Genotypic
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Related Articles from SNS
Integrated Evaluation of Osmotic and Antioxidant Defense Mechanisms in Cotton Genotypes Exposed to NaCl Stress
Salinity stress is one of the major abiotic factors limiting cotton productivity worldwide by inducing osmotic imbalance, oxidative stress, and metabolic disturbances in plant tissues. The present study aimed to evaluate the physiological and biochemical responses of different cotton (Gossypium hirsutum L.) genotypes under NaCl-induced salinity stress through analysis of proline accumulation, antioxidant enzyme activities, and lipid peroxidation intensity. The experiment was conducted under...
Genotypic and multi-environment phenotypic evaluation of the lima bean USDA National Plant Germplasm System collection
Lima bean (Phaseolus lunatus L.) is an economically and agronomically important grain legume. Lima beans (or limas) show a range of climatic adaptations with independent domestications in the Andes (large-seeded) and Mesoamerica (small- or medium-seeded). We generated and integrated genotypic and comprehensive field- and laboratory-based phenotypic information for the available accessions in the USDA National Plant Germplasm System collection across multiple environments to inform germplasm...
Genotype and methylation interact to reconfigure transcriptional regulation in colorectal cancer
Background Transcriptional regulation is shaped by both genomic variants and the environment. Yet, how the regulatory effects of genomic variants are reconfigured by dynamic epigenomic changes during tumorigenesis remains incompletely understood. Methods We investigated methylation context-dependent links between genotype and gene expression in colorectal cancer (CRC) using paired tumor and normal-adjacent tissue (NAT) from 80 patients, thereby controlling for germline genomic background.
Genotype-Conditioned Molecular Generation via Evidence-Grounded Multi-Objective Latent Perturbation in Diffusion Models
arXiv:2606.01461v1 Announce Type: new Abstract: Developing effective anticancer therapeutics remains challenging due to tumor heterogeneity and the absence of well-defined molecular targets across cancer subtypes. Generative models conditioned on cancer genotypes offer a promising avenue for personalized drug discovery, yet existing approaches lack explicit optimization for simultaneous sensitivity, synthesizability, and mechanistic binding plausibility.
Imputed graph-genotyped structural variants identify regulatory haplotypes associated with gene expression in Atlantic salmon
Structural variants (SVs) can affect gene regulation, but they are difficult to include in expression genetic studies when large RNA-seq cohorts lack whole-genome sequencing. This is common in non-human and non-model systems, where whole-genome sequencing at population scale remains costly. As a result, expression quantitative trait locus (eQTL) studies often rely on single nucleotide polymorphism (SNP) markers.
Two Genomes, One Metabolome: Mitonuclear Incompatibility Remodels Developmental Metabolism and Fitness in Drosophila
Mitochondrial-nuclear (hereafter mitonuclear) genetic variation can alter cellular bioenergetics and metabolism via jointly encoding the subunits of oxidative phosphorylation (OXPHOS) system. Here we tested whether genetic variation in biochemical and bioenergetic phenotype can scale up across higher levels of biological organization to affect organismal development. We used a panel of (mtDNA); nDNA genotypes created by asymmetric substitution of divergent mtDNA between Drosophila...
Scalable in vivo cardiac functional genomics with compressed AAV-Perturb-seq reveals a common mitochondrial response to perturbation
Efficient identification of new targets to treat human disease requires a scalable way to link genotype to phenotype directly in the target organ. Pooled CRISPR screening with single-cell RNA sequencing as a readout (Perturb-seq) has emerged as a method for functional genomics but is typically applied in vitro and is limited in scale. Here, we combine in vivo Perturb-seq via adeno-associated virus (AAV)-mediated delivery with a statistical framework allowing for signal deconvolution after...
Modes of natural selection on maternal and zygotic gene expression in Drosophila melanogaster embryos
Early embryonic development involves the coordination of gene expression from two distinct genomes, as mothers load eggs with gene products prior to the beginning of zygotic transcription. Because the maternal transcriptome is controlled by the mothers regulatory genotype rather than that of the embryo, these two sequential developmental programs may experience distinct evolutionary constraints and selection pressures despite both existing within the embryo. To infer modes of selection on...
An interpretable machine learning framework for dog breed inference and ancestry decomposition
The over 300 currently recognized breeds of domesticated dogs are the culmination of centuries of intense artificial selection and recurrent population bottlenecks. While breed labels are widely used in genetic and veterinary studies, inferring breed identity from genomic data remains challenging due to the high dimensionality of genotype data, uneven sampling across breeds, and admixture resulting in mixed-breed individuals. Here, we present an interpretable machine learning framework to...
The canine respiratory epithelium is a permissive ecosystem for influenza interspecies transmission and emergence
The outcome of virus spillover ranges from dead-end infections to pandemics and is underpinned by host-pathogen interactions as well as evolutionary and epidemiological processes. The emergence of novel influenza A viruses (IAVs) has been associated with reassortment events involving multiple species, highlighting the importance of reservoir and intermediate hosts in viral emergence. Highly pathogenic H5N1 IAVs of the 2.3.4.4b genotype have caused a panzootic affecting a broad range of mammals.