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PubMed2026

Integrated functional genomics and safety assessment of plant-growth-promoting Caryophanales from post-maize-cultivation soils.

This study aimed to evaluate six environmental bacterial strains isolated from post-maize cultivation soils as candidates for agricultural biopreparation development, using an integrated functional genomic and safety assessment framework. Building on experimental validation of plant-growth-promoting activities, the analysis included: plant-growth-promoting traits (PGPT-Pred) using PLABase; carbohydrate-active enzymes (CAZymes) relevant for lignocellulosic crop residue degradation (dbCAN3); secondary metabolite profiles (antiSMASH); and screening for virulence factors and antibiotic resistance genes (ABRicate, BTyper3).All analyzed strains possess 1,449-1,617 predicted PGPT-encoding genes (24.1-35.9% of total genes), which are strongly shaped by taxonomic relatedness, as confirmed by congruence testing against ANI-based genomic divergence. Paenibacillus amylolyticus 5mez and Priestia megaterium 7psych showed distinct functional profiles compared to Bacillus spp., while Bacillus subtilis sensu lato strains were most similar to each other. Genomic predictions suggest involvement in nutrient acquisition (N, P, K, Fe) and stress mitigation. Secondary metabolite analysis revealed high biosynthetic potential, with non-Bacillus species harbouring a large proportion of unknown gene clusters, indicating underexplored metabolite diversity. CAZyme profiling identified P. amylolyticus 5mez as the most enzyme-rich strain, while B. cereus s.s. zielonkawy showed ligninolytic potential despite low overall CAZyme abundance. The safety assessment identified B. cereus s.s. zielonkawy as toxigenic and unsuitable for use. Of the remaining strains, P. amylolyticus 5mez and Pr. megaterium 7psych demonstrated the most favourable safety profiles, exhibiting no detectable virulence factors or antibiotic resistance genes, justifying their priority use in agricultural biopreparations, pending phenotypic validation. Given the high-dimensional, low-sample-size nature of multi-trait datasets in applied microbial genomics, tailored statistical approaches, including noise-reduction-validated PCA and distance-based congruence testing, were applied; their rationale and limitations are discussed.

Soil Microbiology↗

PubMed2025

Post-genome-wide association study dissects genetic vulnerability and risk gene expression of Sjögren's disease for cardiovascular disease.

OBJECTIVES: This study aims to clarify the genetic associations between Sjögren's Disease (SD) and cardiovascular disease (CVD) outcomes, and to conduct an in-depth exploration of specific pleiotropic susceptibility genes. METHODS: We performed two-sample and multivariable Mendelian randomization (MR) analysis to investigate the association between SD and the risk of ischemic heart disease (IHD) and stroke. Linkage disequilibrium score regression (LDSC) and Bayesian co-localization analyses were employed to assess the genetic associations between traits. Cross-phenotype analyses were employed to identify shared variants and genes, followed by a Transcriptome-Wide Association Study (TWAS) and Multi-marker Analysis of Genomic Annotation (MAGMA) based on Multi-Trait Analysis of GWAS (MTAG) results. To validate the pleiotropic genes, we further analyzed tissue-specific differentially expressed genes (DEGs) related to SD using RNA sequencing data. RESULTS: The two-sample and multivariable MR analyses revealed that SD confers a genetic vulnerability to IHD and stroke. LDSC and co-localization analyses indicated a strong genetic linkage between SD and CVDs. Cross-phenotype analyses identified 38 and 37 pleiotropic single nucleotide polymorphisms (SNPs) for SD-Stroke and SD-IHD, respectively, primarily located within the MHC class region on 6p21.32:33 loci. Additionally, TWAS and MAGMA analyses identified pleiotropic genes located outside the MHC regions-seven associated with stroke (UHRF1BP1, SNRPC, BLK, FAM167A, ARHGAP27, C8orf12, and PLEKHM1) and two associated with IHD (UHRF1BP1 and SNRPC). Proxy variants within these genes in SD suggested an increased causal risk for stroke or IHD. Co-localization analysis further reinforced that SD and stroke share significant SNPs within the loci of FAM167A, BLK, C8orf12, SNRPC, and UHRF1BP1. DEG analysis revealed a significant up-regulation of the identified genes in SD-specific tissues. CONCLUSIONS: SD appears genetically predisposed to an increased risk of CVDs. Moreover, this research not only identified pleiotropic genes shared between SD and CVDs, but also, for the first time, detected key gene expressions that elevate CVD risk in SD patients-findings that may offer promising therapeutic targets for patient management.

