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Transcriptome analysis of differentially expressed genes (DEGs) induced by RBSDV between the two NILs (NIL-R and NIL-S

ABSTRACT: Transcriptome analysis of differentially expressed genes (DEGs) induced by RBSDV between the two NILs (NIL-R and NIL-S

PROVIDER: PRJNA1049346 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27108974_1.fastq.gz	Fastqsanger.gz
	SRR27108974_2.fastq.gz	Fastqsanger.gz
	SRR27108975_1.fastq.gz	Fastqsanger.gz
	SRR27108975_2.fastq.gz	Fastqsanger.gz
	SRR27108976_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of differentially expressed genes (DEGs) induced by RBSDV between the two NILs (NIL-R and NIL-S

Project description:In the study, RBSDV accumulation was detected in NIL-S starting from 16 days post inoculation (dpi) and increased linearly thereafter to reach a high level. Concurrently, the viral S10 encoding the coat protein exhibited a dramatic accumulation in NIL-S but not in NIL-R, as did the viral S7-1. We performed RNA-seq analysis at 16 dpi between NIL-S and NIL-R. The differentially expressed genes (DEGs) were identified based on the criteria of fold-change > 2 and P < 0.05. Compared to NIL-R, NIL-S exhibited 24 downregulated and 21 upregulated DEGs. Gene Ontology (GO) term analysis revealed that these DEGs are mainly enriched in one molecular process: oxidoreductase activity, and in three biological processes: biology, oxidation-reduction, and single-organism. KEGG analysis demonstrated significant DEG enrichment in three pathways: photosynthesis-antenna proteins, fatty acid elongation, and diterpenoid biosynthesis.

2024-08-07 | GSE249472 | GEO

RNA-sequencing reveals differentially expressed rice genes functionally associated with defense against brown planthopper in NILs pyramiding BPH14 and BPH15

Project description:Brown planthopper (BPH) is one of the most destructive pests in rice production. The pyramiding application of BPH-resistance genes BPH14 and BPH15 can effectively improve rice resistance to BPH, however, the molecular mechanisms underlying BPH14/BPH15 pyramiding lines are poorly understood. Here, a mRNA expression profiling analysis was performed on the near isogenic lines (NILs) containing the BPH14, BPH15 or BPH14/BPH15 and their recurrent parent (RP) Wushansimiao. A total of 14492 differentially expressed mRNAs (DEGs) were identified from 12 mRNA profiles of resistant NILs and RP at different feeding stages. In the transcriptome analysis, 531 DEGs appeared to be common among the resistant NILs compared to RP before and after BPH feeding, which were enriched in defense response, phosphorylation and salt stress response. In addition, 258 DEGs shared only in resistant NILs were obtained among the different feeding stages, which were enriched in oxidative stress response, karrikin response and chloroplast organization. 21 DEGs were further selected as candidates for BPH resistance. OsPOX8.1, a potential candidate DEG related to BPH resistance, increased reactive oxygen species levels in rice protoplast. Our results provide valuable information to further explore the defense mechanism of insect-resistant gene pyramiding lines and develop robust strategies for insect control.

2023-07-03 | GSE232449 | GEO

Transcription profiling of Fusarium head blight resistance in Sumai-3 and two susceptible NILs

Project description:Microarray gene expression analysis were performed to identify genes responding to Fusarium graminearum inoculation and genes that show a differential regulation between the resistant c.v. Sumai-3 and the susceptible near isogenic lines. Sumai-3 is a Chinese wheat cultivar, the most commonly used source of resistance to Fusarium head blight (FHB) disease. NIL-3 and NIL-4 are near isogenic lines susceptible to FHB and are derived from a cross between Sumai-3 and Chuan980, a susceptible wheat cultivar, followed by seven generations of marker assisted backcrossing with the recurrent parent Sumai-3 and selection for FHB susceptibility in each generation by artificial inoculation with F. graminearum. A combination of DNA markers including simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs) were used to screen for DNA polymorphisms between Sumai-3 and its susceptible NILs. Polymorphic markers were mapped using a mapping population. The analysis indicated 7 polymorphisms between the susceptible NILs and the resistant Sumai-3. The analysis indicated that NIL-3 differs from Sumai-3 at chromosome 3BS and NIL-4 differs from Sumai-3 at chromosome 2AL region.

