Genes

18 pages, 467 KiB

Open AccessArticle

Changes in Vertical Jump Parameters After Training Unit in Relation to ACE, ACTN3, PPARA, HIF1A, and AMPD1 Gene Polymorphisms in Volleyball and Basketball Players

by Miroslav Vavak, Iveta Cihova, Katarina Reichwalderova, David Vegh, Ladislava Dolezajova and Miroslava Slaninova

Genes 2025, 16(3), 250; https://doi.org/10.3390/genes16030250 - 21 Feb 2025

Abstract

Background/objectives: The study aims to investigate potential differences in vertical jump performance between elite basketball and volleyball players before and after a standard training session, in comparison to a control group from the general population. The analysis focuses on the influence of selected [...] Read more.

Background/objectives: The study aims to investigate potential differences in vertical jump performance between elite basketball and volleyball players before and after a standard training session, in comparison to a control group from the general population. The analysis focuses on the influence of selected gene polymorphisms that may contribute to variations in the assessed performance parameters. Aims: The aim was to investigate the influence of ACE (rs4646994), ACTN3 (rs1815739), PPARA rs4253778, HIF1A (rs11549465), and AMPD1 (rs17602729) genes polymorphisms on the combined effects of post-activation potentiation (PAP), post-activation performance enhancement (PAPE), and general adaptation syndrome (GAS), as reflected in vertical jump performance, in elite basketball and volleyball players compared to a control group from the general population. Methods: The effects of PAP at the beginning of the training load (acute exercise), and the combined influences of PAPE and GAS following the training load were evaluated using parameters measured by the OptoJump Next^® system (Microgate, Bolzano, Italy). Results: A statistically significant (h, p < 0.05) negative effect of the CT genotype of the AMPD1 gene on jump height was observed in the group of athletes. The CT genotype of the AMPD1 gene negatively impacted on PAPE and GAS adaptive responses (ΔP, Δh, p < 0.001) also in the control group. A positive effect on the power during the active phase of the vertical jump was identified for the II genotype of the ACE gene and the Pro/Ser genotype of the HIF1A gene, both exclusively in the control group (ΔP, p < 0.05). Conclusion: Our findings demonstrate that different gene polymorphisms exert variable influences on the combined effects of PAPE and GAS, as reflected in vertical jump parameters, depending on the participants’ level of training adaptation. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

18 pages, 3249 KiB

Open AccessArticle

Genome-Wide Identification, Gene Duplication, and Expression Pattern of NPC2 Gene Family in Parnassius glacialis

by Zhenyao Zhu, Chengyong Su, Xuejie Guo, Youjie Zhao, Ruie Nie, Bo He and Jiasheng Hao

Genes 2025, 16(3), 249; https://doi.org/10.3390/genes16030249 - 21 Feb 2025

Abstract

Background: The Niemann–Pick C2 (NPC2) gene family plays an important role in olfactory communication, immune response, and the recognition of host plants associated with environmental adaptation for insects. Methods: In this study, we conducted a genomic analysis of the structural characteristics [...] Read more.

Background: The Niemann–Pick C2 (NPC2) gene family plays an important role in olfactory communication, immune response, and the recognition of host plants associated with environmental adaptation for insects. Methods: In this study, we conducted a genomic analysis of the structural characteristics and physicochemical properties of the NPC2 genes of eleven butterfly species available, focusing on the alpine Parnassius species, especially Parnassius glacialis, to investigate their duplication and expression patterns. Results: Our results indicate that a significant expansion of NPC2 genes was detected in P. glacialis compared to other butterflies; in addition, the expansion of these unevenly distributed P. glacialis NPC2 chromosome genes was shaped by tandem duplication mediated by transposons. Furthermore, the PgNPC2 genes had relatively higher expression in P. glacialis antennae and other head tissues. These facts were verified by quantitative real-time PCR (qRT-PCR). Conclusions: These findings suggest that the expansion of NPC2 genes may have contributed to the local adaptation of P. glacialis during its dispersal ‘out of the Qinghai–Tibet Plateau,’ although further functional tests are needed to confirm their specific role in this adaptive process. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)

