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Search Results (1,407)

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Keywords = phenotypic and genetic correlation

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18 pages, 3388 KB  
Article
Impact of Alien Chromosome Introgression from Thinopyrum ponticum on Wheat Grain Traits
by Shuwei Zhang, Yu Zhang, Ting Hu, Linying Li, Zihao Wang, Linyi Qiao, Lifang Chang, Xin Li, Zhijian Chang, Peng Zhang and Xiaojun Zhang
Plants 2025, 14(19), 3072; https://doi.org/10.3390/plants14193072 (registering DOI) - 4 Oct 2025
Abstract
Structural variation (SV) serves as a fundamental driver of phenotypic diversity and environmental adaptation in plants and animals, significantly influencing key agronomic traits in crops. Common wheat (Triticum aestivum L.), an allohexaploid species, harbors extensive chromosomal SVs and distant hybridization-induced recombination events [...] Read more.
Structural variation (SV) serves as a fundamental driver of phenotypic diversity and environmental adaptation in plants and animals, significantly influencing key agronomic traits in crops. Common wheat (Triticum aestivum L.), an allohexaploid species, harbors extensive chromosomal SVs and distant hybridization-induced recombination events that provide critical resources for genetic improvement. This study utilizes non-denaturing fluorescence in situ hybridization (ND-FISH) and oligonucleotide multiplex probe-based FISH (ONPM-FISH) to analyze the karyotypes of 153 BC1F4–BC1F6 lines derived from the hybrid line Xiaoyan 7430 and common wheat Yannong 1212. The results revealed that Xiaoyan 7430 carries 8 alien chromosome pairs and 20 wheat chromosome pairs (lacking 6B), and Yannong 1212 contains 21 pairs of wheat chromosomes. The parental lines exhibited presence/absence variations (PAVs) on chromosomes 2A, 6A, 5B, 1D, and 2D. Chromosomal variations, including numerical chromosomal variation (NCV), structural chromosomal variation (SCV), and complex chromosomal variation (CCV), were detected in the progeny lines through ONPM-FISH analysis. The tracking of alien chromosomes over three consecutive generations revealed a significant decrease in transmission frequency, declining from 61.82% in BC1F4 to 26.83% in BC1F6. Telosomes were also lost during transmission, declining from 21.82% in BC1F4 to 9.76% in BC1F6. Alien chromosome 1JS, 4J, and 6J exhibited the highest transmission stability and were detected across all three generations. Association analysis showed that YN-PAV.2A significantly affected the length/width ratio (LWR) and grain diameter (GD); YN-PAV.6A, XY-PAV.6A, and PAV.5B increased six grain traits (+2.25%~15.36%); YN-PAV.1D negatively affected grain length (GL) and grain circumference (GC); and XY-PAV.2D exerted positive effects on thousand-grain weight (TGW). Alien chromosomes differentially modulated grain characteristics: 1JS and 6J both reduced grain length and grain circumference; 1JS increased LWR; and 4J negatively impacted TGW, grain width (GW), GD, and grain area (GA). Meanwhile, increasing alien chromosome numbers correlated with progressively stronger negative effects on grain traits. These findings elucidate the genetic mechanisms underlying wheat chromosomal variations induced by distant hybridization and their impact on wheat grain traits, and provide critical intermediate materials for genome design breeding and marker-assisted selection in wheat improvement. Full article
(This article belongs to the Section Plant Molecular Biology)
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27 pages, 2015 KB  
Review
The Neuro-Immune Axis in Cardiomyopathy: Molecular Mechanisms, Clinical Phenotypes, and Therapeutic Frontiers
by Dwaipayan Saha, Preyangsee Dutta and Abhijit Chakraborty
Immuno 2025, 5(4), 45; https://doi.org/10.3390/immuno5040045 - 3 Oct 2025
Abstract
Cardiomyopathies affect over 3 million individuals globally, with conventional treatments exhibiting up to 60% resistance and 25% 30-day readmission rates. This review synthesizes the current evidence on the role of neuro-immune interactions in the pathogenesis of cardiomyopathy and evaluates emerging therapies targeting this [...] Read more.
