Genes

14 pages, 1457 KiB

Open AccessArticle

MiR-18a-5p Targets Connective Tissue Growth Factor Expression and Inhibits Transforming Growth Factor β2-Induced Trabecular Meshwork Cell Contractility

by John Knox, George Bou-Gharios, Kevin J. Hamill and Colin E. Willoughby

Genes 2022, 13(8), 1500; https://doi.org/10.3390/genes13081500 - 22 Aug 2022

Cited by 7 | Viewed by 2527

Abstract

Increased trabecular meshwork (TM) cell and tissue contractility is a driver of the reduced outflow facility and elevation of intraocular pressure (IOP) associated with primary open-angle glaucoma (POAG). Connective tissue growth factor (CTGF) is an established mediator of TM cell contractility, and its [...] Read more.

Increased trabecular meshwork (TM) cell and tissue contractility is a driver of the reduced outflow facility and elevation of intraocular pressure (IOP) associated with primary open-angle glaucoma (POAG). Connective tissue growth factor (CTGF) is an established mediator of TM cell contractility, and its expression is increased in POAG due to transforming growth factor β 2 (TGFβ2) signalling. Inhibiting CTGF upregulation using microRNA (miRNA) mimetics could represent a new treatment option for POAG. A combination of in silico predictive tools and a literature review identified a panel of putative CTGF-targeting miRNAs. Treatment of primary human TM cells with 5 ng/mL TGFβ2 for 24 h identified miR-18a-5p as a consistent responder, being upregulated in cells from five different human donors. Transfection of primary donor TM cells with 20 nM synthetic miR-18a-5p mimic reduced TGFβ2-induced CTGF protein expression, and stable lentiviral-mediated overexpression of this miRNA reduced TGFβ2-induced contraction of collagen gels. Together, these findings identify miR-18a-5p as a mediator of the TGFβ2 response and a candidate therapeutic agent for glaucoma via its ability to inhibit CTGF-associated increased TM contractility. Full article

(This article belongs to the Special Issue Small Non-coding RNAs in Normal Physiology, Development and Diseases)

► Show Figures

Figure 1

12 pages, 937 KiB

Open AccessArticle

Predominance of the Rare EGFR Mutation p.L861Q in Tunisian Patients with Non-Small Cell Lung Carcinoma

by Rania Abdelmaksoud-Dammak, Nihel Ammous-Boukhris, Amèna Saadallah-Kallel, Slim Charfi, Souhir Khemiri, Rim Khemakhem, Nesrin Kallel, Wala Ben Kridis-Rejeb, Tahya Sallemi-Boudawara, Afef Khanfir, Ilhem Yangui, Jamel Daoud and Raja Mokdad-Gargouri

Genes 2022, 13(8), 1499; https://doi.org/10.3390/genes13081499 - 22 Aug 2022

Cited by 3 | Viewed by 2806

Abstract

Objectives: Several new cancer therapies targeting signaling pathways involved in the growth and progression of cancer cells were developed as personalized medicine. Our study aimed to identify epidermal growth factor receptor (EGFR) mutations for TKI treatment in non-small-cell lung cancer (NSCLC) [...] Read more.

Objectives: Several new cancer therapies targeting signaling pathways involved in the growth and progression of cancer cells were developed as personalized medicine. Our study aimed to identify epidermal growth factor receptor (EGFR) mutations for TKI treatment in non-small-cell lung cancer (NSCLC) Tunisian patients. Methods: Analysis of the TKI sensitivity mutations in exons 18 to 21 of the EGFR gene and exon 15 of the B-raf gene was performed in 79 formalin fixed-paraffin embedded (FFPE) NSCLC samples using pyrosequencing. Results: EGFR mutations were detected in 34 cases among 79 (43%), with the predominance of the L861Q in exon 21 found in 35.3% of the cases (12 out of 34). Deletions in exon 19 were found in 8 cases (23.5%), and only one young male patient had the T790M mutation. Three patients harbored composite EGFR mutations (p.E746_A750del/p.L861R, p.E746_S752>V/p.S768I, and p.G719A/p.L861Q). Furthermore, the EGFR mutated status was significantly more frequent in female patients (p = 0.019), in non-smoker patients (p = 0.008), and in patients with metastasis (p = 0.044). Moreover, the B-raf V600E was identified in 5 EGFR negative patients among 39 analyzed samples (13.15%). Conclusion: The p.L861Q localized in exon 21 of the EGFR gene was the most common mutation identified in our patients (35.3%), whereas the “classic” EGFR mutations such as Del19 and p.L858R were found in 23.5% and 11.7% of the cases, respectively. Interestingly, most of p.L861X mutation-carrying patients showed good response to TKI treatment. Altogether, our findings suggest a particular distribution of the EGFR-TKIs sensitivity mutations in Tunisian NSCLC patients. Full article

(This article belongs to the Section Genetic Diagnosis)

► Show Figures

Figure 1

14 pages, 628 KiB

Open AccessReview

Relationship between Nutrition, Lifestyle, and Neurodegenerative Disease: Lessons from ADH1B, CYP1A2 and MTHFR

by Shila Barati, Carlo Fabrizio, Claudia Strafella, Raffaella Cascella, Valerio Caputo, Domenica Megalizzi, Cristina Peconi, Julia Mela, Luca Colantoni, Carlo Caltagirone, Andrea Termine and Emiliano Giardina

Genes 2022, 13(8), 1498; https://doi.org/10.3390/genes13081498 - 22 Aug 2022

Cited by 4 | Viewed by 4586

Abstract

In the present review, the main features involved in the susceptibility and progression of neurodegenerative disorders (NDDs) have been discussed, with the purpose of highlighting their potential application for promoting the management and treatment of patients with NDDs. In particular, the impact of [...] Read more.

In the present review, the main features involved in the susceptibility and progression of neurodegenerative disorders (NDDs) have been discussed, with the purpose of highlighting their potential application for promoting the management and treatment of patients with NDDs. In particular, the impact of genetic and epigenetic factors, nutrients, and lifestyle will be presented, with particular emphasis on Alzheimer’s disease (AD) and Parkinson’s disease (PD). Metabolism, dietary habits, physical exercise and microbiota are part of a complex network that is crucial for brain function and preservation. This complex equilibrium can be disrupted by genetic, epigenetic, and environmental factors causing perturbations in central nervous system homeostasis, contributing thereby to neuroinflammation and neurodegeneration. Diet and physical activity can directly act on epigenetic modifications, which, in turn, alter the expression of specific genes involved in NDDs onset and progression. On this subject, the introduction of nutrigenomics shed light on the main molecular players involved in the modulation of health and disease status. In particular, the review presents data concerning the impact of ADH1B, CYP1A2, and MTHFR on the susceptibility and progression of NDDs (especially AD and PD) and how they may be exploited for developing precision medicine strategies for the disease treatment and management. Full article

(This article belongs to the Special Issue Feature Papers in Human Genomics and Genetic Diseases)

► Show Figures

Figure 1

11 pages, 968 KiB

Open AccessCommunication

Genetic Variants Associated with Elevated Plasma Ceramides in Individuals with Metabolic Syndrome

by Sanghoo Lee, Seol-A Kim, Yejin Kim, Juhoon Kim, Gayeon Hong, Jeonghoon Hong, Kyeonghwan Choi, Chun-Sick Eom, Saeyun Baik, Mi-Kyeong Lee and Kyoung-Ryul Lee

Genes 2022, 13(8), 1497; https://doi.org/10.3390/genes13081497 - 22 Aug 2022

Cited by 3 | Viewed by 2209

Abstract

Metabolic syndrome (MetS) is a complex condition of metabolic disorders and shows a steady onset globally. Ceramides are known as intracellular signaling molecules that influence key metabolism through various pathways such as MetS and insulin resistance. Therefore, it is important to identify novel [...] Read more.

