Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction

Javed, Mohammed; Reddy, Bhaskar; Sheoran, Neelam; Prakash, Ganesan; Kumar, Aundy

doi:10.1016/j.gene.2023.147718

Cited by 3 publications

(4 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genes with fragments per kilobase of transcript per million mapped reads (FPKM) ≤ 9.0 were excluded from this annotation process. The expressed genes underwent Gene Ontology (GO) annotation via the Database for Annotation, Visualization, and Integrated Discovery (DAVID) [45,46] v2023q4. Additionally, these genes were assessed for gene enrichment using the functional annotation tool against a background reference, B. graminis f. sp.…”

Section: Comparative Genomic Analysismentioning

confidence: 99%

“…Additionally, these genes were assessed for gene enrichment using the functional annotation tool against a background reference, B. graminis f. sp. hordei DH14n [45]. Furthermore, the raw reads from the conidial transcriptome datasets are deposited to NCBI-SRA with accession number PRJNA1086707.…”

Section: Comparative Genomic Analysismentioning

confidence: 99%

“…tritici Wtn1 genome, 583 tRNA anticodon sequences were identified, including the stop codon. The most prevalent anticodons were for leucine (70), cysteine (61), and alanine (58), followed by arginine (45), serine (37), and methionine (31). Aromatic amino acids were also detected, with tyrosine (21) being the most abundant and then phenylalanine (19) and tryptophan (11).…”

Section: Deciphering the Trna Anticodons In The Genomementioning

confidence: 99%

See 2 more Smart Citations

Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics

Nallathambi,

Umamaheswari,

Reddy

et al. 2024

JoF

Self Cite

View full text Add to dashboard Cite

A high-quality genome sequence from an Indian isolate of Blumeria graminis f. sp. tritici Wtn1, a persistent threat in wheat farming, was obtained using a hybrid method. The assembly of over 9.24 million DNA-sequence reads resulted in 93 contigs, totaling a 140.61 Mb genome size, potentially encoding 8480 genes. Notably, more than 73.80% of the genome, spanning approximately 102.14 Mb, comprises retro-elements, LTR elements, and P elements, influencing evolution and adaptation significantly. The phylogenomic analysis placed B. graminis f. sp. tritici Wtn1 in a distinct monocot-infecting clade. A total of 583 tRNA anticodon sequences were identified from the whole genome of the native virulent strain B. graminis f. sp. tritici, which comprises distinct genome features with high counts of tRNA anticodons for leucine (70), cysteine (61), alanine (58), and arginine (45), with only two stop codons (Opal and Ochre) present and the absence of the Amber stop codon. Comparative InterProScan analysis unveiled “shared and unique” proteins in B. graminis f. sp. tritici Wtn1. Identified were 7707 protein-encoding genes, annotated to different categories such as 805 effectors, 156 CAZymes, 6102 orthologous proteins, and 3180 distinct protein families (PFAMs). Among the effectors, genes like Avra10, Avrk1, Bcg-7, BEC1005, CSEP0105, CSEP0162, BEC1016, BEC1040, and HopI1 closely linked to pathogenesis and virulence were recognized. Transcriptome analysis highlighted abundant proteins associated with RNA processing and modification, post-translational modification, protein turnover, chaperones, and signal transduction. Examining the Environmental Information Processing Pathways in B. graminis f. sp. tritici Wtn1 revealed 393 genes across 33 signal transduction pathways. The key pathways included yeast MAPK signaling (53 genes), mTOR signaling (38 genes), PI3K-Akt signaling (23 genes), and AMPK signaling (21 genes). Additionally, pathways like FoxO, Phosphatidylinositol, the two-component system, and Ras signaling showed significant gene representation, each with 15–16 genes, key SNPs, and Indels in specific chromosomes highlighting their relevance to environmental responses and pathotype evolution. The SNP and InDel analysis resulted in about 3.56 million variants, including 3.45 million SNPs, 5050 insertions, and 5651 deletions within the whole genome of B. graminis f. sp. tritici Wtn1. These comprehensive genome and transcriptome datasets serve as crucial resources for understanding the pathogenicity, virulence effectors, retro-elements, and evolutionary origins of B. graminis f. sp. tritici Wtn1, aiding in developing robust strategies for the effective management of wheat powdery mildew.