Cardiomyopathies affect over 3 million individuals globally, with conventional treatments exhibiting up to 60% resistance and 25% 30-day readmission rates. This review synthesizes the current evidence on the role of neuro-immune interactions in the pathogenesis of cardiomyopathy and evaluates emerging therapies targeting this axis. We systematically examined clinical trials and mechanistic and multi-omics data across cardiomyopathy phenotypes, focusing on autonomic-immune dysregulation. Sympathetic overactivation, present in approximately 85% of patients, correlates with elevated pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6) and contributes significantly to therapeutic non-response. Concurrent parasympathetic withdrawal impairs cholinergic anti-inflammatory pathways, as reflected by reduced heart rate variability and baroreflex sensitivity. At the molecular level, shared mechanisms include inflammasome activation, neuroimmune synaptic signaling, and neurogenic inflammation. Emerging therapies targeting this axis are promising. Vagus nerve stimulation, as demonstrated in the INOVATE-HF trial, improves functional outcomes, whereas IL-1β antagonists reduce cardiovascular events by 15–20% in the context of inflammatory diseases. Bioelectronic interventions, such as transcutaneous vagal nerve stimulation and baroreflex activation therapy, offer noninvasive dual-modulatory strategies that address both neural and immune pathways, positioning the neuroimmune axis as a central driver of cardiomyopathy, regardless of etiology. The integration of genetic and metabolomic profiling may enable precision therapies targeting neuroimmune circuits, thereby overcoming the limitations of hemodynamic-focused care. This mechanistic framework shifts the therapeutic paradigm from symptomatic relief to targeted modulation of pathogenic pathways, with implications for millions of patients with cardiomyopathy and broader inflammatory cardiovascular disorders. Full article
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20 pages, 2313 KB  
Article
Genetic Diversity and Association Analysis of Dioscorea polystachya Germplasm Resources Based on Phenotypic Traits and SSR Markers
by Dan Tan, Rong Tang, Ge Yang, Yinfang Yang, Miao Hu, Min Tang, Tianxu Cao and Ping Du
Horticulturae 2025, 11(10), 1193; https://doi.org/10.3390/horticulturae11101193 - 3 Oct 2025
Abstract
Dioscorea polystachya (Chinese yam) is a crop valued for both medicinal and edible purposes, and exhibits rich genetic diversity. However, research into its germplasm resources remains understudied, and molecular breeding efforts lag behind. To bridge this gap, this study employed an integrated approach, [...] Read more.
Dioscorea polystachya (Chinese yam) is a crop valued for both medicinal and edible purposes, and exhibits rich genetic diversity. However, research into its germplasm resources remains understudied, and molecular breeding efforts lag behind. To bridge this gap, this study employed an integrated approach, combining the analysis of 23 phenotypic traits (17 qualitative and 6 quantitative) with genotyping using 19 polymorphic SSR markers. This combined strategy was applied to 53 accessions collected across 16 Chinese provinces to assess genetic diversity, population structure, and marker–trait associations. Phenotypic analysis revealed high diversity, with the Shannon diversity index (I) ranging from 0.09 to 1.15 for qualitative traits and from 1.45 to 1.79 for quantitative traits. Tuber traits exhibited the highest variability (with a CV up to 71.45%), indicating significant potential for yield improvement. Principal component analysis distilled phenotypic variation into eight principal components (accounting for 73.13% of the cumulative variance), and elite germplasm (e.g., DP24, DP52) was selected for breeding based on this analysis. Stepwise regression prioritized eight core evaluation traits (e.g., flowering rate, tuber length). SSR markers amplified 80 alleles (mean 4.211/locus), showing moderate genetic diversity (He = 0.529, PIC = 0.585). Population structure analysis divided accessions into two subpopulations, correlated with geographic origins: Group 1 (northern/southwestern China) and Group 2 (central/eastern China), reflecting adaptation to local climates and human selection. Association analysis identified 10 SSR loci significantly linked (p < 0.01) to key traits, including YM07_2 (flowering, R2 = 13.94%), YM37_2 (leaf margin color, R2 = 19.03%), and YM19_3 (leaf width, R2 = 19.34%). This study establishes a comprehensive genetic framework for Chinese yam, offering molecular tools for marker-assisted breeding and strategies to conserve high-diversity germplasm, thereby enhancing the utilization of this orphan crop. Full article
(This article belongs to the Section Genetics, Genomics, Breeding, and Biotechnology (G2B2))
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18 pages, 748 KB  
Review
Statistical Methods for Multi-Omics Analysis in Neurodevelopmental Disorders: From High Dimensionality to Mechanistic Insight
by Manuel Airoldi, Veronica Remori and Mauro Fasano
Biomolecules 2025, 15(10), 1401; https://doi.org/10.3390/biom15101401 - 2 Oct 2025
Abstract
Neurodevelopmental disorders (NDDs), including autism spectrum disorder, intellectual disability, and attention-deficit/hyperactivity disorder, are genetically and phenotypically heterogeneous conditions affecting millions worldwide. High-throughput omics technologies—transcriptomics, proteomics, metabolomics, and epigenomics—offer a unique opportunity to link genetic variation to molecular and cellular mechanisms underlying these disorders. [...] Read more.