22 pages, 1816 KiB

Open AccessArticle

The Association Between Statin Drugs and Rhabdomyolysis: An Analysis of FDA Adverse Event Reporting System (FAERS) Data and Transcriptomic Profiles

by Robert Morris, Kun Bu, Weiru Han, Savanah Wood, Paola M. Hernandez Velez, Jacob Ward, Ariana Crescitelli, Madison Martin and Feng Cheng

Genes 2025, 16(3), 248; https://doi.org/10.3390/genes16030248 - 21 Feb 2025

Abstract

Background/Objectives: Rhabdomyolysis, a dangerous breakdown of skeletal muscle, has been reported as an adverse event in those prescribed a statin therapy for the treatment of hypercholesterolemia. Statin drugs are some of the most prescribed treatments for elevated cholesterol levels. The purpose of this [...] Read more.

Background/Objectives: Rhabdomyolysis, a dangerous breakdown of skeletal muscle, has been reported as an adverse event in those prescribed a statin therapy for the treatment of hypercholesterolemia. Statin drugs are some of the most prescribed treatments for elevated cholesterol levels. The purpose of this comparative study was to determine the association between the statin drugs used and the risk of rhabdomyolysis using the FDA Adverse Event Reporting System (FAERS) and transcriptomic data. Methods: A disproportionality analysis was performed to compare the risk of rhabdomyolysis between the reference statin drug (simvastatin) and the treatment group, with patient age assessed as a possible confounder. In addition, association rule mining was utilized to both identify other adverse events that frequently presented with rhabdomyolysis and identify possible drug-drug interactions (DDIs). Finally, public transcriptomic data were explored to identify the possible genetic underpinnings highlighting these differences in rhabdomyolysis risk across statins. Results: Rhabdomyolysis is a commonly reported adverse event for patients treated with statins, particularly those prescribed simvastatin. Simvastatin was associated with a more than 2-fold increased likelihood of rhabdomyolysis compared to other statins. Men were twice as likely to report rhabdomyolysis than women regardless of statin treatment, with the highest risk observed for pravastatin (ROR = 2.30, p < 0.001) and atorvastatin (ROR = 2.03, p < 0.0001). Several possible DDIs were identified, including furosemide/Lasix, allopurinol clopidogrel/Plavix, and pantoprazole, which may elevate rhabdomyolysis risk through impaired muscle function and delayed statin metabolism. Finally, nine myopathic genes were identified as possible regulators of statin-induced rhabdomyolysis, including DYSF, DES, PLEC, CAPN3, SCN4A, TNNT1, SDHA, MYH7, and PYGM in primary human muscle cells. Conclusions: Simvastatin was associated with the highest risk of rhabdomyolysis. The risk of rhabdomyolysis was more pronounced in men than women. Several possible DDIs were identified including furosemide/Lasix, allopurinol clopidogrel/Plavix, and pantoprazole. Full article

(This article belongs to the Section Toxicogenomics)

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18 pages, 3764 KiB

Open AccessArticle

Quantitative Trait Loci Mapping for Yield and Related Traits in Cowpea

by Abdoul Moumouni Iro Sodo, Patrick Obia Ongom, Christian Fatokun, Bunmi Olasanmi, Ibnou Dieng and Ousmane Boukar

Genes 2025, 16(3), 247; https://doi.org/10.3390/genes16030247 - 21 Feb 2025

Abstract

Background/Objectives: Cowpea is a major source of dietary protein and plays a key role in sustainable agriculture across sub-Saharan Africa (SSA), Asia, and Latin America. Research efforts have focused mainly on enhancing productivity through higher yield and resistance to biotic and abiotic stresses [...] Read more.

Background/Objectives: Cowpea is a major source of dietary protein and plays a key role in sustainable agriculture across sub-Saharan Africa (SSA), Asia, and Latin America. Research efforts have focused mainly on enhancing productivity through higher yield and resistance to biotic and abiotic stresses in cowpea. Understanding the genetic basis of yield and associated agronomic traits is crucial for improving crop productivity. This study aims to identify quantitative trait loci (QTL) associated with grain yield and related traits in cowpea under regular rainfed conditions. Methods: We developed a set of 316 F6:7 recombinant inbred lines (RILs) mapping populations derived from a cross between RP270 and CB27 using a single-seed descent breeding method. The RILs and their two parental lines were evaluated in the field for two years, 2022 and 2023, at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. The cowpea mid-density genotyping panel consisting of 2602 quality DArTag single nucleotide polymorphisms (SNPs) was used to genotype the RIL population. Results: Seven major QTLs, each explaining ≥10% of phenotypic variance, were detected for 100-seed weight, number of days to flower, number of pods per plant, number of branches per plant, and number of peduncles per plant. Putative genes associated with yield and related traits were identified within significant flanking markers. Further efforts to validate these loci will help to better understand their roles in yield and associated traits in cowpea. Full article

