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14 pages, 2075 KiB  
Article
Molecular Marker-Assisted Breeding of High-Quality and Salt-Tolerant Hybrid Japonica Rice Combination Shenyanyou 1
by Fuan Niu, Anpeng Zhang, Can Cheng, Huangwei Chu, Jun Fang, Jihua Zhou, Bin Sun, Yuting Dai, Jianming Zhang, Zhizun Feng and Liming Cao
Agronomy 2025, 15(8), 2006; https://doi.org/10.3390/agronomy15082006 - 21 Aug 2025
Viewed by 48
Abstract
The development of a new salt–alkaline-tolerant hybrid japonica rice is crucial for enhancing japonica rice supply and ensuring national food security. Utilizing molecular marker-assisted selection (MAS) technology combining Kompetitive Allele-Specific PCR (KASP) markers and a gene breeding chip, the salt-tolerant gene SKC1 was [...] Read more.
The development of a new salt–alkaline-tolerant hybrid japonica rice is crucial for enhancing japonica rice supply and ensuring national food security. Utilizing molecular marker-assisted selection (MAS) technology combining Kompetitive Allele-Specific PCR (KASP) markers and a gene breeding chip, the salt-tolerant gene SKC1 was introgressed into a rice genotype Fan 14. This led to the development of Shenyanhui 1, a new high-quality, strongly heterotic, and salt-tolerant japonica restorer line. Subsequently, the high-quality, salt-tolerant japonica three-line hybrid rice variety Shenyanyou 1 was developed by crossing the BT-type japonica cytoplasmic male sterile (CMS) line Shen 21A with the restorer line Shenyanhui 1. Shenyanyou 1 carries the major salt tolerance gene SKC1, exhibiting excellent salt tolerance with seedling stage salt tolerance reaching level 5. Under precise salt tolerance evaluation throughout its growth cycle, Shenyanyou 1 achieved a yield of 3640.5 kg/hm2, representing an extremely significant increase of 20.7% over the control variety Yandao 21. Shenyanyou 1 exhibits superior grain quality, meeting the Grade 3 high-quality rice standards issued by the Ministry of Agriculture. Shenyanyou 1 has good comprehensive resistance, aggregating rice blast resistance genes such as Pi2, Pita, Pizt and LHCB5, bacterial blight resistance genes Xa26/Xa3, stripe blast resistance gene STV11, semi-dwarf gene Sdt97, nitrogen-efficient utilization gene NRT1.1B, the light repair activity enhancement gene qUVR-10, the cold resistance gene qLTG3-1, and the iron tolerance gene OsFRO1. It has good resistance to biotic and abiotic stresses. This paper details the breeding process, key agronomic traits, salt tolerance, yield performance, and grain quality characteristics of Shenyanyou 1. Full article
(This article belongs to the Section Crop Breeding and Genetics)
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18 pages, 903 KiB  
Article
Immune Modulation Through KIR–HLA Interactions Influences Cetuximab Efficacy in Colorectal Cancer
by María Gómez-Aguilera, Bárbara Manzanares-Martín, Arancha Cebrián-Aranda, Antonio Rodríguez-Ariza, Rafael González-Fernández, Laura del Puerto-Nevado, Jesús García-Foncillas and Enrique Aranda
Int. J. Mol. Sci. 2025, 26(16), 8062; https://doi.org/10.3390/ijms26168062 - 20 Aug 2025
Viewed by 182
Abstract
Colorectal cancer (CRC) remains a major cause of cancer-related mortality. Cetuximab improves survival by combining EGFR inhibition with immune activation. This study evaluated the influence of killer cell immunoglobulin-like receptor (KIR)-mediated immune responses on cetuximab efficacy in 124 metastatic CRC patients: 55 with [...] Read more.
Colorectal cancer (CRC) remains a major cause of cancer-related mortality. Cetuximab improves survival by combining EGFR inhibition with immune activation. This study evaluated the influence of killer cell immunoglobulin-like receptor (KIR)-mediated immune responses on cetuximab efficacy in 124 metastatic CRC patients: 55 with wild-type (WT) KRAS and 69 with KRAS mutations. Peripheral blood was genotyped for 19 KIR genes and relevant HLA alleles, focusing on key KIR–HLA interactions (2DL1–C2, 3DL1–Bw4, 3DS1–Bw4). KRAS-WT patients showed better outcomes, receiving more treatment cycles (median: 17 vs. 4) and showing slower disease progression (60% vs. 92.8% at 12 months). WT patients had higher frequencies of inhibitory KIRs and the Bw4 allele, with KIR3DS1–Bw4 heterozygosity linked to longer survival (p = 0.013). In KRAS-mutant patients, heterozygous KIR genotypes (AB) and mixed A/B semi-haplotypes were associated with improved survival (p = 0.002). Multivariate analysis confirmed KIR3DS1–Bw4 as a favorable factor in WT patients and AB genotypes as beneficial in KRAS-mutants. In conclusion, KIR–HLA interactions significantly impact cetuximab efficacy in metastatic CRC, with distinct immunogenetic profiles in WT and KRAS-mutant patients. These results highlight the potential of KIR–HLA profiling to guide personalized treatment strategies. Full article
(This article belongs to the Section Molecular Immunology)
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13 pages, 2230 KiB  
Article
Genetic Diversity Analysis of Sugar Beet Multigerm Germplasm Resources Based on SRAP Molecular Markers
by Yue Song, Jinghao Li, Shengnan Li, Zedong Wu and Zhi Pi
Horticulturae 2025, 11(8), 988; https://doi.org/10.3390/horticulturae11080988 - 20 Aug 2025
Viewed by 104
Abstract
This study utilized SRAP molecular markers to analyze the genetic basis of 106 multigerm sugar beet germplasm accessions. By revealing the genetic diversity, population structure, and differentiation patterns, it aimed to tap into the germplasm potential, guide core germplasm construction and hybrid combination [...] Read more.
