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Genes

Genes is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Spanish Society for Biochemistry and Molecular Biology (SEBBM) is affiliated with Genes and their members receive discounts on the article processing charges.

Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
Journal Rank: JCR - Q2 (Genetics and Heredity) / CiteScore - Q2 (Genetics (clinical))
Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 14.9 days after submission; acceptance to publication is undertaken in 2.6 days (median values for papers published in this journal in the second half of 2024).
Recognition of Reviewers: Reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.

Impact Factor: 2.8 (2023); 5-Year Impact Factor: 3.3 (2023)

Imprint Information Journal Flyer Open Access ISSN: 2073-4425

Latest Articles

29 pages, 575 KiB

Open AccessReview

Hereditary Breast Cancer: Comprehensive Risk Assessment and Prevention Strategies

by Eliza Del Fiol Manna, Davide Serrano, Laura Cazzaniga, Sara Mannucci, Cristina Zanzottera, Francesca Fava, Gaetano Aurilio, Aliana Guerrieri-Gonzaga, Matilde Risti, Mariarosaria Calvello, Irene Feroce, Monica Marabelli, Cecilia Altemura, Lucio Bertario, Bernardo Bonanni and Matteo Lazzeroni

Genes 2025, 16(1), 82; https://doi.org/10.3390/genes16010082 - 13 Jan 2025

Women carrying pathogenic/likely pathogenic (P/LP) variants in moderate- or high-penetrance genes have an increased risk of developing breast cancer. However, most P/LP variants associated with breast cancer risk show incomplete penetrance. Age, gender, family history, polygenic risk, lifestyle, reproductive, hormonal, and environmental factors [...] Read more.

Women carrying pathogenic/likely pathogenic (P/LP) variants in moderate- or high-penetrance genes have an increased risk of developing breast cancer. However, most P/LP variants associated with breast cancer risk show incomplete penetrance. Age, gender, family history, polygenic risk, lifestyle, reproductive, hormonal, and environmental factors can affect the expressivity and penetrance of the disease. However, there are gaps in translating how individual genomic variation affects phenotypic presentation. The expansion of criteria for genetic testing and the increasing utilization of comprehensive genetic panels may enhance the identification of individuals carrying P/LP variants linked to hereditary breast cancer. Individualized risk assessment could facilitate the implementation of personalized risk-reduction strategies for these individuals. Preventive interventions encompass lifestyle modifications, chemoprevention, enhanced surveillance through breast imaging, and risk-reducing surgeries. This review addresses the current literature’s inconsistencies and limitations, particularly regarding risk factors and the intensity of preventive strategies for women with P/LP variants in moderate- and high-penetrance genes. In addition, it synthesizes the latest evidence on risk assessment and primary and secondary prevention in women at high risk of breast cancer. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

14 pages, 3490 KiB

Open AccessArticle

Evaluation of Genetic Diversity and Identification of Cultivars in Spray-Type Chrysanthemum Based on SSR Markers

by Manjulatha Mekapogu, So-Hyeon Lim, Youn-Jung Choi, Su-Young Lee and Jae-A Jung

Genes 2025, 16(1), 81; https://doi.org/10.3390/genes16010081 - 13 Jan 2025

Background/Objectives: Chrysanthemum (Chrysanthemum morifolium), a key ornamental and medicinal plant, presents challenges in cultivar identification due to high phenotypic similarity and environmental influences. This study assessed the genetic diversity and discrimination of 126 spray-type chrysanthemum cultivars. Methods: About twenty-three simple sequence [...] Read more.

Background/Objectives: Chrysanthemum (Chrysanthemum morifolium), a key ornamental and medicinal plant, presents challenges in cultivar identification due to high phenotypic similarity and environmental influences. This study assessed the genetic diversity and discrimination of 126 spray-type chrysanthemum cultivars. Methods: About twenty-three simple sequence repeat (SSR) markers were screened for the discrimination of 126 cultivars, among which six SSR markers showed polymorphic fragments. Results: Results showed high polymorphism across six markers, with an average of 3.8 alleles per locus and a mean polymorphism information content (PIC) of 0.52, indicating strong discriminatory efficiency. The average observed heterozygosity (Ho) was 0.72, reflecting significant genetic diversity within the cultivars. Cluster analysis using the unweighted pair group method with arithmetic mean (UPGMA) grouped the cultivars into seven clusters, correlating well with the PCA. Bayesian population structure analysis suggested two primary genetic subpopulations. Conclusions: These findings confirm SSR markers as an effective tool for the genetic characterization and precise discrimination of spray type chrysanthemum cultivars, offering significant applications in breeding, cultivar registration, and germplasm conservation. The SSR marker-based approach thus provides a reliable and efficient strategy to enhance the management and commercialization of diverse chrysanthemum germplasm collections. Full article

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

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16 pages, 3676 KiB

Open AccessArticle

Chromosome 4 Duplication Associated with Strabismus Leads to Gene Expression Changes in iPSC-Derived Cortical Neurons

by Mayra Martinez-Sanchez, William Skarnes, Ashish Jain, Sampath Vemula, Liang Sun, Shira Rockowitz and Mary C. Whitman

Genes 2025, 16(1), 80; https://doi.org/10.3390/genes16010080 - 12 Jan 2025

Background/Objectives: Strabismus is the most common ocular disorder of childhood. Three rare, recurrent genetic duplications have been associated with both esotropia and exotropia, but the mechanisms by which they contribute to strabismus are unknown. This work aims to investigate the mechanisms of the [...] Read more.

