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Barley small RNA sequencing of Mlo near-isogenic lines

ABSTRACT: Small RNA sequencing of a barley powdery mildew susceptible cultivar (cv) Baudin near-isogenic lines (NILs) introgressed with mlo-11 and mlo-11 (cnv2) mutations

PROVIDER: PRJEB40118 | ENA |

REPOSITORIES: ENA

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Barley RNA sequencing of Mlo near-isogenic lines

Project description:Gene expression study for barley powdery mildew susceptible cultivar (cv) Baudin near-isogenic lines (NILs) introgressed with mlo-11 and mlo-11 (cnv2) mutations and cv Palace NILs with and without the mlo-5 null mutation.

| PRJEB39864 | ENA

Expression data in wheat (T. aestivum L.) near isogenic lines in response to powdery mildew infection

2011-02-15 | GSE27320 | GEO

Expression data in wheat (T. aestivum L.) near isogenic lines in response to powdery mildew infection

Project description:We used two wheat genotypes, the susceptible wheat cultivar ‘8866 ’(S) and its near isogenic line with single powdery mildew resistance gene ‘pm30’ (R), to investigate gene expression changes in response to powdery mildew infection by using Wheat Genome Array wheat young leveas of near isogenic lines before or 12 hours after powdery mildew infection were selected for RNA extraction and hybridization on Affymetrix microarrays.The leaf samples were harvested from three independent biological replicates, and the leaves without inoculation were regarded as control.

2011-02-15 | E-GEOD-27320 | biostudies-arrayexpress

mlo5-mediated resistance responses in barley

Project description:Gene expression of a near-isogenic pair of barley lines differing in absence or presence of the mlo5 resistance gene in response to attack by barley powdery mildew (Bgh). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Achim Fischer. The equivalent experiment is BB7 at PLEXdb.] disease type: Control - genotype: Mlo(1-replications); disease type: Control - genotype: mlo5(1-replications); disease type: Treated (Pathogen Infection) - genotype: Mlo(1-replications); disease type: Treated (Pathogen Infection) - genotype: mlo5(1-replications)

2011-11-22 | E-GEOD-33406 | biostudies-arrayexpress

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

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

Barley seed proteome analysis - Genes for seed longevity in barley identified by genomic analysis on near isogenic lines

Project description:Genes controlling differences in seed longevity between two barley (Hordeum vulgare) accessions were identified by combining a quantitative genetics approach with ˈomicsˈ technologies in Near Isogenic Lines (NILs). The NILs were derived from crosses between the spring barley landraces L94 from Ethiopia and Cebada Capa from Argentina, which produce short-lived and long-lived seeds, respectively. The NILs harbor introgressions from Cebada Capa in four QTLs for seed longevity on 1H and 2H in the background of L94. A label-free proteome analysis was performed on mature, non aged seeds of the two parental lines and the L94 NILs.

2018-07-23 | PXD009464 | Pride

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

Metabolomic Discrimination of Near Isogenic Low and High Phytate Soybean Seeds

Project description:Methodologies for untargeted metabolomic profiling using liquid chromatography-mass spectrometry (LC-MS) were developed and applied to lipid-depleted methanolic extracts of soybeans seeds obtained from four near isogenic soybean lines (NILs) that differed in phytate content. The four lines differed in mutations for genes encoding two highly homologous multi-drug resistant proteins (MRPs). The double mutant exhibited the low phytate/emergence phenotype whereas the other three NILs, namely the two single mutants and the wild type, did not. Lipid-depleted aqueous methanol extracts were analyzed by orthogonal chromatographic separations (reversed-phase and hydrophilic interaction) in both positive and negative ionization modes. Principal component analysis (PCA) of the LC-MS data clearly separated the low phytate line from the other three, with the major metabolite differences residing in the soyasaponin composition. Group A soyasaponins containing C22-terminated acetylated glucosides were of much lower concentration in the low phytate line, which favored terminally acetylated xyloside-based soyasaponins (soyasaponin A4, A5 and A6). Differing levels of the allergen Gly m 1 were also detected.

2016-02-04 | MTBLS120 | MetaboLights

Comparative proteomic analysis of near isogenic lines for qDSI.4B.1 QTL on short arm of chromosome 4B conferring drought tolerance in wheat

Project description:This study conducted isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis on near-isogenic lines (NILs) to shed light on the drought tolerance conferring qDSI.4B.1 QTL on short arm of chromosome 4B.

2023-05-24 | PXD036534 | Pride

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