(This article belongs to the Special Issue Genomic Studies of Plant Breeding)

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13 pages, 1853 KiB

Open AccessArticle

Analysis of Transcriptome Differences Between Subcutaneous and Intramuscular Adipose Tissue of Tibetan Pigs

by Xinming Li, Qiuyan Huang, Fanming Meng, Chun Hong, Baohong Li, Yecheng Yang, Zixiao Qu, Junda Wu, Fei Li, Haiyun Xin, Bin Hu, Jie Wu, Chuanhuo Hu, Xiangxing Zhu, Dongsheng Tang, Zongliang Du and Sutian Wang

Genes 2025, 16(3), 246; https://doi.org/10.3390/genes16030246 - 20 Feb 2025

Abstract

Background/Objectives: Fat deposition traits in pigs directly influence pork flavor, tenderness, and juiciness and are closely linked to overall pork quality. The Tibetan pig, an indigenous breed in China, not only possesses a high intramuscular fat content but also exhibits a unique [...] Read more.

Background/Objectives: Fat deposition traits in pigs directly influence pork flavor, tenderness, and juiciness and are closely linked to overall pork quality. The Tibetan pig, an indigenous breed in China, not only possesses a high intramuscular fat content but also exhibits a unique fat metabolism pattern due to long-term adaptation to harsh environments. This makes it an excellent genetic and physiological model for investigating fat deposition characteristics. Adipose tissue from different body regions displays varying morphologies, cytokines, and adipokines. This study aimed to examine adipose tissue deposition characteristics in different parts of Tibetan pigs and provide additional data to explore the underlying mechanisms of differential fat deposition. Methods: Our research identified significant differences in the morphology and gene expression patterns between subcutaneous fat (abdominal fat [AF] and back fat [BF]) and intramuscular fat (IMF) in Tibetan pigs. Results: Histological observations revealed that subcutaneous fat cells were significantly larger in area and diameter compared to IMF cells. The transcriptomic analysis further identified differentially expressed genes (DEGs) between subcutaneous fat and IMF, with a total of 65 DEGs in BF vs. IMF and 347 DEGs in AF vs. IMF, including 25 DEGs common to both comparisons. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these genes were significantly associated with lipid metabolism-related signaling pathways, such as the Wnt, mTOR, and PI3K-Akt signaling pathways. Several DEGs, including DDAH1, ADRA1B, SLCO3A1, and THBS3, may be linked to the differences in fat deposition in different parts of Tibetan pigs, thereby affecting meat quality and nutritional value. Conclusions: These findings provide new insights into the unique fat distribution and deposition characteristics of Tibetan pigs and establish a foundation for breeding strategies aimed at improving pork quality. Full article

(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)

35 pages, 768 KiB

Open AccessReview

Congenital Anomalies of the Kidney and Urinary Tract in Down Syndrome: Prevalence, Phenotypes, Genetics and Clinical Management

by Mirela Leskur, Dario Leskur, Sandra Marijan, Luka Minarik and Bernarda Lozić

Genes 2025, 16(3), 245; https://doi.org/10.3390/genes16030245 - 20 Feb 2025

Abstract

Down syndrome (DS), the most common survivable autosomal aneuploidy, is associated with a high prevalence of congenital anomalies of the kidney and urinary tract (CAKUT), significantly increasing the risk of chronic kidney disease (CKD). This review examines the diversity of CAKUT phenotypes reported [...] Read more.

