Biomedical subjects

Yan Yan

Publications and source records attributed to Yan Yan.

4 recordsLinked to original sources

PubMed2026

Comparative Genome-Wide Association Studies of Metabolites and Grain-Related Traits in Common Wheat.

The metabolome is highly diverse and the closest layer to phenotype; therefore, it is commonly regarded as a bridge between the genome and phenome in plants. Here, we performed large-scale metabolome analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 33 grain-related traits in a diverse panel of natural accessions and a recombinant inbred line (RIL) population. We identified a new network of 2286 associations between 947 metabolites and 33 grain-related traits. Systematic integration of metabolic genome-wide association study (mGWAS) and metabolic quantitative trait locus (mQTL) analyses identified 33 566 significant single-nucleotide polymorphisms (SNPs) and 3128 mQTL. Thirteen annotated metabolites co-localized within a physical interval on 7A. Integration of metabolite-based and phenotype-based GWAS and QTL revealed an overlapped region for gibberellin A4 (GA4) content and grain roundness on 4A. Phenotyping of an ethyl methanesulfonate (EMS)-induced mutant confirmed the role of TaSDR in regulating GA4 content and grain morphology. These findings provide novel insights into the metabolic pathways influencing key grain-related traits and advance our understanding of the complex molecular mechanisms regulating grain metabolites and phenotypes in wheat. The identified metabolic markers and candidate genes provide valuable targets for molecular breeding programs aimed at improving wheat yield and quality.

QTL↗

PubMed2026

Complete genome sequences of three co-occurring Pseudomonas isolates from California Botanic Garden topsoil.

We report the complete genome sequences of three Pseudomonas isolates recovered from topsoil at the California Botanic Garden. Two isolates share ~99.4% average nucleotide identity, enabling investigation of intraspecies microvariation; the third represents a co-occurring distinct species, together capturing species- and strain-level genomic diversity within a natural soil community.

Pseudomonas↗

PubMed2025

Tensor decomposition of multi-dimensional splicing events across multiple tissues to identify splicing-mediated risk genes associated with complex traits.

Identifying risk genes associated with complex traits remains challenging. Integrating gene expression data with Genome-Wide Association Study (GWAS) through Transcriptome-Wide Association Study (TWAS) methods has discovered candidate risk genes for various complex traits. Splicing, which explains a comparable heritability of complex traits as gene expression, is under-explored due to its multidimensionality. To leverage multiple splicing events in a gene and shared splicing across tissues, we develop Multi-tissue Splicing Gene (MTSG), which employs tensor decomposition and sparse Canonical Correlation Analysis (sCCA) to extract meaningful information from high-dimensional multiple splicing events across multiple tissues. We build MTSG models using GTEx data and apply them to GWAS summary statistics of Alzheimer's disease (AD) (111,326 cases and 677,663 controls) and schizophrenia (SCZ) (36,989 cases and 113,075 controls). We identify 174 and 497 significant splicing-mediated risk genes for AD and SCZ, respectively, at Bonferroni correction. For AD, our results demonstrate significant enrichment of AD related pathways and identify additional AD risk genes not detected in the single-tissue analysis, while preserving most top genes identified in the brain frontal cortex. Consistently, for SCZ, genes identified by our brain-wide MTSG model, built from a cluster of 13 brain tissues, exhibit stronger enrichment in SCZ-relevant genes and MTSG identifies unique SCZ risk genes compared to single-tissue models. These results showcase that our MTSG models capture distinctive splicing events across tissues, which might be overlooked when using single tissue alone. Our MTSG models can be applied to other complex traits to help identify splicing-mediated disease risk genes.

Humans↗

PubMed2025

Water shortage reduces PHYTOCHROME INTERACTING FACTOR 4, 5 and 3 expression and shade avoidance in Arabidopsis.

In agricultural crops, forests and grasslands, water deficit often occurs in the presence of cues from neighbouring vegetation. However, most studies have addressed separately the mechanisms of plant growth responses to these two aspects of the environment. Here we show that transferring Arabidopsis thaliana seedlings to agar containing polyethylene glycol (PEG) to restrict water availability reduces hypocotyl growth responses to shade without simultaneously affecting cotyledon expansion or its response to shade. Hypocotyl growth showed significant triple interaction among water availability, shade and the presence of PHYTOCHROME INTERACTING FACTOR 4 (PIF4), PIF5 and PIF3. Water restriction diminished auxin signalling and the activity of the PIF4, PIF5, PIF3 gene promoters and their transcript levels. The responses of PIF4 expression and hypocotyl growth to PEG were reduced in mutants of its positive morning regulators CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). The CCA1 and LHY gene promoters also reduced their activity in response to PEG. In addition to the changes in PIF4 levels, post-transcriptional processes also contributed to the PIF4 protein response to PEG. Collectively, these results unveil PIFs as a hub that interlinks shade and drought information to control growth.

Arabidopsis↗