Background/Objectives: Strabismus is the most common ocular disorder of childhood. Three rare, recurrent genetic duplications have been associated with both esotropia and exotropia, but the mechanisms by which they contribute to strabismus are unknown. This work aims to investigate the mechanisms of the smallest of the three, a 23 kb duplication on chromosome 4 (hg38|4:25,554,985-25,578,843). Methods: Using CRISPR and bridging oligos, we introduced the duplication into the Kolf2.1J iPSC line. We differentiated the parent line and the line with the duplication into cortical neurons using a three-dimensional differentiation protocol, and performed bulk RNASeq on neural progenitors (day 14) and differentiated neurons (day 63). Results: We successfully introduced the duplication into Kolf2.1J iPSCs by nucleofecting a bridging oligo for the newly formed junction along with cas9 ribonucleoparticles. We confirmed that the cells had a tandem duplication without inversion or deletion. The parent line and the line with the duplication both differentiated into neurons reliably. There were a total of 37 differentially expressed genes (DEGs) at day 63, 25 downregulated and 12 upregulated. There were 55 DEGs at day 14, 18 of which were also DEGs at day 63. The DEGs included a number of protocadherins, several genes involved in neuronal development, including SLITRK2, CSMD1, and VGF, and several genes of unknown function. Conclusions: A copy number variant (CNV) that confers risk for strabismus affects gene expression of several genes involved in neural development, highlighting that strabismus most likely results from abnormal neural development, and identifying several new genes and pathways for further research into the pathophysiology of strabismus. Full article

(This article belongs to the Special Issue Genetics of Eye Development and Diseases)

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17 pages, 945 KiB

Open AccessReview

Research Progress on Gene Regulation of Plant Floral Organogenesis

by Lixia Zhou, Amjad Iqbal, Mengdi Yang and Yaodong Yang

Genes 2025, 16(1), 79; https://doi.org/10.3390/genes16010079 - 12 Jan 2025

Flowers, serving as the reproductive structures of angiosperms, perform an integral role in plant biology and are fundamental to understanding plant evolution and taxonomy. The growth and organogenesis of flowers are driven by numerous factors, such as external environmental conditions and internal physiological [...] Read more.

Flowers, serving as the reproductive structures of angiosperms, perform an integral role in plant biology and are fundamental to understanding plant evolution and taxonomy. The growth and organogenesis of flowers are driven by numerous factors, such as external environmental conditions and internal physiological processes, resulting in diverse traits across species or even within the same species. Among these factors, genes play a central role, governing the entire developmental process. The regulation of floral genesis by these genes has become a significant focus of research. In the AE model of floral development, the five structural whorls (calyx, corolla, stamens, pistils, and ovules) are controlled by five groups of genes: A, B, C, D, and E. These genes interact to give rise to a complex control system that governs the floral organsgenesis. The activation or suppression of specific gene categories results in structural modifications to floral organs, with variations observed across different species. The present article examines the regulatory roles of key genes, including genes within the MADS-box and AP2/ERF gene clusters, such as AP1, AP2, AP3, AG, STK, SHP, SEP, PI, and AGL6, as well as other genes, like NAP, SPL, TGA, PAN, and WOX, in shaping floral organ genesis. In addition, it analyzes the molecular-level effects of these genes on floral organ formation. The findings offer a deeper understanding of the genetic governance of floral organ genesis across plant species. Full article

(This article belongs to the Special Issue Forest Genetics and Plant Physiology)

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11 pages, 634 KiB

Open AccessArticle

The Impact of Storage Conditions on DNA Preservation in Human Skeletal Remains: A Comparison of Freshly Excavated Samples and Those Stored for 12 Years in a Museum Depot

by Tonja Jeromelj, Tamara Leskovar and Irena Zupanič Pajnič

Genes 2025, 16(1), 78; https://doi.org/10.3390/genes16010078 - 11 Jan 2025

Background: As the field of ancient DNA research continues to evolve and produce significant discoveries, it is important to address the crucial limitations it still faces. Under conducive conditions, DNA can persist for thousands of years within human skeletal remains, but, as excavation [...] Read more.

Background: As the field of ancient DNA research continues to evolve and produce significant discoveries, it is important to address the crucial limitations it still faces. Under conducive conditions, DNA can persist for thousands of years within human skeletal remains, but, as excavation occurs, the environment abruptly changes, often leading to the loss of DNA and valuable genetic information. Proper storage procedures are needed to mediate DNA degradation and maintain sample integrity. This study aimed to investigate the impact of long-term storage under unregulated temperatures and humidity conditions on DNA preservation in human skeletal remains. Methods: To achieve this, archaeological petrous bones were used for DNA recovery. The DNA yield and degree of DNA degradation were compared for samples originating from historically and geographically equivalent archaeological sites, which differed in times of excavation and, consequently, in storage durations and conditions. DNA yield and the degree of DNA degradation were determined using real time PCR. Results: A significant reduction in the DNA yield and a borderline significant increase in the degree of DNA degradation were detected for samples stored at unregulated conditions for approximately 12 years. Conclusions: Our results show the imperative need for adhering to scientific recommendations regarding the optimal temperature and humidity in the long-term storage of human skeletal material. Full article

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

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12 pages, 509 KiB

Open AccessReview

ADAR Therapeutics as a New Tool for Personalized Medicine

by Matteo Bertoli, Luca La Via and Alessandro Barbon

Genes 2025, 16(1), 77; https://doi.org/10.3390/genes16010077 - 11 Jan 2025

In the field of RNA therapy, innovative approaches based on adenosine deaminases acting on RNA (ADAR)-mediated site-directed RNA editing (SDRE) have been established, providing an exciting opportunity for RNA therapeutics. ADAR1 and ADAR2 enzymes are accountable for the predominant form of RNA editing [...] Read more.

