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Keywords = genome-wide study

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12 pages, 1076 KiB  
Article
Rapid Identification of the SNP Mutation in the ABCD4 Gene and Its Association with Multi-Vertebrae Phenotypes in Ujimqin Sheep Using TaqMan-MGB Technology
by Yue Zhang, Min Zhang, Hong Su, Jun Liu, Feifei Zhao, Yifan Zhao, Xiunan Li, Yanyan Yang, Guifang Cao and Yong Zhang
Animals 2025, 15(15), 2284; https://doi.org/10.3390/ani15152284 - 5 Aug 2025
Abstract
Ujimqin sheep, known for its distinctive multi-vertebrae phenotypes (T13L7, T14L6, and T14L7) and economic value, has garnered significant attention. However, conventional phenotypic detection methods suffer from low efficiency and high costs. In this study, based on a key SNP locus (ABCD4 gene, [...] Read more.
Ujimqin sheep, known for its distinctive multi-vertebrae phenotypes (T13L7, T14L6, and T14L7) and economic value, has garnered significant attention. However, conventional phenotypic detection methods suffer from low efficiency and high costs. In this study, based on a key SNP locus (ABCD4 gene, Chr7:89393414, C > T) identified through a genome-wide association study (GWAS), a TaqMan-MGB (minor groove binder) genotyping system was developed. the objective was to establish a high-throughput and efficient molecular marker-assisted selection (MAS) tool. Specific primers and dual fluorescent probes were designed to optimize the reaction system. Standard plasmids were adopted to validate genotyping accuracy. A total of 152 Ujimqin sheep were subjected to TaqMan-MGB genotyping, digital radiography (DR) imaging, and Sanger sequencing. the results showed complete concordance between TaqMan-MGB and Sanger sequencing, with an overall agreement rate of 83.6% with DR imaging. For individuals with T/T genotypes (127/139), the detection accuracy reached 91.4%. This method demonstrated high specificity, simplicity, and cost-efficiency, significantly reducing the time and financial burden associated with traditional imaging-based approaches. the findings indicate that the TaqMan-MGB technique can accurately identify the T/T genotype at the SNP site and its strong association with the multi-vertebrae phenotypes, offering an effective and reliable tool for molecular breeding of Ujimqin sheep. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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16 pages, 2443 KiB  
Article
Contralateral Structure and Molecular Response to Severe Unilateral Brain Injury
by Xixian Liao, Xiaojian Xu, Ming Li, Runfa Tian, Yuan Zhuang and Guoyi Gao
Brain Sci. 2025, 15(8), 837; https://doi.org/10.3390/brainsci15080837 (registering DOI) - 5 Aug 2025
Abstract
Background: Severe damage to one side of the brain often leads to adverse consequences and can also cause widespread changes throughout the brain, especially in the contralateral area. Studying molecular changes in the contralateral cerebral hemisphere, especially with regard to genetic regulation, [...] Read more.
Background: Severe damage to one side of the brain often leads to adverse consequences and can also cause widespread changes throughout the brain, especially in the contralateral area. Studying molecular changes in the contralateral cerebral hemisphere, especially with regard to genetic regulation, can help discover potential treatment strategies to promote recovery after severe brain trauma on one side. Methods: In our study, the right motor cortex was surgically removed to simulate severe unilateral brain injury, and changes in glial cells and synaptic structure in the contralateral cortex were subsequently assessed through immunohistological, morphological, and Western blot analyses. We conducted transcriptomic studies to explore changes in gene expression levels associated with the inflammatory response. Results: Seven days after corticotomy, levels of reactive astrocytes and hypertrophic microglia increased significantly in the experimental group, while synapsin-1 and PSD-95 levels in the contralateral motor cortex increased. These molecular changes are associated with structural changes, including destruction of dendritic structures and the encapsulation of astrocytes by synapses. Genome-wide transcriptome analysis showed a significant increase in gene pathways involved in inflammatory responses, synaptic activity, and nerve fiber regeneration in the contralateral cortex after corticorectomy. Key transcription factors such as NF-κB1, Rela, STAT3 and Jun were identified as potential regulators of these contralateral changes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) confirmed that the mRNA expression levels of Cacna1c, Tgfb1 and Slc2a1 genes related to STAT3, JUN, and NF-κB regulation significantly increased in the contralateral cortex of the experimental group. Conclusions: After unilateral brain damage occurs, changes in the contralateral cerebral hemisphere are closely related to processes involving inflammation and synaptic function. Full article
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16 pages, 4328 KiB  
Article
High-Throughput Study on Nanoindentation Deformation of Al-Mg-Si Alloys
by Tong Shen, Guanglong Xu, Fuwen Chen, Shuaishuai Zhu and Yuwen Cui
Materials 2025, 18(15), 3663; https://doi.org/10.3390/ma18153663 - 4 Aug 2025
Abstract
Al-Mg-Si (6XXX) series aluminum alloys are widely applied in aerospace and transportation industries. However, exploring how varying compositions affect alloy properties and deformation mechanisms is often time-consuming and labor-intensive due to the complexity of the multicomponent composition space and the diversity of processing [...] Read more.