2009-11-16 | E-TABM-281 | biostudies-arrayexpress

NILS

Project description:NILS

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Transcriptome analysis of differentially expressed genes (DEGs) induced by Sporisorium reilianum between the two lines of ZmWRKY-KO and B73

Project description:The 7d-mesocotyls of wild type B73 and its ZmWRKY53-KO counterparts were treated with or without S. reilianum for RNA sequencing.The differentially expressed genes (DEGs) were identified based on the criteria of fold-change > 2 and P < 0.05. Under normal conditions, we found 1,025 downregulated and 599 upregulated differentially expressed genes (DEGs) in the ZmWRKY53-KO plant compared to its wild-type B73 counterpart. Under S. reilianum-infected conditions, 1,041 downregulated and 1,268 upregulated DEGs were identified in the ZmWRKY53-KO plant.

2024-10-04 | GSE278385 | GEO

The transcriptomes for primary panicle in four near-isogenic lines combined of different allele of two major grain length loci GS3 and qGL3 in rice

Project description:To investigate the genetic relationship between two major grain length loci GS3 and qGL3, we developed the near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3), NIL-qgl3 (gs3/qgl3), NIL-GS3/qgl3 (GS3/qgl3) in the background of 93-11 (gs3/qGL3) by crossing and MAS approach. Four samples was analyzed: three near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3), NIL-qgl3 (gs3/qgl3), NIL-GS3/qgl3 (GS3/qgl3) and their background of 93-11. Every sample had three independed duplications. And the primary panicle with 3-6 cm length from the three NILs and 93-11 were used for RNA preparation and hybrid with Rice Genome OneArray Microarray (Phalanx Biotech Group).

2014-07-22 | E-GEOD-59619 | biostudies-arrayexpress

Differentially expressed genes (DEGs) analysis in control and hsa_circ_0004287 knockdown THP1-derived macrophages

Project description:Differentially expressed genes (DEGs) analysis in control and hsa_circ_0004287 knockdown THP1-derived macrophages

| PRJNA713406 | ENA

The transcriptomes for primary panicle in four near-isogenic lines combined of different allele of two major grain length loci GS3 and qGL3 in rice

2014-07-22 | GSE59619 | GEO

Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae

Project description:Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is effectively controlled by Rps genes in soybean. Rps genes are race-specific, yet the mechanism of resistance, as well as susceptibility, remains largely unclear. Taking advantage of RNA-seq technology, we sequenced the transcriptomes of 10 near isogenic lines (NIL), each with a unique Rps gene, and the recurrent susceptible parent ‘Williams’. A total of 4330 differentially expressed genes (DEGs) were identified in ‘Williams’ while 2075 to 5499 DEGs were identified in each NIL. Comparisons between the NILs and ‘Williams’ allowed classification of two major groups of DEGs of interest: incompatible reaction associated genes (IRAGs) and compatible reaction associated genes (CRAGs). Hierarchical cluster analysis divided NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6). Heatmap analysis, along with GO analysis suggested that the diversity of clusters for NILs were likely due to variation of the number of DEGs and the intensity of gene expression, rather than functional differentiation. Further analysis suggested that transcription factors might play pivotal role in determination of the cluster pattern, and that WRKY family were strongly associated with incompatible reactions. Analysis of IRAGs and CRAGs with putative functions suggested that the regulation of many phytohormone signaling pathways were associated with incompatible or compatible interactions with potential crosstalk between each other. As such, our study provides an in depth view of both incompatible and compatible interactions between soybean and P. sojae, which provides further insight into the mechanisms involved in host-pathogen interactions. 22 samples were sequenced, 11 inoculated with P. sojae, the other 11 were mock-inoculated

2014-04-16 | E-GEOD-48524 | biostudies-arrayexpress

Comparitive transcriptome study of resistant NILs PB1+Pi1 and PB1+Pi54 and susceptible rice line (PB1) after M oryzae inoculation

Project description:Purpose: This study gives insight into transcriptomic dynamics and the set of important candidate acting as modules to regulate the changes in resistant NIL upon M.oryzae infection. Methods: Rice leaves were collected after M. Oryza (Mo-nwi-53) infection from resistant NILs and suceptible line were frozen in liquid nitrogen. RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma). Standard Illumina protocols was used for preparing RNA sequencing libraries. Results: Around 30 million pairs of filtered 101 base paired reads were obtained for each biological replicate. Conclusions: Pathway, gene set enrichment and co-expression analysis of SDEL unique to each resistant NIL respectively decipher the common broad spectrum resistance mechanism found in resistant NIL and provide important candidate genes.

2019-12-04 | GSE117030 | GEO

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