show abstract

Section: Comparative Genomic Analysismentioning

confidence: 99%

Section: Comparative Genomic Analysismentioning

confidence: 99%

Section: Deciphering the Trna Anticodons In The Genomementioning

confidence: 99%

See 1 more Smart Citation

Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics

Nallathambi,

Umamaheswari,

Reddy

et al. 2024

JoF

Self Cite

View full text Add to dashboard Cite

show abstract

“…Therefore, engineering the endogenous Bsr-d1 gene by gene-editing can enhance blast resistance of JG88 against different M. oryzae races in Jinlin province.When plants are not stressed, reactive oxygen species (ROS) are produced and removed to maintain dynamic equilibrium. SOD, CAT and POD are the main protective enzymes in plants, when plants are infected by pathogens, the activities of the three enzymes change to inhibit the pathogens(Javed et al 2023). Many studies have proposed that the production of ROS is closely related to plant disease resistance(Huang et al.…”

mentioning

confidence: 99%

CRISPR/Cas9-mediated knockout of Bsr-d1 enhances blast resistance of rice in Northeast China

Zhang,

Lin,

et al. 2024

Preprint

View full text Add to dashboard Cite

Rice blast is a globaldisease, which has a significant negative impact on rice yield and quality. Due to the complexity and changeability of the physiological races of rice blast, controlling the rice blast is challenging in agricultural production. Bsr-d1, a negative transcription factor confers broad-spectrum resistance to rice blast which was identified from the indica rice cultivar Digu, however, the biological function in japonica rice varieties is still unclear. In this study, we analyzed the blast resistance allele of OsBsr-d1 in a total of 256 japonica rice varieties of Jilin province in Northeast China and found that it does not exist in these varieties. Therefore, we developed Bsr-d1 knockout mutants by CRISPR/Cas9 system using a japonica rice variety Jigeng88 (JG88) as a recipient variety. Compared with the wild-type JG88, the homozygous Bsr-d1 mutant lines, KO#1 and KO#2, showed enhanced leaf blast resistance at seedling stage to several Magnaporthe oryzae (M. oryzae) races collected from Jilin Province in Northeast China. Physiological and biochemical indicators revealed that the homozygous mutant lines produced more hydrogen peroxide compared to JG88 when infected by M. oryzae. Comparative RNA-seq revealed that the DEGs were mainly involved in the synthesis of amide compounds, zinc finger proteins and transmembrane transporters, etc. In summary, our results indicate that the Bsr-d1 knockout mutants developed through gene editing technology can enhance the broad-spectrum resistance of rice in Northeast China to rice blast. This study not only provides a theoretical basis for disease resistance breeding of Bsr-d1 gene in Northeast China, but also provides new germplasm resources for disease resistance rice breeding.

show abstract

CRISPR/Cas9-mediated knockout of Bsr-d1 enhances the blast resistance of rice in Northeast China

Zhang,

Lin,

et al. 2024

Plant Cell Rep

View full text Add to dashboard Cite

Rice blast is a globaldisease, which has a signi cant negative impact on rice yield and quality. Due to the complexity and changeability of the physiological races of rice blast, controlling the rice blast is challenging in agricultural production. Bsr-d1, a negative transcription factor confers broad-spectrum resistance to rice blast which was identi ed from the indica rice cultivar Digu, however, the biological function in japonica rice varieties is still unclear. In this study, we analyzed the blast resistance allele of OsBsr-d1 in a total of 256 japonica rice varieties of Jilin province in Northeast China and found that it does not exist in these varieties. Therefore, we developed Bsr-d1 knockout mutants by CRISPR/Cas9 system using a japonica rice variety Jigeng88 (JG88) as a recipient variety. Compared with the wild-type JG88, the homozygous Bsr-d1 mutant lines, KO#1 and KO#2, showed enhanced leaf blast resistance at seedling stage to several Magnaporthe oryzae (M. oryzae) races collected from Jilin Province in Northeast China. Physiological and biochemical indicators revealed that the homozygous mutant lines produced more hydrogen peroxide compared to JG88 when infected by M. oryzae. Comparative RNA-seq revealed that the DEGs were mainly involved in the synthesis of amide compounds, zinc nger proteins and transmembrane transporters, etc. In summary, our results indicate that the Bsr-d1 knockout mutants developed through gene editing technology can enhance the broad-spectrum resistance of rice in Northeast China to rice blast. This study not only provides a theoretical basis for disease resistance breeding of Bsr-d1 gene in Northeast China, but also provides new germplasm resources for disease resistance rice breeding. Key MessageBlast resistance allele of OsBsr-d1 doesn't exist in most Japonica rice varieties of Jilin province in China. Bsr-d1 knockout mutants developed by CRISPR/Cas9 enhance the broad-spectrum resistance to rice blast in Northeast China.

show abstract

Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction

Cited by 3 publications

References 72 publications

Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics

Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics

CRISPR/Cas9-mediated knockout of Bsr-d1 enhances blast resistance of rice in Northeast China

CRISPR/Cas9-mediated knockout of Bsr-d1 enhances the blast resistance of rice in Northeast China

Contact Info

Product

Resources

About