Metabolic syndrome (MetS) is a complex condition of metabolic disorders and shows a steady onset globally. Ceramides are known as intracellular signaling molecules that influence key metabolism through various pathways such as MetS and insulin resistance. Therefore, it is important to identify novel genetic factors related to increased plasma ceramides in subjects with MetS. Here we first measured plasma ceramides levels in 37 subjects with MetS and in 38 healthy subjects by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Specifically, levels of C16 ceramide (Cer-16), C18 ceramide (Cer-18), C20 ceramide (Cer-20), C18 dihydroceramide (DhCer-18), C24 dihydroceramide (DhCer-24), and C24:1 dihydroceramide (DhCer-24:1) were significantly increased in MetS group (p < 5.0 × 10⁻²). We then performed single nucleotide polymorphism (SNP) genotyping to identify variants associated with elevated plasma ceramides in MetS group using Axiom^® Korea Biobank Array v1.1 chip. We also performed linear regression analysis on genetic variants involved in ceramide synthesis and significantly elevated plasma ceramides and dihydroceramides. Ten variants (rs75397325, rs4246316, rs80165332, rs62106618, rs12358192, rs11006229, rs10826014, rs149162405, rs6109681, and rs3906631) across six genes (ACER1, CERS3, CERS6, SGMS1, SPTLC2, and SPTLC3) functionally involved in ceramide biosynthesis showed significant associations with the elevated levels of at least one of the ceramide species in MetS group at a statistically significant threshold of false discovery rate (FDR)-adjusted p < 5.0 × 10⁻². Our findings suggest that the variants may be genetic determinants associated with increased plasma ceramides in individuals with MetS. Full article

(This article belongs to the Section Genetic Diagnosis)

► Show Figures

Figure 1

20 pages, 2229 KiB

Open AccessArticle

Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox (Urocyon littoralis catalinae)

by Sarah A. Hendricks, Julie L. King, Calvin L. Duncan, Winston Vickers, Paul A. Hohenlohe and Brian W. Davis

Genes 2022, 13(8), 1496; https://doi.org/10.3390/genes13081496 - 22 Aug 2022

Cited by 3 | Viewed by 3152

Abstract

Small effective population sizes raise the probability of extinction by increasing the frequency of potentially deleterious alleles and reducing fitness. However, the extent to which cancers play a role in the fitness reduction of genetically depauperate wildlife populations is unknown. Santa Catalina island [...] Read more.

Small effective population sizes raise the probability of extinction by increasing the frequency of potentially deleterious alleles and reducing fitness. However, the extent to which cancers play a role in the fitness reduction of genetically depauperate wildlife populations is unknown. Santa Catalina island foxes (Urocyon littoralis catalinae) sampled in 2007–2008 have a high prevalence of ceruminous gland tumors, which was not detected in the population prior to a recent bottleneck caused by a canine distemper epidemic. The disease appears to be associated with inflammation from chronic ear mite (Otodectes) infections and secondary elevated levels of Staphyloccus pseudointermedius bacterial infections. However, no other environmental factors to date have been found to be associated with elevated cancer risk in this population. Here, we used whole genome sequencing of the case and control individuals from two islands to identify candidate loci associated with cancer based on genetic divergence, nucleotide diversity, allele frequency spectrum, and runs of homozygosity. We identified several candidate loci based on genomic signatures and putative gene functions, suggesting that cancer susceptibility in this population may be polygenic. Due to the efforts of a recovery program and weak fitness effects of late-onset disease, the population size has increased, which may allow selection to be more effective in removing these presumably slightly deleterious alleles. Long-term monitoring of the disease alleles, as well as overall genetic diversity, will provide crucial information for the long-term persistence of this threatened population. Full article

(This article belongs to the Special Issue Advances in Canine Genetics)

► Show Figures

Figure 1

13 pages, 3415 KiB

Open AccessEditor’s ChoiceArticle

Cathepsin D Plays a Vital Role in Macrobrachium nipponense of Ovary Maturation: Identification, Characterization, and Function Analysis

by Dan Cheng, Wenyi Zhang, Sufei Jiang, Yiwei Xiong, Shubo Jin, Fangyan Pan, Junpeng Zhu, Yongsheng Gong, Yan Wu, Hui Qiao and Hongtuo Fu

Genes 2022, 13(8), 1495; https://doi.org/10.3390/genes13081495 - 21 Aug 2022

Cited by 5 | Viewed by 2101

Abstract

The oriental river prawn Macrobrachium nipponense is an economically important aquacultural species. However, its aquaculture is negatively impacted by the rapid sexual maturation of female M. nipponense. The fast sexual maturation produces a large number of offspring which leads to a reduction [...] Read more.

The oriental river prawn Macrobrachium nipponense is an economically important aquacultural species. However, its aquaculture is negatively impacted by the rapid sexual maturation of female M. nipponense. The fast sexual maturation produces a large number of offspring which leads to a reduction in resilience, a low survival rate, and an increased risk of hypoxia, this in turn, seriously affects the economic benefits of prawn farming. Cathepsin D is a lysosomal protease involved in the ovarian maturation of M. nipponense. In the current study, the cDNA of the gene encoding cathepsin D (Mn-CTSD) was cloned from M. nipponense. The total length was 2391 bp and consisted of an open reading frame (ORF) of 1158 bp encoding 385 amino acids. Sequence analysis confirmed the presence of conserved N-glycosylation sites and characteristic sequences of nondigestive cathepsin D. The qPCR analysis indicated that Mn-CTSD was highly expressed in all tissues tested, most significantly in the ovaries, whereas in situ hybridization showed that expression occurred mainly in oocyte nuclei. Analysis of its expression during development showed that Mn-CTSD peaked during the O-IV stage of ovarian maturation. For the RNAi interference experiment, female M. nipponense specimens in the ovary stage I were selected. Injection of Mn-CTSD double-stranded (ds)RNA into female M. nipponense decreased the expression of Mn-CTSD in the ovaries, such that the Gonad Somatic Index (GSI) of the experimental group was significantly lower than that of the control group (1.79% versus 4.57%; p < 0.05). Ovary development reached the O-III stage in 80% of the control group, compared with 0% in the experimental group. These results suggest that Mn-CTSD dsRNA inhibits ovarian maturation in M. nipponense, highlighting its important role in ovarian maturation in this species and suggesting an approach to controlling ovarian maturation during M. nipponense aquaculture. Full article

(This article belongs to the Special Issue Genetic Breeding of Aquaculture)

► Show Figures

Figure 1

21 pages, 1094 KiB

Open AccessArticle

A Comparison of Three Machine Learning Methods for Multivariate Genomic Prediction Using the Sparse Kernels Method (SKM) Library

by Osval A. Montesinos-López, Abelardo Montesinos-López, Bernabe Cano-Paez, Carlos Moisés Hernández-Suárez, Pedro C. Santana-Mancilla and José Crossa

Genes 2022, 13(8), 1494; https://doi.org/10.3390/genes13081494 - 21 Aug 2022

Cited by 6 | Viewed by 3098

Abstract

Genomic selection (GS) changed the way plant breeders select genotypes. GS takes advantage of phenotypic and genotypic information to training a statistical machine learning model, which is used to predict phenotypic (or breeding) values of new lines for which only genotypic information is [...] Read more.