This study utilized SRAP molecular markers to analyze the genetic basis of 106 multigerm sugar beet germplasm accessions. By revealing the genetic diversity, population structure, and differentiation patterns, it aimed to tap into the germplasm potential, guide core germplasm construction and hybrid combination optimization, and ultimately design a molecular breeding route to break through bottlenecks in sugar beet genetic breeding. In total, 24 core primer combinations were screened from 546 initial primer pairs for genomic DNA amplification. The results demonstrated that each primer combination amplified an average of five alleles. Genetic parameter calculations revealed moderate variation potential. Population structure analysis divided the germplasm into four genetic groups (G1–G4), highly consistent with cluster analysis and DAPC analysis results. Its reliability was jointly confirmed by STRUCTURE convergence verification (LnP(K) standard deviation) and cluster goodness-of-fit testing (r = 0.63166, p < 0.0001). Key findings indicated that Group G4 possesses a unique genetic background, and the maximum genetic distance exists between Group G1 and the other three groups, indicating its significant genetic differentiation characteristics. Gene exchange exists between the G3 and G4 populations. Genetic variation primarily originated from within populations (93%, FST = 0.1283). Genetic distances spanned from 0.385 (between accessions 66 and 71 within a group) to 0.836 (between accessions 47 and 85 across groups). Concurrently, gene flow analysis (Nm = 3.3977) indicated moderate genetic exchange among populations. This achievement established the first SRAP marker-based genetic architecture for multigerm sugar beet germplasm resources. It provides a quantitative population genetics basis for formulating targeted strategies for germplasm resource conservation and utilization, and lays the foundation for constructing an innovation system for sugar beet germplasm resources. Full article
(This article belongs to the Special Issue Genomics and Genetic Diversity in Vegetable Crops)
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9 pages, 1246 KiB  
Brief Report
ERBB2 Mutation Testing in NSCLC: A Pan-European Real-World Evaluation of the Oncomine Precision Assay
by Ilaria Alborelli, Melanie Demes, Peter Wild, Susana Hernandez, Fernando Lopez-Rios, Olivier Bordone, Christophe Bontoux, Paul Hofman, Caterina De Luca, Giancarlo Troncone, Luisella Righi, Umberto Malapelle, Ricella Souza da Silva, Luis Cirnes, Fernando Schmitt, Eveline Keller, Philip M. Jermann, John Longshore and Lukas Bubendorf
J. Mol. Pathol. 2025, 6(3), 19; https://doi.org/10.3390/jmp6030019 - 14 Aug 2025
Viewed by 329
Abstract
Background/Objectives: The non-small-cell lung cancer (NSCLC) therapeutic landscape has undergone a profound transformation with the introduction of multiple personalized treatment options. Mutations in ERBB2 (HER2) have recently emerged as promising novel targets for the treatment of non-squamous NSCLC (nsNSCLC). Accurate, rapid, [...] Read more.
Background/Objectives: The non-small-cell lung cancer (NSCLC) therapeutic landscape has undergone a profound transformation with the introduction of multiple personalized treatment options. Mutations in ERBB2 (HER2) have recently emerged as promising novel targets for the treatment of non-squamous NSCLC (nsNSCLC). Accurate, rapid, and efficient molecular profiling is crucial for identifying patients who may benefit from targeted therapies, including HER2-directed agents. Materials and Methods: Here, we aimed to retrospectively assess the performance of the Oncomine™ Precision Assay* (OPA) in combination with the Ion Torrent Genexus™ Integrated Sequencer* (Thermo Fisher Scientific. Waltham, MA, USA) for detecting ERBB2 mutations in nsNSCLC. A total of 108 archived nsNSCLC samples, consisting of biopsies, resections, and cytological specimens, were used to assess concordance with in-house-validated orthogonal tests. Results: The OPA showed high sensitivity and specificity with an overall accuracy of 100% for single-nucleotide variants (SNVs) and insertions and deletions (Indels). SNVs and Indels with allele frequencies as low as 5% were correctly identified across samples with a tumor cell content ranging from 5% to 95%. Additionally, the assay demonstrated high reproducibility across the six participating laboratories. The turnaround time of the OPA was notably shorter compared to traditional orthogonal methods, facilitating rapid molecular report generation. Conclusions: The OPA in combination with the Ion Torrent Genexus™ System allows for highly sensitive and specific detection of relevant ERBB2 mutations. The assay’s streamlined workflow, coupled with its automated data analysis pipeline, enables a fast turnaround time for testing across a range of sample types. This includes samples with reduced tumor cell content and limited available input. This study demonstrates the future potential of using this assay in a clinical setting. Full article
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10 pages, 1645 KiB  
Article
Molecular Characterization of Citrus Accessions Grown for Pre-Breeding Purposes
by Israel Felipe Gonçalves Soares, Felipe Cruz Paula, Conceição de Maria Batista Oliveira, José Dias de Souza Neto, Talles de Oliveira Santos, Rafael Nunes de Almeida, Ana Paula Candido Gabriel Berilli, Sávio da Silva Berilli, Taís Cristina Bastos Soares, Jardel Oliveira Santos, Alexandre Cristiano Santos Júnior and Monique Moreira Moulin
Curr. Issues Mol. Biol. 2025, 47(8), 656; https://doi.org/10.3390/cimb47080656 - 14 Aug 2025
Viewed by 287
Abstract
The objective of this work was to analyse the genetic diversity of a population of Citrus spp. in the south of the State of Espírito Santo, Brazil, for pre-breeding studies. For that, a total of sixty genotypes were analysed, including ten citrus varieties [...] Read more.
