Integrated genomics and metabolomics analysis revealed the metabolic mechanisms by which genetic variations affect the growth performance of local chickens.

Exploring genetic diversity and grouping genetic materials into distinguished clusters are basic steps in developing sustainable crop varieties within any breeding program. In this line, the molecular marker systems serve as one of the most important biological tools that provide valuable information at the molecular level. In this dataset, three molecular marker techniques, including inter-primer binding site (iPBS), Start codon-targeted (SCoT), and CAAT box-derived polymorphism (CBDP) in terms of their potential to explore genetic diversity and group the 111 Aegilops tauschii accessions. Based on the results, iPBS primers showed higher values for total amplified fragments (TAF = 14.70), polymorphic amplified fragments (PAF = 14.70), polymorphism information content (PIC = 0.41), marker index (MI = 16.31), and resolving power (Rp = 6.13) compare to SCoT (TAF = 10.80; PAF = 10.80; PIC = 0.38; MI = 12.90; Rp = 4.12) and CBDP (TAF = 9.93; PAF = 9.33; PIC = 0.37; MI = 4.12; Rp = 3.44) markers. In all analysis of molecular variance (AMOVA) based each marker technique, the genetic variation within populations was exceeded the variation among them (SCoT = 57 % vs 42 %; CBDP = 58 % vs 42 %; iPBS = 68 % vs 32 %). However, gene-targeted markers (SCoT and CBDP) showed more efficiency in grouping the accessions compared to iPBS technique. In more detail, CBDP markers revealed a clearer and more stable grouping of Ae. tauschii accessions, so grouping patterns were consistent with the geographical distributions of the studied accessions. Overall, this report suggests that the CBDP marker technique can serve as a powerful genotyping tool with substantial potential for assessing genetic diversity and further phylogenetic studies.

Expanding horizons of ecological and evolutionary research in urban heat islands.

Stomatal and leaf hydraulic conductivity responses to changing light and CO2 conditions in Phaseolus vulgaris.

Monkeypox virus: Pandemic and antiviral drugs.

Phakopsora pachyrhizi, the causative agent of Asian soybean rust, poses a major threat to soybean production in South America. The rising incidence of fungicide resistance underscores the need for a deeper understanding of its underlying genetic mechanisms. This study characterized fungicide resistance profiles in P. pachyrhizi from Paraguay, integrating genetic mutation analyses with molecular dynamics simulations to elucidate resistance mechanisms and inform disease management strategies. The first characterization of fungicide resistance profiles in P. pachyrhizi from eastern Paraguay (2022-2023) revealed multiple resistance patterns to demethylation inhibitor (DMI), succinate dehydrogenase inhibitor (SDHI), and quinone outside inhibitor (QoI) fungicides. Detached leaf assays demonstrated reduced fungicidal efficacy relative to susceptible control strains. Pyrosequencing revealed mutations in CYP51 (F120L, V130A, Y131H/F, I145V), SDH-C (I86F), and CYTB (F129L), with variable mutation values across populations and isolates. Notably, isolates from a single field displayed substantial genetic and phenotypic variability, indicating complex intra-field resistance dynamics. CYP51 mutations were markedly overexpressed in cDNA relative to gDNA, reinforcing their contribution to DMI resistance. Molecular dynamics simulations of prothioconazole-desthio interactions revealed key structural determinants of resistance, in which protein-water-ligand networks played a critical role in modulating fungicide efficacy. These findings provide critical insights into the genetic basis of fungicide resistance in P. pachyrhizi and highlight the necessity for continuous molecular surveillance, resistance management, and strategic adaptation of fungicide applications to mitigate the spread of resistant strains in soybean-growing regions of South America. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Decoding metabolic reprogramming heterogeneity across bladder cancer stages using single-cell and spatial multi-omics approaches.

Cell-type-specific genetic architecture of postpartum depression: A single-cell Mendelian randomization framework for causal gene discovery.

Microsatellite-based assessment of genetic variation, bottleneck signatures and population structure in Omani and exotic goats

Rapid evolution of marine phytoplankton under global change: mechanisms, constraints, and ecological consequences.

