Identification of a novel gene GmCESA7 encoding cellulose synthase controlling plant height in soybean.

Sorghum (Sorghum bicolor L. Moench) is a drought-tolerant crop, with its resilience essentially attributed to high transpiration efficiency (TE), and simply defined as the biomass produced per unit of water transpired. Understanding the genetic architecture of TE is crucial for breeding water-efficient varieties. This study undertook a genome-wide association study (GWAS) using SNP marker on 112 sorghum genotypes to identify genomic regions controlling TE and related physiological traits at the flag leaf stage using 17,637 imputed SNP markers. Phenotypic evaluation revealed significant variation for key traits like root dry wight (RDW), shoot dry weight (SDW), plant dry weight (PDW), water used efficiency (WUE), Root plant ratio (RTR), chlorophyll a concentration (Chla), Transpiration rate (TR) and TE, with moderate to high heritability. Using a multi-locus GWAS approach, we identified 23 robust quantitative trait nucleotides (QTNs) associated with eight traits except WUE. Notably, we discovered pleiotropic genomic hotspots on chromosomes 2, 3, 6, and 9 that simultaneously influence biomass (PDW, SDW) and TE. A meta-analysis showed that 86.9% of these QTNs co-located with previously reported QTLs, validating these regions, while three QTNs were novel. Candidate gene analysis within the QTN regions pinpointed 218 genes with different functions such as hormone signaling (auxin, cytokinin), stomatal regulation (S-type anion channel), root development (glutamate synthase), and photosynthesis (chlorophyll biosynthesis). Six QTNs also found intergenic, between start/end regions of the genes. Our findings provide valuable molecular tools for marker-assisted selection and highlight key candidate genes for enhancing transpiration efficiency and drought adaptation in sorghum.

Being a staple crop and growing over larger area, rice (Oryza sativa L.) generates a vast quantity of straw as a by-product. However, high fibre and silica content present in rice straw makes it difficult to utilize as a quality livestock feed or for industrial utilization, thus necessitating to identify genetic resources with lower silica content and enhanced straw digestibility. In this study, 207 diverse rice germplasm accessions belonging to 2K rice diversity panel and 25 cultivated varieties were evaluated for straw cell wall components (silica, lignin and cellulose), agronomic traits (plant height, number of tillers, stem thickness) and in-vitro digestibility (acid detergent fibre). Wide variation was observed for silica (4.3-15.7%), lignin (4.9-29.5%), cellulose (20.3-45.2%), plant height (65.6-197.0cm), number of tillers (4.0-19.0), stem thickness (0.9-9.2mm) acid detergent fibre (ADF; 45.1-73.0%). Correlation analysis revealed a strong negative relationship between silica and organic as well as dry matter digestibility while lignin displayed variable effects depending on its interaction with other components. Multi-locus-Genome-wide Association Studies (ML-GWAS) with a subset of 154 rice accessions using 208,846 SNPs identified 33 significant marker-trait associations (MTAs) across genome for straw silica, lignin, cellulose, and ADF content. Major MTAs co-localized with known genes involved in silicon uptake (OsOPT2, OsOPT3, OsUCP2), lignin biosynthesis (4CL3, WRKY71, OsACS7), and cellulose synthesis (WAK12, BGLU4, OsMPS). Haplotype analyses of key candidate genes revealed superior alleles associated with up to 15.9% lower silica and 26.9% lower lignin content, with corresponding higher expression in relevant tissues. Selected rice accessions with favourable alleles and balanced ADF, lignin, and silica showed improved in-vitro digestibility, providing promising genetic resources for enhancing rice straw palatability. These findings offer valuable insights into the genetic basis of straw quality traits and identify potential donors for breeding programs aimed at developing rice varieties with improved straw value for sustainable agriculture and bioenergy use.