Al-Mg-Si (6XXX) series aluminum alloys are widely applied in aerospace and transportation industries. However, exploring how varying compositions affect alloy properties and deformation mechanisms is often time-consuming and labor-intensive due to the complexity of the multicomponent composition space and the diversity of processing and heat treatments. This study, inspired by the Materials Genome Initiative, employs high-throughput experimentation—specifically the kinetic diffusion multiple (KDM) method—to systematically investigate how the pop-in effect, indentation size effect (ISE), and creep behavior vary with the composition of Al-Mg-Si alloys at room temperature. To this end, a 6016/Al-3Si/Al-1.2Mg/Al KDM material was designed and fabricated. After diffusion annealing at 530 °C for 72 h, two junction areas were formed with compositional and microstructural gradients extending over more than one thousand micrometers. Subsequent solution treatment (530 °C for 30 min) and artificial aging (185 °C for 20 min) were applied to simulate industrial processing conditions. Comprehensive characterization using electron probe microanalysis (EPMA), nanoindentation with continuous stiffness measurement (CSM), and nanoindentation creep tests across these gradient regions revealed key insights. The results show that increasing Mg and Si content progressively suppresses the pop-in effect. When the alloy composition exceeds 1.0 wt.%, the pop-in events are nearly eliminated due to strong interactions between solute atoms and mobile dislocations. In addition, adjustments in the ISE enabled rapid evaluation of the strengthening contributions from Mg and Si in the microscale compositional array, demonstrating that the optimum strengthening occurs when the Mg-to-Si atomic ratio is approximately 1 under a fixed total alloy content. Furthermore, analysis of the creep stress exponent and activation volume indicated that dislocation motion is the dominant creep mechanism. Overall, this enhanced KDM method proves to be an effective conceptual tool for accelerating the study of composition–deformation relationships in Al-Mg-Si alloys. Full article
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21 pages, 6621 KiB  
Article
Genome-Wide Identification and Expression Pattern Analysis of the Late Embryogenesis Abundant (LEA) Family in Foxtail Millet (Setaria italica L.)
by Yingying Qin, Yiru Zhao, Xiaoyu Li, Ruifu Wang, Shuo Chang, Yu Zhang, Xuemei Ren and Hongying Li
Genes 2025, 16(8), 932; https://doi.org/10.3390/genes16080932 (registering DOI) - 4 Aug 2025
Abstract
Background/Objectives: Late embryogenesis abundant (LEA) proteins regulate stress responses and contribute significantly to plant stress tolerance. As a model species for stress resistance studies, foxtail millet (Setaria italica) lacks comprehensive characterization of its LEA gene family. This study aimed to [...] Read more.
