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High yield and wide adaptation rice are crucial for grain supply and food security. Here the authors report OsPI4Kγ7 which contributes to different “adaptability-yield” trade-offs in japonica and indica, and provides an alternative breeding strategy for raising grain yield in different latitudes.

Expression quantitative trait loci (eQTL) analysis in patients with inflammatory bowel disease identify potential target genes for IBD GWAS loci not readily detected in individuals without disease highlighting the importance disease-focused studies.

Cell-free DNA is widely used in clinical testing, but its genetic basis remains unclear. Here, the authors perform cfGWAS in 28,016 pregnant women, identifying 15 loci linked to cfDNA end motifs and confirming roles for neutrophils through validation studies.

Here the authors identify via an East Asian mQTL study (n = 7,619) nearly 29,000 novel mCpG. It shows that mQTLs are strongly enriched for disease heritability, especially when ancestry is matched, underscoring their utility in interpreting GWAS results.

ATRX mutations are associated with developmental disorders and cancer, but how they affect gene regulation is unclear. Here, the authors report that ATRX loss can perturb alpha-globin gene expression by promoting G4- and R-loop-associated DNA damage via a G-rich repeat.

Most GWAS have focused on common variants or rare protein coding variants. Here, the authors interrogate the contribution of rare non-coding variants for anthropometric traits, identifying new genes associated with increased BMI and height.

molQTL mapping helps link genetic variants to molecular traits, but common tools overlook relatedness. Here, the authors develop OmiGA, a mixed‑model toolkit that increases power, fine‑mapping accuracy, colocalization performance, and efficiency for complex populations.

Here the authors report that a missense variant in ASCL5 causes lobodontia, a rare dental anomaly. Genetic analysis and mouse models confirm that the variant disrupts tooth and jaw development, overturning previous theories and defining the genetic basis of this rare condition.

CRISPR/Cas9 screens have identified genetic contributions to many phenotypes. However, studying combinations of genes or regulatory elements remains challenging. Here, the authors use CRISPR/Cas12a to overcome those challenges and enable new approaches to study combinatorial genetic mechanisms.

Using RAMPAGE across 115 human biosamples, this study maps over 26,000 transposable element–derived transcription start sites and shows how their evolutionary age and promoter features shape tissue-specific gene regulation in primates.

Crabgrasses (Digitaria spp.) are invasive upland weeds distributed globally. Here, the authors assemble a telomere-to-telomere reference genome of D. sanguinalis along with its diploid and tetraploid progenitors and reveal lineage-specific introgression of a herbicide resistance-associated gene through population genetics analyses.

Low outcrossing rate of sterile lines limits hybrid rice seed production. Here, the authors report that mutation of a SET domain-containing protein HER1 leads to enlarged stigma, enhanced stigma exsertion, and hybrid seed production in rice.

Chromatin loops are key to gene regulation, but standard normalisation can obscure regulatory interactions. Here, the authors present Raichu, a normalisation method that preserves enhancer-promoter signals and improves the detection of regulatory chromatin loops across platforms and conditions.

Here, the authors conduct a GWAS for eGFR, then a three-stage regional meta-analysis using GWAS summary data from the Eastern, Western, and Southern African geographical regions. Followed by fine mapping, colocalization, functional annotation, pathway analysis, and phenome-wide association studies showing weaker APOL1 effects in Africa.

The APOE-ε4/ε4 genotype is the strongest genetic risk factor for sporadic Alzheimer’s disease. Here, Brutman et al. identify a deletion common in people of African ancestry that reduces the relative risk conferred by the APOE-ε4/ε4 genotype.

The changing cellular, transcriptional, and genomic landscape of human lung aging can be characterized using single-cell RNA sequencing. Here, the authors show that lung aging is cell-type dyssynchronous, with alveolar epithelial and endothelial cells exhibiting the greatest changes in gene expression, transcriptional entropy, and a high level of somatic mutations.