In the field of RNA therapy, innovative approaches based on adenosine deaminases acting on RNA (ADAR)-mediated site-directed RNA editing (SDRE) have been established, providing an exciting opportunity for RNA therapeutics. ADAR1 and ADAR2 enzymes are accountable for the predominant form of RNA editing in humans, which involves the hydrolytic deamination of adenosine (A) to inosine (I). This inosine is subsequently interpreted as guanosine (G) by the translational and splicing machinery because of their structural similarity. Intriguingly, the novel SDRE system leverages this recoding ability of ADAR proteins to correct the pathogenic G to A nucleotide mutations through a short, engineered guide RNA (gRNA). Thus, ADAR-mediated SDRE is emerging as a powerful tool to manipulate the genetic information at the RNA level and correct disease-causing mutations without causing damage to the genome. Further it is emerging as a new instrument for personalized medicine, since treatments can be tailored to the unique genetic mutations present in an individual patient. In this short review, we aimed to described the main approached bases on ADARs activity, highlighting their advantages and disadvantages. Full article

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

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11 pages, 4814 KiB

Open AccessCase Report

Compound Heterozygous p.(R124C) (Classic Lattice Corneal Dystrophy) and p.(R124H) (Granular Corneal Dystrophy Type 2) in TGFBI: Phenotype, Genotype, and Treatment

by Ji Sang Min, Tae-im Kim, Ikhyun Jun, R. Doyle Stulting, Changrae Rho, Sang Beom Han, Heeyoung Kim, Jinseok Choi, Jinu Han and Eung Kweon Kim

Genes 2025, 16(1), 76; https://doi.org/10.3390/genes16010076 - 11 Jan 2025

(1) Background: The phenotypes of classic lattice corneal dystrophy (LCD) and granular corneal dystrophy type 2 (GCD2) that result from abnormalities in transforming growth factor β-induced gene (TGFBI) have previously been described. The phenotype of compound heterozygous classic LCD and GCD2, [...] Read more.

(1) Background: The phenotypes of classic lattice corneal dystrophy (LCD) and granular corneal dystrophy type 2 (GCD2) that result from abnormalities in transforming growth factor β-induced gene (TGFBI) have previously been described. The phenotype of compound heterozygous classic LCD and GCD2, however, has not yet been reported. (2) Case report: A 39-year-old male (proband) presented to our clinic complaining of decreased vision bilaterally. A slit-lamp examination revealed corneal opacities consistent with classic LCD. Contrast sensitivity (CS) was decreased. A genetic analysis performed with commercially available real-time polymerase chain reaction (PCR) showed both homozygous classic LCD and homozygous GCD2. Sanger sequencing performed in our lab suggested compound heterozygosity for c.370C>T and c.371G>A variants, which was confirmed by the TA cloning of exon 4 of TGFBI and sequencing of clones. Phototherapeutic keratectomy (PTK) was performed on the right eye of the proband, and the CS improved. (3) Conclusions: Compound heterozygous classic LCD and GCD2 produces clinical findings like that of severe, classic LCD. PTK can improve VA and CS, delaying the need for keratoplasty. Full article

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

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19 pages, 6027 KiB

Open AccessArticle

The X-Linked Tumor Suppressor TSPX Regulates Genes Involved in the EGFR Signaling Pathway and Cell Viability to Suppress Lung Adenocarcinoma

by Tatsuo Kido, Hui Kong and Yun-Fai Chris Lau

Genes 2025, 16(1), 75; https://doi.org/10.3390/genes16010075 - 11 Jan 2025

Background: TSPX is an X-linked tumor suppressor that was initially identified in non-small cell lung cancer (NSCLC) cell lines. However, its expression patterns and downstream mechanisms in NSCLC remain unclear. This study aims to investigate the functions of TSPX in NSCLC by identifying [...] Read more.

Background: TSPX is an X-linked tumor suppressor that was initially identified in non-small cell lung cancer (NSCLC) cell lines. However, its expression patterns and downstream mechanisms in NSCLC remain unclear. This study aims to investigate the functions of TSPX in NSCLC by identifying its potential downstream targets and their correlation with clinical outcomes. Methods: RNA-seq transcriptome and pathway enrichment analyses were conducted on the TSPX-overexpressing NSCLC cell lines, A549 and SK-MES-1, originating from lung adenocarcinoma and squamous cell carcinoma subtypes, respectively. In addition, comparative analyses were performed using the data from clinical NSCLC specimens (515 lung adenocarcinomas and 502 lung squamous cell carcinomas) in the Cancer Genome Atlas (TCGA) database. Results: TCGA data analysis revealed significant downregulation of TSPX in NSCLC tumors compared to adjacent non-cancerous tissues (Wilcoxon matched pairs signed rank test p < 0.0001). Notably, the TSPX expression levels were inversely correlated with the cancer stage, and higher TSPX levels were associated with better clinical outcomes and improved survival in lung adenocarcinoma, a subtype of NSCLC (median survival extended by 510 days; log-rank test, p = 0.0025). RNA-seq analysis of the TSPX-overexpressing NSCLC cell lines revealed that TSPX regulates various genes involved in the cancer-related signaling pathways and cell viability, consistent with the suppression of cell proliferation in cell culture assays. Notably, various potential downstream targets of TSPX that correlated with patient survival (log-rank test, p = 0.016 to 4.3 × 10⁻¹⁰) were identified, including EGFR pathway-related genes AREG, EREG, FOSL1, and MYC, which were downregulated. Conclusions: Our results suggest that TSPX plays a critical role in suppressing NSCLC progression by downregulating pro-oncogenic genes, particularly those in the EGFR signaling pathway, and upregulating the tumor suppressors, especially in lung adenocarcinoma. These findings suggest that TSPX is a potential biomarker and therapeutic target for NSCLC management. Full article