Background/Objectives: Late embryogenesis abundant (LEA) proteins regulate stress responses and contribute significantly to plant stress tolerance. As a model species for stress resistance studies, foxtail millet (Setaria italica) lacks comprehensive characterization of its LEA gene family. This study aimed to comprehensively identify SiLEA genes in foxtail millet and elucidate their functional roles and tissue-specific expression patterns. Methods: Genome-wide identification of SiLEA genes was conducted, followed by phylogenetic reconstruction, cis-acting element analysis of promoters, synteny analysis, and expression profiling. Results: Ninety-four SiLEA genes were identified and classified into nine structurally distinct subfamilies, which are unevenly distributed across all nine chromosomes. Phylogenetic analysis showed closer clustering of SiLEA genes with sorghum and rice orthologs than with Arabidopsis thaliana AtLEA genes. Synteny analysis indicated the LEA gene family expansion through tandem and segmental duplication. Promoter cis-element analysis linked SiLEA genes to plant growth regulation, stress responses, and hormone signaling. Transcriptome analysis revealed tissue-specific expression patterns among SiLEA members, while RT-qPCR verified ABA-induced transcriptional regulation of SiLEA genes. Conclusions: This study identified 94 SiLEA genes grouped into nine subfamilies with distinct spatial expression profiles. ABA treatment notably upregulated SiASR-2, SiASR-5, and SiASR-6 in both shoots and roots. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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14 pages, 1805 KiB  
Data Descriptor
Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) Trial: Genetic Resource for Precision Nutrition
by Yuxi Liu, Hailie Fowler, Dong D. Wang, Lisa L. Barnes and Marilyn C. Cornelis
Nutrients 2025, 17(15), 2548; https://doi.org/10.3390/nu17152548 - 4 Aug 2025
Abstract
Background: The Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) was a 3-year, multicenter, randomized controlled trial to test the effects of the MIND diet on cognitive decline in 604 individuals at risk for Alzheimer’s dementia. Here, we describe the genotyping, imputation, and quality control [...] Read more.
Background: The Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) was a 3-year, multicenter, randomized controlled trial to test the effects of the MIND diet on cognitive decline in 604 individuals at risk for Alzheimer’s dementia. Here, we describe the genotyping, imputation, and quality control (QC) procedures for the genetic data of trial participants. Methods: DNA was extracted from either whole blood or serum, and genotyping was performed using the Infinium Global Diversity Array. Established sample and SNP QC procedures were applied to the genotyping data, followed by imputation using the 1000 Genomes Phase 3 v5 reference panel. Results: Significant study-site, specimen type, and batch effects were observed. A total of 494 individuals of inferred European ancestry and 58 individuals of inferred African ancestry were included in the final imputed dataset. Evaluation of the imputed APOE genotype against gold-standard sequencing data showed high concordance (98.2%). We replicated several known genetic associations identified from previous genome-wide association studies, including SNPs previously linked to adiponectin (rs16861209, p = 1.5 × 10−5), alpha-linolenic acid (rs174547, p = 1.3 × 10−7), and alpha-tocopherol (rs964184, p = 0.003). Conclusions: This dataset represents the first genetic resource derived from a dietary intervention trial focused on cognitive outcomes. It enables investigation of genetic contributions to variability in cognitive response to the MIND diet and supports integrative analyses with other omics data types to elucidate the biological mechanisms underlying cognitive decline. These efforts may ultimately inform precision nutrition strategies to promote cognitive health. Full article
(This article belongs to the Section Nutrigenetics and Nutrigenomics)
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19 pages, 764 KiB  
Systematic Review
Single Nucleotide Polymorphisms of Leptin and Calpain/Calpastatin in Key Traits of Pork Meat Quality
by Ofelia Limón-Morales, Herlinda Bonilla-Jaime, Marcela Arteaga-Silva, Patricia Roldán-Santiago, Luis Alberto de la Cruz-Cruz, Héctor Orozco-Gregorio, Marco Cerbón and José Luis Cortes-Altamirano
Animals 2025, 15(15), 2270; https://doi.org/10.3390/ani15152270 - 4 Aug 2025
Abstract
The increasing demand for food to meet the needs of the planet’s growing population requires, among other factors, greater and improved meat production. Meat quality is determined by key consumer-preferred traits, particularly tenderness, juiciness, and flavor. Recently, interest has grown in analyzing the [...] Read more.