Down syndrome (DS), the most common survivable autosomal aneuploidy, is associated with a high prevalence of congenital anomalies of the kidney and urinary tract (CAKUT), significantly increasing the risk of chronic kidney disease (CKD). This review examines the diversity of CAKUT phenotypes reported in individuals with DS, focusing on anomalies affecting the kidney, ureter, bladder, and urethra. According to available literature, hydronephrosis is the most common renal anomaly, often secondary to other CAKUT phenotypes, followed by renal hypoplasia and glomerulocystic disease. Furthermore, obstructive uropathies are also frequent but usually lack detailed characterization in the literature. Key features of CAKUT in DS, including reduced kidney size, renal cystic diseases, acquired glomerulopathies, reduced nephron number, and immature glomeruli heighten the risk of CKD. Also, early detection of lower urinary tract dysfunction (LUTD) is critical to prevent progressive upper urinary tract damage and CKD. Despite the prevalence of CAKUT in DS, reported between 0.22% and 21.16%, there is a lack of standardized diagnostic criteria, consistent terminology, and extended follow-up studies. Systematic screening from infancy, including regular renal monitoring via urinalysis and ultrasound, plays a critical role in the timely diagnosis and intervention of CAKUT. To further enhance diagnostic accuracy and develop effective therapeutic strategies, increased awareness and focused research into the genetic factors underlying these anomalies are essential. Moreover, a multidisciplinary approach is indispensable for managing CAKUT and its associated complications, ultimately ensuring better long-term outcomes and an improved quality of life for individuals with DS. Full article

(This article belongs to the Special Issue From Genetic to Molecular Basis of Kidney Diseases)

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23 pages, 1673 KiB

Open AccessReview

Multiomics with Evolutionary Computation to Identify Molecular and Module Biomarkers for Early Diagnosis and Treatment of Complex Disease

by Han Cheng, Mengyu Liang, Yiwen Gao, Wenshan Zhao and Wei-Feng Guo

Genes 2025, 16(3), 244; https://doi.org/10.3390/genes16030244 - 20 Feb 2025

Abstract

It is important to identify disease biomarkers (DBs) for early diagnosis and treatment of complex diseases in personalized medicine. However, existing methods integrating intelligence technologies and multiomics to predict key biomarkers are limited by the complex dynamic characteristics of omics data, making it [...] Read more.

It is important to identify disease biomarkers (DBs) for early diagnosis and treatment of complex diseases in personalized medicine. However, existing methods integrating intelligence technologies and multiomics to predict key biomarkers are limited by the complex dynamic characteristics of omics data, making it difficult to meet the high-precision requirements for biomarker characterization in large dimensions. This study reviewed current analysis methods of evolutionary computation (EC) by considering the essential characteristics of DB identification problems and the advantages of EC, aiming to explore the complex dynamic characteristics of multiomics. In this study, EC-based biomarker identification strategies were summarized as evolutionary algorithms, swarm intelligence and other EC methods for molecular and module DB identification, respectively. Finally, we pointed out the challenges in current research and future research directions. This study can enrich the application of EC theory and promote interdisciplinary integration between EC and bioinformatics. Full article

(This article belongs to the Special Issue Bioinformatics and Computational Biology for Cancer Prediction and Prognosis, 2nd Edition)

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10 pages, 1459 KiB

Open AccessCommunication

MicroRNA Expression Profile Analysis in Blood During Giant Panda (Ailuropoda melanoleuca) Growth and Development

by Shanshan Ling, Die Deng, Fuxing Yang, Pingfeng Wang, Ming He, Qian Wang, Linhua Deng, Xun Wang, Ling Zhao, Gang Ye and Xiaoyu Huang

Genes 2025, 16(3), 243; https://doi.org/10.3390/genes16030243 - 20 Feb 2025

Abstract

Background/Objectives: Blood is an essential component of the immune system. As post-transcriptional regulators, miRNAs, abundant in blood, are necessary aspects in blood’s immune and physiological functions. However, there is limited knowledge about the expression and function of miRNAs in the blood of giant [...] Read more.

