Ontology highlight
ABSTRACT:
PROVIDER: PRJNA861912 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20755400.fastq.gz | Fastqsanger.gz | |||
| SRR20755389.fastq.gz | Fastqsanger.gz | |||
| SRR20755390.fastq.gz | Fastqsanger.gz | |||
| SRR20755391.fastq.gz | Fastqsanger.gz | |||
| SRR20755392.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:<p>Free asparagine content is a key factor in acrylamide formation in wheat derivatives after high temperature processing. Therefore, the control of free asparagine levels is of interest in crop and food sciences. Our study aims to explore the natural variation in durum wheat to identify candidate genes controlling this trait. Durum wheat genotypes were selected from an international germplasm collection and sown in an experimental field in Italy for three years. Free asparagine content was measured on whole grain using an enzymatic assay. A genome-wide association study was performed, and six associated quantitative trait nucleotides were identified. Moreover, the whole grain metabolome of the durum wheat genotypes was investigated to identify metabolic pathways associated to free asparagine accumulation. Specific enriched pathways involved in amino acids metabolism were detected and four candidate genes were identified. This study paved the way to characterize the genetic determinants of free asparagine accumulation in wheat grain.</p>
2025-05-23 | MTBLS10381 | MetaboLights
Project description:Regulation of grain size is a crucial strategy for improving crop yield and is also a fundamental aspect of developmental biology. However, the underlying molecular mechanisms governing grain development in wheat remain largely unknown. In this study, we identified a wheat atypical basic helix-loop-helix (bHLH) transcription factor, TabHLH489, which is tightly associated with grain length through genome-wide association study and map-based cloning. Knockout of TabHLH489 and its homologous genes resulted in increased grain length and weight, whereas overexpression led to decreased grain length and weight. TaSnRK1α1, the α-catalytic subunit of plant energy sensor SnRK1, interacted with and phosphorylated TabHLH489 to induce its degradation, thereby promoting wheat grain development. Sugar treatment induced TaSnRK1α1 protein accumulation while reducing TabHLH489 protein levels. Moreover, brassinosteroid (BR) promotes grain development by decreasing TabHLH489 expression through the transcription factor BRASSINAZOLE RESISTANT1 (BZR1). Importantly, natural variations in the promoter region of TabHLH489 affect the TaBZR1 binding ability, thereby influencing TabHLH489 expression. Taken together, our findings reveal that the TaSnRK1α1-TabHLH489 regulatory module integrates BR and sugar signaling to regulate grain length, presenting potential targets for enhancing grain size in wheat.
2024-02-04 | GSE253343 | GEO
Project description:Introduction: Pre-harvest Sprouting (PHS) seriously affects wheat quality and yield. However, to date there have been limited reports. It is of great urgency to breed resistance varieties via quantitative trait nucleotides (QTNs) or genes for PHS resistance in white-grained wheat. Methods: 629 Chinese wheat varieties, including 373 local wheat varieties from 70 years ago and 256 improved wheat varieties were phenotyped for spike sprouting (SS) in two environments and genotyped by wheat 660K microarray. These phenotypes were used to associate with 314,548 SNP markers for identifying QTNs for PHS resistance using several multi-locus genome-wide association study (GWAS) methods. Their candidate genes were verified by RNA-seq, and the validated candidate genes were further exploited in wheat breeding. Results: As a result, variation coefficients of 50% and 47% for PHS in 629 wheat varieties, respectively, in 2020-2021 and 2021-2022 indicated large phenotypic variation, in particular, 38 white grain varieties appeared at least medium resistance, such as Baipimai, Fengchan 3, and Jimai 20. In GWAS, 22 significant QTNs, with the sizes of 0.06% ~ 38.11%, for PHS resistance were stably identified by multiple multi-locus methods in two environments, e.g., AX-95124645 (chr3D:571.35Mb), with the sizes of 36.390% and 45.850% in 2020-2021 and 2021-2022, respectively, was detected by several multi-locus methods in two environments. As compared with previous studies, the AX-95124645 was used to develop Kompetitive Allele-Specific PCR marker QSS.TAF9-3D (chr3D:569.17Mb~573.55Mb) for the first time, especially, it is available in white-grain wheat varieties. Around this locus, nine genes were significantly differentially expressed, and two of them (TraesCS3D01G466100 and TraesCS3D01G468500) were found by GO annotation to be related to PHS resistance and determined as candidate genes. Discussion: The QTN and two new candidate genes related to PHS resistance were identified in this study. The QTN can be used to effectively identify the PHS resistance materials, especially, all the white-grained varieties with QSS.TAF9-3D-TT haplotype are resistant to spike sprouting. Thus, this study provides candidate genes, materials, and methodological basis for breeding wheat PHS resistance in the future.
2023-01-08 | GSE222342 | GEO
Project description:Genome-wide association analysis to identify candidate genes for growth rate traits in Chinese endemic geese
| PRJNA1309086 | ENA
Project description:Genome-wide association analysis to identify candidate genes for growth rate traits in Chinese endemic geese
| PRJNA1305644 | ENA
Project description:Abstract Lysine crotonylation (Kcr) is a recently identified post-translational modification (PTM) in the prokaryotic and eukaryotic organisms. However, the function of lysine-crotonylated proteins in response to abiotic stress in plants remains largely unknown. Here, we report the first global profiling of the Kcr proteome in common wheat, identifying 4,696 Kcr sites on 1,726 substrate proteins, participating in a wide variety of biological and metabolic pathways. Combination of transcriptome and proteome in a RIL (recombinant inbred line) population, Kcr proteome, and genome-wide association study, a candidate gene phosphoglycerate kinase (TaPGK) was identified to potentially affect on cold tolerance in common wheat. Using EMS-mutants, overexpressed transgenic wheat plants and CRISPR/Cas9-mediated know-out mutants, we demonstrated that TaPGK played a positively key role in regulation of plant cold tolerance. Moreover, TaPGK protein strongly interacted with sirtuin-like (TaSRT1). EMS-mutant tetraploid and overexpressed transgenic wheat experiments confirmed that TaSRT1 gene negatively regulated wheat cold tolerance. Immunoprecipitation demonstrated that TaSRT1 promoted the degradation of TaPGK by erasing Kcr. Additionally, RNA-sequencing results showed that overexpressed TaPGK significantly improved expression of peroxidase genes. It concluded that a large number of Kcr sites were present in wheat important proteins and TaPGK crotonylated by TaSRT1 played a key role in wheat response to cold stress through scavenging the accumulation of ROS.
2023-07-20 | PXD030768 | Pride
Project description:Genome-wide transcriptional analyses of islet-specific CD4+ T cells identify Idd9 genes controlling diabetogenic T cell function
| PRJNA271610 | ENA