This study aimed to identify genetic markers for body weight in adult male Dongfeng sika deer (Cervus nippon) using a genome-wide association study (GWAS). A cohort of 266 healthy, five-year-old stags was phenotyped and genotyped via whole-genome resequencing. Population structure was assessed, and a mixed linear model (MLM) was employed for association testing, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of candidate genes. The GWAS identified twelve genome-wide significant SNP loci, which were annotated to seven candidate genes: ERC2, LOC122708028, FHIT, CASP14, UBE3A, NRXN3, and GABRA5. Functional enrichment analyses revealed these genes are significantly involved in the γ-aminobutyric acid (GABA)ergic synaptic transmission pathway and pathways related to DNA damage repair and cell cycle regulation. This study provides insights into the genetic mechanisms underlying body weight traits in adult male Dongfeng sika deer and offers a reference for subsequent functional exploration of candidate genes.

Genome-wide analysis of inbreeding patterns and candidate genes for adaptation in indigenous chickens of Botswana.

We aimed to investigate whether genetic variation is associated with venous thromboembolism after immunization with SARS-CoV-2 vaccines. We conducted a genome-wide association study (GWAS) on cases of venous thromboembolism within 42 days after SARS-CoV-2 vaccination, recruited from reports of adverse drug reactions sent to the Swedish Medical Products Agency. Two hundred one cases (43% women, 91% Swedish) were compared with 4891 Swedish population controls. Analyses were performed on two candidate variants in coagulation factor II (rs1799963) and coagulation factor V (rs6025), on 14 prespecified candidate genes and across the whole genome. To support the findings, we conducted an observational register study of the Swedish general population with/without a diagnosis of thrombophilia and the risks of venous thromboembolism after SARS-CoV-2 vaccination. In the GWAS, the main findings were that the candidate variants of coagulation factors II rs1799963 and V rs6025 were significantly associated with venous thromboembolism (odds ratio [OR] 2.4 [95% confidence interval (CI) 1.2-4.8], p = .015 and OR 1.8 [95% CI 1.3-2.6], p = .0022). No genetic marker passed the significance threshold in the candidate gene analysis or the full genome-wide analysis. In the register study, people with a thrombophilia diagnosis had a five-fold elevated risk of venous thromboembolism within 42 days after vaccination, adjusted for potential confounders, OR 5.06 [95% CI 3.98-6.44]. Well-characterized genetic variants in the genes of coagulation factors II and V were associated with thromboembolism after SARS-CoV-2 immunization. Further research is recommended to elucidate their potential role in vaccine-related thromboembolic events.

qHSW_11, a major quantitative trait locus controlling seed weight in soybean, was fine-mapped to a 340-kb region on chromosome 11, and Glyma.11G239000 is the candidate gene responsible for seed weight. A KASP marker could therefore be useful for selecting high-seed-weight lines in soybean breeding. Seed weight is a critical determinant of yield in soybean. The mechanism underlying seed weight remains poorly understood in soybean. In this study, a recombinant inbred line (RIL) population derived from the cross between Jidou17 and Zhonghuang13 was employed to identify QTLs associated with seed weight. A major locus, qHSW_11, which was consistently detected across three consecutive years, explained 9.51-15.13% of the phenotypic variance. To further refine this locus, we developed a BC1F4 population, which narrowed qHSW_11 to a 340-kb genomic interval harboring four putative candidate genes. Among them, Glyma.11G239000, a soybean homolog of ETHYLENE INSENSITIVE 3 (EIN3), carried an 8-bp insertion within the EIN3 DNA-binding domain and six SNPs distinguishing the parental alleles and exhibited differential expression between the parents during seed development stages. Haplotype analysis revealed that Hap2 (Zhonghuang13) was significantly associated with higher seed weight compared with Hap1 (Jidou17). Furthermore, we designed a site-specific Kompetitive Allele-Specific PCR (KASP) marker based on resequencing data of Glyma.11G239000 and confirmed its effectiveness in a germplasm collection comprising 247 soybean accessions. Overall, the comprehensive results provide new insights into the genetic regulation of seed weight and establish a functional marker for marker-assisted selection to enhance soybean yield.