The objective of this work was to analyse the genetic diversity of a population of Citrus spp. in the south of the State of Espírito Santo, Brazil, for pre-breeding studies. For that, a total of sixty genotypes were analysed, including ten citrus varieties from four species of the Citrus genus. The methodology involved DNA extraction, amplification via polymerase chain reaction, and the use of a set of 16 Simple Sequence Repeat markers. These markers identified 42 alleles, with a variation of one to four alleles per locus, an average heterozygosity value of 0.53, and an average polymorphic information content of up to 0.29 per species. After the analysis, a dissimilarity matrix was generated using Jaccard distance and a dendrogram, revealing the formation of two groups: Group I, comprising Citrus sinensis varieties, and Group II, comprising varieties of Citrus latifolia, Citrus aurantifolia, and Citrus reticulata. Our study demonstrated that the combination of these markers allowed for the differentiation of genotypes within the collection. The results obtained are valuable for the future management of the collection and the efficient use of genetic diversity estimation in Citrus spp. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants, 2nd Edition)
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19 pages, 1119 KiB  
Article
Analysis of the Genetic Mechanism of Yield-Related Traits of Maize in Cold Regions
by Chao Gao, Zimeng Li, Guogang Zheng, Hong Di, Lin Zhang, Zhenhua Wang and Ling Dong
Genes 2025, 16(8), 941; https://doi.org/10.3390/genes16080941 - 8 Aug 2025
Viewed by 361
Abstract
Background: Maize is an important food crop in cold regions, especially in Northeast China. However, its short growth period and low-temperature stress pose challenges to the breeding of high-yield hybrids. With climate warming, the maize planting area continues to expand to high latitudes. [...] Read more.
Background: Maize is an important food crop in cold regions, especially in Northeast China. However, its short growth period and low-temperature stress pose challenges to the breeding of high-yield hybrids. With climate warming, the maize planting area continues to expand to high latitudes. Research on cold-region maize is of great significance to ensure food security and sustainable agricultural development. However, most of the current maize research is concentrated in temperate and tropical regions, and there are few studies on cold-region maize. Methods: Based on this, this study selected some representative cold-region maize materials and materials whose adaptability has not yet been verified, and used a semi-diallel hybrid design for hybridization to determine the general combining ability (GCA) and specific combining ability (SCA) to screen out excellent breeding materials suitable for cold regions. Field experiments were carried out under four different cold environments, and 55 hybrid progenies and their parents were evaluated. The double allele hybridization analysis based on the Griffing method 2 (model 1) showed that the specific combining ability (SCA) and general combining ability (GCA) effects of each trait were significant. Results: The GCA mean square of all traits except yield and number of grains per row was greater than the SCA mean square, indicating that additive gene effects were dominant and genetic improvement through selective breeding was feasible. Hayman plot analysis under four environments showed that yield, ear length, number of grains per row, water content, and plant height were mainly controlled by superdominant genes, while stem thickness, number of nodes, and ear position were controlled by some dominant genes. Conclusions: Parent P1 contained more recessive genes in yield traits, but more dominant genes in number of grains per row, number of nodes, and ear position; P3 contained more dominant genes in yield and water content, but more recessive genes in number of nodes and ear position; P7 contained more recessive genes in most traits; and P9 contained more dominant genes in most traits. P9 and P6 represent excellent parental germplasm, among which the hybrid combinations P1 × P9, P2 × P5, P3 × P10, P4 × P6, P5 × P8, P6 × P9, P7 × P10, and P8 × P10 all show hybrid vigor exceeding that of their parents and have high breeding value. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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21 pages, 3401 KiB  
Article
Allelic Variation of Helicobacter pylori vacA Gene and Its Association with Gastric Pathologies in Clinical Samples Collected in Jordan
by Mamoon M. Al-Hyassat, Hala I. Al-Daghistani, Lubna F. Abu-Niaaj, Sima Zein and Talal Al-Qaisi
Microorganisms 2025, 13(8), 1841; https://doi.org/10.3390/microorganisms13081841 - 7 Aug 2025
Viewed by 647
Abstract
Helicobacter pylori is a well-established causative agent of gastritis, peptic ulcers, gastric adenocarcinoma, and primary gastric lymphoma. It colonizes the human stomach and expresses numerous virulent factors that influence disease progression. Among these factors is the cytotoxin vacA gene, which encodes the vacuolating [...] Read more.