The increasing demand for food to meet the needs of the planet’s growing population requires, among other factors, greater and improved meat production. Meat quality is determined by key consumer-preferred traits, particularly tenderness, juiciness, and flavor. Recently, interest has grown in analyzing the genes associated with these phenotypic characteristics. Single-nucleotide polymorphisms (SNPs) are common genomic variations in cattle and represent the most widely used molecular markers. Research on SNP variation is now a major focus of genomic studies aimed at improving meat quality. Leptin levels reflect the amount of adipose tissue in meat, also known as marbling. Several SNPs in the leptin gene and its receptor have been linked to this meat quality trait. Similarly, SNPs in the calpain/calpastatin system play a significant role in postmortem muscle proteolysis and pork tenderness. This review examines these genetic variants as markers involved in the expression of phenotypic traits in meat products and explores their mechanisms of action. Additionally, it provides insights into the genetic variants associated with production-related characteristics. Full article
(This article belongs to the Special Issue Genetic Improvement in Pigs)
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21 pages, 3086 KiB  
Article
Integrative Population Genomics Reveals Niche Differentiation and Gene Flow in Chinese Sclerophyllous Oaks (Quercus Sect. Ilex)
by Miao-Miao Ju, Ming Yue and Gui-Fang Zhao
Plants 2025, 14(15), 2403; https://doi.org/10.3390/plants14152403 - 3 Aug 2025
Viewed by 139
Abstract
Elucidating the coexistence mechanisms of rapidly diverging species has long been a challenge in evolutionary biology. Genome-wide polymorphic loci are expected to provide insights into the speciation processes of these closely related species. This study focused on seven Chinese sclerophyllous oaks, represented by [...] Read more.
Elucidating the coexistence mechanisms of rapidly diverging species has long been a challenge in evolutionary biology. Genome-wide polymorphic loci are expected to provide insights into the speciation processes of these closely related species. This study focused on seven Chinese sclerophyllous oaks, represented by Quercus spinosa, Quercus aquifolioides, Quercus rehderiana, Quercus guyavifolia, Quercus monimotricha, Quercus semecarpifolia, and Quercus senescens, employing 27,592 single-nucleotide polymorphisms to examine their phylogenetic relationships at the genomic level. Combined with genetic structure analysis, phylogenetic trees revealed that the genetic clustering of individuals was influenced by both geographic distance and ancestral genetic components. Furthermore, this study confirmed the existence of reticulate evolutionary relationships among the species. Frequent gene flow and introgression within the seven species were primarily responsible for the ambiguous interspecies boundaries, with hybridization serving as a major driver of reticulate evolution. Additionally, the seven species exhibited distinct differences in niche occupancy. By reconstructing the climatic adaptability of ancestral taxonomic units, we found that the climatic tolerance of each species displayed differential responses to 19 climatic factors. Consequently, ecological niche differentiation and variations in habitat adaptation contributed to the preservation of species boundaries. This study provides a comprehensive understanding of the speciation processes in rapidly diverging genera and underscores the significance of both genetic and ecological factors in the formation and maintenance of species boundaries. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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10 pages, 588 KiB  
Article
Genome-Wide Association Study of Gluteus Medius Muscle Size in a Crossbred Pig Population
by Yu He, Chunyan Bai, Junwen Fei, Juan Ke, Changyi Chen, Xiaoran Zhang, Wuyang Liu, Jing Li, Shuang Liang, Boxing Sun and Hao Sun
Vet. Sci. 2025, 12(8), 730; https://doi.org/10.3390/vetsci12080730 - 3 Aug 2025
Viewed by 49
Abstract
The size of the gluteus medius muscle (GM) in swine significantly impacts both hindlimb conformation and carcass yield, while little is known about the genetic architecture of this trait. This study aims to estimate genetic parameters and identify candidate genes associated with this [...] Read more.