Genomic selection (GS) changed the way plant breeders select genotypes. GS takes advantage of phenotypic and genotypic information to training a statistical machine learning model, which is used to predict phenotypic (or breeding) values of new lines for which only genotypic information is available. Therefore, many statistical machine learning methods have been proposed for this task. Multi-trait (MT) genomic prediction models take advantage of correlated traits to improve prediction accuracy. Therefore, some multivariate statistical machine learning methods are popular for GS. In this paper, we compare the prediction performance of three MT methods: the MT genomic best linear unbiased predictor (GBLUP), the MT partial least squares (PLS) and the multi-trait random forest (RF) methods. Benchmarking was performed with six real datasets. We found that the three investigated methods produce similar results, but under predictors with genotype (G) and environment (E), that is, E + G, the MT GBLUP achieved superior performance, whereas under predictors E + G + genotype

\times

environment (GE) and G + GE, random forest achieved the best results. We also found that the best predictions were achieved under the predictors E + G and E + G + GE. Here, we also provide the R code for the implementation of these three statistical machine learning methods in the sparse kernel method (SKM) library, which offers not only options for single-trait prediction with various statistical machine learning methods but also some options for MT predictions that can help to capture improved complex patterns in datasets that are common in genomic selection. Full article

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

► Show Figures

Figure 1

18 pages, 2998 KiB

Open AccessArticle

Identification of Alkaline Salt Tolerance Genes in Brassica napus L. by Transcriptome Analysis

by Yu Xu, Shunxian Tao, Yunlin Zhu, Qi Zhang, Ping Li, Han Wang, Yan Zhang, Aldiyar Bakirov, Hanming Cao, Mengfan Qin, Kai Wang, Yiji Shi, Xiang Liu, Lin Zheng, Aixia Xu and Zhen Huang

Genes 2022, 13(8), 1493; https://doi.org/10.3390/genes13081493 - 21 Aug 2022

Cited by 3 | Viewed by 2650

Abstract

Soil salt alkalization is one major abiotic factor reducing the productivity of crops, including rapeseed, an indispensable oil crop and vegetable. The mechanism studies of alkali salt tolerance can help breed highly resistant varieties. In the current study, rapeseed (B. napus) [...] Read more.

Soil salt alkalization is one major abiotic factor reducing the productivity of crops, including rapeseed, an indispensable oil crop and vegetable. The mechanism studies of alkali salt tolerance can help breed highly resistant varieties. In the current study, rapeseed (B. napus) line 2205 exhibited more tolerance to alkaline salt than line 1423 did. In line 2205, the lesser plasma membrane damage index, the accumulated osmotic solute, and higher antioxidant enzyme activities contributed to alkaline tolerance. A more integrated mesophyll-cell structure was revealed under alkali salt stress by ultrastructure observation in line 2205, which also implied a lesser injury. Transcriptome analysis showed that more genes responded to alkaline salt in line 2205. The expression of specific-response genes in line 1423 was lower than in line 2205. However, most of the specific-response genes in line 2205 had higher expression, which was mainly enriched in carbohydrate metabolism, photosynthetic processes, ROS regulating, and response to salt stress. It can be seen that the tolerance to alkaline salt is attributed to the high expression of some genes in these pathways. Based on these, twelve cross-differentially expressed genes were proposed as candidates. They provide clues for further analysis of the resistance mechanism of rapeseed. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

► Show Figures

Figure 1

14 pages, 2968 KiB

Open AccessArticle

Association Analysis for Some Biochemical Traits in Wild Relatives of Wheat under Drought Stress Conditions

by Alireza Pour-Aboughadareh, Omid Jadidi, Lia Shooshtari, Peter Poczai and Ali Ashraf Mehrabi

Genes 2022, 13(8), 1491; https://doi.org/10.3390/genes13081491 - 21 Aug 2022

Cited by 8 | Viewed by 2108

Abstract

In the present study, we estimated genetic diversity and population structure in 186 accessions of Triticum and Aegilops species using 24 simple sequence repeat markers (SSR). Furthermore, an association analysis was performed for antioxidant activities, including guaiacol peroxidase (GPX), ascorbate peroxidase (APX), peroxidase [...] Read more.

In the present study, we estimated genetic diversity and population structure in 186 accessions of Triticum and Aegilops species using 24 simple sequence repeat markers (SSR). Furthermore, an association analysis was performed for antioxidant activities, including guaiacol peroxidase (GPX), ascorbate peroxidase (APX), peroxidase (POX), catalase (CAT), and dry matter (DM) under two control and drought stress conditions. Our findings showed that drought treatment significantly decreased DM, whereas activities of all antioxidant enzymes were increased compared to the control conditions. The results of correlation analysis indicated that, under drought stress conditions, all biochemical traits had a positive and significant association with each other and with dry matter. In the molecular section, the results of the analysis of molecular variance (AMOVA) indicated that the molecular variation within species is more than within them. The dendrogram obtained by cluster analysis showed that grouping the investigated accessions was in accordance with their genomic constitutions. The results of association analysis revealed 8 and 9 significant marker–trait associations (MTA) under control and drought stress conditions, respectively. Among identified MTAs, two associations were simultaneously found in both growing conditions. Moreover, several SSR markers were associated with multiple traits across both conditions. In conclusion, our results could provide worthwhile information regarding marker-assisted selection for the activity of antioxidant enzymes in future breeding programs. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation and Utilization of Plant Genetic Resources)

► Show Figures

Figure 1

15 pages, 5519 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analyses of the Cotton AGO Genes and Their Potential Roles in Fiber Development and Stress Response

by Mingchuan Fu, Yizhen Chen, Hao Li, Liguo Wang, Renzhong Liu and Zhanji Liu

Genes 2022, 13(8), 1492; https://doi.org/10.3390/genes13081492 - 20 Aug 2022

Cited by 4 | Viewed by 2211

Abstract

Argonaute proteins (AGOs) are indispensable components of RNA silencing. However, systematic characterization of the AGO genes have not been completed in cotton until now. In this study, cotton AGO genes were identified and analyzed with respect to their evolution and expression profile during [...] Read more.

Argonaute proteins (AGOs) are indispensable components of RNA silencing. However, systematic characterization of the AGO genes have not been completed in cotton until now. In this study, cotton AGO genes were identified and analyzed with respect to their evolution and expression profile during biotic and abiotic stresses. We identified 14 GaAGO, 14 GrAGO, and 28 GhAGO genes in the genomes of Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum. Cotton AGO proteins were classified into four subgroups. Structural and functional conservation were observed in the same subgroups based on the analysis of the gene structure and conserved domains. Twenty-four duplicated gene pairs were identified in GhAGO genes, and all of them exhibited strong purifying selection during evolution. Moreover, RNA-seq analysis showed that most of the GhAGO genes exhibit high expression levels in the fiber initiation and elongation processes. Furthermore, the expression profiles of GhAGO genes tested by quantitative real-time polymerase chain reaction (qPCR) demonstrated that they were sensitive to Verticillium wilt infection and salt and drought stresses. Overall, our results will pave the way for further functional investigation of the cotton AGO gene family, which may be involved in fiber development and stress response. Full article

(This article belongs to the Section Genes & Environments)

► Show Figures

Figure 1

10 pages, 788 KiB

Open AccessArticle

Inherited Retinal Dystrophy in Southeastern United States: Characterization of South Carolina Patients and Comparative Literature Review

by Joseph Griffith III, Kareem Sioufi, Laurie Wilbanks, George N. Magrath, Emil A. T. Say, Michael J. Lyons, Meg Wilkes, Gurpur Shashidhar Pai and Mae Millicent Winfrey Peterseim

Genes 2022, 13(8), 1490; https://doi.org/10.3390/genes13081490 - 20 Aug 2022

Cited by 5 | Viewed by 2495

Abstract

Inherited retinal dystrophies (IRDs) are a group of rare diseases involving more than 340 genes and a variety of clinical phenotypes that lead to significant visual impairment. The aim of this study is to evaluate the rates and genetic characteristics of IRDs in [...] Read more.