Neurodevelopmental disorders (NDDs), including autism spectrum disorder, intellectual disability, and attention-deficit/hyperactivity disorder, are genetically and phenotypically heterogeneous conditions affecting millions worldwide. High-throughput omics technologies—transcriptomics, proteomics, metabolomics, and epigenomics—offer a unique opportunity to link genetic variation to molecular and cellular mechanisms underlying these disorders. However, the high dimensionality, sparsity, batch effects, and complex covariance structures of omics data present significant statistical challenges, requiring robust normalization, batch correction, imputation, dimensionality reduction, and multivariate modeling approaches. This review provides a comprehensive overview of statistical frameworks for analyzing high-dimensional omics datasets in NDDs, including univariate and multivariate models, penalized regression, sparse canonical correlation analysis, partial least squares, and integrative multi-omics methods such as DIABLO, similarity network fusion, and MOFA. We illustrate how these approaches have revealed convergent molecular signatures—synaptic, mitochondrial, and immune dysregulation—across transcriptomic, proteomic, and metabolomic layers in human cohorts and experimental models. Finally, we discuss emerging strategies, including single-cell and spatially resolved omics, machine learning-driven integration, and longitudinal multi-modal analyses, highlighting their potential to translate complex molecular patterns into mechanistic insights, biomarkers, and therapeutic targets. Integrative multi-omics analyses, grounded in rigorous statistical methodology, are poised to advance mechanistic understanding and precision medicine in NDDs. Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
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13 pages, 1027 KB  
Article
Quantitative Trait Locus Mapping and Candidate Gene Identification for Fruit Acidity in Chinese Dwarf Cherry (Cerasus humilis) Using a High-Density Genetic Map
by Caizhen Guo, Fenglan Hu and Yuqi Li
Genes 2025, 16(10), 1157; https://doi.org/10.3390/genes16101157 - 29 Sep 2025
Abstract
Background/Objectives: The Chinese dwarf cherry (Cerasus humilis) is an endemic shrub fruit tree species in China. Its fruit is flavorful, nutrient-rich, and has considerable research and utilization potential. However, most currently cultivated varieties of C. humilis are highly acidic and primarily [...] Read more.
Background/Objectives: The Chinese dwarf cherry (Cerasus humilis) is an endemic shrub fruit tree species in China. Its fruit is flavorful, nutrient-rich, and has considerable research and utilization potential. However, most currently cultivated varieties of C. humilis are highly acidic and primarily used for processing. Consumer-preferred, low-acid, fresh-eating varieties are scarce, limiting industrial development. We used 208 F1 individuals derived from a cross between high-acid “Nongda 4” and the low-acid “DS-1”. Methods: Restriction site-associated DNA sequencing (RAD-seq) was used to develop single-nucleotide polymorphism (SNP) markers and construct a high-density genetic linkage map. Using two years of fruit titratable acidity phenotypic data, quantitative trait locus (QTL) mapping and candidate gene screening were performed. Results: The genetic map contained 2491 SNP markers, assigned to eight linkage groups. The total genetic distance was 672.71 cm, with an average distance of 0.27 cm between markers, indicating high map quality. QTL mapping identified 18 loci associated with fruit titratable acidity, including 11 major-effect QTLs (logarithm of odds, LOD ≥ 3.5). These major-effect QTLs were concentrated on linkage groups LG2 and LG5, with an explained phenotypic variation of 8.6–31.13%. Two candidate genes were identified within QTL intervals: phosphoester phosphatase and MATE transmembrane transporter. The phosphatase gene’s expression showed a strong correlation with titratable acid content (p < 0.01, correlation coefficient 0.93), suggesting that it plays an important role regulating fruit acidity in C. humilis. Conclusions: This study supports marker-assisted breeding of low-acid, fresh-eating varieties, aiding commercial promotion of C. humilis. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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14 pages, 2279 KB  
Article
Development of KASP Molecular Markers and Candidate Gene Mining for Heat Tolerance-Related Traits in Gossypium hirsutum
by Zhaolong Gong, Ni Yang, Shiwei Geng, Juyun Zheng, Zhi Liu, Fenglei Sun, Shengmei Li, Xueyuan Li, Yajun Liang and Junduo Wang
Genes 2025, 16(10), 1154; https://doi.org/10.3390/genes16101154 - 28 Sep 2025
Abstract
Background: High-temperature stress is one of the major abiotic stresses limiting cotton production. Identifying genetic loci and genes for heat tolerance is crucial for breeding heat-tolerant varieties. Methods: Given the complexity of heat tolerance phenotypes in cotton, this study, which focused [...] Read more.