The size of the gluteus medius muscle (GM) in swine significantly impacts both hindlimb conformation and carcass yield, while little is known about the genetic architecture of this trait. This study aims to estimate genetic parameters and identify candidate genes associated with this trait through a genome-wide association study (GWAS). A total of 439 commercial crossbred pigs, possessing both Landrace and Yorkshire ancestry, were genotyped using the Porcine 50K chip. The length and width of the GM were directly measured, and the area was then calculated from these values. The heritabilities were estimated by HIBLUP (V1.5.0) software, and the GWAS was conducted employing the BLINK model implemented in GAPIT3. The heritability estimates for the length, width, and area of the GM were 0.43, 0.40, and 0.46, respectively. The GWAS identified four genome-wide significant SNPs (rs81381267, rs697734475, rs81298447, and rs81458910) associated with the gluteus medius muscle area. The PDE4D gene was identified as a promising candidate gene potentially involved in the regulation of gluteus medius muscle development. Our analysis revealed moderate heritability estimates for gluteus medius muscle size traits. These findings enhance our understanding of the genetic architecture underlying porcine muscle development. Full article
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12 pages, 1647 KiB  
Article
Detection of Burkholderia mallei in Microbiological Culture: A Comparative Analysis of PCR Primer Sets
by Jéssica Cristine K. Moriya, Paula Adas P. Suniga, Ana Clara L. Araújo, Maria Goretti Santos, Juliana S. G. Rieger, Cynthia Mantovani, Rodrigo Jardim, Márcio Roberto Silva, Flábio R. Araújo and Lenita R. Santos
Pathogens 2025, 14(8), 766; https://doi.org/10.3390/pathogens14080766 (registering DOI) - 2 Aug 2025
Viewed by 190
Abstract
Glanders is a highly contagious and often fatal zoonotic disease of equids caused by Burkholderia mallei, a pathogen of significant concern due to its potential for bioterrorism. In Brazil, glanders remains endemic, particularly among working equids in the Northeast region. Diagnostic confirmation [...] Read more.
Glanders is a highly contagious and often fatal zoonotic disease of equids caused by Burkholderia mallei, a pathogen of significant concern due to its potential for bioterrorism. In Brazil, glanders remains endemic, particularly among working equids in the Northeast region. Diagnostic confirmation typically involves serology, culture, and polymerase chain reaction (PCR), although false-negative PCR results have been increasingly reported. This study aimed to evaluate the diagnostic performance and analytical sensitivity of four B. mallei-specific PCR primer sets using samples from 30 seropositive equids. Microbiological cultures were obtained from various organs and swabs, followed by PCR targeting four genomic regions: fliP-IS407A(a), fliP-IS407A(b), Burk457, and Bm17. All animals were confirmed positive for B. mallei via culture, but PCR detection rates varied significantly across primer sets. The fliP-IS407A(b) primer set showed the highest sensitivity, detecting 86% of samples, while the WOAH-recommended fliP-IS407A(a) set had the lowest performance (13.4%). Analytical sensitivity assays confirmed that fliP-IS407A(b) and Bm17 primers detected DNA concentrations as low as 0.007 ng, outperforming the others. These findings suggest that certain widely used primer sets may lack sufficient sensitivity for reliable detection of B. mallei, especially in chronically infected animals with low bacterial loads. The study underscores the need for ongoing validation of molecular diagnostics to improve the detection and control of glanders in endemic regions. Full article
(This article belongs to the Section Bacterial Pathogens)
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19 pages, 9488 KiB  
Article
Proteus mirabilis from Captive Giant Pandas and Red Pandas Carries Diverse Antimicrobial Resistance Genes and Virulence Genes Associated with Mobile Genetic Elements
by Yizhou Yang, Yan Liu, Jiali Wang, Caiwu Li, Ruihu Wu, Jialiang Xin, Xue Yang, Haohong Zheng, Zhijun Zhong, Hualin Fu, Ziyao Zhou, Haifeng Liu and Guangneng Peng
Microorganisms 2025, 13(8), 1802; https://doi.org/10.3390/microorganisms13081802 - 1 Aug 2025
Viewed by 148
Abstract
Proteus mirabilis is a zoonotic pathogen that poses a growing threat to both animal and human health due to rising antimicrobial resistance (AMR). It is widely found in animals, including China’s nationally protected captive giant and red pandas. This study isolated Proteus mirabilis [...] Read more.