Humans↗

PubMed2024

Genomic selection for tolerance to aluminum toxicity in a synthetic population of upland rice.

Over half of the world's arable land is acidic, which constrains cereal production. In South America, different rice-growing regions (Cerrado in Brazil and Llanos in Colombia and Venezuela) are particularly affected due to high aluminum toxicity levels. For this reason, efforts have been made to breed for tolerance to aluminum toxicity using synthetic populations. The breeding program of CIAT-CIRAD is a good example of the use of recurrent selection to increase productivity for the Llanos in Colombia. In this study, we evaluated the performance of genomic prediction models to optimize the breeding scheme by hastening the development of an improved synthetic population and elite lines. We characterized 334 families at the S0:4 generation in two conditions. One condition was the control, managed with liming, while the other had high aluminum toxicity. Four traits were considered: days to flowering (FL), plant height (PH), grain yield (YLD), and zinc concentration in the polished grain (ZN). The population presented a high tolerance to aluminum toxicity, with more than 72% of the families showing a higher yield under aluminum conditions. The performance of the families under the aluminum toxicity condition was predicted using four different models: a single-environment model and three multi-environment models. The multi-environment models differed in the way they integrated genotype-by-environment interactions. The best predictive abilities were achieved using multi-environment models: 0.67 for FL, 0.60 for PH, 0.53 for YLD, and 0.65 for ZN. The gain of multi-environment over single-environment models ranged from 71% for YLD to 430% for FL. The selection of the best-performing families based on multi-trait indices, including the four traits mentioned above, facilitated the identification of suitable families for recombination. This information will be used to develop a new cycle of recurrent selection through genomic selection.

Oryza↗

PubMed2026

Genomic dimensions deconstruct the clinical heterogeneity of bipolar disorder.

Bipolar disorder's (BD) clinical heterogeneity has an unresolved genetic basis. We meta-analyzed genome-wide association studies (GWAS) of 16 BD subphenotypes in 226,032 individuals from 57 cohorts (38,022 cases); 10 advanced to multivariate and multi-trait analyses. Four factors (compulsive, psychotic, dysregulated, internalizing) explained 82.8% of shared genetic variance. BD1 and BD2 loaded on distinct factors despite a high genetic correlation; 87.0% of common-factor loci were significant in neither subtype. Unipolar mania aligned with psychosis over internalizing, and was distinguishable from BD1, and rapid cycling showed heritable cross-domain liability. We identified 356 risk loci, 158 novel, including the first univariate-GWAS associations for psychosis, unipolar mania, rapid cycling and schizoaffective disorder-and 249 credible genes (89 high-confidence), 12 with approved-drug or clinical-phase annotations. Cell-type association showed a midbrain dopaminergic-GABAergic gradient along the psychotic factor. BD's genetic architecture appears hierarchical-a general liability resolving into dimensions of course and comorbidity, beyond subtypes.

Journal Article↗

PubMed2026

Accounting for voluntary waiting period changes in US dairy herds: Adjusting daughter pregnancy rate and introducing first-service to conception.