Seedling height is an important agronomic trait for early vigor and crop establishment in rice. It is controlled by multiple genes, as shown by the continuous variation and normal distribution observed in the Cheongcheong × Nagdong double haploid population measured from 6 to 24days after sowing. This study identified 32 quantitative trait loci QTLs associated with seedling height across multiple chromosomes. Subsequent candidate gene analysis within overlapping QTL regions identified 44 genes associated with growth, metabolism, and stress responses. A key finding was the identification of Os06g0282000 on chromosome 6 between RM540 and RM586, which encodes a putative UDP-glucuronosyl/UDP-glucosyltransferase (UGT). This gene showed consistently higher expression in tall CNDH lines and increased expression during the 12-24 DAS period, indicating a positive correlation with seedling growth. Gene Ontology enrichment showed the role of QTL-associated genes in hormone signaling and carbohydrate metabolism, emphasizing their roles in early seedling development. Comparative genomic analysis showed that Os06g0282000 is part of a conserved gene family that includes 51 homologous genes in rice. Phylogenetic analysis supported its close relationship with UGTs involved in regulating plant growth. These findings position Os06g0282000 as a strong candidate gene that may play a key role in seedling height QTLs and emphasize the role of UGT-mediated regulation of phytohormone homeostasis in controlling rice seedling growth and development.

Obesity and periodontitis are chronic diseases that share inflammatory and metabolic pathways. The RBFOX1 gene was selected as an exploratory candidate gene because it encodes an RNA-binding splicing regulator, has been implicated in obesity-related phenotypes, and has been reported in candidate-gene analyses of periodontitis/metabolic traits. This study investigated the association between obesity, periodontal disease severity, and RBFOX1 rs6500744 polymorphism. This case–control study enrolled 106 adults: 53 with obesity (BMI ≥ 30 kg/m2) and 53 normoweight controls. Clinical and radiographic periodontal assessments determined disease severity, complexity, staging, and grading. Genotyping of the RBFOX1 rs6500744 polymorphism (CC, CT, TT) was performed using the TaqMan® SNP Genotyping Assay and the 7500 Fast Dx Real-Time PCR system. Multivariable models adjusted for age, sex, smoking status, and clinically confirmed type 2 diabetes. Participants with obesity showed higher levels of periodontal disease than normoweight controls, indicated by greater pocket depths, attachment loss, and bone loss. Advanced stage (Stage III/IV; p = 5.35 × 10−6) and Grade C periodontitis (p = 2.08 × 10−7) were significantly more frequent in the obese group. The rs6500744 T allele was more common among individuals with obesity (46.2% vs. 30.2%; OR 1.99, p = 0.023). Periodontal damage appeared to increase progressively from CC to CT to TT genotype, but genotype-stratified estimates, particularly for TT homozygotes, were interpreted cautiously because of the small subgroup size and multiple testing. Both obesity and the number of T alleles were associated with increased periodontal severity in adjusted statistical models. VIFs were low, residual diagnostics did not indicate major assumption violations, smoking-stratified sensitivity analyses were directionally consistent, and the obesity × T-allele interaction was not statistically significant. Obesity is associated with more severe and extensive periodontal disease in this exploratory case–control cohort; however, residual confounding from significant smoking imbalances between groups cannot be excluded. The RBFOX1 rs6500744 T allele may mark increased susceptibility to periodontal tissue destruction, but the findings do not establish causality or clinical prognostic utility and require longitudinal validation in larger, ancestry-controlled populations.

Chronic pelvic pain syndrome (CPPS) is a multifactorial condition with unclear pathophysiology and a lack of objective biomarkers for assessing disease activity. To investigate its molecular basis, we generated patient-derived prostate organoids from biopsy tissues of nine patients with CPPS, categorized as mild, moderate, or severe according to the NIH CP Symptom Index scores. The organoids were treated with Eviprostat or tadalafil, followed by transcriptomic profiling, quantitative RT-PCR validation, and immunohistochemical analysis of candidate genes. Among the differentially expressed genes, monoamine oxidase A (MAOA) and calbindin-D28K (CALB1) were consistently associateds with symptom severity. Expression of both genes decreased in organoids and prostate tissues as symptom severity increased, whereas serum MAOA levels were significantly elevated in patients with severe CPPS. These findings suggest that MAOA and CALB1 reflect molecular alterations linked to symptom intensity and may serve as potential biomarkers for CPPS. Furthermore, patient-derived prostate organoids offer a valuable experimental platform for elucidating disease mechanisms and evaluating therapeutic interventions in prostatitis-related disorders.