This dataset illustrates the genetic diversity and evolutionary linkages of five underutilized Nigerian native legume species: Parkia biglobosa, Albizia lebbeck, Cassia fistula, Leucaena leucocephala, and Senna alata. These species are vital sources of sustenance, nutrition, revenue, and natural fertilizer, significantly contributing to sustainable agriculture. Nevertheless, limited knowledge exists regarding their genomes and their genetic diversity. We examined 22 high-quality chloroplast matK (Maturase K) gene sequences to assess the genetic divergence among the species and their phylogenetic relationships. The analysis of sequence alignment and diversity recorded 888 nucleotide positions, identified 10 segregating sites, 11 mutations, and 3 distinct haplotypes. Gene diversity was 0.654, whereas nucleotide diversity was negligible at 0.028. The analysis of molecular variance (AMOVA) indicated that 88.04% (p < 0.001) of genetic variation was shared among populations, whereas 11.96% was detected within populations. Employing the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithm for phylogenetic analysis, the species examined were classified into unique evolutionary lineages along species lines with a minimal exception. This information serves as a valuable genetic resource for enhancing conservation, breeding initiatives, and the sustainable utilization of underutilized native legumes in tropical settings. It impacts food security, agroforestry, and environmental restoration.

Mobile genetic elements drive the assembly of high-risk resistance and virulence configurations at the riverine water-sediment interface.

Development and efficacy of autogenous multivalent vaccine to prevent Motile Aeromonas Septicemia (MAS) and Bacillary Necrosis of Pangasius (BNP) in striped catfish (Pangasianodon hypophthalmus).

Bovine viral diarrhea virus (BVDV) is globally endemic, with the ability to establish persistent infection (PI) being central to its complex epidemiology. Currently the genetic variability of BVDV in Bangladesh remains poorly understood. This study involved a survey in commercial dairy herds in the south-eastern part of Bangladesh in 2024/2025. A total of 373 blood samples were collected from cattle in 24 dairy herds. Serum and buffy coat samples were analyzed using antibody-ELISA and RT-qPCR targeting the 5'-UTR region, followed by sequencing. The MDBK cell line was used for virus isolation and biotyping. Herd and animal-level seroprevalences were 83.3% and 15.3%, respectively, while the corresponding viremic rates were 79.2% and 11.0%. Analysis of 41 sequences identified nine distinct BVDV-1 subgenotypes (1a, 1b, 1c, 1d, 1e, 1k, 1p, 1o, and 1v), with BVDV-1b (41.5%) and BVDV-2a (14.6%) predominating. Additionally, five HoBiPeV-a pestiviruses were detected. Among antigen-positive cattle, 38 (92.68%) were identified as transiently infected and 3 (7.3%) were confirmed as PI. Six (14.6%) and 27 (65.9%) were identified as cytopathic and non-cytopathic biotypes, respectively. Risk factors for BVDV seropositivity included: female sex (OR: 3.0), clinical disease in the past three months (OR: 2.4), crowding (OR: 2.9), and lack of dedicated clothing for farm workers (OR: 5.7). Active infection was associated with calves (OR: 6.2), heifers (OR: 2.3), stunted growth (OR: 3.0), technician-performed artificial insemination (OR: 10.4), and frequent neighboring farm visits (OR: 3.1). This study has provided data crucial for formulating prevention and control strategies against BVDV to safeguard the Bangladeshi dairy industry.

Combination immunization with mRNAs encoding PRRSV antigens enhances immune responses and confers protective immunity against highly pathogenic PRRSV in piglets.

There is a burgeoning body of research suggesting a possible relationship between thyroid function and carpal tunnel syndrome (CTS). This study aimed to investigate the potential causal relationship between various aspects of thyroid function and CTS using a two-sample mendelian randomization (MR) approach. However, their causal relationship has yet to be conclusively determined. Using summary data from extensive genome-wide association studies, we conducted a two-sample MR analysis to investigate the potential genetic causal relationship between thyroid function-encompassing hyperthyroidism, hypothyroidism, thyroid-stimulating hormone, free thyroxine (FT4), free triiodothyronine, total triiodothyronine, and their ratios (free triiodothyronine/FT4 and total triiodothyronine/FT4)-and CTS. Our analytical strategy included the inverse-variance weighted (IVW) method, supplemented by MR-Egger regression, weighted median, and weighted mode analyses, with the IVW method regarded the primary analytical approach. Sensitivity analyses were done using Cochran Q test, the MR pleiotropy residual sum and outlier test, MR-Egger regression, and the leave-one-out method. Robust sets of genetic instrumental variables were identified for different aspects of thyroid function using stringent selection criteria (including F-statistics >10). The IVW method, relying on genome-wide association studies summary data for thyroid function, did not provide evidence a supporting causal effect of genetically predicted thyroid function on CTS (all P > 0.05). Despite observed heterogeneity and pleiotropy in some relationships, the overall findings were consistent and robust across all sensitivity analyses. Our two-sample MR analysis did not establish a potential causal relationship between thyroid function and CTS, highlighting the necessity for further studies to clarify the complex interplay between these two entities.