Inherited retinal dystrophies (IRDs) are a group of rare diseases involving more than 340 genes and a variety of clinical phenotypes that lead to significant visual impairment. The aim of this study is to evaluate the rates and genetic characteristics of IRDs in the southeastern region of the United States (US). A retrospective chart review was performed on 325 patients with a clinical diagnosis of retinal dystrophy. Data including presenting symptoms, visual acuity, retinal exam findings, imaging findings, and genetic test results were compiled and compared to national and international IRD cohorts. The known ethnic groups included White (64%), African American or Black (30%), Hispanic (3%), and Asian (2%). The most prevalent dystrophies identified clinically were non-syndromic retinitis pigmentosa (29.8%), Stargardt disease (8.3%), Usher syndrome (8.3%), cone-rod dystrophy (8.0%), cone dystrophy (4.9%), and Leber congenital amaurosis (4.3%). Of the 101 patients (31.1%) with genetic testing, 54 (53.5%) had causative genetic variants identified. The most common pathogenic genetic variants were USH2A (n = 11), ABCA4 (n = 8), CLN3 (n = 7), and CEP290 (n = 3). Our study provides initial information characterizing IRDs within the diverse population of the southeastern US, which differs from national and international genetic and diagnostic trends with a relatively high proportion of retinitis pigmentosa in our African American or Black population and a relatively high frequency of USH2A pathogenic variants. Full article

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

► Show Figures

Figure 1

13 pages, 2704 KiB

Open AccessArticle

The Rm1 and Rm2 Resistance Genes to Green Peach Aphid (Myzus persicae) Encode the Same TNL Proteins in Peach (Prunus persica L.)

by Henri Duval, Laure Heurtevin, Naïma Dlalah, Caroline Callot and Jacques Lagnel

Genes 2022, 13(8), 1489; https://doi.org/10.3390/genes13081489 - 20 Aug 2022

Cited by 3 | Viewed by 2404

Abstract

The green peach aphid (GPA), Myzus persicae, is an important pest of the peach crop. Three major dominant resistance genes have already been detected, Rm1 in the Weeping Flower Peach (WFP) clone, Rm2 in the Rubira clone, and Rm3 in the Fen [...] Read more.

The green peach aphid (GPA), Myzus persicae, is an important pest of the peach crop. Three major dominant resistance genes have already been detected, Rm1 in the Weeping Flower Peach (WFP) clone, Rm2 in the Rubira clone, and Rm3 in the Fen Shouxing clone. In this study, after NGS resequencing of WFP and Rubira, we found that their genomic sequences in the Rm1 and Rm2 region were similar but very different from that of the susceptible reference peach Lovell. We constructed a BAC library for the GPA-resistant WFP and screened four BAC clones to sequence the target region. The new sequence was 61.7 Kb longer than Lovell and was annotated with four different TIR_NBS_LRR genes. Among them, the TNL1 gene was very overexpressed in WFP leaves 24 h after GPA infestation. This gene was also present and expressed in the Rubira clone and had the same sequence as the candidate Rm3 gene, supporting the hypothesis that the three genes share the same origin. In addition, we identified a second TNL, TNL2, located at 35.4 Kb from TNL1 and slightly overexpressed after GPA infestation. Kasp and size molecular markers were designed for use in marker-assisted selection and were validated in a peach segregating population. Full article

(This article belongs to the Special Issue Genetics and Genomics of Edible Rosaceae)

► Show Figures

Figure 1

15 pages, 1813 KiB

Open AccessArticle

Prediction of Synaptically Localized RNAs in Human Neurons Using Developmental Brain Gene Expression Data

by Anqi Wei and Liangjiang Wang

Genes 2022, 13(8), 1488; https://doi.org/10.3390/genes13081488 - 20 Aug 2022

Cited by 1 | Viewed by 2075

Abstract

In the nervous system, synapses are special and pervasive structures between axonal and dendritic terminals, which facilitate electrical and chemical communications among neurons. Extensive studies have been conducted in mice and rats to explore the RNA pool at synapses and investigate RNA transport, [...] Read more.

In the nervous system, synapses are special and pervasive structures between axonal and dendritic terminals, which facilitate electrical and chemical communications among neurons. Extensive studies have been conducted in mice and rats to explore the RNA pool at synapses and investigate RNA transport, local protein synthesis, and synaptic plasticity. However, owing to the experimental difficulties of studying human synaptic transcriptomes, the full pool of human synaptic RNAs remains largely unclear. We developed a new machine learning method, called PredSynRNA, to predict the synaptic localization of human RNAs. Training instances of dendritically localized RNAs were compiled from previous rodent studies, overcoming the shortage of empirical instances of human synaptic RNAs. Using RNA sequence and gene expression data as features, various models with different learning algorithms were constructed and evaluated. Strikingly, the models using the developmental brain gene expression features achieved superior performance for predicting synaptically localized RNAs. We examined the relevant expression features learned by PredSynRNA and used an independent test dataset to further validate the model performance. PredSynRNA models were then applied to the prediction and prioritization of candidate RNAs localized to human synapses, providing valuable targets for experimental investigations into neuronal mechanisms and brain disorders. Full article

(This article belongs to the Section RNA)

► Show Figures

Figure 1

10 pages, 1748 KiB

Open AccessArticle

Evaluation of the Impact of the Peregrine Falcon (Falco peregrinus peregrinus) Reintroduction Process on Captive-Bred Population

by Karol O. Puchała, Zuzanna Nowak-Życzyńska, Sławomir Sielicki and Wanda Olech

Genes 2022, 13(8), 1487; https://doi.org/10.3390/genes13081487 - 20 Aug 2022

Viewed by 2206

Abstract

The main objective of this study was to determine the impact of increased demand for peregrine falcons via breeding (mainly Polish, Czech, German and Slovak) on the genetic structure of the birds. In the analysis, 374 specimens from six countries were sampled in [...] Read more.

The main objective of this study was to determine the impact of increased demand for peregrine falcons via breeding (mainly Polish, Czech, German and Slovak) on the genetic structure of the birds. In the analysis, 374 specimens from six countries were sampled in 2008–2019 (omitting 2009), and all the birds analyzed were released into the wild as part of the Polish reintroduction program. The assessment of genetic variation was based on a well-known panel of 10 microsatellite markers described for the species. We calculated a fixation index for the samples from each year, and based on this, we determined the level of inbreeding. We also performed an analysis using the Bayesian cluster method, assuming that 1–19 hypothetical populations would define the division that best fit the samples. The most probable division was into two groups; in the first group, the samples from individuals delivered in 2013 were most often segregated; moreover, in this year, a jump in inbreeding, expressed by the fixation index, was observed. Full article

(This article belongs to the Special Issue Genetic Structure of World Animal Populations)

► Show Figures

Figure 1

16 pages, 2848 KiB

Open AccessArticle

Selection of Suitable Reference Genes for Gene Expression Normalization Studies in Dendrobium huoshanense

by Shanyong Yi, Haibo Lu, Chuanjun Tian, Tao Xu, Cheng Song, Wei Wang, Peipei Wei, Fangli Gu, Dong Liu, Yongping Cai and Bangxing Han

Genes 2022, 13(8), 1486; https://doi.org/10.3390/genes13081486 - 19 Aug 2022

Cited by 10 | Viewed by 2074

Abstract

Dendrobium huoshanense is a kind of precious herb with important medicinal and edible value in China, which is widely used in traditional Chinese medicine for various diseases. Recent studies have paid close attention to the genetic expression of the biosynthetic pathway of the [...] Read more.