Helicobacter pylori is a well-established causative agent of gastritis, peptic ulcers, gastric adenocarcinoma, and primary gastric lymphoma. It colonizes the human stomach and expresses numerous virulent factors that influence disease progression. Among these factors is the cytotoxin vacA gene, which encodes the vacuolating capacity of the cytotoxin and plays a key role in the bacterium’s pathogenic potential. This study investigated the allelic diversity of the vacA among H. pylori strains infecting patients in Jordan with various gastric conditions and examined potential associations between vacA s-and m- genotypes, histopathological and endoscopic findings, and the development of gastric diseases. Gastric biopsies were collected from 106 patients at two hospitals in Jordan who underwent endoscopic examination. The collected biopsies for each patient were subjected to histopathological assessment, urease detection using the Rapid Urease Test (RUT), a diagnostic test for H. pylori, and molecular detection of the vacA gene and its s and m alleles. The histopathology reports indicated that 83 of 106 patients exhibited gastric disorders, of which 81 samples showed features associated with H. pylori infection. The RUT was positive in 76 of 106 with an accuracy of 93.8%. Real-time polymerase chain reaction (RT-PCR) targeting the 16S rRNA gene confirmed the presence of H. pylori in 79 of 81 histologically diagnosed cases as infected (97.5%), while the vacA gene was detected only in 75 samples (~95%). To explore genetic diversity, PCR-amplified fragments underwent sequence analysis of the vacA gene. The m-allele was detected in 58 samples (73%), the s-allele was detected in 45 (57%), while both alleles were not detected in 13% of samples. The predominant genotype combination among Jordanians was vacA s2/m2 (50%), significantly linked to mild chronic gastritis, followed by s1/m2 (35%) and s1/m1 (11.8%) which are linked to severe gastric conditions including malignancies. Age-and gender-related differences in vacA genotype were observed with less virulent s2m2 and s1m2 genotypes predominating in younger adults specially males, while the more virulent m1 genotypes were found exclusively in females and middle-aged patients. Genomic sequencing revealed extensive diversity within H. pylori, likely reflecting its long-standing co-evolution with human hosts in Jordan. This genetic variability plays a key role in modulating virulence and influencing clinical outcomes. Comprehensive characterization of vacA genotypic variations through whole-genome sequencing is essential to enhance diagnostic precision, strengthen epidemiological surveillance, and inform targeted therapeutic strategies. While this study highlights the significance of the vacA m and s alleles, future research is recommended in order to investigate the other vacA allelic variations, such as the i, d, and c alleles, to achieve a more comprehensive understanding of H. pylori pathogenicity and associated disease severity across different strains. These investigations will be crucial for improving diagnostic accuracy and guiding the development of targeted therapeutic strategies. Full article
(This article belongs to the Special Issue Helicobacter pylori Infection: Detection and Novel Treatment)
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19 pages, 1016 KiB  
Article
Genetic Associations of ITGB3, FGG, GP1BA, PECAM1, and PEAR1 Polymorphisms and the Platelet Activation Pathway with Recurrent Pregnancy Loss in the Korean Population
by Eun Ju Ko, Eun Hee Ahn, Hyeon Woo Park, Jae Hyun Lee, Da Hwan Kim, Young Ran Kim, Ji Hyang Kim and Nam Keun Kim
Int. J. Mol. Sci. 2025, 26(15), 7505; https://doi.org/10.3390/ijms26157505 - 3 Aug 2025
Viewed by 405
Abstract
Recurrent pregnancy loss (RPL) is defined as the occurrence of two or more pregnancy losses before 20 weeks of gestation. RPL is a common medical condition among reproductive-age women, with approximately 23 million cases reported annually worldwide. Up to 5% of pregnant women [...] Read more.
