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Related Articles from SNS
Integrative genomics reveals shared and stress-specific adaptive pathways underlying acidic soil-associated metal toxicity in rice
Soil acidity-associated toxicities of aluminum (Al), cadmium (Cd), and manganese (Mn) severely constrain rice productivity in upland ecosystems. To investigate the genomic basis of adaptation to acidic soil-related metal stress, we conducted an integrated meta-QTL (M-QTL) and functional genomics analysis in rice. Meta-analysis of 681 QTLs and MTAs from 53 QTL mapping and GWAS studies identified 79 robust M-QTLs, including ten overlapping regions associated with Al-, Cd-, and Mn-responsive...
The genetics of transcriptional responses to stress in yeast
Alteration of gene expression levels is a key cellular strategy for responding to internal and external challenges. While expression quantitative trait loci (eQTLs) are known to influence steady-state transcript levels, their role in mediating rapid physiological transitions remains poorly understood. Using a high-throughput, "one-pot" single-cell RNA-seq approach, we mapped eQTLs in yeast immediately before and after two acute environmental shifts: salt perturbation of actively cycling...
Long-read RNA-seq resolves isoform-level and context-specific regulatory architecture of complex traits in cattle
Traditional short-read RNA-seq lacks the resolution to fully capture full-length isoforms and complex alternative splicing, leaving a "missing regulation" gap in existing molecular atlases. Here, we present a population-scale, multi-omics dissection of bovine complex traits using matched deep whole-genome sequencing (30), long-read (ONT) and short-read RNA-seq, as well as metabolome data from 432 dairy cows across four distinct lactation stages. We expanded the bovine transcript atlas with...
Cell-specific regulatory circuits connect genetic variation to disease susceptibility
Genome-wide association studies have identified thousands of variants associated with immune-related diseases, yet most lie in non-coding regions, complicating mechanistic interpretation. Regulatory quantitative trait loci (QTLs), such as expression QTLs (eQTLs) and chromatin accessibility QTLs (caQTLs), offer a powerful framework for prioritization and interpretation of these disease-associated genetic variants. When analyzed together, they offer deeper insights into the regulatory...
Genomic Dimensionality Bounds Mixed-Model Association Power and Fine-Mapping Resolution
Mixed-model genome-wide association studies (GWAS) behave differently in livestock than in humans, yet a unified explanation is lacking. Analyses using the full genomic relationship matrix (full-GRM; from genome-wide SNPs) yield only a few significant peaks even with hundreds of thousands of animals, whereas leave-one-chromosome-out (LOCO), numerator-relationship-matrix, and sparse-GRM approaches report many broad associations over similar data. Here we develop a framework that traces these...