Background/Objectives: Blood is an essential component of the immune system. As post-transcriptional regulators, miRNAs, abundant in blood, are necessary aspects in blood’s immune and physiological functions. However, there is limited knowledge about the expression and function of miRNAs in the blood of giant pandas. Methods: We comparatively analyzed miRNA expression profiles in the blood of giant pandas of different ages using small-RNA sequencing technology. Results: We identified 393 known miRNAs, 219 conserved miRNAs, and 71 novel miRNAs in the blood of giant pandas, and functional enrichment analysis showed that the genes regulated by DE (differentially expressed) miRNAs were mainly enriched in the regulation of enzyme-linked receptor protein signaling pathways and the signaling pathways of MAPK, Hippo, and FoXO. Conclusions: Our study clarified giant pandas’ blood miRNA expression profiles at different developmental stages, which will help elucidate the blood immunity and regulation of blood cell physiological functions in giant pandas. Full article

(This article belongs to the Special Issue Gene Regulation of Development and Evolution in Mammals)

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20 pages, 1868 KiB

Open AccessArticle

Chromosome Morphology and Heterochromatin Patterns in Paspalum notatum: Insights into Polyploid Genome Structure

by Ana I. Honfi, A. Verena Reutemann, Juan S. Schneider, Lucas M. Escobar, Eric J. Martínez and Julio R. Daviña

Genes 2025, 16(3), 242; https://doi.org/10.3390/genes16030242 - 20 Feb 2025

Abstract

Background/Objectives: Paspalum notatum is a key multipurpose species native to American grasslands. This study provides, for the first time, a detailed karyotype analysis of diploid (2n = 2x = 20) and tetraploid (2n = 4x = 40) accessions of [...] Read more.

Background/Objectives: Paspalum notatum is a key multipurpose species native to American grasslands. This study provides, for the first time, a detailed karyotype analysis of diploid (2n = 2x = 20) and tetraploid (2n = 4x = 40) accessions of P. notatum, the most common cytotypes within the species. Methods: The constitutive heterochromatin patterns revealed using CMA-DA-DAPI staining and genome size estimations are novel contributions to the understanding of the N genome in Paspalum. Results: Chromosomes were small (1.1–2.3 µm), with the diploid karyotype comprising nine metacentric pairs (one bearing microsatellites on the short arms, pair 6) and one submetacentric pair. In tetraploids, the diploid karyotype was duplicated. Heterochromatin analysis revealed two CMA⁺⁺/DAPI⁻ bands located on the short arm and satellite of chromosome 6 in diploids, while tetraploids exhibited two to three CMA⁺⁺/DAPI⁻ and one to two CMA⁺⁺/DAPI⁰ bands. The proportion of GC-rich heterochromatin represented 2.8 and 3.47% of the total chromosome length in diploid and tetraploid cytotypes, respectively. Genome size analysis revealed a reduction in monoploid genome size in tetraploids (1Cx = 0.678 pg) compared to diploids (1Cx = 0.71 pg), consistent with the autopolyploid origin hypothesis. Conclusions: These findings provide essential cytogenetic insights and suggest only minor structural changes in the N genome following polyploidization, which could guide future studies integrating genomic and cytogenetic maps of P. notatum. Full article

(This article belongs to the Special Issue Genetics and Breeding of Polyploid Plants)

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17 pages, 10020 KiB

Open AccessArticle

Membranous Nephropathy Target Antigens Display Podocyte-Specific and Non-Specific Expression in Healthy Kidneys

by Ying Dong, Hui Xu and Damu Tang

Genes 2025, 16(3), 241; https://doi.org/10.3390/genes16030241 - 20 Feb 2025

Abstract

Background/Objectives: Autoimmunity towards podocyte antigens causes membranous nephropathy (MN). Numerous MN target antigens (MNTAgs) have been reported, including PLA2R1, THSD7A, NTNG1, TGFBR3, HTRA1, NDNF, SEMA3B, FAT1, EXT1, CNTN1, NELL1, PCDH7, EXT2, PCSK6, and NCAM1, but their podocyte expression has not been thoroughly studied. [...] Read more.

Background/Objectives: Autoimmunity towards podocyte antigens causes membranous nephropathy (MN). Numerous MN target antigens (MNTAgs) have been reported, including PLA2R1, THSD7A, NTNG1, TGFBR3, HTRA1, NDNF, SEMA3B, FAT1, EXT1, CNTN1, NELL1, PCDH7, EXT2, PCSK6, and NCAM1, but their podocyte expression has not been thoroughly studied. Methods: We screened CZ CELLxGene single-cell RNA (scRNA) sequence datasets for those of adult, fetal, and mouse kidneys and analyzed the above MNTAgs’ expression. Results: In adult kidneys, most MNTAgs are present in podocytes, except PCSK6 and NCAM1. PLA2R1 is expressed significantly more than other MNTAgs in podocytes and is a major podocyte marker, consistent with PLA2R1 as the dominant MNTAg. Additionally, PLA2R1 is a top-upregulated gene in the podocytes of chronic kidney disease, acute kidney injury, and diabetic nephropathy, indicating its general role in causing podocyte injury. PLA2R1, NTNG1, HTRA1, and NDNF display podocyte-enriched expression along with elevated chromatin accessibility in podocytes, suggesting transcription initiation contributing to their preference expression in podocytes. In the fetal kidney, most MNTAgs are expressed in podocytes. While PLA2R1 is weakly present in podocytes, SEMA3B is abundantly expressed in immature and mature podocytes, supporting SEMA3B as a childhood MNTAg. In mouse kidneys, Thsd7a is the only MNTAg with a prominent level and podocyte-specific expression. Conclusions: Most MNTAgs are present in podocytes in adults and during renal development. In adults, PLA2R1 expression is highly enriched in podocytes and significantly upregulated in multiple kidney diseases accompanied by proteinuria. In mouse kidneys, Thsd7a is specifically expressed in podocytes at an elevated level. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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24 pages, 15348 KiB

Open AccessArticle

A TFAIII-Type Transcription Factor OsZFPH Regulating a Signaling Pathway Confers Resistance to Xanthomonas oryzae pv. Oryzae in Rice

by Chunyun Yang, Xinxiang A, Cuifeng Tang, Chao Dong, Feifei Zhang, Chunmei He, Yiding Sun, Yi Yang, Sandan Yan, Yanhong Liu, Yayun Yang and Luyuan Dai

Genes 2025, 16(3), 240; https://doi.org/10.3390/genes16030240 - 20 Feb 2025

Abstract

Background: Rice bacterial leaf blight, caused by the Gram-negative bacterium Xanthomonas oryzae pv. Oryzae (Xoo), significantly impacts rice production. To address this disease, research efforts have focused on discovering and utilizing novel disease-resistant genes and examining their functional mechanisms. Methods and [...] Read more.

Background: Rice bacterial leaf blight, caused by the Gram-negative bacterium Xanthomonas oryzae pv. Oryzae (Xoo), significantly impacts rice production. To address this disease, research efforts have focused on discovering and utilizing novel disease-resistant genes and examining their functional mechanisms. Methods and Results: In this study, a variety of bacterial strains were utilized. CX28-3, AX-11, JC12-2, and X10 were isolated from the high-altitude japonica rice-growing region on the Yunnan Plateau. Additionally, PXO61, PXO86, PXO99, and PXO339, sourced from the International Rice Research Institute (IRRI), were included in the analysis. To evaluate the resistance characteristics of Haonuoyang, artificial leaf cutting and inoculation methods were applied. Results indicated that Haonuoyang exhibited broad-spectrum resistance. Additionally, to explore the genetic mechanisms of resistance, the TFAIII-type transcription factor OsZFPH was cloned from Haonuoyang using PCR amplification. The subcellular localization method identified the precise location of the OsZFPH gene within the cell. The expression of OsZFPH was induced by Xoo stress. The overexpression of OsZFPH resulted in increased activities of enzymes, including SOD, CAT, and POD, while silencing the gene led to reduced enzyme activities. Furthermore, the hormones SA (salicylic acid), JA (jasmonic acid), and GA (gibberellin) were shown to positively regulate the gene expression. Protein interactions with OsZFPH were verified through a yeast two-hybrid system and BiFC technology. Hap5, which aligned with the sequence of Haonuoyang, was found to belong to a haplotype consisting of Jingang 30, 40 resequenced rice varieties, 18 Oryza rufipogon, and 29 Oryza granulata. Conclusions: The findings of this study emphasize the vital role of OsZFPH in rice resistance to bacterial leaf blight. The identification of broad-spectrum resistance in Haonuoyang and the understanding of OsZFPH gene functions provide valuable insights for the future development of rice varieties with improved resistance to this destructive disease. Full article

(This article belongs to the Special Issue Plant Disease Resistance-Related Signaling Pathways and Their Interactions)

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20 pages, 17654 KiB

Open AccessArticle

Comparative and Phylogenetic Analysis of the Chloroplast Genomes of Four Wild Species of the Genus Prunus

by Mengfan Cui, Chenxi Liu, Xingling Yang, Mingyu Li, Liqiang Liu, Kai Jia and Wenwen Li

Genes 2025, 16(3), 239; https://doi.org/10.3390/genes16030239 - 20 Feb 2025

Abstract

Background: Prunus armeniaca, Prunus divaricata, Prunus tianshanica, and Prunus domestica are valuable ancient tree species that have persisted since the end of the Tertiary period within the Tianshan wild fruit forest. However, the evolutionary relationships among Prunus species in the [...] Read more.