Dendrobium huoshanense is a kind of precious herb with important medicinal and edible value in China, which is widely used in traditional Chinese medicine for various diseases. Recent studies have paid close attention to the genetic expression of the biosynthetic pathway of the main active components (polysaccharides, alkaloids, and flavonoids), and real-time polymerase chain reaction (qPCR) is one of the most widely used methods for doing so. However, so far, no reference gene selections have been reported in D. huoshanense. In this study, 15 reference gene candidates (GAPDH, eIF, EF-1α, PP2A, UBCE, RPL5, TBP, APT1, MDH, PTBP3, PEPC, CYP71, NCBP2, TIP41, and F-box) were selected and evaluated for their expression stability in D. huoshanense under various experimental conditions, including in different tissues (root, stem, and leaf), abiotic stresses (oxidative, drought, cold, and UV), and hormone treatment (methyl jasmonate) using three statistical programs (geNorm, NormFinder, and BestKeeper). Then, the RefFinder program was employed to comprehensively validate the stability of the selected reference genes. Finally, the expression profiles of the CESA and GMPP genes were further analyzed, and these results indicated that TBP, NCBP2, and CYP71 were the top three most stable reference genes after comprehensive comparison, which could be used as stable reference genes for normalizing the genes expression in D. huoshanense. This study described here provides the first data regarding on reference gene selection in D. huoshanense, which will be extremely beneficial for future research on the gene expression normalization in D. huoshanense. Full article

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

► Show Figures

Figure 1

8 pages, 1189 KiB

Open AccessEditor’s ChoiceArticle

When a Synonymous Variant Is Nonsynonymous

by Mauno Vihinen

Genes 2022, 13(8), 1485; https://doi.org/10.3390/genes13081485 - 19 Aug 2022

Cited by 21 | Viewed by 3701

Abstract

Term synonymous variation is widely used, but frequently in a wrong or misleading meaning and context. Twenty three point eight % of possible nucleotide substitution types in the universal genetic code are for synonymous amino acid changes, but when these variants have a [...] Read more.

Term synonymous variation is widely used, but frequently in a wrong or misleading meaning and context. Twenty three point eight % of possible nucleotide substitution types in the universal genetic code are for synonymous amino acid changes, but when these variants have a phenotype and functional effect, they are very seldom synonymous. Such variants may manifest changes at DNA, RNA and/or protein levels. Large numbers of variations are erroneously annotated as synonymous, which causes problems e.g., in clinical genetics and diagnosis of diseases. To facilitate precise communication, novel systematics and nomenclature are introduced for variants that when looking only at the genetic code seem like synonymous, but which have phenotypes. A new term, unsense variant is defined as a substitution in the mRNA coding region that affects gene expression and protein production without introducing a stop codon in the variation site. Such variants are common and need to be correctly annotated. Proper naming and annotation are important also to increase awareness of these variants and their consequences. Full article

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

► Show Figures

Figure 1

9 pages, 1079 KiB

Open AccessArticle

Circular Noncoding RNA hsa_circ_0003570 as a Prognostic Biomarker for Hepatocellular Carcinoma

by Se Young Jang, Gyeonghwa Kim, Won Young Tak, Young Oh Kweon, Yu Rim Lee, Young Seok Han, Ja Ryung Han, Jung Gil Park, Min Kyu Kang, Hye Won Lee, Won Kee Lee, Soo Young Park and Keun Hur

Genes 2022, 13(8), 1484; https://doi.org/10.3390/genes13081484 - 19 Aug 2022

Cited by 7 | Viewed by 2211

Abstract

Circular RNAs (circRNAs) are potential biomarkers owing to their stability, tissue specificity, and abundance. This study aimed to evaluate the clinical significance of hsa_circ_0003570 expression and to investigate its potential as a biomarker in hepatocellular carcinoma (HCC). We evaluated hsa_circ_0003570 expression in 121 [...] Read more.

Circular RNAs (circRNAs) are potential biomarkers owing to their stability, tissue specificity, and abundance. This study aimed to evaluate the clinical significance of hsa_circ_0003570 expression and to investigate its potential as a biomarker in hepatocellular carcinoma (HCC). We evaluated hsa_circ_0003570 expression in 121 HCC tissue samples, its association with clinicopathological characteristics, and overall and progression-free survival. Hsa_circ_0003570 expression was downregulated in HCC tissues. Low hsa_circ_0003570 expression was more common in tumors larger than 5 cm (odds ratio (OR), 6.369; 95% confidence interval (CI), 2.725–14.706; p < 0.001), vessel invasion (OR, 5.128; 95% CI, 2.288–11.494; p < 0.001); advanced tumor-node metastasis stage (III/IV; OR, 4.082; 95% CI, 1.866–8.929; p < 0.001); higher Barcelona Clinic Liver Cancer stage (B/C; OR, 3.215; 95% CI, 1.475–6.993; p = 0.003); and higher AFP (>200 ng/mL; OR, 2.475; 95% CI, 1.159–5.291; p = 0.018). High hsa_circ_0003570 expression was an independent prognostic factor for overall survival (hazard ratio (HR), 0.541; 95% confidence interval (CI), 0.327–0.894; p = 0.017) and progression-free survival (HR, 0.633; 95% CI, 0.402–0.997; p = 0.048). Hsa_circ_0003570 is a potential prognostic biomarker in patients with HCC, and further validation of hsa_circ_0003570 is needed. Full article

(This article belongs to the Special Issue Non-coding RNAs in Human Health and Diseases)

► Show Figures

Figure 1

9 pages, 829 KiB

Open AccessCase Report

An Atypical Presentation of Upper Motor Neuron Predominant Juvenile Amyotrophic Lateral Sclerosis Associated with TARDBP Gene: A Case Report and Review of the Literature

by Daniel Sánchez-Tejerina, Juan Luis Restrepo-Vera, Eulalia Rovira-Moreno, Marta Codina-Sola, Arnau Llauradó, Javier Sotoca, Maria Salvado, Núria Raguer, Elena García-Arumí and Raúl Juntas-Morales

Genes 2022, 13(8), 1483; https://doi.org/10.3390/genes13081483 - 19 Aug 2022

Cited by 2 | Viewed by 2251

Abstract

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that can rarely affect young individuals. Juvenile ALS (JALS) is defined for individuals with an onset of the disease before the age of 25. The contribution of genetics to ALS pathology is a field of [...] Read more.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that can rarely affect young individuals. Juvenile ALS (JALS) is defined for individuals with an onset of the disease before the age of 25. The contribution of genetics to ALS pathology is a field of growing interest. One of the differences between adult-onset ALS and JALS is their genetic background, with a higher contribution of genetic causes in JALS. We report a patient with JALS and a pathogenic variant in the TARDBP gene (c.1035C > G; p.Asn345Lys), previously reported only in adult-onset ALS, and with an atypical phenotype of marked upper motor neuron predominance. In addition, the proband presented an additional variant in the NEK1 gene, c.2961C > G (p.Phe987Leu), which is classified as a variant of unknown significance. Segregation studies showed a paternal origin of the TARDBP variant, while the variant in NEK1 was inherited from the mother. We hypothesize that the NEK1 variant acts as a disease modifier and suggests the possibility of a functional interaction between both genes in our case. This hypothesis could explain the peculiarities of the phenotype, penetrance, and the age of onset. This report highlights the heterogeneity of the phenotypic presentation of ALS associated with diverse pathogenic genetic variants. Full article

(This article belongs to the Special Issue Advances in Genetics of Motor Neuron Diseases)

► Show Figures

Figure 1

11 pages, 1375 KiB

Open AccessArticle

Metabolomic Profiling Reveals Common Metabolic Alterations in Plasma of Patients with Toxoplasma Infection and Schizophrenia

by Emelia Osman, Anis Safirah Mohammad Zahariluddin, Shalisah Sharip, Zulkarnain Md Idris and Jen Kit Tan

Genes 2022, 13(8), 1482; https://doi.org/10.3390/genes13081482 - 19 Aug 2022

Cited by 5 | Viewed by 2260

Abstract

Toxoplasma gondii is an opportunistic protozoan parasite known to affect the human brain. The infection has been associated with an increased incidence of schizophrenia; however, the link between the two conditions remains unclear. This study aimed to compare the plasma metabolome of schizophrenia [...] Read more.