Background: High-temperature stress is one of the major abiotic stresses limiting cotton production. Identifying genetic loci and genes for heat tolerance is crucial for breeding heat-tolerant varieties. Methods: Given the complexity of heat tolerance phenotypes in cotton, this study, which focused on resource materials, identified an A/C SNP mutation at position 5486185 on chromosome D06 within the heat tolerance interval through genome-wide association studies (GWAS) of natural Gossypium hirsutum populations. Results: A total of 308 resource materials were identified and evaluated for their heat tolerance phenotypes over two years of field research. Kompetitive allele-specific PCR (KASP) molecular markers were developed on the basis of the D06-5486185 SNP to characterize the heat tolerance phenotypes of these 308 resource materials. Genotyping for heat tolerance-related traits and agronomic traits was also performed. Materials with the C/C haplotype at position D06-5486185 presented increased heat tolerance (higher pollen viability (PV), leaf area (LA), chlorophyll (Chl) and number of bolls on the third fruit branch (FB3) and a lower number of dry buds (DBs) and drop rate (DR)) without negatively impacting key yield traits. This locus is located in the intergenic region of two adjacent bZIP transcription factor genes (GH_D06G0408 and GH_D06G0409). Expression analysis revealed that the expression levels of these two genes were significantly greater in heat-tolerant accessions (C/C type) than in sensitive accessions and that their expression levels were significantly correlated with multiple heat-tolerant phenotypes. Conclusions: In summary, this study developed a Kompetitive Allele Specific PCR (KASP) marker associated with heat tolerance in G. hirsutum and identified two key heat tolerance candidate genes. These results provide an efficient marker selection tool and important genetic resources for the molecular breeding of heat-tolerant G. hirsutum, laying an important foundation for further establishing a molecular marker-assisted breeding system for heat tolerance in G. hirsutum. Full article
(This article belongs to the Special Issue Genetic Research on Crop Stress Resistance and Quality Traits)
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25 pages, 1134 KB  
Article
Genetic Etiology of Developmental and Epileptic Encephalopathy in a Turkish Cohort: A Single-Center Study with Targeted Gene Panel and Whole Exome Sequencing
by Deniz Sunnetci-Akkoyunlu, Bulent Kara, Tolgahan Ozer, Adnan Deniz, Ayfer Sakarya-Gunes, Elif Busra Isik, Buket Dogruoglu, Zeynep Ilkay, Mehtap Yilmaz, Sumeyye Sahin, Seda Eren-Keskin, Naci Cine and Hakan Savli
Genes 2025, 16(10), 1152; https://doi.org/10.3390/genes16101152 - 28 Sep 2025
Abstract
Background: Developmental and Epileptic Encephalopathy (DEE) is a severe and heterogeneous neurological disorder in infancy/early childhood. DEE’s genetic and phenotypic variability complicates diagnosis and treatment. This retrospective study aimed to identify genetic variants and explore genotype–phenotype correlations in children with DEE using a [...] Read more.
Background: Developmental and Epileptic Encephalopathy (DEE) is a severe and heterogeneous neurological disorder in infancy/early childhood. DEE’s genetic and phenotypic variability complicates diagnosis and treatment. This retrospective study aimed to identify genetic variants and explore genotype–phenotype correlations in children with DEE using a targeted epilepsy gene panel (TGP) and Whole Exome Sequencing (WES). Patients and Methods: Medical records of children who underwent custom-designed 55-gene TGP and WES were reviewed. The diagnostic yield of each method was determined based on the detection of pathogenic (P) and likely pathogenic (LP) variants. Results: A total of 129 patients (66 males, 63 females) underwent TGP, which identified P/LP variants in 29 cases (22.48%). Variants were detected in SCN1A, KCNQ2, STXBP1, CDKL5, PCDH19, PLCB1, WWOX, SCN2A, FGF12, HCN1, SCN8A, and SLC35A2. WES further identified several variants in children with West syndrome. A TSC1 variant was detected in a patient without cutaneous stigmata of tuberous sclerosis complex. The NALCN variant in a patient was linked to Infantile Hypotonia with Psychomotor Retardation and Characteristic Facies 1. A CTBP1 variant associated with extremely rare Hypotonia, Ataxia, Developmental Delay, and Tooth Enamel Defect Syndrome was detected in another patient. A PIEZO2 variant—associated with Marden–Walker syndrome—was found in a child with Early Infantile Developmental and Epileptic Encephalopathy. Conclusions: These findings highlight the extensive genetic heterogeneity and phenotypic variability of DEE. WES demonstrates substantial value in identifying novel gene-disease associations and may be considered as a first-tier diagnostic tool in epilepsy and DEE. Full article
(This article belongs to the Section Genetic Diagnosis)
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20 pages, 9291 KB  
Article
Atad1 Is a Potential Candidate Gene for Prepulse Inhibition
by Akhilesh K. Bajpai, Timothy G. Freels, Lu Lu and Melloni N. Cook
Genes 2025, 16(10), 1139; https://doi.org/10.3390/genes16101139 - 26 Sep 2025
Abstract
Background/Objectives: Prepulse inhibition (PPI) is a robust, reproducible phenotype associated with schizophrenia and other psychiatric disorders. This study was carried out to identify gene(s) influencing PPI. Methods: We performed Quantitative Trait Locus (QTL) analysis of PPI in 59 strains from [...] Read more.