The genetic evaluation of female fertility traits in dairy cattle in the United States has progressed over the past 2 decades, with 4 additional traits integrated into the national evaluation system since the introduction of daughter pregnancy rate (DPR) in 2004. However, concerns have arisen in the dairy sector, with reports of producers extending the voluntary waiting period (VWP), which is the time of initial breeding after calving, due to more persistent lactation yields. Since its inception, DPR calculations in the US evaluation have assumed a fixed 50-d VWP, which may not reflect modern reproductive strategies. Furthermore, producers may determine that some of their cows should have their VWP extended while others may follow the standard time. A re-evaluation of the current female fertility evaluation is necessary to ensure traits align with current management practices. Therefore, this study explores the addition of a potential new trait, First Service to Conception (FSC), along with a revised DPR formula that permits more flexibility with VWP. About 32 million records from the National Cooperator Database, covering 5 major dairy breeds (2003-2023), were used for this study. Data for cows calving before 2003 were unavailable because insemination records were not recorded prior. The findings suggest FSC enhances female fertility evaluations, providing a more comprehensive reproductive assessment independent of VWP. Another approach was an adjustment to the DPR calculation (DPRadj) to account for herd VWP on a herd-year and lactation group basis. The mean DPR value was 45.06%, while DPRadj increased the mean value to 52.58%. The mean FSC was 62.64 d. In an analysis using first lactation cows for cow traits and heifers for heifer traits, genetic correlations of FSC with other fertility traits were 0.97 with Cow Conception Rate (CCR) and DPR, 0.98 with DPRadj, 0.40 with Heifer Conception Rate (HCR), and 0.32 with Early First Calving (EFC). Predicted transmitting abilities (PTA) were calculated to assess the implications of adding FSC to, or replacing DPR with DPRadj within the CDCB multi-trait evaluation index, Net Merit $ (NM$). The highest correlation among the top 10% of bulls occurred when replacing DPR with DPRadj (0.99). Adding FSC to the original model reduced the latter correlation to 0.88, which indicates slight re-ranking of top bulls. Among animals with PTA reliability above 50%, the lowest correlation was between the original index and the index replacing DPR with FSC (0.95). This work advances genetic evaluation in dairy cattle, improving reproductive efficiency and productivity.

daughter pregnancy rate↗

PubMed2026

Dissecting the genetics of forage quality traits in soft red winter wheat in the U.S. southeast region.

Winter wheat plays a viable role in agriculture, not only as a primary grain crop but also as a valuable forage source that bridges fall-spring forage gaps in many regions, including the southeastern (SE) U.S. Despite its nutritive potential, genetic basis of forage-quality traits remains insufficiently understood, limiting breeding efforts for dual-purpose cultivars. This study aimed to dissect the genetic architecture of forage quality in 182 soft red winter wheat (SRWW) genotypes adapted to the SE U.S. using genome-wide association study (GWAS). Field experiments were carried out in randomized complete block design across three Georgia locations over two growing seasons (2023-2025), with forage sampled at the end of tillering and evaluated using near-infrared reflectance spectroscopy. Significant phenotypic variation was observed for dry matter (DM), crude protein (CP), acid and neutral detergent fiber (ADF, NDF), acid detergent lignin (ADL), total digestible nutrients (TDN), sugars (SUG), and relative forage quality (RFQ). Heritability estimates ranged from low-to-moderate in combined environments and from low-to-high within individual locations. Correlation analysis revealed strong positive associations among fiber-related traits and negative associations with TDN, RFQ, and SUG, while CP declined with increasing fiber. Genome-wide association analysis identified 282 significant marker-trait associations (P < 1×10-4) across 19 chromosomes, which were consolidated into 121 QTLs, including 27 major-effect QTLs. Three QTLs QRfq.uga-3B.1, QRfq.uga-3B.2 (RFQ) and QDm/Sug.uga-7A (DM, SUG) were stable across locations while QAdf/Adl.uga-2A (ADF, ADL) and QDm/Sug.uga-7A (DM, SUG) indicated multi-trait control. Notably, 25 of the 27 major QTLs were putatively novel, highlighting substantial untapped allelic diversity for forage-quality improvement in SE SRWW. Favorable allele accumulation resulted in an overall improvement in forage quality, increasing desirable nutritive traits (DM, RFQ, SUG, CP) while reducing undesirable traits (ADF, ADL). Candidate gene analysis linked six major QTLs with genes implicated in abiotic stress response, plant development, and metabolic regulation, supporting their functional relevance in forage-quality determination. Incorporating these loci into breeding programs provides a robust genetic framework for marker-assisted selection, enabling the development of dual-purpose wheat cultivars with enhanced forage quality, thereby strengthening wheat's utility as a reliable forage resource during periods of seasonal feed scarcity in SE production systems.