Termite reproductives are long-lived and their genomes have abundant selfish genetic elements. Using long-read sequencing to profile transposable elements and DNA methylation, Qiu et al. uncover evolutionary arms races between TEs and host defences.

Structural variants are an underexplored source of genetic diversity. Here, the authors use phased pangenome graphs to improve detection of these variants in dairy cattle and link these variants to traits of economic importance.

Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid evolution through genome reshuffling, which can alter fungal pathogenicity.

In maize, ZmDapF1 suppresses the activity of ZmMDH6 in chloroplasts, exacerbating oxidative damage under drought. Knocking out ZmDapF1 or using its favourable allele with lower gene expression enhances drought resilience without yield penalty.

RNA modifications influence gene regulation, but global mapping was limited. Here, the authors introduce ORCA, a deep learning framework using nanopore RNA sequencing to detect multiple modification types, revealing isoform-specific patterns and regulatory interactions.

Many vascular‑disease risk loci lack defined causal genes. Here, the authors integrate functional genomics and CRISPR screens to identify genes influencing smooth muscle cell behaviour, validating roles for FES, BCAR1, CARF and SMARCA4, with Fes loss promoting atherosclerosis and hypertension.

Genome evolutionary history of wild Arachis species remains unclear. Here, the authors report the origin of small chromosome A08 and genome evolution of Arachis species via comparative oligopainting and genomic analysis of A. hoehnei.

Here the authors present scLong, a billion parameter foundation model trained on 48M single cells, using self attention across all 28k human genes and Gene Ontology knowledge. It captures long range gene context in single Cell transcriptomics.

The emergence and persistence of cellular life are the result of the integration of metabolic and genetic networks. Here the authors create a model synthetic cell that produces the key building blocks of life—DNA, RNA, proteins, and lipids—from a self-replicating genome encapsulated in liposomes.

Maternal mRNA regulation in growing oocytes is poorly understood. Here, the authors identify hnRNPM as a key splicing regulator during oogenesis. Its deletion causes severe cytoplasmic defects, meiotic arrest, and female infertility.

Papaya is a trioecious species with XX females, XY males, and XY^h hermaphrodites, and the combination of Y and Y^h chromosomes is lethal. Here, the authors identify the degeneration of the YY lethality gene on the Y chromosome as the causal balancing lethal factor that reenforces dioecy and stabilizes balanced sex ratios.

Genetic regulation of RNA splicing in immune cells remains incompletely understood in European populations. Here, the authors use single-cell data to map cell-type specific splicing QTLs, revealing how genetic variation influences complex trait risk through splicing regulation.

Here the authors systematically benchmark 13 polygenic score (PGS) methods in UK Biobank European and African populations, revealing factors that affect prediction accuracy. They also introduce an automated platform for standardized and reproducible PGS computation.

Natural variation in the promoter of OsTPS8 contributes to differences in grain chalkiness and seed vigor between indica and japonica rice subspecies by altering trehalose-6-phosphate biosynthesis and α-amylase levels.

Grain number per panicle (GNP) is a yield-determining trait of rice. Here, the authors identify a GSK3-like kinase-encoding gene GNP2 and a bZIP transcription factor-encoding gene GNP5, demonstrating their synergistic regulation of GNP and showing that specific allele combinations of these genes enhance rice yield in field conditions.

Large-effect variants in autism remain elusive. Here, the authors use long-read sequencing to assemble phased genomes for 189 individuals, identifying pathogenic variants in TBL1XR1, MECP2, and SYNGAP1, plus nine candidate structural variants missed by short-read methods.

Current mapping of fork progression in the human genome suffers from drastically low throughput. Here, the authors introduce ForkML, a nanopore sequencing-based method automatically positioning thousands of individual fork velocities by tracking BrdU incorporation into asynchronously growing cells.

The absence of a generic feature reference for single-cell scATAC-seq data limits analyses and hinders the development of comprehensive cell atlases. Here, the authors built cPeaks, a reference of 1.4 million consensus chromatin accessibility peaks to improve scATAC-seq analysis resolution.