Recurrent pregnancy loss (RPL) is defined as the occurrence of two or more pregnancy losses before 20 weeks of gestation. RPL is a common medical condition among reproductive-age women, with approximately 23 million cases reported annually worldwide. Up to 5% of pregnant women may experience two or more consecutive pregnancy losses. Previous studies have investigated risk factors for RPL, including maternal age, uterine pathology, genetic anomalies, infectious agents, endocrine disorders, thrombophilia, and immune dysfunction. However, RPL is a disease caused by a complex interaction of genetic factors, environmental factors (e.g., diet, lifestyle, and stress), epigenetic factors, and the immune system. In addition, due to the lack of research on genetics research related to RPL, the etiology remains unclear in up to 50% of cases. Platelets play a critical role in pregnancy maintenance. This study examined the associations of platelet receptor and ligand gene variants, including integrin subunit beta 3 (ITGB3) rs2317676 A > G, rs3809865 A > T; fibrinogen gamma chain (FGG) rs1049636 T > C, rs2066865 T > C; glycoprotein 1b subunit alpha (GP1BA) rs2243093 T > C, rs6065 C > T; platelet endothelial cell adhesion molecule 1 (PECAM1) rs2812 C > T; and platelet endothelial aggregation receptor 1 (PEAR1) rs822442 C > A, rs12137505 G > A, with RPL prevalence. In total, 389 RPL patients and 375 healthy controls (all Korean women) were enrolled. Genotyping of each single nucleotide polymorphism was performed using polymerase chain reaction–restriction fragment length polymorphism and the TaqMan genotyping assay. All samples were collected with approval from the Institutional Review Board at Bundang CHA Medical Center. The ITGB3 rs3809865 A > T genotype was strongly associated with RPL prevalence (pregnancy loss [PL] ≥ 2: adjusted odds ratio [AOR] = 2.505, 95% confidence interval [CI] = 1.262–4.969, p = 0.009; PL ≥ 3: AOR = 3.255, 95% CI = 1.551–6.830, p = 0.002; PL ≥ 4: AOR = 3.613, 95% CI = 1.403–9.307, p = 0.008). The FGG rs1049636 T > C polymorphism was associated with a decreased risk in women who had three or more pregnancy losses (PL ≥ 3: AOR = 0.673, 95% CI = 0.460–0.987, p = 0.043; PL ≥ 4: AOR = 0.556, 95% CI = 0.310–0.997, p = 0.049). These findings indicate significant associations of the ITGB3 rs3809865 A > T and FGG rs1049636 T > C polymorphisms with RPL, suggesting that platelet function influences RPL in Korean women. Full article
(This article belongs to the Special Issue Molecular Research in Gynecological Diseases—2nd Edition)
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26 pages, 11108 KiB  
Article
Warming in the Maternal Environment Alters Seed Performance and Genetic Diversity of Stylosanthes capitata, a Tropical Legume Forage
by Priscila Marlys Sá Rivas, Fernando Bonifácio-Anacleto, Ivan Schuster, Carlos Alberto Martinez and Ana Lilia Alzate-Marin
Genes 2025, 16(8), 913; https://doi.org/10.3390/genes16080913 - 30 Jul 2025
Viewed by 513
Abstract
Background/Objectives: Global warming and rising CO2 concentrations pose significant challenges to plant systems. Amid these pressures, this study contributes to understanding how tropical species respond by simultaneously evaluating reproductive and genetic traits. It specifically investigates the effects of maternal exposure to [...] Read more.
Background/Objectives: Global warming and rising CO2 concentrations pose significant challenges to plant systems. Amid these pressures, this study contributes to understanding how tropical species respond by simultaneously evaluating reproductive and genetic traits. It specifically investigates the effects of maternal exposure to warming and elevated CO2 on progeny physiology, genetic diversity, and population structure in Stylosanthes capitata, a resilient forage legume native to Brazil. Methods: Maternal plants were cultivated under controlled treatments, including ambient conditions (control), elevated CO2 at 600 ppm (eCO2), elevated temperature at +2 °C (eTE), and their combined exposure (eTEeCO2), within a Trop-T-FACE field facility (Temperature Free-Air Controlled Enhancement and Free-Air Carbon Dioxide Enrichment). Seed traits (seeds per inflorescence, hundred-seed mass, abortion, non-viable seeds, coat color, germination at 32, 40, 71 weeks) and abnormal seedling rates were quantified. Genetic diversity metrics included the average (A) and effective (Ae) number of alleles, observed (Ho) and expected (He) heterozygosity, and inbreeding coefficient (Fis). Population structure was assessed using Principal Coordinates Analysis (PCoA), Analysis of Molecular Variance (AMOVA), number of migrants per generation (Nm), and genetic differentiation index (Fst). Two- and three-way Analysis of Variance (ANOVA) were used to evaluate factor effects. Results: Compared to control conditions, warming increased seeds per inflorescence (+46%), reduced abortion (−42.9%), non-viable seeds (−57%), and altered coat color. The germination speed index (GSI +23.5%) and germination rate (Gr +11%) improved with warming; combined treatments decreased germination time (GT −9.6%). Storage preserved germination traits, with warming enhancing performance over time and reducing abnormal seedlings (−54.5%). Conversely, elevated CO2 shortened GSI in late stages, impairing germination efficiency. Warming reduced Ae (−35%), He (−20%), and raised Fis (maternal 0.50, progeny 0.58), consistent with the species’ mixed mating system; A and Ho were unaffected. Allele frequency shifts suggested selective pressure under eTE. Warming induced slight structure in PCoA, and AMOVA detected 1% (maternal) and 9% (progeny) variation. Fst = 0.06 and Nm = 3.8 imply environmental influence without isolation. Conclusions: Warming significantly shapes seed quality, reproductive success, and genetic diversity in S. capitata. Improved reproduction and germination suggest adaptive advantages, but higher inbreeding and reduced diversity may constrain long-term resilience. The findings underscore the need for genetic monitoring and broader genetic bases in cultivars confronting environmental stressors. Full article
(This article belongs to the Special Issue Genetics and Breeding of Forage)
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10 pages, 1920 KiB  
Case Report
Junctional Epidermolysis Bullosa Caused by a Hemiallelic Nonsense Mutation in LAMA3 Revealed by 18q11.2 Microdeletion
by Matteo Iacoviello, Marilidia Piglionica, Ornella Tabaku, Antonella Garganese, Aurora De Marco, Fabio Cardinale, Domenico Bonamonte and Nicoletta Resta
Int. J. Mol. Sci. 2025, 26(15), 7343; https://doi.org/10.3390/ijms26157343 - 29 Jul 2025
Viewed by 413
Abstract
Inherited epidermolysis bullosa (EB) is a heterogeneous clinical entity that includes over 30 phenotypically and/or genotypically distinct inherited disorders, characterized by mechanical skin fragility and bullae formation. Junctional EB (JEB) is an autosomal recessive disease characterized by an intermediated cleavage level within the [...] Read more.