Background/Objectives: Prepulse inhibition (PPI) is a robust, reproducible phenotype associated with schizophrenia and other psychiatric disorders. This study was carried out to identify gene(s) influencing PPI. Methods: We performed Quantitative Trait Locus (QTL) analysis of PPI in 59 strains from the BXD recombinant inbred (BXD RI) mouse family and used a 2-LOD region for candidate gene identification. Genes significantly correlated with the candidate gene were identified based on genetic, partial, and literature correlation, and were further studied through gene enrichment and protein–protein interaction analyses. Phenome-wide association study (PheWAS) and differential expression analyses of the candidate gene were performed using human data. Results: We identified one significant (GN Trait 11428) and two suggestive male-specific QTLs (GN Traits 11426 and 11427) on Chromosome 19 between 27 and 36 Mb with peak LRS values of 19.2 (−logP = 4.2), 14.4 (−logP = 3.1), and 13.3 (−logP = 2.9), respectively. Atad1, ATPase family, AAA domain containing 1 was identified as the strongest candidate for the male-specific PPI loci. Atad1 expression in BXDs is strongly cis-modulated in the nucleus accumbens (NAc, LRS = 26.5 (−logP = 5.7). Many of the Atad1-correlated genes in the NAc were enriched in neurotransmission-related categories. Protein–protein interaction analysis suggested that ATAD1 functions through its direct partners, GRIA2 and ASNA1. PheWAS revealed significant associations between Atad1 and psychiatric traits, including schizophrenia. Analysis of a human RNA-seq dataset revealed differential expression of Atad1 between schizophrenia patients and the control group. Conclusions: Collectively, our analyses support Atad1 as a potential candidate gene for PPI and suggest that this gene should be further investigated for its involvement in psychiatric disorders. Full article
(This article belongs to the Special Issue Genetics of Neuropsychiatric Disorders)
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20 pages, 5636 KB  
Communication
Bridging Breeds: Transcriptomic Insights into Immune Traits of Yili, Thoroughbred, and Kazakh Horses
by Tongliang Wang, Xixi Yang, Chuankun Wang, Jianwen Wang, Jun Meng, Xinkui Yao, Yaqi Zeng and Wanlu Ren
Life 2025, 15(10), 1496; https://doi.org/10.3390/life15101496 - 23 Sep 2025
Viewed by 157
Abstract
Background: Studying the genetic characteristics and molecular mechanisms of immune regulation in horses is of great significance for protecting their genetic resources, improving breeding strategies, and enhancing their disease resistance, thereby ensuring their healthy performance in both sports and production. Aims/objectives: This study [...] Read more.
Background: Studying the genetic characteristics and molecular mechanisms of immune regulation in horses is of great significance for protecting their genetic resources, improving breeding strategies, and enhancing their disease resistance, thereby ensuring their healthy performance in both sports and production. Aims/objectives: This study investigates the genetic characteristics and molecular mechanisms underlying immune regulation in Yili horses, comparing them with Thoroughbreds and Kazakh horses. Methods: Blood samples from each breed were analyzed for physiological, biochemical, and immune indices alongside transcriptome sequencing to identify differentially expressed genes (DEGs). Results: The results revealed significant differences in neutrophil counts, monocytes, red blood cell parameters, glucose levels, and immunoglobulins (IgA, IgG, IgM) among breeds. Yili horses exhibited intermediate values for most parameters, aligning more closely with Thoroughbreds. Transcriptomic analysis identified 3574 DEGs, enriched in immune-related pathways such as platelet activation, antigen processing, and cytokine signaling. Key genes, including TNFRSF14, IFIT3, and IL21R, correlated with immune traits, highlighting hybrid vigor in Yili horses. Functional enrichment underscored pathways like IL-17 signaling and NF-κB regulation, linking genetic differences to immune adaptability. Conclusions: These findings provide molecular insights into breed-specific immune traits, supporting strategies to enhance disease resilience in Yili horses while preserving their athletic performance. This study underscores the importance of integrating transcriptomic and phenotypic data for informed breeding practices in equine conservation and improvement. Full article
(This article belongs to the Section Animal Science)
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19 pages, 1503 KB  
Review
Rethinking Childhood-Onset Hypertrophic Cardiomyopathy: A Review of Molecular Mechanisms and Unique Therapy Considerations
by Caitlin Menzies and Vernon W. Dolinsky
J. Cardiovasc. Dev. Dis. 2025, 12(10), 374; https://doi.org/10.3390/jcdd12100374 - 23 Sep 2025
Viewed by 206
Abstract
Childhood-onset hypertrophic cardiomyopathy (HCM) is a cardiac disorder presenting unique diagnostic and therapeutic challenges in children that require tailored clinical attention compared to HCM arising at other life stages. Despite this, current treatment strategies specific to childhood-onset HCM are lacking and are predominantly [...] Read more.