Toxoplasma gondii is an opportunistic protozoan parasite known to affect the human brain. The infection has been associated with an increased incidence of schizophrenia; however, the link between the two conditions remains unclear. This study aimed to compare the plasma metabolome of schizophrenia and non-schizophrenia subjects with or without Toxoplasma infection. Untargeted metabolomic profiling was carried out by liquid chromatography-mass spectrometry. Elevation of the α-hydroxyglutaric acid level and reduced adenosine monophosphate, inosine, hypoxanthine and xanthine were found in the subjects with either toxoplasmosis or schizophrenia alone. These results suggest that purine catabolism is a common metabolic alteration in Toxoplasma infection and schizophrenia. The roles of these metabolites on the pathogenesis of schizophrenia in relation to Toxoplasma infection warrant further studies. Full article

(This article belongs to the Special Issue Genetic Basis of - and Biomarker Exploration in - Neurodevelopmental and Psychiatric Disorders)

► Show Figures

Graphical abstract

13 pages, 4464 KiB

Open AccessArticle

Genome-Wide Analysis of the WOX Transcription Factor Genes in Dendrobium catenatum Lindl.

by Hefan Li, Cheng Li, Yuhua Wang, Xiangshi Qin, Lihua Meng and Xudong Sun

Genes 2022, 13(8), 1481; https://doi.org/10.3390/genes13081481 - 19 Aug 2022

Cited by 7 | Viewed by 2256

Abstract

The WUSCHEL-related homeobox (WOX) proteins are a class of transcription factors exclusive to plants. They can promote cell division or inhibit stem cell differentiation to regulate plant growth and development. However, the WOX transcription factor genes in the monocotyledon Dendrobium catenatum Lindl. remain [...] Read more.

The WUSCHEL-related homeobox (WOX) proteins are a class of transcription factors exclusive to plants. They can promote cell division or inhibit stem cell differentiation to regulate plant growth and development. However, the WOX transcription factor genes in the monocotyledon Dendrobium catenatum Lindl. remain relatively uncharacterized. Specifically, the effects of phytohormones on their expression levels are unclear. In this study, we identified and analyzed 10 candidate DcaWOX transcription factor genes in D. catenatum. The DcaWOX family was divided into the modern/WUS, intermediate, and ancient clades. The subcellular localization analysis detected DcaWOX-GFP fusion proteins in the tobacco epidermal leaf cell nucleus. In DcaWOX, members of the WUS clade with the WUS-box motif can significantly activate the expression of TPL in vivo, while members of the intermediate and ancient clades cannot. The expression of the DcaWOX genes varied among the examined tissues. Moreover, the DcaWOX expression patterns were differentially affected by the phytohormone treatments, with differences detected even between homologs of the same gene. Furthermore, the gene expression patterns were consistent with the predicted cis-acting elements in the promoters. The above results suggest that DcaWOX may have an important role in its growth and development and resistance to stress. The results of this comprehensive investigation of the DcaWOX gene family provide the basis for future studies on the roles of WOX genes in D. catenatum. Full article

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

► Show Figures

Graphical abstract

13 pages, 6746 KiB

Open AccessEditor’s ChoiceArticle

Gene–microRNA Network Analysis Identified Seven Hub Genes in Association with Progression and Prognosis in Non-Small Cell Lung Cancer

by Zhiyuan Yang, Hongqi Wang, Zixin Zhao, Yunlong Jin, Zhengnan Zhang, Jiayi Tan and Fuyan Hu

Genes 2022, 13(8), 1480; https://doi.org/10.3390/genes13081480 - 19 Aug 2022

Cited by 5 | Viewed by 2462

Abstract

Introduction: Lung cancer is the leading cause of cancer deaths in the world and is usually divided into non-small cell lung cancer (NSCLC) and small cell lung cancer. NSCLC is dominant and accounts for 85% of the total cases. Currently, the therapeutic method [...] Read more.

Introduction: Lung cancer is the leading cause of cancer deaths in the world and is usually divided into non-small cell lung cancer (NSCLC) and small cell lung cancer. NSCLC is dominant and accounts for 85% of the total cases. Currently, the therapeutic method of NSCLC is not so satisfactory, and thus identification of new biomarkers is critical for new clinical therapy for this disease. Methods: Datasets of miRNA and gene expression were obtained from the NCBI database. The differentially expressed genes (DEGs) and miRNAs (DEMs) were analyzed by GEO2R tools. The DEG-DEM interaction was built via miRNA-targeted genes by miRWalk. Several hub genes were selected via network topological analysis in Cytoscape. Results: A set of 276 genes were found to be significantly differentially expressed in the three datasets. Functional enrichment by the DAVID tool showed that these 276 DEGs were significantly enriched in the term “cancer”, with a statistic p-value of 1.9 × 10⁻⁵. The subdivision analysis of the specific cancer types indicated that “lung cancer” occupies the largest category with a p-value of 2 × 10⁻³. Furthermore, 75 miRNAs were shown to be differentially expressed in three representative datasets. A group of 13 DEGs was selected by analysis of the miRNA–gene interaction of these DEGs and DEMs. The investigation of these 13 genes by GEPIA tools showed that eight of them had consistent results with NSCLC samples in the TCGA database. In addition, we applied the KMplot to conduct the survival analysis of these eight genes and found that seven of them have a significant effect on the prognosis survival of patients. We believe that this study could provide effective research clues for the prevention and treatment of non-small cell lung cancer. Full article

(This article belongs to the Special Issue Bioinformatics of Disease Genes)

► Show Figures

Figure 1

8 pages, 530 KiB

Open AccessReview

Emerging Role of microRNA Dysregulation in Diagnosis and Prognosis of Extrahepatic Cholangiocarcinoma

by Christian Prinz, Robin Frese, Mashiba Grams and Leonard Fehring

Genes 2022, 13(8), 1479; https://doi.org/10.3390/genes13081479 - 19 Aug 2022

Cited by 3 | Viewed by 1948

Abstract

Extrahepatic cholangiocarcinomas, also called bile duct carcinomas, represent a special entity in gastrointestinal tumors, and histological specimens of the tumors are often difficult to obtain. A special feature of these tumors is the strong neovascularization, which can often be seen in the endoluminal [...] Read more.

Extrahepatic cholangiocarcinomas, also called bile duct carcinomas, represent a special entity in gastrointestinal tumors, and histological specimens of the tumors are often difficult to obtain. A special feature of these tumors is the strong neovascularization, which can often be seen in the endoluminal endoscopic procedure called cholangioscopy, performed alone or in combination with laserscanning techniques. The additional analysis of microRNA expression profiles associated with inflammation and neovascularization in bile duct tumors or just the bile duct fluid of these patients could be of enormous additional importance. In particular, the dysregulation of microRNA in these cholangiocarcinomas (CCA) was previously reported to affect epigenetics (reported for miR-148, miR-152), inflammation (determined for miR-200, miR-125, and miR-605), and chemoresistance (miR-200b, 204) in patients with cholangiocarcinoma. More importantly, in the context of malignant neovascularization, well-defined microRNAs including miR-141, miR-181, miR-191, and miR-200b have been found to be dysregulated in cholangiocarcinoma and have been associated with an increased proliferation and vascularization in CCA. Thus, a panel of these microRNA molecules together with the clinical aspects of these tumors might facilitate tumor diagnosis and early treatment. To our knowledge, this is the first review that outlines the unique potential of combining macroscopic findings from cholangioscopy with microRNA expression. Full article

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

► Show Figures

Figure 1

6 pages, 203 KiB

Open AccessArticle

Predisposition to Myocardial Infarction Influenced by Interleukin 13 Gene Polymorphisms: A Case-Control Study

by Seyyed Fatemeh Hosseini, Khalil Khashei Varnamkhasti, Raziyeh Naeimi, Leila Naeimi and Sirous Naeimi

Genes 2022, 13(8), 1478; https://doi.org/10.3390/genes13081478 - 19 Aug 2022

Cited by 1 | Viewed by 1740

Abstract

Background: Additional inflammatory responses and subsequent damage—arising from enhance transcriptional activity or forming the more active protein due to existence of polymorphic sites in the pro-inflammatory cytokines gene loci—give rise to myocardial infarction susceptibility. Objectives: The aim of our study was to explore [...] Read more.