Inherited epidermolysis bullosa (EB) is a heterogeneous clinical entity that includes over 30 phenotypically and/or genotypically distinct inherited disorders, characterized by mechanical skin fragility and bullae formation. Junctional EB (JEB) is an autosomal recessive disease characterized by an intermediated cleavage level within the skin layers, commonly at the “lamina lucida”. Laryngo-onycho-cutaneous syndrome (LOC) is an extremely rare variant of JEB, characterized by granulation tissue formation in specific body sites (skin, larynx, and nails). Although most cases of JEB are caused by pathogenic variants occurring in the genes encoding for classical components of the lamina lucida, such as laminin 332 (LAMA3, LAMB3, LAMC2), integrin α6β4 (ITGA6, ITGB4), and collagen XVII (COL17A1), other variants have also been described. We report the case of a 4-month-old male infant who presented with recurrent bullous and erosive lesions from the first month of life. At the first dermatological evaluation, the patient was agitated and exhibited hoarse breathing, a clinical sign suggestive of laryngeal involvement. Multiple polygonal skin erosions were observed on the cheeks, along with similar isolated, roundish lesions on the scalp and legs. Notably, nail dystrophy and near-complete anonychia were evident on the left first and fifth toes. Due to the coexistence of skin erosions and nail dystrophy in such a young infant, a congenital bullous disorder was suspected, prompting molecular analysis of all potentially involved genes. In the patient’s DNA, clinical exome sequencing (CES) identified a pathogenic variant, apparently in homozygosity, in the exon 1 of the LAMA3 gene (18q11.2; NM_000227.6): c.47G > A;p.Trp16*. The presence of this variant was confirmed, in heterozygosity, in the genomic DNA of the patient’s mother, while it was absent in the father’s DNA. Subsequently, trio-based SNP array analysis was performed, revealing a paternally derived pathogenic microdeletion encompassing the LAMA3 locus (18q11.2). To our knowledge, this is the first reported case of JEB with a LOC-like phenotype caused by a maternally inherited monoallelic nonsense mutation in LAMA3, unmasked by an almost complete deletion of the paternal allele. The combined use of exome sequencing and SNP array is proving essential for elucidating autosomal recessive diseases with a discordant segregation. This is pivotal for providing accurate genetic counseling to parents regarding future pregnancies. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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11 pages, 671 KiB  
Article
Genetic Factors of Elite Wrestling Status: A Multi-Ethnic Comparative Study
by Ayumu Kozuma, Celal Bulgay, Hirofumi Zempo, Mika Saito, Minoru Deguchi, Hiroki Homma, Shingo Matsumoto, Ryutaro Matsumoto, Anıl Kasakolu, Hasan H. Kazan, Türker Bıyıklı, Seyrani Koncagül, Giyasettin Baydaş, Mehmet A. Ergun, Attila Szabo, Ekaterina A. Semenova, Andrey K. Larin, Nikolay A. Kulemin, Edward V. Generozov, Takanobu Okamoto, Koichi Nakazato, Ildus I. Ahmetov and Naoki Kikuchiadd Show full author list remove Hide full author list
Genes 2025, 16(8), 906; https://doi.org/10.3390/genes16080906 - 29 Jul 2025
Viewed by 453
Abstract
Background: In recent years, comprehensive analyses using a genome-wide association study (GWAS) have been conducted to identify genetic factors related to athletic performance. In this study, we investigated the association between genetic variants and elite wrestling status across multiple ethnic groups using a [...] Read more.