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

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14 pages, 2318 KiB

Open AccessReview

Hypertrophic Cardiomyopathy: New Clinical and Therapeutic Perspectives of an “Old” Genetic Myocardial Disease

by Chiara Calore, Mario Mangia, Cristina Basso, Domenico Corrado and Gaetano Thiene

Genes 2025, 16(1), 74; https://doi.org/10.3390/genes16010074 - 10 Jan 2025

Since its first pathological description over 65 years ago, hypertrophic cardiomyopathy (HCM), with a worldwide prevalence of 1:500, has emerged as the most common genetically determined cardiac disease. Diagnostic work-up has dramatically improved over the last decades, from clinical suspicion and abnormal electrocardiographic [...] Read more.

Since its first pathological description over 65 years ago, hypertrophic cardiomyopathy (HCM), with a worldwide prevalence of 1:500, has emerged as the most common genetically determined cardiac disease. Diagnostic work-up has dramatically improved over the last decades, from clinical suspicion and abnormal electrocardiographic findings to hemodynamic studies, echocardiography, contrast-enhanced cardiac magnetic resonance, and genetic testing. The implementation of screening programs and the use of implantable cardioverter defibrillators (ICDs) for high-risk individuals have notably reduced arrhythmic sudden deaths, altering the disease’s mortality profile. Therapeutic breakthroughs, including surgical myectomy, alcohol septal ablation, and the novel introduction of “myosin inhibitors”, have revolutionized symptom management and reduced progression to advanced heart failure (HF) and death. Despite this progress, refractory HF—both with preserved and reduced systolic function—has become the predominant cause of HCM-related mortality. While most patients with HCM experience a favorable clinical course with low morbidity and mortality, timely identification and targeted treatment of high-risk subgroups progressing toward progressive HF remain a pressing challenge, even for expert clinicians. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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15 pages, 1390 KiB

Open AccessArticle

Population Genetics of Haliotis discus hannai in China Inferred Through EST-SSR Markers

by Hongsu Yang, Zhou Wu, Guangyu Ge, Xiujun Sun, Biao Wu, Zhihong Liu, Tao Yu, Yanxin Zheng and Liqing Zhou

Genes 2025, 16(1), 73; https://doi.org/10.3390/genes16010073 - 10 Jan 2025

Background/Objectives: The Pacific abalone Haliotis discus hannai originated in cold waters and is an economically important aquaculture shellfish in China. Our goal was to clarify the current status of the genetic structure of Pacific abalone in China. Methods: In this study, eighteen polymorphic [...] Read more.

Background/Objectives: The Pacific abalone Haliotis discus hannai originated in cold waters and is an economically important aquaculture shellfish in China. Our goal was to clarify the current status of the genetic structure of Pacific abalone in China. Methods: In this study, eighteen polymorphic EST-SSR loci were successfully developed based on the hemolymph transcriptome data of Pacific abalone, and thirteen highly polymorphic EST-SSR loci were selected for the genetic variation analysis of the six populations collected. Results: The results showed that the average number of observed alleles was 8.0769 (RC)-11.3848 (DQ) in each population. The number of observed alleles in the DQ, NH, and TJ populations was significantly higher than that in the RC population. The cultivated population outside the Changshan Islands has experienced a 22.79% reduction in allele diversity compared to the wild population of DQ. The pairwise F_st values and analysis of molecular variance (AMOVA) revealed significant population differentiation among all populations except DQ and NH populations, with RC and ZZ cultured populations exhibiting the largest population differentiation (F_st = 0.1334). The phylogenetic tree and structural analysis divided the six populations into two groups (group 1: NH, DQ, and ZZ; group 2: DL, TJ, and RC), and there was no relationship between geographical distance and genetic distance. Conclusions: These results may reflect the large-scale culture from different populations in China and the exchange of juveniles between hatcheries. Different breeding conditions have led to a higher degree of genetic differentiation between the RC and ZZ populations. This study enables a better understanding of the genetic diversity and structure of current Pacific abalone populations. Full article

(This article belongs to the Special Issue Genetic Studies of Fish)

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13 pages, 559 KiB

Open AccessReview

22q11.21 Deletions: A Review on the Interval Mediated by Low-Copy Repeats C and D

by Veronica Bertini, Francesca Cambi, Annalisa Legitimo, Giorgio Costagliola, Rita Consolini and Angelo Valetto

Genes 2025, 16(1), 72; https://doi.org/10.3390/genes16010072 - 9 Jan 2025

22q11.2 is a region prone to chromosomal rearrangements due to the presence of eight large blocks of low-copy repeats (LCR22s). The 3 Mb 22q11.2 “typical deletion”, between LCR22-A and D, causes a fairly well-known clinical picture, while the effects of smaller CNVs harbored [...] Read more.

