Project description:Rice blast disease is a major threat to rice production worldwide, but the mechanisms underlying rice resistance to the causal agent Magnaporthe oryzae remain elusive. In this whole-genome transcriptome study of rice early defense response to M. oryzae, we applied Affymetrix Rice Genome Genechip to compare the compatible and incompatible rice-M. oryzae interactions in 24 hours post-inoculation.

2012-12-25 | GSE41798 | GEO

OsELP3/ELP4, rice Elongator factor complex subunits, epigenetically regulates rice blast resistance

Project description:Rice blast, caused by Magnaporthe oryzae (M.oryzae), is one of the three most devastating rice diseases, significantly reducing both yield and grain quality. The Elongator complex, first characterized in Arabidopsis thaliana, regulates growth, development, and innate immunity by tightly associating with hyperphosphorylated RNA polymerase II. However, its immunological role in rice remains unexplored. Here, we demonstrate that Elongator plays an essential role in rice blast resistance. The OsELP3 subunit mutant exhibited susceptibility to M.oryzae, while its overexpression increased resistance. OsELP3 interacts with its homologous subunit OsELP4 in the nucleus, and that OsELP4 also positively regulates rice blast resistance. RNA-seq and histone acetylation analyses demonstrated that OsELP3/ELP4 enhances transcriptional activation of key rice blast resistance genes by modulating histone acetylation levels in both the jasmonic acid (JA) signaling pathway (OsAOS1, OsLOX6, OsPROPEP3) and lignin biosynthesis pathway (OsMYB30, OsMYB55, OsMYB110), thereby strengthening plant defense mechanisms against M. oryzae. These findings reveal that OsELP3/ELP4 regulates histone acetylation-mediated defense responses against M.oryzae, providing both theoretical foundations and genetic resources for developing blast-resistant rice cultivars.

2026-06-06 | GSE333984 | GEO

Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycemic index and texture in rice

Project description:Reliably generating rice varieties with low glycemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa) explained the intermediate-to-high GI variation. A SNP (C>T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non‑starch polysaccharide pathway in lowering GI.

2019-02-01 | GSE123616 | GEO

Epigenome wide association study of post-mortem Alzheimer’s Disease samples

Project description:Samples from 72 AD patients and 62 age-matched cognitively normal controls were assayed using Illumina© Infinium MethylationEPIC BeadChip. We performed an epigenome-wide association study (EWAS) to evaluate the epigenetic differences using post-mortem superior temporal gyrus (STG) and inferior frontal gyrus (IFG) samples. We performed an epigenome-wide association study (EWAS) to evaluate the epigenetic differences using post-mortem superior temporal gyrus (STG) and inferior frontal gyrus (IFG) samples.

2020-10-20 | GSE156984 | GEO

rice sheath blight resistance

Project description:novel rice sheath blight resistance marker

| PRJEB28811 | ENA

Identification of bakanae disease resistance loci in japonica rice through genome wide association study.

Project description: Not available

| S-EPMC5465229 | biostudies-literature

CIDR_NIA Late Onset Alzheimer's Disease:Genome-Wide Association Study

Project description:CIDR_NIA Late Onset Alzheimer's Disease:Genome-Wide Association Study

| PRJNA75485 | ENA