Background: In recent years, comprehensive analyses using a genome-wide association study (GWAS) have been conducted to identify genetic factors related to athletic performance. In this study, we investigated the association between genetic variants and elite wrestling status across multiple ethnic groups using a genome-wide genotyping approach. Methods: This study included 168 elite wrestlers (64 Japanese, 67 Turkish, and 36 Russian), all of whom had competed in international tournaments, including the Olympic Games. Control groups consisted of 306 Japanese, 137 Turkish, and 173 Russian individuals without elite athletic backgrounds. We performed a GWAS comparing allele frequencies of single-nucleotide polymorphisms (SNPs) between elite wrestlers and controls in each ethnic cohort. Cross-population analysis comprised (1) identifying SNPs with nominal significance (p < 0.05) in all three groups, then (2) meta-analyzing overlapped SNPs to assess effect consistency and combined significance. Finally, we investigated whether the most significant SNPs were associated with gene expression in skeletal muscle in 23 physically active men. Results: The GWAS identified 328,388 (Japanese), 23,932 (Turkish), and 30,385 (Russian) SNPs reaching nominal significance. Meta-analysis revealed that the ATP2A3 rs6502758 and UNC5C rs265061 polymorphisms were associated (p < 0.0001) with elite wrestling status across all three populations. Both variants are located in intronic regions and influence the expression of their respective genes in skeletal muscle. Conclusions: This is the first study to investigate gene polymorphisms associated with elite wrestling status in a multi-ethnic cohort. ATP2A3 rs6502758 and UNC5C rs265061 polymorphisms may represent important genetic factors associated with achieving an elite status in wrestling, irrespective of ethnicity. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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16 pages, 3903 KiB  
Article
Identification of Salt Tolerance-Related NAC Genes in Wheat Roots Based on RNA-Seq and Association Analysis
by Lei Zhang, Aili Wei, Weiwei Wang, Xueqi Zhang, Zhiyong Zhao and Linyi Qiao
Plants 2025, 14(15), 2318; https://doi.org/10.3390/plants14152318 - 27 Jul 2025
Viewed by 427
Abstract
Excavating new salt tolerance genes and utilizing them to improve salt-tolerant wheat varieties is an effective way to utilize salinized soil. The NAC gene family plays an important role in plant response to salt stress. In this study, 446 NAC sequences were isolated [...] Read more.
Excavating new salt tolerance genes and utilizing them to improve salt-tolerant wheat varieties is an effective way to utilize salinized soil. The NAC gene family plays an important role in plant response to salt stress. In this study, 446 NAC sequences were isolated from the whole genome of common wheat and classified into 118 members based on subgenome homology, named TaNAC1 to TaNAC118. Transcriptome analysis of salt-tolerant wheat breeding line CH7034 roots revealed that 144 of the 446 TaNAC genes showed significant changes in expression levels at least two time points after NaCl treatment. These differentially expressed TaNACs were divided into four groups, and Group 4, containing the largest number of 78 genes, exhibited a successive upregulation trend after salt treatment. Single nucleotide polymorphisms (SNPs) of the TaNAC gene family in 114 wheat germplasms were retrieved from the public database and were subjected to further association analysis with the relative salt-injury rates (RSIRs) of six root phenotypes, and then 20 SNPs distributed on chromosomes 1B, 2B, 2D, 3B, 3D, 5B, 5D, and 7A were correlated with phenotypes involving salt tolerance (p < 0.0001). Combining the results of RT-qPCR and association analysis, we further selected three NAC genes from Group 4 as candidate genes that related to salt tolerance, including TaNAC26-D3.2, TaNAC33-B, and TaNAC40-B. Compared with the wild type, the roots of the tanac26-d3.2 mutant showed shorter length, less volume, and reduced biomass after being subjected to salt stress. Four SNPs of TaNAC26-D3.2 formed two haplotypes, Hap1 and Hap2, and germplasms with Hap2 exhibited better salt tolerance. Snp3, in exon 3 of TaNAC26-D3.2, causing a synonymous mutation, was developed into a Kompetitive Allele-Specific PCR marker, K3, to distinguish the two haplotypes, which can be further used for wheat germplasm screening or marker-assisted breeding. This study provides new genes and molecular markers for improvement of salt tolerance in wheat. Full article
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17 pages, 810 KiB  
Article
Association Analysis Between Ischemic Stroke Risk Single Nucleotide Polymorphisms and Alzheimer’s Disease
by Wei Dong, Wei Wang and Mingxuan Li
Bioengineering 2025, 12(8), 804; https://doi.org/10.3390/bioengineering12080804 - 26 Jul 2025
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Abstract
Alzheimer’s disease (AD) and ischemic stroke (IS) are prevalent neurological disorders that frequently co-occur in the same individuals. Recent studies have demonstrated that AD and IS share several common risk factors and pathogenic elements, including an overlapping genomic architecture. However, the relationship between [...] Read more.