GWAS↗

PubMed2025

Shared Genetic Architecture Between Atopic Dermatitis and Autoimmune Diseases.

Atopic dermatitis (AD) and autoimmune diseases exhibit epidemiological comorbidity, yet the shared genetic architecture remains incompletely understood. We investigated the genetic overlap between AD and three autoimmune disorders including inflammatory bowel disease (IBD), rheumatoid arthritis (RA), and vitiligo, leveraging genome-wide association data. Despite modest evidence for global genetic correlations, we found 113 independent pleiotropic loci shared among AD and autoimmune diseases, with 11 displaying a concordant effect across all 3 pairwise comparisons. Gene-set and tissue enrichment analyses evidenced the inflammatory background of pleiotropic associations. Multi-trait colocalization analysis prioritized 22 loci, linking the tissue-specific expression of DOK2, GPR132, RERE, RERE-AS1, SUOX, TNFRSF11A, and TRAF1 pleiotropic genes with AD risk. Mendelian randomization revealed no causal effect of genetic liability to AD on autoimmune diseases. Nevertheless, genetic liability to IBD increased AD risk, while vitiligo exhibited a protective effect post outlier correction. Our findings provide mechanistic insights into the multimorbidity of atopic dermatitis (AD) and autoimmune diseases, offering additional evidence for the pleiotropic genetic architecture of AD that contributes to systemic immune dysregulation across multiple organ systems.

Humans↗

PubMed2026

Advances in Understanding Salt Stress Effects on Growth and Productivity in Sorghum (Sorghum bicolor L. Moench).

Salinity is a growing problem for cereal cultivation because it imposes multiple stresses, including osmotic, ionic, nutritional, and oxidative constraints, on the crop. Sorghum (Sorghum bicolor L. Moench) is considered a climate-smart C4 cereal for food, feed, fodder, forage, and bioenergy, but recent studies indicate that salinity continues to hinder establishment, biomass formation, reproductive growth, and yield. This review compiles the literature on the impacts of salinity on sorghum from 2021 to 2026, with a focus on germination, vegetative growth, physiological and biochemical responses, ion homeostasis, genetic control, productivity, mitigation, and future breeding priorities. In total, 160 records were identified, 118 records were screened after duplicate removal, and 44 recent sources were included in the synthesis. Across comparable sorghum studies, saline/NaCl treatments of approximately 60-200 mM commonly reduced germination by about 20-40%, root and shoot elongation by 25-50%, and biomass by 20-55%, while tolerant genotypes generally maintained higher K+/Na+ balance, 40-60% greater biomass retention, or two- to five-fold stronger ion homeostasis indicators than sensitive lines under similar conditions. Salt stress also lowers leaf expansion, chlorophyll stability, gas exchange, dry matter accumulation, panicle fertility, and grain filling. Tolerant genotypes show greater antioxidant potential, osmotic adjustment, photosynthetic stability, and root system resilience. Recent omics and genome-wide association studies suggest that salinity tolerance in sorghum is polygenic and involves genes related to ion transport, stress signalling, antioxidant regulation, osmolyte metabolism, and growth maintenance. This review recommends a shift from descriptive trait lists to full-cycle field validation, multi-trait selection indices, and integrated packages combining breeding with seed priming, soil water management, amendments, and beneficial microorganisms.

PRISMA↗