Childhood-onset hypertrophic cardiomyopathy (HCM) is a cardiac disorder presenting unique diagnostic and therapeutic challenges in children that require tailored clinical attention compared to HCM arising at other life stages. Despite this, current treatment strategies specific to childhood-onset HCM are lacking and are predominantly extrapolated from adult-specific treatment guidelines. This review explores the molecular basis, clinical implications, and management strategies specific to childhood-onset HCM. Advances in molecular genetics have elucidated diverse pathogenic pathways and genotype-phenotype correlations, revealing age-specific disease modifiers distinct from adult-onset forms. Current management includes pharmacologic, surgical, and device-based interventions, tailored to individualized needs. However, there is a lack of evidence for the efficacy and safety profiles of these treatments in children, meaning children may be receiving sub-optimal care. Emerging approaches, such as gene-targeted therapies and precision medicine frameworks, show promise, but require further investigation. Enhancing early diagnosis and personalized care is crucial for improving outcomes and reducing long-term disease burden in affected children. This review underscores the necessity for specific research to refine risk stratification and treatment paradigms for childhood-onset HCM. Full article
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20 pages, 3813 KB  
Article
Molecular and Phytopathological Characterization of Fusarium Wilt-Resistant Chickpea Genotypes for Breeding Applications
by Raushan Yerzhebayeva, Alfiya Abekova, Kuralay Baitarakova, Mukhtar Kudaibergenov, Aydarkhan Yesserkenov, Bekzhan Maikotov and Svetlana Didorenko
Agriculture 2025, 15(19), 1992; https://doi.org/10.3390/agriculture15191992 - 23 Sep 2025
Viewed by 173
Abstract
Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (Foc), is a devastating disease of chickpea (Cicer arietinum L.), leading to vascular necrosis and plant death. This study evaluated 120 chickpea genotypes under natural infection field conditions during spring sowing [...] Read more.
Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (Foc), is a devastating disease of chickpea (Cicer arietinum L.), leading to vascular necrosis and plant death. This study evaluated 120 chickpea genotypes under natural infection field conditions during spring sowing in southeastern Kazakhstan, assessing disease incidence (DI) and severity (DS) to identify resistant germplasm. Molecular screening using eight SSR markers linked to Foc-1, Foc-2, Foc-3, and Foc-5 loci detected resistant alleles in 18, 26, 19, and 42 genotypes, respectively. The correlation between molecular marker data and phenotypic resistance evaluations confirmed UBC-170 (Foc-2) and TA-194 (Foc-5) as the most predictive diagnostic markers (p < 0.01). Ten genotypes showed complete disease resistance (DI < 5%, R), corresponding to the resistant control (cultivar “WR-315”), with confirmed presence of multiple Foc resistance genes. The results of this study revealed valuable genetic resources for marker-assisted breeding programs aimed at developing Fusarium wilt-resistant chickpea cultivars adapted to Central Asian agroclimatic conditions. Full article
(This article belongs to the Section Crop Protection, Diseases, Pests and Weeds)
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17 pages, 10184 KB  
Article
Genome-Wide Association Studies of Fiber Content in Sugarcane
by Yongsheng Chen, Xiaomin Feng, Nannan Zhang, Yawen Lei, Zilin Wu and Jiayun Wu
Agronomy 2025, 15(10), 2249; https://doi.org/10.3390/agronomy15102249 - 23 Sep 2025
Viewed by 149
Abstract
Lignocellulosic biomass may play a major role in the production of biofuels, bioplastics, sugar, paper, and various other industrial products. In addition, it is a key trait in plants due to its contribution to lodging resistance. Fiber also shows a significant negative correlation [...] Read more.