Ex-situ breeding programs often utilize pedigree-analysis to select breeding pairs with the goal of maximizing retention of genetic variation and establishing self-sustaining populations. These efforts are limited when selected pairs fail to reproduce successfully. Because mate-choice serves an important role in many mating systems, providing the opportunity to engage in this behavior could lead to greater pair compatibility and offspring survival. In this study, we investigated the impact of female mate-choice on reproductive success and animal welfare of two passerine species: blue-gray tanagers (Thraupis episcopus) and red-capped cardinals (Paroaria gularis). One group of females were allowed to demonstrate a preference between three potential males and were subsequently paired with their preferred mate. A second group of females were paired with their pedigree-assigned partner. We measured a variety of reproductive parameters (onset of nesting, number of eggs, and number of fledglings) and evaluated animal welfare using positive (behavioral diversity) and negative (fecal glucocorticoid metabolite) indicators of welfare. There was no statistically significant difference in reproductive success based on pairing method for either species. Females allowed to choose their mate had significantly higher behavioral diversity than those assigned a mate (p < 0.03), however there was no difference in male behavioral diversity between the two groups. These findings suggest that the opportunity for mate-choice may lead to greater welfare, but only for the individual expressing preference. Outcomes of the study highlight the many variables that can affect reproductive success and the considerable research still needed.

With the increasing accuracy and decreasing cost of sequencing technology, the extent of structural variation (SV) and its importance in crop species has become increasingly evident. SVs such as insertions, deletions, and inversions have been associated with genetic variation of agronomically important traits and the diversification of crop species. Pangenomes aim to capture the genetic diversity of a species, population or genus, by incorporating the genomes of multiple individuals. The additional genetic diversity represented by a pangenome compared to a single-genome reference can aid the association of variation with traits and support crop improvement. Genus-wide pangenomes representing related crop species as well as their wild relatives can be used to identify and introduce novel genetic variation associated with agronomically important traits into crops. Pangenomes can aid crop improvement through pangenome assisted breeding (PAB) and genome editing. PAB is an adaption of marker assisted breeding that associates pangenome-based markers, including single nucleotide polymorphisms (SNPs) and SVs, with a trait of interest. Genome editing can use CRISPR/cas9 or similar tools to introduce or change the expression of agronomically important SVs. Pan-epigenomics is an emerging field that can complement pangenomics studies by identifying epigenetic modifications such as DNA methylation, histone modifications, and chromatin accessibility, which play important roles in regulating gene expression and have been shown to contribute to intraspecific diversity and agronomically important traits. We highlight the advances of crop pangenomics and their use in crop breeding and improvement.

Traumatic brain injury (TBI) is a leading cause of disability and death, with outcome severity varying widely even among individuals with comparable injuries. A major challenge is to identify pathways that underlie this variation and could be targeted to improve therapies. Innate immune pathways are candidates because they are rapidly activated after TBI and contribute to neurodegenerative disorders. Using a Drosophila melanogaster TBI model, we examined how genetic background, age, and diet modify effects of evolutionarily conserved Toll and Immune deficiency (Imd) pathways on injury outcomes. These pathways signal through nuclear factor-kappa B (NF-κB) transcription factors Dorsal-related immunity factor (Dif) and Relish (Rel) to activate antimicrobial peptide (AMP) gene expression. We found that genetic diversity among lines from the Drosophila Genetic Reference Panel (DGRP) contributed to variation in AMP expression before and after TBI, with additional effects of age and diet. AMP expression tended to be correlated positively with early mortality following TBI in young flies, but negatively in older flies, suggesting an age-dependent shift in AMP effects from detrimental to protective. Furthermore, heterozygous mutations in Dif or Rel lowered AMP expression in a diet-dependent manner and led to correspondingly reduced early mortality after TBI. These findings show that genetic, biological, and environmental factors influence innate immune pathways, which in turn determine TBI outcomes. Innate immune gene expression before injury emerges as a potential prognostic indicator, pointing to potential new therapeutic strategies.

The ecology of horizontal gene transfer.