Background: Prunus armeniaca, Prunus divaricata, Prunus tianshanica, and Prunus domestica are valuable ancient tree species that have persisted since the end of the Tertiary period within the Tianshan wild fruit forest. However, the evolutionary relationships among Prunus species in the Tianshan wild fruit forest have long posed a challenge. Methods: We sequenced and assembled the chloroplast genomes of P. armeniaca, P. divaricata, and P. tianshanica, and incorporated the chloroplast genome data of P. domestica for comparative analysis to elucidate their phylogenetic positions within the genus Prunus. Results: The lengths of these chloroplast genomes ranged from 157,395 bp to 158,090 bp, with a total of 130 to 131 genes annotated, comprising 85 to 86 protein-coding genes, 8 rRNA genes, and 35 to 36 tRNA genes. Notably, the four wild Prunus species predominantly used high-frequency codons ending in A/U. Additionally, we identified 300 simple repetitive sequences and 166 long repetitive sequences across the four wild Prunus species. The mutation sites were mainly found in the non-coding regions, with seven regions of high mutation frequency identified. The phylogenetic tree revealed five branches: subgenus Armeniaca, subgenus Microcerasus, subgenus Prunus, subgenus Amygdalus, and subgenus Cerasus. The estimated deviation time for the crown group of Prunus is roughly 61.41 million years ago. Conclusions: This study provides exhaustive genetic evidence for the classification and systematic relationships of the four wild Prunus species and establishes a crucial foundation for subsequent research into the diversity and evolutionary history of the Prunus genus. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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20 pages, 1945 KiB

Open AccessArticle

Considerations for the Implementation of Massively Parallel Sequencing into Routine Kinship Analysis

by Lucinda Davenport, Laurence Devesse, Somruetai Satmun, Denise Syndercombe Court and David Ballard

Genes 2025, 16(3), 238; https://doi.org/10.3390/genes16030238 - 20 Feb 2025

Abstract

Background: Investigating the way in which individuals are genetically related has been a long-standing application of forensic DNA typing. Whilst capillary electrophoresis (CE)-based STR analysis is likely to provide sufficient data to resolve regularly encountered paternity cases, its power to adequately resolve [...] Read more.

Background: Investigating the way in which individuals are genetically related has been a long-standing application of forensic DNA typing. Whilst capillary electrophoresis (CE)-based STR analysis is likely to provide sufficient data to resolve regularly encountered paternity cases, its power to adequately resolve more distant or complex relationships can be limited. Massively parallel sequencing (MPS) has become a popular alternative method to CE for analysing genetic markers for forensic applications, including kinship analysis. Data workflows used in kinship testing are well-characterised for CE-based methodologies but are much less established for MPS. When incorporating this technology into routine relationship casework, modifications to existing procedures will be required to ensure that the full power of MPS can be utilised whilst maintaining the authenticity of results. Methods: Empirical data generated with MPS for forensically relevant STRs and SNPs and real-world case experience have been used to determine the necessary workflow adaptations. Results: The four considerations highlighted in this work revolve around the distinctive properties of sequence-based data and the need to adapt CE-based data analysis workflows to ensure compatibility with existing kinship software. These considerations can be summarised as the need for a suitable sequence-based allele nomenclature; methods to account for mutational events; appropriate population databases; and procedures for dealing with rare allele frequencies. Additionally, a practical outline of the statistical adjustments required to account for genetic linkage between loci, within the expanded marker sets associated with MPS, has been presented. Conclusions: This article provides a framework for laboratories wishing to implement MPS into routine kinship analysis, with guidance on aspects of the data analysis and statistical interpretation processes. Full article

(This article belongs to the Special Issue Strategies and Techniques in DNA Forensic Investigations)

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