Lignocellulosic biomass may play a major role in the production of biofuels, bioplastics, sugar, paper, and various other industrial products. In addition, it is a key trait in plants due to its contribution to lodging resistance. Fiber also shows a significant negative correlation with most yield traits and all sugar traits. As the most harvested crop globally by tonnage, sugarcane is an important resource for both sugar and bioenergy production. In this study, a panel of sugarcane clones was utilized to investigate the fiber content. This panel included 17 core parental lines derived from 11 countries involved in sugarcane cultivation and breeding. It represented the genetic base of commercial sugarcane breeding programs in China and other countries. The objective of this research was to identify molecular markers and candidate genes associated with fiber content in sugarcane using genome-wide association studies (GWASs). By integrating 5,964,084 high-quality single-nucleotide polymorphisms (SNPs) with phenotypic data collected across five different environments, a total of 69 SNPs spanning 41 quantitative trait loci (QTLs) were identified. Based on functional annotations and genomic positions, these QTLs contained 52 candidate genes. These candidate genes encoded the ultraviolet-B receptor (UVR8), leucine-rich repeat receptor-like kinases (LRR-RLKs), serine/threonine kinases (STKs), cellulose synthase (CESA), vegetative cell wall protein glycoproteins1 (gp1), F-box protein, MYB transcription factor, and so on. These genes could directly or indirectly influence the fiber content in sugarcane. Furthermore, according to previous studies, among these candidate genes, five located in four QTL regions were proposed to be the most critical. They included Sspon.02G0041160-2C, encoding CESA; Sspon.03G0039010-1C and Sspon.03G0039030-1C, both encoding gp1; Sspon.06G0023090-1B, encoding an F-box protein; and Sspon.07G0019440-2C, encoding a MYB transcription factor. The genetic basis of the fiber content was explored using elite breeding lines and their derivatives from the Chinese sugarcane breeding program. These candidate genes represent promising targets for future functional studies and may contribute to the development of different types of sugarcane varieties with correspondingly suitable fiber content through marker-assisted selection. Full article
(This article belongs to the Section Crop Breeding and Genetics)
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14 pages, 2636 KB  
Article
Efficiency of Genomic Selection for Developing Superior Pure Lines
by Jean Paulo Aparecido da Silva and José Marcelo Soriano Viana
Agronomy 2025, 15(10), 2247; https://doi.org/10.3390/agronomy15102247 - 23 Sep 2025
Viewed by 148
Abstract
The objectives were to assess the efficacy of genomic selection in pure line breeding, using a simulated dataset, the significance of several factors, including model updating, selection intensity, early generation (F2) selection, dominance, and the presence of major-effect genes (QTLs). The [...] Read more.
The objectives were to assess the efficacy of genomic selection in pure line breeding, using a simulated dataset, the significance of several factors, including model updating, selection intensity, early generation (F2) selection, dominance, and the presence of major-effect genes (QTLs). The simulated genome included 1000 biallelic genes and 49,825 SNPs, distributed on 10 chromosomes of 100 cM. We used genomic selection with partial phenotyping over generations and other scenarios. The efficacy of genomic selection was based on total realized genetic gain and probability of selecting superior pure lines. The results showed that genomic selection with model updating maximized the probability of selecting superior F8 progeny and provided the highest total genetic gain, comparable to selection based on the true genotypic value. Larger training sets (achieved through model updating) and higher selection intensity were key factors affecting the development of elite pure lines. Dominance did not significantly affect genomic selection efficiency. Including QTLs increased genomic selection efficiency. Direct selection imposed within the F2 generation was no more effective than selection started in F3. All selection methods provided a high decrease in the genotypic variance at F8. The realized genetic gains per cycle were positively correlated with the prediction accuracies. Full article
(This article belongs to the Section Crop Breeding and Genetics)
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21 pages, 6852 KB  
Article
Phenotypic and Genetic Diversity of Chickpea (Cicer arietinum L.) Accessions from Kazakhstan
by Alibek Zatybekov, Yuliya Genievskaya, Shynar Anuarbek, Mukhtar Kudaibergenov, Yerlan Turuspekov and Saule Abugalieva
Diversity 2025, 17(9), 664; https://doi.org/10.3390/d17090664 - 22 Sep 2025
Viewed by 204
Abstract
Chickpea (Cicer arietinum L.) is a key legume crop of global economic and nutritional importance, yet its cultivation in Kazakhstan is constrained by a narrow genetic base and exposure to stress-prone environments. To characterize the diversity available for breeding and conservation, 27 [...] Read more.