Grain chalkiness is an undesirable trait that severely compromises rice quality. Here, the authors report the cloning of an E3 ubiquitin ligase encoding gene Chalk9 and reveal its crucial role in regulating grain chalkiness through mediating the ubiquitination-dependent degradation of OsEBP89.

Cholera remains a significant public health burden in sub-Saharan Africa, but the mechanisms of continental and regional spread remain undefined. Here, the authors investigate recent patterns of spread using Vibrio cholerae genomic surveillance data collected by a consortium of seven African Union member states from 2019-2024.

Here the authors present a compendium of avirulence genotypes for epidemiologically significant strains of wheat stem rust based on nuclear phased genome assemblies and functional assays to inform resistance gene deployment and pathogen surveillance.

Precise and efficient CRISPR genome editing requires specialized delivery systems. Here, the authors develop Coomassie lipidoids that deliver purified adenine base editors into retinal tissues, making it possible to achieve robust genome editing with a defined, non-viral nanomedicine.

Symbiotic bacteria can have exceedingly small genomes. This study finds that ancient bacterial symbionts of planthoppers have repeatedly evolved the smallest known genomes, losing most biosynthetic functions, revealing how extreme genome reduction shapes life at the edge of cellular complexity.

CRISPR-Cas9 genome editing is constrained by the need for a protospacer adjacent motif (PAM) at the target site. Here, the authors combine metagenomic mining with machine learning to map and predict PAM specificities across thousands of Cas9 enzymes, expanding the genomic target space.

Apomixis allows plants to reproduce clonally, yet it is unclear how rare sexual events shape their genomes. This study shows that residual sex in apomictic hickories causes recombination-driven loss of heterozygosity that exposes harmful mutations to selection and helps maintain clonality.

Changes in gene regulation are a major driver of human traits and disease. Here, authors develop e2MPRA, a high-throughput technology that simultaneously measures enhancer activity and associated epigenetic modifications, revealing how sequence variants influence regulatory function.

The authors in this work present a study with multiplexed gene editing that is used to assess all possible mutations at a native drug binding site. The approach yields data that predicts spontaneous resistance, that aligns with in silico predictions, and that promises to facilitate drug discovery.

Genetic and protein-protein interaction networks can be used to infer gene function and genotype-phenotype relationships. Here, the authors show that genetic interaction patterns reflect protein binding affinities.

Japonica subspecies has a lower nitrogen use efficiency (NUE) than that of indica rice. Here, the authors show that natural variations in the NIN-like protein 4 (OsNLP4) encoding gene are responsible for the divergence and introgression of the indica OsNLP4 allele into elite japonica cultivar can increase NUE and grain yield.

Schizophrenia risk at 1p36.23 lacked functional insight. Here, the authors identify two enhancer variants that upregulate RERE, which disrupts neurogenesis and synaptic function by regulating Grin2a, linking genetic risk to neuronal development and excitatory signaling.

Two-input chemogenetic tools remain limited. Here, authors develop ligand-responsive systems based on human nuclear receptors, using agonists and antagonists to reversibly control protein interactions and cellular processes, including synthetic protein condensate formation to enhance transcription.

The complexity of the evolved metabolic networks of flavonoids complicates pathway elucidation and design. Here, the authors identify enzymes that modify isoflavan scaffolds from the genome and transcriptome data of Glycyrrhiza glabra, and reconstruct de novo glabridin biosynthesis in yeast.

The factors contributing to the onset of Barrett’s esophagus, a precancerous stage of the highly lethal esophageal cancer, remain elusive. Here, the authors identify inherited mutations in the VSIG10L gene as a key etiologic determinant affecting esophageal biology and facilitating the development of Barrett’s esophagus.

For proper mitochondrial inheritance, paternal sperm mitochondria must be eliminated. Here, authors identify ALKB-1 mediated tRNA demethylation as essential for this clearance in Caenorhabditis elegans, revealing an epitranscriptomic quality checkpoint tied to male fertility.