22q11.2 is a region prone to chromosomal rearrangements due to the presence of eight large blocks of low-copy repeats (LCR22s). The 3 Mb 22q11.2 “typical deletion”, between LCR22-A and D, causes a fairly well-known clinical picture, while the effects of smaller CNVs harbored in this interval are still to be fully elucidated. Nested deletions, flanked by LCR22B-D, LCR22B-C, or LCR22C-D, are very rare and are collectively described as “central deletions”. The LCR22C-D deletion (CDdel) has never been separately analyzed. In this paper, we focused only on CDdel, evaluating its gene content and reviewing the literature and public databases in order to obtain new insights for the classification of this CNV. At first glance, CDdels are associated with a broad phenotypic spectrum, ranging from clinically normal to quite severe phenotypes. However, the frequency of specific clinical traits highlights that renal/urinary tract abnormalities, cardiac defects, and neurological/behavioral disorders are much more common in CDdel than in the general population. This frequency is too high to be fortuitous, indicating that CDdel is a predisposing factor for these phenotypic traits. Among the genes present in this interval, CRKL is an excellent candidate for cardiac and renal defects. Even if further data are necessary to confirm the role of CDdels, according to our review, this CNV fits into the class of ‘likely pathogenic’ CNVs. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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17 pages, 1057 KiB

Open AccessReview

Liquid Biopsy and Challenge of Assay Heterogeneity for Minimal Residual Disease Assessment in Colon Cancer Treatment

by Giovanni Crisafulli

Genes 2025, 16(1), 71; https://doi.org/10.3390/genes16010071 - 9 Jan 2025

This review provides a comprehensive overview of the evolving role of minimal residual disease (MRD) for patients with Colon Cancer (CC). Currently, the standard of care for patients with non-metastatic CC is adjuvant chemotherapy (ACT) for all patients with stage III and high-risk [...] Read more.

This review provides a comprehensive overview of the evolving role of minimal residual disease (MRD) for patients with Colon Cancer (CC). Currently, the standard of care for patients with non-metastatic CC is adjuvant chemotherapy (ACT) for all patients with stage III and high-risk stage II CC following surgical intervention. Despite a 5–20% improvement in long-term survival outcomes, this approach also results in a significant proportion of patients receiving ACT without any therapeutic benefit and being unnecessarily exposed to the risks of secondary side effects. This underscores an unmet clinical need for more precise stratification to distinguish patients who necessitate ACT from those who can be treated with surgery alone. By employing liquid biopsy, it is possible to discern MRD enabling the categorization of patients as MRD-positive or MRD-negative, potentially revolutionizing the management of ACT. This review aimed to examine the heterogeneity of methodologies currently available for MRD detection, encompassing the state-of-the-art technologies, their respective advantages, limitations, and the technological challenges and multi-omic approaches that can be utilized to enhance assay performance. Furthermore, a discussion was held regarding the clinical trials that employ an MRD assay focusing on the heterogeneity of the assays used. These differences in methodology, target selection, and performance risk producing inconsistent results that may not solely reflect biological/clinical differences but may be the consequence of the preferential use of particular products in studies conducted in different countries. Standardization and harmonization of MRD assays will be crucial to ensure the liquid revolution delivers reliable and clinically actionable outcomes for patients. Full article

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

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17 pages, 5012 KiB

Open AccessArticle

Comprehensive Analysis of the NHX Gene Family and Its Regulation Under Salt and Drought Stress in Quinoa (Chenopodium quinoa Willd.)

by Yalla Santhoshi, Asha Bindhu Anjana, Harshvardhan Zala, Tejas Bosamia, Kapil Tiwari, Ketan Prajapati, Pranay Patel, Nishit Soni, Nitin Patel, Satyanarayan Solanki and Ulhas Sopanrao Kadam

Genes 2025, 16(1), 70; https://doi.org/10.3390/genes16010070 - 9 Jan 2025

Background/Objectives: Abiotic stresses such as salinity and drought significantly constrain crop cultivation and affect productivity. Quinoa (Chenopodium quinoa Willd.), a facultative halophyte, exhibits remarkable tolerance to drought and salinity stresses, making it a valued model for understanding stress adaptation mechanisms. The [...] Read more.

Background/Objectives: Abiotic stresses such as salinity and drought significantly constrain crop cultivation and affect productivity. Quinoa (Chenopodium quinoa Willd.), a facultative halophyte, exhibits remarkable tolerance to drought and salinity stresses, making it a valued model for understanding stress adaptation mechanisms. The objective of this study was to identify and characterize Sodium/Hydrogen antiporter (NHX) genes from the quinoa genome and study their role in stress tolerance. Methods: We identified and characterized 10 NHX genes from the quinoa genome, which belong to the monovalent cation/proton antiporter 1 (CPA1) superfamily. Comprehensive analysis, including phylogenetic relationships, motif patterns, and structural characteristics, was performed to classify these genes into three subfamilies. Physicochemical properties such as isoelectric point (pI), GRAVY, and transmembrane domains were examined. Promoter analysis was conducted to identify cis-elements linked to abiotic stress responses, phytohormone signalling, and light regulation. qPCR analysis was used to assess the differential expression patterns of CqNHX genes under salt and drought stress. Results: The analysis revealed that the NHX genes were divided into three subfamilies localized to vacuolar, plasma, and endosomal membranes. These genes exhibited structural and functional diversity. Promoter analysis indicated the presence of cis-elements associated with abiotic stress responses, phytohormone signalling, and light regulation, suggesting diverse regulatory roles. qPCR analysis revealed differential expression patterns of CqNHX genes under salt and drought stress, with vacuolar NHXs showing higher induction in leaf tissues under salinity. This underscores their critical role in sodium sequestration and ion homeostasis. Evolutionary analysis indicated a high degree of conservation within subfamilies, alongside evidence of purifying selection. Conclusions: The findings enhance our understanding of the molecular basis of stress tolerance in quinoa and provide valuable targets for genetic engineering to improve crop resilience to environmental challenges. Full article

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

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13 pages, 5621 KiB

Open AccessArticle

Molecular Characterization, Recombinant Expression, and Functional Analysis of Carboxypeptidase B in Litopenaeus vannamei

by Hongmei Li, Hai Lin, Hao Yang, Chunhua Ren, Yi He, Xiao Jiang, Ting Chen and Chaoqun Hu

Genes 2025, 16(1), 69; https://doi.org/10.3390/genes16010069 - 9 Jan 2025

Background/Objectives: The Pacific white shrimp (L. vannamei) is economically significant, and its growth is regulated by multiple factors. Carboxypeptidase B (CPB) is related to protein digestion, but its gene sequence and features in L. vannamei are not fully understood. This study [...] Read more.

