regulated Genes Associated with Rice Immunity and Seed Set

Cao,

Lu,

Chen

et al. 2024

Plants

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Sucrose non-fermenting–1-related protein kinase–1 (SnRK1) is a highly conserved serine–threonine kinase complex regulating plants’ energy metabolisms and resistance to various types of stresses. However, the downstream genes regulated by SnRK1 in these plant physiological processes still need to be explored. In this study, we found that the knockout of OsSnRK1a resulted in no obvious defects in rice growth but notably decreased the seed setting rate. The ossnrk1a mutants were more sensitive to blast fungus (Magnaporthe oryzae) infection and showed compromised immune responses. Transcriptome analyses revealed that SnRK1a was an important intermediate in the energy metabolism and response to biotic stress. Further investigation confirmed that the transcription levels of OsNADH-GOGAT2, which positively controls rice yield, and the defense-related gene pathogenesis-related protein 1b (OsPR1b) were remarkably decreased in the ossnrk1a mutant. Moreover, we found that OsSnRK1a directly interacted with the regulatory subunits OsSnRK1β1 and OsSnRK1β3, which responded specifically to blast fungus infection and starvation stresses, respectively. Taken together, our findings provide an insight into the mechanism of OsSnRK1a, which forms a complex with specific β subunits, contributing to rice seed set and resistance by regulating the transcription of related genes.

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Section: Resultsmentioning

confidence: 99%

Identification of Ossnrk1a−1 Regulated Genes Associated with Rice Immunity and Seed Set

Cao,

Lu,

Chen

et al. 2024

Plants

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“…TraesCS5A02G077600 is within the interval of a fusarium head blight resistance QTL, termed Qfhs.ifa‐5AS , and is orthologous to the rice Osmotin‐like protein Os12g0569300 (National Center for Biotechnology Information, 2021; Steiner et al., 2019). TraesCS5A02G059000 is orthologous to the rice defense response gene OsPR1b, which is constitutively expressed at background levels (Luan & Zhou, 2015). Although the physical gene cluster of TraesCS5A02G046300 , TraesCS5A02G046400 , and TraesCS5A02G046500 has no known orthologs in Arabidopsis or rice, they share the additional GO terms defense response to fungus (GO:0050832), binding (GO:0005488), peptidase activity (GO:0008233), extracellular region (GO:0005576), cell wall (GO:0005618), integral component of membrane (GO:0016021), cellular component organization (GO:0016043), and cellular metabolic process (GO:0044237).…”

Section: Resultsmentioning

confidence: 99%

Positional‐based cloning ‘fail‐safe’ approach is overpowered by wheat chromosome structural variation

et al. 2021

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Positional-based cloning is a foundational method for understanding the genes and gene networks that control valuable agronomic traits such as grain yield components.In this study, we sought to positionally clone the causal genetic variant of a 1000-grain weight (TGW) quantitative trait loci (QTL) on wheat (Triticum aestivum L.) chromosome arm 5AL. We developed heterogenous inbred families (HIFs) (>5,000 plants)for enhanced genotypic resolution and fine-mapped the QTL to a 10-Mbp region. The transcriptome of developing grains from positive and negative control HIF haplotypes revealed presence-absence chromosome arm 5AS structural variation and unexpectedly no differential expression of genes within the chromosome arm 5AL candidate region. Evaluation of genomic, transcriptomic, and phenotypic data, and predicted function of genes, identified that the 5AL QTL was the result of strong linkage disequilibrium (LD) with chromosome arm 5AS presence or absence (HIF r 2 = 0.91). Structural variation is common in wheat, and our results highlight that the redundant polyploid genome's masking of such variation is a significant barrier to positional cloning. We propose recommendations for more efficient and robust detection of structural variation, including transitioning from a single nucleotide polymorphism (SNP) to a haplotype-based approach to identify positional cloning targets. We also present nine candidate genes for grain yield components based on chromosome arm 5AS presence or absence, which may unveil hidden variation of homoeolog dosage-dependent genes across the group five chromosome short arms. Taken together, our discovery demonstrates the phenotypic resiliency of polyploid genomic structural variation and highlights a considerable challenge to routine positional cloning in wheat.

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“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted January 20, 2023. ; https://doi.org/10.1101/2023.01.18.523945 doi: bioRxiv preprint application of JA and ET significantly increased the expression level of PR1b in the seedlings. Whereas, the control sample was treated with a pathogen (Xoo) and water treatment (Luan and Zhou, 2015). M. oryzae induced the expression of PR genes such as PR1b, PR2 and PR5 (Schweizer et al, 1997).…”

Section: Discussionmentioning

confidence: 99%

“…Exogenous application of JA and ET significantly increased the expression level of PR 1b in the seedlings. Whereas, the control sample was treated with a pathogen ( Xoo ) and water treatment (Luan and Zhou, 2015). M. oryzae induced the expression of PR genes such as PR 1b, PR 2 and PR 5 (Schweizer et al ., 1997).…”

Section: Discussionmentioning

confidence: 99%

Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes

Jimmy

Karn

Kumari

et al. 2023

Preprint

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In plants, pathogen resistance is brought about due to the binding of certain transcription factors (TF) proteins to the cis-elements of certain target genes. These cis-elements are present up-stream in the motif of the promoters of each gene. This ensures the binding of a specific transcription factor to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific transcription factor. Rice 1kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using gene ontology and gene set enrichment analysis. Gene with more than 4 TFbm in their promoter was selected. Nine genes reported to have a role in rice disease resistance were selected for further analysis. Cis-acting regulatory element analysis was carried out to find the cis-elements and to confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding nine genes were built and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY13 was also considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped to provide the mechanism of interaction. Further co-expression network drew light on the interaction of these selected diseases resistance-related genes with WRKY13 TF protein. This study suggests the target downstream genes that are regulated by WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.

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Screening of rice (Oryza sativa L.) OsPR1b-interacting factors and their roles in resisting bacterial blight

Cited by 8 publications

References 11 publications

Identification of Ossnrk1a−1 Regulated Genes Associated with Rice Immunity and Seed Set

Identification of Ossnrk1a−1 Regulated Genes Associated with Rice Immunity and Seed Set

Positional‐based cloning ‘fail‐safe’ approach is overpowered by wheat chromosome structural variation

Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes

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