Sympetaly (fused petals) is a major innovation driving floral diversity, yet its genetic basis in the highly successful Asteraceae family is elusive. We therefore investigated the molecular mechanisms controlling this trait in Chrysanthemum morifolium. We conducted functional analyses of candidate genes, examined their spatiotemporal expression patterns, and performed biochemical assays to investigate the interaction between the transcription factors CmYAB1 and CmCUC2. Abaxially expressed CmYAB1 regulates floret fusion: its suppression enhanced fusion, while its overexpression caused petal splitting and curling. CmCUC2, a NAM/ATAF1/2/CUC2 (NAC)transcription factor and homolog of the Arabidopsis boundary-specific genes CUC1/2, was downregulated in CmYAB1-silenced lines. Interestingly, its expression shifts dynamically from early floral organ boundaries to later abaxial petal domains, overlapping CmYAB1. CmCUC2 knockdown also increased fusion, while its overexpression led to unfused, curved petals. CmYAB1 directly activates CmCUC2 by binding its promoter, and transient CmCUC2 knockdown in CmYAB1-overexpressing plants rescued the unfused phenotype. Furthermore, silencing either gene upregulated and sustained CmCYC2c expression in dorsal petals, correlating with their elongation. This study delineates the CmYAB1-CmCUC2 regulatory pathway, thereby revealing a novel module of polarity and boundary genes that controls sympetalous development in Asteraceae, advancing our understanding of floral diversity, and enabling the targeted engineering of ornamental traits.

This study identified and validated novel QTL controlling GPC, predicted the underlying candidate genes, and provides valuable insights for improving wheat nutritional quality while minimizing yield penalties. Grain protein content (GPC) is a key determinant of wheat quality, but its improvement is often limited by a negative correlation with yield. To elucidate the genetic architecture of GPC, a genome-wide association study was conducted on 224 wheat cultivars genotyped with a 120K SNP array and phenotyped across three environments. We identified three stable quantitative trait loci (QTL) on chromosome 6D, QGPC.sau-SCV-6D.1, QGPC.sau-SCV-6D.2, and QGPC.sau-SCV-6D.3 which were consistently detected across environments and in best linear unbiased prediction analyses. These loci explained 4.94-9.12% of the phenotypic variance. Notably, the GPC increasing alleles exhibited no adverse effect on major yield components, including thousand-grain weight and grain number per spike. Validation in two independent recombinant inbred line populations confirmed the stable effects of these three QTL. Candidate gene analysis within the QTL intervals highlighted five genes with putative roles in regulating GPC. These findings establish chromosome 6D as a valuable genomic region for breeding high-protein wheat and provide practical markers for marker-assisted selection with minimal yield penalties.

Urochloa grasses are among the most widely used forage grasses across the tropics. Spittlebugs (Hemiptera: Cercopidae) are major pests of tropical Urochloa (syn. Brachiaria) grass pastures, severely reducing forage productivity and quality. Understanding the genetic basis of host-plant resistance is essential for developing durable resistant cultivars. Here, we combined high-throughput image-based phenotyping and genome-wide association studies (GWAS) to dissect the genetic architecture of response to Aeneolamia varia nymphs in 339 interspecific F1 hybrids derived from crosses between resistant sexual and susceptible apomictic Urochloa parents. Digital image analysis using both unsupervised (DQU) and supervised (DTR) quantification pipelines enabled accurate estimation of plant damage, yielding moderate to high broad-sense heritability estimates (H2 = 0.49 to 0.66). In contrast, insect survival (NTS) exhibited low to moderate correlations with all damage traits and lower heritability estimates (H2 = 0.42). Using 57,051 high-quality SNPs aligned to the genome of the hybrid cultivar Basilisk, GWAS models identified 18 quantitative trait loci (QTLs) for plant damage traits, but none for insect survival (antibiosis). Six robust QTLs on chromosomes 1, 6, 7, 27, 29, and 36 were consistently detected across models and phenotyping methods, explaining up to 21.5% of phenotypic variance. Candidate gene analysis revealed proteins involved in hormone signaling, oxidative stress response, and cell wall modification, suggesting multifaceted plant-insect interaction mechanisms. These results provide a foundational set of molecular markers associated with spittlebug response in Urochloa grasses, useful for marker-assisted and genomic selection in the forage breeding program.