Alzheimer’s disease (AD) and ischemic stroke (IS) are prevalent neurological disorders that frequently co-occur in the same individuals. Recent studies have demonstrated that AD and IS share several common risk factors and pathogenic elements, including an overlapping genomic architecture. However, the relationship between IS risk gene polymorphisms and AD has been less extensively studied. We aimed at determining whether IS risk gene polymorphisms were associated with the risk of AD and the severity of AD in AD patients. We utilized data of AD patients and normal controls (NCs) sourced from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. IS risk single nucleotide polymorphisms (SNPs) were identified through the most recent and largest IS genome-wide association study (GWAS) meta-analysis. Subsequently, we conducted SNP-based association analysis of IS-risk SNPs with the risk of AD, along with amyloid, tau, and neuroimaging for AD. The generalized multifactor dimensionality reduction (GMDR) model was used to assess the interactions among IS-risk SNPs and apolipoprotein E (ApoE) ε4. Protein–protein interactions (PPIs) of the IS-risk genes product and APOE were explored using the STRING database. Seven IS-risk SNPs were involved in the study. Five SNPs were found to be associated with at least one measurement of cerebrospinal fluid (CSF) levels of amyloid-beta 1–42 (Aβ42), total tau (t-tau), and phosphorylated tau 181 (p-tau181), as well as the volumes of the hippocampus, whole brain, entorhinal cortex, and mid-temporal regions. After multiple testing corrections, we found that T allele of rs1487504 contributed to an increased risk of AD in non-ApoE ε4 carriers. The combination of rs1487504 and ApoE ε4 emerged as the optimal two-factor model, and its interaction was significantly related to the risk of AD. Additionally, C allele of rs880315 was significantly associated with elevated levels of CSF Aβ42 in AD patients, and A allele of rs10774625 was significantly related to a reduction in the volume of the entorhinal cortex in AD patients. This study found that IS risk SNPs were associated with both the risk of AD and AD major indicators in the ADNI cohort. These findings elucidated the role of IS in AD from a genetic perspective and provided an innovative approach to predict AD through IS-risk SNPs. Full article
(This article belongs to the Section Biomedical Engineering and Biomaterials)
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12 pages, 274 KiB  
Article
Nullity of GSTM1 and GSTT1 Associated with CD4+ T Cells in HIV-Positive Patients from Southern Brazil
by Marcela Gonçalves Trevisan, Marcieli Borba do Nascimento, Valdir Spada Juníor, Volmir Pitt Benedetti, Lirane Elize Defante Ferreto and Léia Carolina Lucio
Antioxidants 2025, 14(8), 909; https://doi.org/10.3390/antiox14080909 - 25 Jul 2025
Viewed by 407
Abstract
Scientific evidence has suggested, in most cases, that nullity of the GSTM1 and GSTT1 genes is associated with worse pathological outcomes and viral infections. In this sense, the main objective of this work was to determine the genotypic frequencies of GSTM1 and GSTT1 [...] Read more.
Scientific evidence has suggested, in most cases, that nullity of the GSTM1 and GSTT1 genes is associated with worse pathological outcomes and viral infections. In this sense, the main objective of this work was to determine the genotypic frequencies of GSTM1 and GSTT1 polymorphisms in individuals with HIV and to establish a possible relationship with CD4+ T lymphocyte count. This was a cross-sectional study, with a quantitative approach, composed of 182 HIV-positive patients. To detect GSTM1 and GSTT1 polymorphisms by the multiplex polymerase chain reaction (PCR), oral mucosa samples were collected. Regarding genotypic frequencies, GST nullity was high in the population, being 97.5% and 97.6%, respectively, for GSTM1− and GSTT1−. Although there was no association between the GST polymorphism and the viral load and CD4+ T lymphocyte counts at diagnosis, when related to the current CD4+ count, the isolated and combined null alleles, GSTT1 (ORadj: 0.219; p = 0.004), GSTM1 (ORadj: 0.219; p = 0.004), and GSTM1/T1 (ORadj: 0.219; p = 0.004), were defined as factors favorable to a minimum CD4+ T lymphocyte count of 350 cells. Therefore, this study demonstrated a probable relationship between the GSTT1 and GSTM1 genetic polymorphisms and HIV. Full article
(This article belongs to the Special Issue Glutathione and Health: From Development to Disease)
19 pages, 259 KiB  
Article
Dietary and Genetic Aspects of Polycystic Ovary Syndrome (PCOS) in Polish Women—Part II: Association of CYP19, FTO, MC4R and INSR Gene Polymorphisms with Clinical Symptoms of PCOS
by Karolina Nowosad, Małgorzata Ostrowska, Paweł Glibowski, Katarzyna Iłowiecka and Wojciech Koch
Genes 2025, 16(7), 840; https://doi.org/10.3390/genes16070840 - 18 Jul 2025
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Abstract
Background/Objectives: Polycystic ovary syndrome (PCOS) is a multifactorial disorder influenced by both environmental and genetic factors. The aim of this study was to evaluate associations between selected polymorphisms (CYP19, INSR, FTO, MC4R) and the clinical manifestations of PCOS [...] Read more.
Background/Objectives: Polycystic ovary syndrome (PCOS) is a multifactorial disorder influenced by both environmental and genetic factors. The aim of this study was to evaluate associations between selected polymorphisms (CYP19, INSR, FTO, MC4R) and the clinical manifestations of PCOS in a Polish female population. Methods: A total of 50 women (25 with PCOS and 25 healthy controls) were included. Genetic variants were identified using Polymerase Chain Reaction (PCR)-based methods. The frequencies of genotypes and alleles were compared between groups. Clinical symptoms such as irregular menstruation, hirsutism, acne, androgenetic alopecia, and overweight were assessed in relation to genotype. Results: No significant differences were found in genotype distributions for CYP19, FTO, INSR, or MC4R between PCOS and control groups. The MC4R polymorphisms showed deviations from Hardy–Weinberg equilibrium, possibly reflecting population-specific effects. Conclusions: Although most analyzed variants were not directly associated with PCOS in this cohort, the observed link between INSR rs1799817 and acne suggests a role in androgen-related symptoms. These findings contribute new insights to the genetic background of PCOS in Polish women and support the need for further studies combining genetic and phenotypic data in diverse populations. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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