Background: Additional inflammatory responses and subsequent damage—arising from enhance transcriptional activity or forming the more active protein due to existence of polymorphic sites in the pro-inflammatory cytokines gene loci—give rise to myocardial infarction susceptibility. Objectives: The aim of our study was to explore whether two interleukin-13 gene polymorphisms (−1512A/C and +2044G/A) could serve as underpins genetic susceptibility of myocardial infarction. Methods: The Iranian population that belong to the Parsis ethnic group was involved in the present study. A total 250 patients with definite myocardial infarction—meeting hypertension, hypercholesterolemia, hyperglycemia, and coronary artery disease requirements—were recruited from the Shiraz urban hospitals. 250 age- and sex-matched healthy individuals without a history of cardiovascular disease and heart disease related risk factors constituted the control group. PCR-restriction fragment length polymorphism technique applied to genotyping at −1512A/C and +2044G/A loci. Hardy–Weinberg equilibrium test was performed (combined cases and controls). The differences of the genotype frequencies in cases and controls were analyzed using a chi-square test. Logistic regression analysis was performed to assess the association between the genotypes and most important risk factors for myocardial infarction. All statistical analyses were performed in SPSS Version 22.0. p-values below 0.05 were hailed as statistically significant. Results: Deviation from Hardy–Weinberg equilibrium was not significant in the −1512A/C locus. Statistically significant difference between our study groups was found in genotype frequency of the −1512A/C. This variant was found in associated with myocardial infarction risk factors. The +2044G/A polymorphism was not in Hardy–Weinberg equilibrium and no significant difference observed in the distribution of +2044G/A genotype frequency among cases and controls. However, further analysis revealed that this genotype associated with an increased susceptibility to myocardial infarction risk factors. Conclusions: The presence of interleukin-13 −1512A/C and +2044G/A gene polymorphisms underpin myocardial infarction predisposition in the ethnic Parsis of the Iranian population. Full article

(This article belongs to the Special Issue Genetics and Mechanistic Basis of Cardiomyopathies)

14 pages, 4598 KiB

Open AccessArticle

Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane

by Hui Zhang, Pingping Lin, Yanming Liu, Chaohua Huang, Guoqiang Huang, Hongtao Jiang, Liangnian Xu, Muqing Zhang, Zuhu Deng and Xinwang Zhao

Genes 2022, 13(8), 1477; https://doi.org/10.3390/genes13081477 - 19 Aug 2022

Cited by 11 | Viewed by 2492

Abstract

A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was [...] Read more.

A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation and Utilization of Plant Genetic Resources)

► Show Figures

Figure 1

20 pages, 4337 KiB

Open AccessEditor’s ChoiceArticle

IbMYB308, a Sweet Potato R2R3-MYB Gene, Improves Salt Stress Tolerance in Transgenic Tobacco

by Chong Wang, Lianjun Wang, Jian Lei, Shasha Chai, Xiaojie Jin, Yuyan Zou, Xiaoqiong Sun, Yuqin Mei, Xianliang Cheng, Xinsun Yang, Chunhai Jiao and Xiaohai Tian

Genes 2022, 13(8), 1476; https://doi.org/10.3390/genes13081476 - 18 Aug 2022

Cited by 18 | Viewed by 2932

Abstract

The MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factor family plays an important role in plant growth, development, and response to biotic and abiotic stresses. However, the gene functions of MYB transcription factors in sweet potato (Ipomoea batatas (L.) Lam) have [...] Read more.

The MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factor family plays an important role in plant growth, development, and response to biotic and abiotic stresses. However, the gene functions of MYB transcription factors in sweet potato (Ipomoea batatas (L.) Lam) have not been elucidated. In this study, an MYB transcription factor gene, IbMYB308, was identified and isolated from sweet potato. Multiple sequence alignment showed that IbMYB308 is a typical R2R3-MYB transcription factor. Further, quantitative real-time PCR (qRT-PCR) analysis revealed that IbMYB308 was expressed in root, stem, and, especially, leaf tissues. Moreover, it showed that IbMYB308 had a tissue-specific profile. The experiment also showed that the expression of IbMYB308 was induced by different abiotic stresses (20% PEG-6000, 200 mM NaCl, and 20% H₂O₂). After a 200 mM NaCl treatment, the expression of several stress-related genes (SOD, POD, APX, and P5CS) was upregulation in transgenic plants, and the CAT activity, POD activity, proline content, and protein content in transgenic tobacco had increased, while MDA content had decreased. In conclusion, this study demonstrated that IbMYB308 could improve salt stress tolerance in transgenic tobacco. These findings lay a foundation for future studies on the R2R3-MYB gene family of sweet potato and suggest that IbMYB308 could potentially be used as an important positive factor in transgenic plant breeding to improve salt stress tolerance in sweet potato plants. Full article

(This article belongs to the Special Issue Sweet Potato Genetics and Genomics)

► Show Figures

Figure 1

15 pages, 39180 KiB

Open AccessEditor’s ChoiceArticle

Cytogenetic Analysis in the Toad Species Bufo spinosus, Bufotes viridis and Epidalea calamita (Anura, Bufonidae) from the Mediterranean Area

by Katerina Guzmán-Markevich, Álvaro S. Roco, Adrián Ruiz-García and Mónica Bullejos

Genes 2022, 13(8), 1475; https://doi.org/10.3390/genes13081475 - 18 Aug 2022

Cited by 4 | Viewed by 2063

Abstract

Taxonomy in Bufonidae witnessed notable transformations. Bufotes viridis and Epidalea calamita, previously included in genus Bufo, were relocated in other genera, while the genus Bufo was restricted to members of the earlier Bufo bufo group. On the other hand, Bufo bufo [...] Read more.

Taxonomy in Bufonidae witnessed notable transformations. Bufotes viridis and Epidalea calamita, previously included in genus Bufo, were relocated in other genera, while the genus Bufo was restricted to members of the earlier Bufo bufo group. On the other hand, Bufo bufo sensu lato now includes four species: Bufo bufo, Bufo spinosus, Bufo verrucosissimus and Bufo eichwaldi. In this study, we examined three species of three Bufonidae genera (B. spinosus, B. viridis and E. calamita) by conventional (C-banding and Ag-NOR staining) and molecular (in situ hybridization with probes for telomeric repeats and rDNA loci, and genomic in situ hybridization (GISH)) cytogenetic methods. C-banding patterns are reported for the first time for B. spinosus and E. calamita populations from Iberian Peninsula and for B. viridis from Greece, and reveal several differences with the reported C-banded karyotypes described for other European populations of these species. Silver staining shows size heteromorphisms of the signals at the Nucleolar Organizing Region (NOR). By contrast, FISH with ribosomal probes only reveal size heteromorphism of rDNA sequences in E. calamita, suggesting that the differences observed after silver staining in B. spinosus and B. viridis should be attributed to differences in chromosomal condensation and/or gene activity rather than to differences in the copy number for ribosomal genes. Regarding telomeric repeats, E. calamita is the only species with interstitial telomeric sequences (ITS) located on centromeric regions, probably originated by accumulation of telomeric sequences in the centromeric heterochromatin. Finally, we analyzed the composition and distribution of repetitive sequences by genome in situ hybridization. These experiments reveal the accumulation of repetitive sequences in centromeric regions of the three species, although these sequences are not conserved when species from different genera are compared. Full article

(This article belongs to the Special Issue Chromosome Evolution and Karyotype Analysis)

► Show Figures

Figure 1

20 pages, 1276 KiB

Open AccessReview

Genetic and Epigenetic Regulation of Lipoxygenase Pathways and Reverse Cholesterol Transport in Atherogenesis

by Stanislav Kotlyarov

Genes 2022, 13(8), 1474; https://doi.org/10.3390/genes13081474 - 18 Aug 2022

Cited by 4 | Viewed by 2959

Abstract

Atherosclerosis is one of the most important medical and social problems of modern society. Atherosclerosis causes a large number of hospitalizations, disability, and mortality. A considerable amount of evidence suggests that inflammation is one of the key links in the pathogenesis of atherosclerosis. [...] Read more.