Postharvest physiological deterioration (PPD) is a rapid and severe process in cassava that causes root discoloration and spoilage soon after harvest, limiting shelf life and commercial value of the storage roots. Although environmental interventions can temporarily delay PPD, they are impractical for large-scale use. Previous studies have focused mainly on transcriptome, proteome, and candidate-gene analyses, with a few reporting robust and independently validated quantitative trait loci (QTLs). Identifying PPD-linked-QTLs is essential to breeding PPD-tolerant cassava varieties. In this study, a genome-wide association study (GWAS) was conducted to identify genomic regions associated with PPD tolerance using both human visual scoring (VS) and an artificial intelligence (AI)-powered phenotyping method. A mapping population of 298 cassava accessions was genotyped using two platforms: DArTag mid-density panel and genotyping-by-sequencing (GBS). Across both genotyping platforms, 6 significant SNPs were identified using VS dataset and 6 using the AI phenotypic dataset. Consistent associations on chromosomes 1 and 12 across both phenotyping and genotyping platforms indicate potentially robust genomic regions influencing PPD response. Overall, the AI-powered phenotyping approach presents a standardized and reproducible PPD scoring procedure over the traditional visual scoring in future breeding programs for PPD. Despite differences in marker density, both DArTag and GBS markers capture comparable insights into the genetic structure of the GWAS panel. These findings provide insights into the genetic basis of PPD in cassava and offer valuable targets for marker-assisted and genomic selection toward developing cassava varieties with delayed PPD.

Rice (Oryza sativa L.) tillering is a critical determinant of grain yield, yet the genetic mechanisms underlying non-productive tillers remain poorly understood. Here, we report a novel high-tillering (HT) phenotype derived from a cross between the elite cultivar Milyang23 and weedy rice Hapcheonaengmi3. The HT phenotype was absent in parental lines, suggesting it arises from unique allelic interactions. To elucidate the genetic basis of HT, we conducted quantitative trait locus sequencing and linkage analysis using recombinant inbred lines and an F2 population. We identified and fine-mapped two major loci, qHT1 and qHT6, where alleles from Hapcheonaengmi3 induce the HT phenotype in the Milyang23 background. Advanced fine mapping facilitated by window-size adjustments further resolved qHT1 into two candidate intervals (qHT1.1 and qHT1.2). Candidate gene analysis highlighted a putative SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor within qHT6. Furthermore, transcriptomic profiling of HT plants uncovered extensive reprogramming of hormone signaling, specifically affecting the gibberellin, auxin, and cytokinin pathways. Notably, the miR156-SPL module, previously implicated in bushy tillering, exhibited significant expression changes, identifying it as a key regulatory candidate. These findings provide crucial insights into a novel polygenic mechanism controlling rice tillering and highlight the value of cryptic variation in weedy rice.