Proteus mirabilis is a zoonotic pathogen that poses a growing threat to both animal and human health due to rising antimicrobial resistance (AMR). It is widely found in animals, including China’s nationally protected captive giant and red pandas. This study isolated Proteus mirabilis from panda feces to assess AMR and virulence traits, and used whole-genome sequencing (WGS) to evaluate the spread of resistance genes (ARGs) and virulence genes (VAGs). In this study, 37 isolates were obtained, 20 from red pandas and 17 from giant pandas. Multidrug-resistant (MDR) strains were present in both hosts. Giant panda isolates showed the highest resistance to ampicillin and cefazolin (58.8%), while red panda isolates were most resistant to trimethoprim/sulfamethoxazole (65%) and imipenem (55%). Giant panda-derived strains also exhibited stronger biofilm formation and swarming motility. WGS identified 31 ARGs and 73 VAGs, many linked to mobile genetic elements (MGEs) such as plasmids, integrons, and ICEs. In addition, we found frequent co-localization of drug resistance genes/VAGs with MGEs, indicating a high possibility of horizontal gene transfer (HGT). This study provides crucial insights into AMR and virulence risks in P. mirabilis from captive pandas, supporting targeted surveillance and control strategies. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and the Use of Antibiotics in Animals)
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18 pages, 1711 KiB  
Article
Genome-Wide Association Analysis of Fresh Maize
by Suying Guo, Rengui Zhao and Jinhao Lan
Int. J. Mol. Sci. 2025, 26(15), 7431; https://doi.org/10.3390/ijms26157431 - 1 Aug 2025
Viewed by 83
Abstract
This study measured eight key phenotypic traits across 259 fresh maize inbred lines, including plant height and spike length. A total of 82 single nucleotide polymorphisms (SNPs) significantly associated with these phenotypes were identified by applying a mixed linear model to calculate the [...] Read more.
This study measured eight key phenotypic traits across 259 fresh maize inbred lines, including plant height and spike length. A total of 82 single nucleotide polymorphisms (SNPs) significantly associated with these phenotypes were identified by applying a mixed linear model to calculate the best linear unbiased prediction (BLUP) values and integrating genome-wide genotypic data through genome-wide association analysis (GWAS). A further analysis of significant SNPs contributed to the identification of 63 candidate genes with functional annotations. Notably, 11 major candidate genes were identified from multi-trait association loci, all of which exhibited highly significant P-values (<0.0001) and explained between 7.21% and 12.78% of phenotypic variation. These 11 genes, located on chromosomes 1, 3, 4, 5, 6, and 9, were functionally involved in signaling, metabolic regulation, structural maintenance, and stress response, and are likely to play crucial roles in the growth and physiological processes of fresh maize inbred lines. The functional genes identified in this study have significant implications for the development of molecular markers, the optimization of breeding strategies, and the enhancement of quality in fresh maize. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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16 pages, 938 KiB  
Review
Enhancing Oil Content in Oilseed Crops: Genetic Insights, Molecular Mechanisms, and Breeding Approaches
by Guizhen Gao, Lu Zhang, Panpan Tong, Guixin Yan and Xiaoming Wu
Int. J. Mol. Sci. 2025, 26(15), 7390; https://doi.org/10.3390/ijms26157390 - 31 Jul 2025
Viewed by 266
Abstract
Vegetable oils are essential for human nutrition and industrial applications. With growing global demand, increasing oil content in oilseed crops has become a top priority. This review synthesizes recent progress in understanding the genetic, environmental, and molecular mechanisms regulating oil content, and presents [...] Read more.
Vegetable oils are essential for human nutrition and industrial applications. With growing global demand, increasing oil content in oilseed crops has become a top priority. This review synthesizes recent progress in understanding the genetic, environmental, and molecular mechanisms regulating oil content, and presents biotechnological strategies to enhance oil accumulation in major oilseed crops. Oil biosynthesis is governed by intricate genetic–environmental interactions. Environmental factors and agronomic practices significantly impact oil accumulation dynamics. Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) have identified key loci and candidate genes involved in lipid biosynthesis pathways. Transcription factors and epigenetic regulators further fine-tune oil accumulation. Biotechnological approaches, including marker-assisted selection (MAS) and CRISPR/Cas9-mediated genome editing, have successfully generated high-oil-content variants. Future research should integrate multi-omics data, leverage AI-based predictive breeding, and apply precision genome editing to optimize oil yield while maintaining seed quality. This review provides critical references for the genetic improvement and breeding of high- and ultra-high-oil-content varieties in oilseed crops. Full article
(This article belongs to the Special Issue Rapeseed: Genetic Breeding, Key Trait Mining and Genome)
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18 pages, 3259 KiB  
Article
Lactic Acid Bacteria in Chinese Sauerkraut: Its Isolation and In Vitro Probiotic Properties
by Ming-Yang Han, Wen-Yong Lou and Meng-Fan Li
Foods 2025, 14(15), 2690; https://doi.org/10.3390/foods14152690 - 30 Jul 2025
Viewed by 285
Abstract
Probiotics have been widely explored for their potential in managing hyperuricemia. However, their isolation and identification are fundamental prerequisites for practical application. In this study, 254 lactic acid bacteria (LAB) strains were isolated from Chinese sauerkraut and screened for probiotic potential based on [...] Read more.
Probiotics have been widely explored for their potential in managing hyperuricemia. However, their isolation and identification are fundamental prerequisites for practical application. In this study, 254 lactic acid bacteria (LAB) strains were isolated from Chinese sauerkraut and screened for probiotic potential based on genomic and phenotypic characteristics, as well as nucleoside-degrading activity relevant to decrease serum urate. Among them, Lactiplantibacillus plantarum (L. plantarum) F42 exhibited the highest bile salt tolerance (survivor rate: 19.46 ± 4.33%), strong adhesion to Caco-2 cells (1.89 ± 0.12%), effective nucleoside degradation (inosine: 5.46 ± 0.67 mg∙L−1∙min−1; guanosine: 3.84 ± 0.11 mg∙L−1∙min−1), and notable anti-listeria activity (inhibition zone: 6.9 ± 0.3 mm). Based on its functional profile, L. plantarum F42 was selected as a promising probiotic candidate for further investigation of its urate-lowering effects. This work provides a new insight into anti-hyperuricemia probiotic selection based on in vitro nucleoside-degrading activity. Full article
(This article belongs to the Section Food Biotechnology)
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24 pages, 1508 KiB  
Article
Genomic Prediction of Adaptation in Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) Hybrids
by Felipe López-Hernández, Diego F. Villanueva-Mejía, Adriana Patricia Tofiño-Rivera and Andrés J. Cortés
Int. J. Mol. Sci. 2025, 26(15), 7370; https://doi.org/10.3390/ijms26157370 - 30 Jul 2025
Viewed by 260
Abstract
Climate change is jeopardizing global food security, with at least 713 million people facing hunger. To face this challenge, legumes as common beans could offer a nature-based solution, sourcing nutrients and dietary fiber, especially for rural communities in Latin America and Africa. However, [...] Read more.
Climate change is jeopardizing global food security, with at least 713 million people facing hunger. To face this challenge, legumes as common beans could offer a nature-based solution, sourcing nutrients and dietary fiber, especially for rural communities in Latin America and Africa. However, since common beans are generally heat and drought susceptible, it is imperative to speed up their molecular introgressive adaptive breeding so that they can be cultivated in regions affected by extreme weather. Therefore, this study aimed to couple an advanced panel of common bean (Phaseolus vulgaris L.) × tolerant Tepary bean (P. acutifolius A. Gray) interspecific lines with Bayesian regression algorithms to forecast adaptation to the humid and dry sub-regions at the Caribbean coast of Colombia, where the common bean typically exhibits maladaptation to extreme heat waves. A total of 87 advanced lines with hybrid ancestries were successfully bred, surpassing the interspecific incompatibilities. This hybrid panel was genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Three yield components (yield per plant, and number of seeds and pods) and two biomass variables (vegetative and seed biomass) were recorded for each genotype and inputted in several Bayesian regression models to identify the top genotypes with the best genetic breeding values across three localities on the Colombian coast. We comparatively analyzed several regression approaches, and the model with the best performance for all traits and localities was BayesC. Also, we compared the utilization of all markers and only those determined as associated by a priori genome-wide association studies (GWAS) models. Better prediction ability with the complete SNP set was indicative of missing heritability as part of GWAS reconstructions. Furthermore, optimal SNP sets per trait and locality were determined as per the top 500 most explicative markers according to their β regression effects. These 500 SNPs, on average, overlapped in 5.24% across localities, which reinforced the locality-dependent nature of polygenic adaptation. Finally, we retrieved the genomic estimated breeding values (GEBVs) and selected the top 10 genotypes for each trait and locality as part of a recommendation scheme targeting narrow adaption in the Caribbean. After validation in field conditions and for screening stability, candidate genotypes and SNPs may be used in further introgressive breeding cycles for adaptation. Full article
(This article belongs to the Special Issue Plant Breeding and Genetics: New Findings and Perspectives)
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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, Seyran Koncagul, 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 249
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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