Background/Objectives: The Pacific white shrimp (L. vannamei) is economically significant, and its growth is regulated by multiple factors. Carboxypeptidase B (CPB) is related to protein digestion, but its gene sequence and features in L. vannamei are not fully understood. This study aimed to explore the molecular and functional properties of CPB in L. vannamei. Methods: The Lv-CPB gene was cloned, and bioinformatics analysis, qRT-PCR, in situ hybridization, recombinant protein expression in Escherichia coli, and an enzyme activity assay were performed. Results: The Lv-CPB gene is 1414 bp long with a 1263 bp ORF encoding a 420-amino-acid protein. It is stable, hydrophilic, and is highly expressed in the hepatopancreas. The recombinant protein was efficiently expressed with a molecular weight of about 47 kDa. The optimal pH and temperature for Lv-CPB were 8.0 and 50 °C, respectively. Conclusions: This study revealed the molecular and functional characteristics of Lv-CPB, providing insights into its role in shrimp digestion, as well as suggestions for improving aquaculture practices. Full article

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

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19 pages, 2164 KiB

Open AccessArticle

Chromosomal rDNA Distribution Patterns in Clonal Cobitis Triploid Hybrids (Teleostei, Cobitidae): Insights into Parental Genomic Contributions

by Alicja Boroń, Anna Grabowska, Olga Jablonska, Lech Kirtiklis, Sara Duda and Dorota Juchno

Genes 2025, 16(1), 68; https://doi.org/10.3390/genes16010068 - 9 Jan 2025

Background: Interspecific hybridization between relative species Cobitis taenia (with a diploid genome designated as TT), Cobitis elongatoides (EE) and Cobitis tanaitica (NN) and the successive polyploidization with transitions from sexuality to asexuality experienced by triploid Cobitis hybrids likely influence their chromosomal rearrangements, including [...] Read more.

Background: Interspecific hybridization between relative species Cobitis taenia (with a diploid genome designated as TT), Cobitis elongatoides (EE) and Cobitis tanaitica (NN) and the successive polyploidization with transitions from sexuality to asexuality experienced by triploid Cobitis hybrids likely influence their chromosomal rearrangements, including rearrangements of ribosomal DNA (rDNA) distribution patterns. Previously, we documented distinct karyotypic differences: C. elongatoides exhibited bi-armed chromosomes while C. taenia showed uni-armed chromosomes with rDNA-positive hybridization signals, respectively. Methods: In this study, fluorescence in situ hybridization (FISH) with 5S rDNA and 28S rDNA probes was used to analyze and compare chromosomal distribution patterns of rDNAs in clonally reproduced triploid Cobitis hybrids of different genomic constitutions ETT, ETN, EEN and EET (referred to using acronyms denoting the haploid genomes of their parent species), and their parental species. Results: Cobitis triploid hybrids exhibited intermediate karyotypes with ribosome synthesis sites on chromosomes inherited from both parents, showing no evidence of nucleolar dominance. The rDNA pattern derived from the C. elongatoides genome was more stable in the hybrids’ karyotypes. Two and one submetacentric chromosomes with co-localized rDNAs were effective markers to ascertain C. elongatoides diploid (EE) and haploid (E) genomes within the genome of triploid hybrids, respectively. Fewer 5S rDNA loci were observed in diploid (TT) and haploid (T) chromosome sets from C. taenia in ETT and EET females. C. taenia and C. tanaitica exhibited similar rDNA distribution patterns. Conclusions: The karyotypes of triploid Cobitis hybrids reflect the genomic contributions of their parental species. Variability in rDNA distribution patterns suggests complex genomic interactions in Cobitis hybrids resulting from polyploidization and hybridization, potentially influencing their reproductive potential. Full article

(This article belongs to the Special Issue Fish Cytogenetics: Insights into Genome Diversity)

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11 pages, 1353 KiB

Open AccessArticle

Concordant Patterns of Population Genetic Structure in Food-Deceptive Dactylorhiza Orchids

by Ada Wróblewska, Beata Ostrowiecka, Edyta Jermakowicz and Izabela Tałałaj

Genes 2025, 16(1), 67; https://doi.org/10.3390/genes16010067 - 8 Jan 2025

Background: The patterns of inbreeding coefficients (F_IS) and fine spatial genetic structure (FSGS) were evaluated regarding the mating system and inbreeding depression of food-deceptive orchids, Dactylorhiza majalis, Dactylorhiza incarnata var. incarnata, and Dactylorhiza fuchsii, from NE Poland. [...] Read more.