Abstract Purpose To study the genetic risk factors of Fuchs endothelial corneal dystrophy (FECD) in the Finnish population using hospital‐based and large biobank cohorts. Methods We genotyped a cohort of 107 Finnish patients with FECD for the primary associated genetic risk factor, the TCF4 (CTG) >50 expansion, and studied their clinical phenotype. For 18 TCF4 (CTG) ≤50 patients, we performed exome‐based candidate gene analysis. We also utilised FinnGen biobank‐based samples to perform a genome‐wide association study (GWAS). Results In the cohort, 83% (89/107) carried one allele with the TCF4 (CTG) >50 expansion. Those without the expansion were younger at enrolment and at the time of first keratoplasty ( p = 0.011, p = 0.044, respectively). A genome‐wide association study of 892 patients and 497 827 controls identified a lead variant rs11659764 (AF = 2.3%, OR = 8.2, p = 2.9 × 10 −195 ). Genotyping showed that 89% of TCF4 (CTG) >50 carriers had the associated TA genotype rather than the TT genotype, whereas none of the TCF4 (CTG) ≤50 carriers did. Exome‐based analyses of the 18 TCF4 (CTG) ≤50 carriers identified a candidate gene variant, AGBL1 c.901 + 2 T>G in one patient. Conclusion In Finland, the TCF4 (CTG) >50 expansion is a significant risk factor for FECD. A nearby single‐nucleotide polymorphism (SNP) was found to perform well as a surrogate for genotyping. However, not all patients carried the expanded repeat, and a variant in a previously associated gene was observed in a single patient. Further research is needed to investigate the origins of FECD in individuals without the repeat expansion.

Genome-wide association studies (GWAS) and candidate gene analyses have identified possible suicide risk genes that are highly conserved during evolution and enriched in genes essential for life. However, functional roles for these risk genes have not been confirmed and pathways from risk variant to relevant phenotype to suicidality-related behavior remain unknown, highlighting critical gaps in our knowledge. Here, we report findings from the largest behavioral and mechanistic study of suicide risk genes to date. In Caenorhabditis elegans, mutations in risk gene counterparts caused exaggerated threat evaluation (social feeding) and diminished motivation to seek food, which represent ancient strategies for avoiding harm and ensuring survival (foraging). Genetic variation affected neuropeptide (NPY and TGF-β) function and kinase signaling. Remarkably, the altered behaviors were corrected with drugs that reduce suicidal behavior including antidepressants and clozapine. Taken together, these findings reveal that risk genes predisposing a person to take their life normally promote strategies to survive.

Genotyping by sequencing of wild interspecific mapping population detected novel genetic locus harbouring OsPT11 for rice yield under nutrient stress conditions.

Arginine Vasopressin (AVP) modulates social and sexual behaviors in mammals through its receptor V1a. Differences inreceptor expression and the resulting behavioral changes have been linked to population-level variation in the 5' flanking region of the AVPR1A gene, specifically, length polymorphism of the composite microsatellite RS3 ((CT)4TT(CT)n(GT)m). However, the source of this length variation is unknown. Here, using a genetically tractable system in Saccharomyces cerevisiae, we recapitulated the full spectrum of the RS3 length polymorphism observed in humans resulting from genetic recombination between two RS3 sequences. Our candidate gene analysis shows that transcription elevates the rate of these recombination events and implicates double-strand break repair via single-strand annealing.

Tomato fruit firmness is a critical determinant of postharvest quality, dictating storage, ultimate shelf life, and market value. While previous research on tomato fruit firmness has largely confined to wild or heirloom accessions, the genetic basis underlying this trait in modern elite breeding lines remains largely unexplored. In this study, we dissect the genetic architecture of fruit firmness using a recombinant inbred line (RIL) population derived from a cross between the modern inbred line CF-1 and the conventional cultivar Moneymaker. Quantitative trait locus (QTL) mapping revealed three firmness-associated loci on chromosomes 3, 4, and 5. The major-effect QTL qFF3.1 on chromosome 3 accounted for 11.10% of the phenotypic variation and was further confirmed by bulked segregant analysis (BSA-seq). Fine-mapping in the F2:3 population delimited qFF3.1 to a 111 kb interval containing 26 predicted gene models. After combined analysis of functional annotations and RNA-seq data from near-isogenic lines (NILs), we prioritized six candidate genes associated with cell wall development and ethylene response, and four of which exhibiting differential expression patterns across fruit ripening stages. To our knowledge, qFF3.1 is the first major-effect QTL for fruit firmness identified in a modern tomato breeding line. Our findings offer molecular insights into the regulation of fruit firmness, and provide a strategy for improving shelf life and other postharvest traits.