Chickpea (Cicer arietinum L.) is a key legume crop of global economic and nutritional importance, yet its cultivation in Kazakhstan is constrained by a narrow genetic base and exposure to stress-prone environments. To characterize the diversity available for breeding and conservation, 27 accessions (22 kabuli and 5 desi) were evaluated for phenotypic and molecular diversity to assess its potential for use in breeding programs. Seven agronomic traits were assessed, including plant height, the first pod’s height, the number of main stems per plant, and seed yield components. The collection showed considerable variability across traits, with the plant height ranging from 37 to 75 cm and hundred-seed weight ranging from 21 to 42 g. Strong positive correlations between the number of fertile nodes, number of seeds per plant, and yield per plant (r > 0.83) highlighted their utility as indirect selection criteria. Genotyping with 28 SSR markers revealed 110 alleles (mean 3.9 ± 0.4 per locus) with moderate polymorphism (PIC = 0.493 ± 0.089). Loci CaM00495 and TAI71 were highly informative (PIC > 0.804), while two accessions showed low polymorphism, indicating genetic uniformity. Population structure analysis grouped accessions into four highly admixed clusters. Overall, Kazakh chickpea germplasm exhibits substantial phenotypic and genetic diversity under optimal conditions, providing valuable preliminary data for selecting parental lines for future breeding programs, which should include targeted stress screening to evaluate resilience. Full article
(This article belongs to the Special Issue Economic Plant Diversity in the Anthropocene)
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Article
Early Detection of Subclinical Myocardial Dysfunction in Familial Dilated Cardiomyopathy Using Myocardial Work Analysis
by Apostolos Vrettos, Ricardo Prista Monteiro, Miltiadis Triantafyllou, Uzma Gul, Sanjeev Bhattacharyya, Luís R. Lopes, Alexios Antonopoulos, Alexandros Protonotarios, Guy Lloyd, Thomas Gossios and Konstantinos Savvatis
Diagnostics 2025, 15(18), 2363; https://doi.org/10.3390/diagnostics15182363 - 17 Sep 2025
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Abstract
Background/Objectives: Early detection of familial dilated cardiomyopathy (DCM) is crucial for initiating timely interventions. Myocardial work (MW) analysis, which integrates strain imaging and blood pressure, shows promise in identifying subclinical disease. To assess the utility of MW in detecting early myocardial changes [...] Read more.
Background/Objectives: Early detection of familial dilated cardiomyopathy (DCM) is crucial for initiating timely interventions. Myocardial work (MW) analysis, which integrates strain imaging and blood pressure, shows promise in identifying subclinical disease. To assess the utility of MW in detecting early myocardial changes in relatives of DCM patients with a positive genotype (G+) compared to genotype-negative (G−) controls. Methods: This study involved asymptomatic relatives of DCM patients who underwent comprehensive echocardiographic evaluation, including MW analysis. Subjects (N = 77) were classified into G+ (n = 39) and (n = 38) groups based on genetic testing. Myocardial work parameters—myocardial global work index (GWI), global constructive work (GCW), global wasted work (GWW), and global work efficiency (GWE)—were measured. Statistical analyses compared these parameters between groups and assessed their predictive value for genotype status. Follow-up data were collected and analysed accordingly. Results: Among 77 participants (mean age 36 ± 14 years; 49% women), there were no significant differences in baseline characteristics between G+ and G− groups. S’ septal, s′ average, e′ lateral, E max and E/A were found to be significantly different between the two groups. G+ individuals had significantly reduced GWE (94% vs. 96%, p < 0.001) and increased GWW (113 mmHg% vs. 80 mmHg%, p = 0.001). After adjustment for significant echocardiographic parameters, GWE (OR = 0.746, 95% CI: 0.560–0.994, p = 0.045) and GWW (OR = 1.012, 95% CI: 1.002–1.024, p = 0.047) remained significant predictors of gene carrier status in multivariable analysis. The addition of GWE and GWW significantly increased the area under the curve of a model identifying G+ individuals (p < 0.05). During a median period of follow-up of 53 months, 16 (21%) individuals expressed a cardiomyopathy phenotype. There was a significant correlation between increased baseline GWW, reduced GWE, and the expression of cardiomyopathy phenotype. Conclusions: Myocardial work analysis, specifically GWE and GWW, identifies early myocardial dysfunction in asymptomatic carriers of genetic variants for DCM. These findings suggest that MW could complement traditional imaging in the early detection and management of familial DCM. Full article
(This article belongs to the Special Issue Insights into Imaging Diagnosis of Heart Disease)
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