Background: The patterns of inbreeding coefficients (F_IS) and fine spatial genetic structure (FSGS) were evaluated regarding the mating system and inbreeding depression of food-deceptive orchids, Dactylorhiza majalis, Dactylorhiza incarnata var. incarnata, and Dactylorhiza fuchsii, from NE Poland. Methods: We used 455 individuals, representing nine populations of three taxa and AFLPs, to estimate percent polymorphic loci and Nei’s gene diversity, which are calculated using the Bayesian method; F_IS; F_ST; FSGS with the pairwise kinship coefficient (Fij); and AMOVA in populations. Results: We detected a relatively high proportion of polymorphic fragments (40.4–68.4%) and Nei’s gene diversity indices (0.140–0.234). The overall F_IS was relatively low to moderate (0.071–0.312). The average Fij for the populations of three Dactylorhiza showed significantly positive values, which were observed between plants at distances of 1–10 m (20 m). F_ST was significant in each Dactylorhiza taxon, ranging from the lowest values in D. fuchsii and D. majalis (0.080–0.086, p < 0.05) to a higher value (0.163, p < 0.05) in D. incarnata var. incarnata. Molecular variance was the highest within populations (76.5–86.6%; p < 0.001). Conclusions: We observed concordant genetic diversity patterns in three food-deceptive, allogamous, pollinator-dependent, and self-compatible Dactylorhiza. F_IS is often substantially higher than Fij with respect to the first class of FSGSs, suggesting that selfing (meaning of geitonogamy) is at least responsible for homozygosity. A strong FSGS may have evolutionary consequences in Dactylorhiza, and combined with low inbreeding depression, it may impact the establishment of inbred lines of D. majalis and D. incarnata var. incarnata. Full article

(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics 2024)

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27 pages, 4250 KiB

Open AccessArticle

The RAD6-like Ubiquitin Conjugase Gene OsUBC7 Has a Positive Role in the Early Cold Stress Tolerance Response of Rice

by Huy Phan and Michael Schläppi

Genes 2025, 16(1), 66; https://doi.org/10.3390/genes16010066 - 8 Jan 2025

Background/Objectives: Cold stress poses a significant threat to Asian rice cultivation, disrupting important physiological processes crucial for seedling establishment and overall plant growth. It is, thus, crucial to elucidate genetic pathways involved in cold stress tolerance response mechanisms. Methods: We mapped OsUBC7, [...] Read more.

Background/Objectives: Cold stress poses a significant threat to Asian rice cultivation, disrupting important physiological processes crucial for seedling establishment and overall plant growth. It is, thus, crucial to elucidate genetic pathways involved in cold stress tolerance response mechanisms. Methods: We mapped OsUBC7, a Radiation-sensitive 6 (RAD6)-type homolog of rice, to a low-temperature seedling survivability (LTSS) QTL and used genomics, molecular genetics, and physiological assays to assess its role in plant resilience against low-temperature stress. Results: OsUBC7 is cold responsive and has higher expression levels in cold-tolerant japonica than cold-sensitive indica. Overexpression of OsUBC7 enhances LTSS of indica and freezing tolerance of Arabidopsis, increases levels of soluble sugars and chlorophyll A, boosts leaf development after cold exposure, and increases leaf cell numbers and plants size, but it does not affect membrane stability after cold stress exposure. Additionally, OsUBC7 has a positive role for germinability in the presence of salt and for flowering and yield-related traits. The OsUBC7 protein physically interacts with the developmental stage-specific and histone-modifying E3 ligases OsRFPH2-12 and OsHUB1/2, respectively, and potential target genes such as cell cycle dependent kinases were identified. Conclusions: OsUBC7 might contribute to cold resilience by regulating sugar metabolism to provide energy for promoting cellular homeostasis restoration after cold stress exposure via new cell growth, particularly in leaf cells crucial for photosynthesis and metabolic activity, possibly by interacting with cell cycle regulating proteins. Overall, the present study suggests that OsUBC7 may be involved in plant development, reproduction, and stress adaptation, and contributes to a deeper understanding of rice plant cold stress tolerance response mechanisms. OsUBC7 may be a promising candidate for improving crop productivity and resilience to stressful environments. Full article

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

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14 pages, 3211 KiB

Open AccessArticle

Transcriptome Analysis of Muscle Growth-Related circRNA in the Pacific Abalone Haliotis discus hanna

by Jianfang Huang, Jian He, Zhenghan She, Mingcan Zhou, Dongchang Li, Jianming Chen and Caihuan Ke

Genes 2025, 16(1), 65; https://doi.org/10.3390/genes16010065 - 8 Jan 2025

(1) Background: Animal growth is a complex process, involving the coordination of a wide variety of genes, non-coding RNAs, and pathways. Circular RNAs (circRNAs) belong to a novel class of functional non-coding RNAs (ncRNAs). They have a distinctive ring structure and are involved [...] Read more.

(1) Background: Animal growth is a complex process, involving the coordination of a wide variety of genes, non-coding RNAs, and pathways. Circular RNAs (circRNAs) belong to a novel class of functional non-coding RNAs (ncRNAs). They have a distinctive ring structure and are involved in various biological processes, including the proliferation, differentiation, and apoptosis of muscle cells. The Pacific abalone Haliotis discus hannai is an economically valuable mollusk species cultivated in China. However, the modulation of muscle growth by circRNAs in this species is poorly understood. (2) Methods: In this study, we analyzed the muscle transcriptomes of 6 H. discus hannai specimens: three small (S_HD) and three large (L_HD) groups via RNA-seq and bioinformatics technology. (3) Results: The results indicated the presence of 11,744 circRNAs in abalone adductor muscle. Furthermore, the L_HD group had 250 significantly differentially expressed circRNAs (106 upregulated and 144 downregulated) relative to the S_HD group. Moreover, the bioinformatics assessment revealed that circRNAs were related to lipid transporter activity, lipid biosynthetic process, fat digestion and absorption, the single-organism metabolic process, the thyroid hormone signaling pathway, and the hippo signaling pathway, which regulates growth. Seventeen key candidate circRNAs were identified, and a core functional circRNA-miRNA-mRNA network associated with abalone muscle growth was described. Gene expression was verified using qRT-PCR, confirming the accuracy of the RNA-seq data. (4) Conclusion: Overall, this investigation furnishes novel evidence for the potential muscle growth modulatory mechanisms in Pacific abalone. These high-quality circRNA data of abalone muscle provide a reference for functional studies on the abalone genome. Full article

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

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33 pages, 1758 KiB

Open AccessArticle

Quantitative Trait Loci for Phenology, Yield, and Phosphorus Use Efficiency in Cowpea

by Saba B. Mohammed, Patrick Obia Ongom, Nouhoun Belko, Muhammad L. Umar, María Muñoz-Amatriaín, Bao-Lam Huynh, Abou Togola, Muhammad F. Ishiyaku and Ousmane Boukar

Genes 2025, 16(1), 64; https://doi.org/10.3390/genes16010064 - 8 Jan 2025

Background/Objectives: Cowpea is an important legume crop in sub-Saharan Africa (SSA) and beyond. However, access to phosphorus (P), a critical element for plant growth and development, is a significant constraint in SSA. Thus, it is essential to have high P-use efficiency varieties to [...] Read more.

Background/Objectives: Cowpea is an important legume crop in sub-Saharan Africa (SSA) and beyond. However, access to phosphorus (P), a critical element for plant growth and development, is a significant constraint in SSA. Thus, it is essential to have high P-use efficiency varieties to achieve increased yields in environments where little-to- no phosphate fertilizers are applied. Methods: In this study, crop phenology, yield, and grain P efficiency traits were assessed in two recombinant inbred line (RIL) populations across ten environments under high- and low-P soil conditions to identify traits’ response to different soil P levels and associated quantitative trait loci (QTLs). Single-environment (SEA) and multi-environment (MEA) QTL analyses were conducted for days to flowering (DTF), days to maturity (DTM), biomass yield (BYLD), grain yield (GYLD), grain P-use efficiency (gPUE) and grain P-uptake efficiency (gPUpE). Results: Phenotypic data indicated significant variation among the RILs, and inadequate soil P had a negative impact on flowering, maturity, and yield traits. A total of 40 QTLs were identified by SEA, with most explaining greater than 10% of the phenotypic variance, indicating that many major-effect QTLs contributed to the genetic component of these traits. Similarly, MEA identified 23 QTLs associated with DTF, DTM, GYLD, and gPUpE under high- and low-P environments. Thirty percent (12/40) of the QTLs identified by SEA were also found by MEA, and some of those were identified in more than one P environment, highlighting their potential in breeding programs targeting PUE. QTLs on chromosomes Vu03 and Vu08 exhibited consistent effects under both high- and low-P conditions. In addition, candidate genes underlying the QTL regions were identified. Conclusions: This study lays the foundation for molecular breeding for PUE and contributes to understanding the genetic basis of cowpea response in different soil P conditions. Some of the identified genomic loci, many being novel QTLs, could be deployed in marker-aided selection and fine mapping of candidate genes. Full article

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

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16 pages, 3031 KiB

Open AccessArticle

Genome-Wide Insights into Internalizing Symptoms in Admixed Latin American Children

by Gabriela de Sales Guerreiro Britto, Alberto O. Moreira, Edson Henrique Bispo Amaral, Daniel Evangelista Santos, Raquel B. São Pedro, Thaís M. M. Barreto, Caroline Alves Feitosa, Darci Neves dos Santos, Eduardo Tarazona-Santos, Maurício Lima Barreto, Camila Alexandrina Viana de Figueiredo, Ryan dos Santos Costa, Ana Lúcia Brunialti Godard and Pablo Rafael Silveira Oliveira

Genes 2025, 16(1), 63; https://doi.org/10.3390/genes16010063 - 8 Jan 2025

Background/Objectives: Internalizing disorders, including depression and anxiety, are major contributors to the global burden of disease. While the genetic architecture of these disorders in adults has been extensively studied, their early-life genetic mechanisms remain underexplored, especially in non-European populations. This study investigated the [...] Read more.

Background/Objectives: Internalizing disorders, including depression and anxiety, are major contributors to the global burden of disease. While the genetic architecture of these disorders in adults has been extensively studied, their early-life genetic mechanisms remain underexplored, especially in non-European populations. This study investigated the genetic mechanisms underlying internalizing symptoms in a cohort of Latin American children. Methods: This study included 1244 Brazilian children whose legal guardians completed the Child Behavior Checklist (CBCL) questionnaire. Genotyping was performed using the Illumina HumanOmni 2.5-8v1 BeadChip. Results: The genome-wide association analysis revealed a significant association of rs7196970 (p = 4.5 × 10⁻⁸, OR = 0.61), in the ABCC1 gene, with internalizing symptoms. Functional annotation highlighted variants in epigenetically active regulatory regions, with multiple variants linked to differential expression of ABCC1 across several human tissues. Pathway enrichment analysis identified 42 significant pathways, with notable involvement in neurobiological processes such as glutamatergic, GABAergic, and dopaminergic synapses. Conclusions: This study identifies ABCC1 variants as novel genetic factors potentially associated with early-life internalizing symptoms. These results may contribute to future research on targeted interventions for childhood internalizing conditions. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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