Atherosclerosis is one of the most important medical and social problems of modern society. Atherosclerosis causes a large number of hospitalizations, disability, and mortality. A considerable amount of evidence suggests that inflammation is one of the key links in the pathogenesis of atherosclerosis. Inflammation in the vascular wall has extensive cross-linkages with lipid metabolism, and lipid mediators act as a central link in the regulation of inflammation in the vascular wall. Data on the role of genetics and epigenetic factors in the development of atherosclerosis are of great interest. A growing body of evidence is strengthening the understanding of the significance of gene polymorphism, as well as gene expression dysregulation involved in cross-links between lipid metabolism and the innate immune system. A better understanding of the genetic basis and molecular mechanisms of disease pathogenesis is an important step towards solving the problems of its early diagnosis and treatment. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Vascular Disease)

► Show Figures

Graphical abstract

17 pages, 1122 KiB

Open AccessArticle

Life-Course Associations between Blood Pressure-Related Polygenic Risk Scores and Hypertension in the Bogalusa Heart Study

by Xiao Sun, Yang Pan, Ruiyuan Zhang, Ileana De Anda-Duran, Zhijie Huang, Changwei Li, Mengyao Shi, Alexander C. Razavi, Lydia A. Bazzano, Jiang He, Tamar Sofer and Tanika N. Kelly

Genes 2022, 13(8), 1473; https://doi.org/10.3390/genes13081473 - 18 Aug 2022

Cited by 3 | Viewed by 2155

Abstract

Genetic information may help to identify individuals at increased risk for hypertension in early life, prior to the manifestation of elevated blood pressure (BP) values. We examined 369 Black and 832 White Bogalusa Heart Study (BHS) participants recruited in childhood and followed for [...] Read more.

Genetic information may help to identify individuals at increased risk for hypertension in early life, prior to the manifestation of elevated blood pressure (BP) values. We examined 369 Black and 832 White Bogalusa Heart Study (BHS) participants recruited in childhood and followed for approximately 37 years. The multi-ancestry genome-wide polygenic risk scores (PRSs) for systolic BP (SBP), diastolic BP (DBP), and hypertension were tested for an association with incident hypertension and stage 2 hypertension using Cox proportional hazards models. Race-stratified analyses were adjusted for baseline age, age2, sex, body mass index, genetic principal components, and BP. In Black participants, each standard deviation increase in SBP and DBP PRS conferred a 38% (p = 0.009) and 22% (p = 0.02) increased risk of hypertension and a 74% (p < 0.001) and 50% (p < 0.001) increased risk of stage 2 hypertension, respectively, while no association was observed with the hypertension PRSs. In Whites, each standard deviation increase in SBP, DBP, and hypertension PRS conferred a 24% (p < 0.05), 29% (p = 0.01), and 25% (p < 0.001) increased risk of hypertension, and a 27% (p = 0.08), 29% (0.01), and 42% (p < 0.001) increased risk of stage 2 hypertension, respectively. The addition of BP PRSs to the covariable-only models generally improved the C-statistics (p < 0.05). Multi-ancestry BP PRSs demonstrate the utility of genomic information in the early life prediction of hypertension. Full article

(This article belongs to the Special Issue Genetic and Epigenetic Contributions to Hypertension and Blood Pressure Response to Interventions)

► Show Figures

Figure 1

17 pages, 2004 KiB

Open AccessArticle

Analysis of Common SNPs across Continents Reveals Major Genomic Differences between Human Populations

by Larisa Fedorova, Andrey Khrunin, Gennady Khvorykh, Jan Lim, Nicholas Thornton, Oleh A. Mulyar, Svetlana Limborska and Alexei Fedorov

Genes 2022, 13(8), 1472; https://doi.org/10.3390/genes13081472 - 18 Aug 2022

Cited by 7 | Viewed by 4857

Abstract

Common alleles tend to be more ancient than rare alleles. These common SNPs appeared thousands of years ago and reflect intricate human evolution including various adaptations, admixtures, and migration events. Eighty-four thousand abundant region-specific alleles (ARSAs) that are common in one continent but [...] Read more.

Common alleles tend to be more ancient than rare alleles. These common SNPs appeared thousands of years ago and reflect intricate human evolution including various adaptations, admixtures, and migration events. Eighty-four thousand abundant region-specific alleles (ARSAs) that are common in one continent but absent in the rest of the world have been characterized by processing 3100 genomes from 230 populations. Also computed were 17,446 polymorphic sites with regional absence of common alleles (RACAs), which are widespread globally but absent in one region. A majority of these region-specific SNPs were found in Africa. America has the second greatest number of ARSAs (3348) and is even ahead of Europe (1911). Surprisingly, East Asia has the highest number of RACAs (10,524) and the lowest number of ARSAs (362). ARSAs and RACAs have distinct compositions of ancestral versus derived alleles in different geographical regions, reflecting their unique evolution. Genes associated with ARSA and RACA SNPs were identified and their functions were analyzed. The core 100 genes shared by multiple populations and associated with region-specific natural selection were examined. The largest part of them (42%) are related to the nervous system. ARSA and RACA SNPs are important for both association and human evolution studies. Full article

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

► Show Figures

Figure 1

39 pages, 2813 KiB

Open AccessReview

Epigenetic Alterations in Sports-Related Injuries

by Maciej Tarnowski, Patrycja Tomasiak, Marta Tkacz, Katarzyna Zgutka and Katarzyna Piotrowska

Genes 2022, 13(8), 1471; https://doi.org/10.3390/genes13081471 - 17 Aug 2022

Cited by 7 | Viewed by 4070

Abstract

It is a well-known fact that physical activity benefits people of all age groups. However, highly intensive training, maladaptation, improper equipment, and lack of sufficient rest lead to contusions and sports-related injuries. From the perspectives of sports professionals and those performing regular–amateur sports [...] Read more.

It is a well-known fact that physical activity benefits people of all age groups. However, highly intensive training, maladaptation, improper equipment, and lack of sufficient rest lead to contusions and sports-related injuries. From the perspectives of sports professionals and those performing regular–amateur sports activities, it is important to maintain proper levels of training, without encountering frequent injuries. The bodily responses to physical stress and intensive physical activity are detected on many levels. Epigenetic modifications, including DNA methylation, histone protein methylation, acetylation, and miRNA expression occur in response to environmental changes and play fundamental roles in the regulation of cellular activities. In the current review, we summarise the available knowledge on epigenetic alterations present in tissues and organs (e.g., muscles, the brain, tendons, and bones) as a consequence of sports-related injuries. Epigenetic mechanism observations have the potential to become useful tools in sports medicine, as predictors of approaching pathophysiological alterations and injury biomarkers that have already taken place. Full article

(This article belongs to the Special Issue Sports Medicine, Injuries, and Genetics)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Genes, Volume 13, Issue 8 (August 2022) – 208 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI