2 pages, 571 KiB  
Correction
Correction: Leske, B.A.; Biddulph, T.B. Estimating Effects of Radiation Frost on Wheat Using a Field-Based Frost Control Treatment to Stop Freezing Damage. Genes 2022, 13, 578
by Brenton A. Leske 1,2 and Thomas Ben Biddulph 1,*
1 The Department of Primary Industries and Regional Development, 3 Baron Hay Court, South Perth, WA 6151, Australia
2 The School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
Genes 2023, 14(3), 728; https://doi.org/10.3390/genes14030728 - 16 Mar 2023
Cited by 1 | Viewed by 1092
Abstract
In the original publication [...] Full article
(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)
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12 pages, 1205 KiB  
Article
Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data
by Draga Toncheva 1,2,*, Maria Marinova 3, Todor Chobanov 4 and Dimitar Serbezov 1
1 Medical Faculty, Department of Medical Genetics, Medical University of Sofia, Sofia 1000, Bulgaria
2 Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
3 Department of Computer Systems and Technologies, Faculty of Electronics and Automation, Technical University of Sofia, Branch Plovdiv, Plovdiv 4000, Bulgaria
4 Institute of Balkan Studies, Centre of Tracology at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
Genes 2023, 14(3), 727; https://doi.org/10.3390/genes14030727 - 16 Mar 2023
Viewed by 4080
Abstract
Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. [...] Read more.
Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans. Full article
(This article belongs to the Special Issue Advances in Ancient Genomes)
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12 pages, 5188 KiB  
Article
Design and Outcomes of a Novel Multidisciplinary Ophthalmic Genetics Clinic
by Bela Parekh 1,2, Adelyn Beil 3, Bridget Blevins 2, Adam Jacobson 2, Pamela Williams 2, Jeffrey W. Innis 3,4, Amanda Barone Pritchard 3 and Lev Prasov 2,4,*
1 University of Michigan Medical School, Ann Arbor, MI 48109, USA
2 Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
3 Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
4 Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
Genes 2023, 14(3), 726; https://doi.org/10.3390/genes14030726 - 15 Mar 2023
Cited by 4 | Viewed by 2228
Abstract
The Multidisciplinary Ophthalmic Genetics Clinic (MOGC) at the University of Michigan Kellogg Eye Center aims to provide medical and ophthalmic genetics care to patients with inherited ocular conditions. We have developed a clinical and referral workflow where each patient undergoes coordinated evaluation by [...] Read more.
The Multidisciplinary Ophthalmic Genetics Clinic (MOGC) at the University of Michigan Kellogg Eye Center aims to provide medical and ophthalmic genetics care to patients with inherited ocular conditions. We have developed a clinical and referral workflow where each patient undergoes coordinated evaluation by our multidisciplinary team followed by discussions on diagnosis, prognosis, and genetic testing. Testing approaches are specific to each patient and can be targeted (single-gene, gene panel), broad (chromosomal microarray, whole-exome sequencing), or a combination. We hypothesize that this clinic model improves patient outcomes and quality of care. A retrospective chart review of patients in the MOGC from July 2020 to October 2022 revealed that the most common referral diagnoses were congenital cataracts, optic neuropathy, and microphthalmia, with 52% syndromic cases. Within this patient cohort, we saw a 76% uptake for genetic testing, among which 33% received a diagnostic test result. Our results support a tailored approach to genetic testing for specific conditions. Through case examples, we highlight the power and impact of our clinic. By integrating ophthalmic care with medical genetics and counseling, the MOGC has not only helped solve individual patient diagnostic challenges but has aided the greater population in novel genetic discoveries and research towards targeted therapeutics. Full article
(This article belongs to the Special Issue Genetics of Eye Development and Disease)
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13 pages, 657 KiB  
Article
Expanding the Chromosomal Evolution Understanding of Lygaeioid True Bugs (Lygaeoidea, Pentatomomorpha, Heteroptera) by Classical and Molecular Cytogenetic Analysis
by Natalia V. Golub 1, Anna Maryańska-Nadachowska 2, Boris A. Anokhin 1 and Valentina G. Kuznetsova 1,*
1 Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, 199034 St. Petersburg, Russia
2 Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, Poland
Genes 2023, 14(3), 725; https://doi.org/10.3390/genes14030725 - 15 Mar 2023
Cited by 6 | Viewed by 2055
Abstract
The Lygaeoidea comprise about 4660 species in 790 genera and 16 families. Using standard chromosome staining and FISH with 18S rDNA and telomeric (TTAGG)n probes, we studied male karyotypes and meiosis in 10 species of Lygaeoidea belonging to eight genera of the [...] Read more.
The Lygaeoidea comprise about 4660 species in 790 genera and 16 families. Using standard chromosome staining and FISH with 18S rDNA and telomeric (TTAGG)n probes, we studied male karyotypes and meiosis in 10 species of Lygaeoidea belonging to eight genera of the families Blissidae, Cymidae, Heterogastridae, Lygaeidae, and Rhyparochromidae. Chromosome numbers were shown to range from 12 to 28, with 2n = 14 being predominant. All species have an XY system and all but one have a pair of m-chromosomes. The exception is Spilostethus saxatilis (Lygaeidae: Lygaeinae); in another species of Lygaeinae, Thunbergia floridulus, m-chromosomes were present, which represents the first finding for this subfamily. All species have an inverted sequence of sex chromosome divisions (“post-reduction”). The 18S rDNA loci were observed on one or both sex chromosomes in Kleidocerys resedae and Th. floridulus, respectively (Lygaeidae), while on an autosomal bivalent in all other species. The rDNA loci tended to be close to the end of the chromosome. Using (TTAGG)n—FISH, we were able to show for the first time that the Lygaeoidea lack the canonical “insect” telomere motif (TTAGG)n. We speculate that this ancestral motif is absent from the entire infraorder Pentatomomorpha being replaced by some other telomere repeat motif sequences. Full article
(This article belongs to the Special Issue State-of-the-Art in Insect Cytogenetics)
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12 pages, 8731 KiB  
Case Report
FGF9-Associated Multiple Synostoses Syndrome Type 3 in a Multigenerational Family
by Ariane Schmetz 1,*, Jörg Schaper 2, Simon Thelen 3, Majeed Rana 4, Thomas Klenzner 5, Katharina Schaumann 5, Jasmin Beygo 6, Harald Surowy 1, Hermann-Josef Lüdecke 1 and Dagmar Wieczorek 1,2
1 Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
2 Center for Rare Diseases, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
3 Department of Orthopedic and Trauma Surgery, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
4 Department of Oral, Maxillo- and Plastic Facial Surgery, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
5 Department of Otorhinolaryngology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
6 Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
Genes 2023, 14(3), 724; https://doi.org/10.3390/genes14030724 - 15 Mar 2023
Cited by 4 | Viewed by 1800
Abstract
Multiple synostoses syndrome (OMIM: #186500, #610017, #612961, #617898) is a genetically heterogeneous group of autosomal dominant diseases characterized by abnormal bone unions. The joint fusions frequently involve the hands, feet, elbows or vertebrae. Pathogenic variants in FGF9 have been associated with multiple synostoses [...] Read more.
Multiple synostoses syndrome (OMIM: #186500, #610017, #612961, #617898) is a genetically heterogeneous group of autosomal dominant diseases characterized by abnormal bone unions. The joint fusions frequently involve the hands, feet, elbows or vertebrae. Pathogenic variants in FGF9 have been associated with multiple synostoses syndrome type 3 (SYNS3). So far, only five different missense variants in FGF9 that cause SYNS3 have been reported in 18 affected individuals. Unlike other multiple synostoses syndromes, conductive hearing loss has not been reported in SYNS3. In this report, we describe the clinical and selected radiological findings in a large multigenerational family with a novel missense variant in FGF9: c.430T>C, p.(Trp144Arg). We extend the phenotypic spectrum of SYNS3 by suggesting that cleft palate and conductive hearing loss are part of the syndrome and highlight the high degree of intrafamilial phenotypic variability. These findings should be considered when counseling affected individuals. Full article
(This article belongs to the Special Issue Identification of Genes in Rare Syndromes)
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15 pages, 6491 KiB  
Article
Identification of Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs for Xp11 Translocation Renal Cell Carcinoma (RCC) Based on Whole-Transcriptome Sequencing
by Changqi Deng 1,†, Chengcheng Wei 1,†, Yaxin Hou 2, Ming Xiong 1, Dong Ni 1, Yu Huang 1, Miao Wang 1, Xiong Yang 1, Ke Chen 2,* and Zhaohui Chen 1,*
1 Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
2 Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
These authors contributed equally to this work.
Genes 2023, 14(3), 723; https://doi.org/10.3390/genes14030723 - 15 Mar 2023
Cited by 1 | Viewed by 2699
Abstract
We carried out whole transcriptome sequencing (WTS) on the tumor and the matching adjacent normal tissues from five patients having Xp11 translocation renal cell carcinoma (RCC). This was performed in terms of obtaining more understanding of the genomic panorama and molecular basis of [...] Read more.
We carried out whole transcriptome sequencing (WTS) on the tumor and the matching adjacent normal tissues from five patients having Xp11 translocation renal cell carcinoma (RCC). This was performed in terms of obtaining more understanding of the genomic panorama and molecular basis of this cancer. To examine gene-regulatory networks in XP11 translocation RCC, variance expression analysis was carried out, followed by functional enrichment analysis. Gene Expression Omnibus (GEO) of Xp11 translocation RCC data was used to validate the results. As per inclusion criteria, a total of 1886 differentially expressed mRNAs (DEmRNAs), 56 differentially expressed miRNAs (DEmiRNAs), 223 differentially expressed lncRNAs (DElncRNAs), and 1764 differentially expressed circRNAs (DEcircRNAs) were found. KEGG enrichment study of DEmiRNA, DElncRNA, and DEcircRNA target genes identified the function of protein processing in the endoplasmic reticulum, lysosome, and neutrophil-mediated immunity. Three subnetwork modules integrated from the PPI network also revealed the genes involved in protein processing in the endoplasmic reticulum, lysosome, and protein degradation processes, which may regulate the Xp11 translocation RCC process. The ceRNA complex network was created by Cytoscape, which included three upregulated circRNAs, five upregulated lncRNAs, 24 upregulated mRNAs, and two downregulated miRNAs (hsa-let-7d-5p and hsa-miR-433-3p). The genes as a prominent component of the complex ceRNA network may be key factors in the pathogenesis of Xp11 translocation RCC. Our findings clarified the genomic and transcriptional complexity of Xp11 translocation RCC while also pointing to possible new targets for Xp11 translocation RCC characterization. Full article
(This article belongs to the Section RNA)
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11 pages, 1595 KiB  
Article
Should Prenatal Chromosomal Microarray Analysis Be Offered for Pulmonary Atresia? A Single-Center Retrospective Study in China
by You Wang 1,2,†, Chunling Ma 1,2,†, Fang Fu 2, Hang Zhou 2, Ken Cheng 2,3, Ruibin Huang 2, Ru Li 2, Dongzhi Li 2 and Can Liao 1,2,*
1 The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
2 Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
3 School of Medicine, South China University of Technology, Guangzhou 510641, China
These authors contributed equally to this work.
Genes 2023, 14(3), 722; https://doi.org/10.3390/genes14030722 - 15 Mar 2023
Viewed by 1817
Abstract
(1) Objective: To evaluate the application of chromosomal microarray analysis (CMA) in fetuses with pulmonary atresia (PA) and to explore the risk factors for predicting chromosomal imbalances and adverse perinatal outcomes. (2) Methods: This study investigated 428 cases of PA singleton pregnancies that [...] Read more.
(1) Objective: To evaluate the application of chromosomal microarray analysis (CMA) in fetuses with pulmonary atresia (PA) and to explore the risk factors for predicting chromosomal imbalances and adverse perinatal outcomes. (2) Methods: This study investigated 428 cases of PA singleton pregnancies that were tested using CMA and quantitative fluorescent polymerase chain reaction (QF-PCR) as first-line genetic testing. The PA cases were divided into two groups: an isolated group and a non-isolated group. (3) Results: CMA revealed clinically relevant copy number variations (CNVs) in 9/139 (6.47%) PA fetuses, i.e., pathogenic copy number variations (pCNVs) in 8/139 (5.76%) fetuses and likely pathogenic CNVs in 1/139 (0.72%) fetuses. Stratified analysis showed that the incidence of clinically significant variants was higher in non-isolated PA fetuses than in isolated PA fetuses (12.50%, 6/48 vs. 3.30%, 3/91, p = 0.036). Regression analysis showed that a combination of other structural abnormalities at diagnosis of PA represented the principal risk factor for chromosomal imbalances (OR = 2.672). A combination of other structural abnormalities and a high maternal age increased the risk of adverse pregnancy outcomes in PA cases, including intrauterine fetal death (IUFD), termination of pregnancy (TOP), and preterm delivery. (4) Conclusions: The value of CMA for locating imbalanced genetic variations in fetuses with PA was highlighted by this study, particularly when combined with additional structural abnormalities. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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15 pages, 1337 KiB  
Article
Hypercholesterolemia in the Malaysian Cohort Participants: Genetic and Non-Genetic Risk Factors
by Nor Azian Abdul Murad 1, Yusuf Mohammad Noor 1,2, Zam Zureena Mohd. Rani 1, Siti Aishah Sulaiman 1, Yock Ping Chow 1, Noraidatulakma Abdullah 1, Norfazilah Ahmad 1,3, Norliza Ismail 1, Nazihah Abdul Jalal 1, Mohd. Arman Kamaruddin 1, Amalia Afzan Saperi 1 and Rahman Jamal 1,*
1 UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Cheras, Kuala Lumpur 56000, Malaysia
2 Malaysian Genome Institute (MGI), Jalan Bangi, Bangi 43000, Malaysia
3 Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Cheras, Kuala Lumpur 56000, Malaysia
Genes 2023, 14(3), 721; https://doi.org/10.3390/genes14030721 - 15 Mar 2023
Cited by 4 | Viewed by 3787
Abstract
Hypercholesterolemia was prevalent in 44.9% of The Malaysian Cohort participants, of which 51% were Malay. This study aimed to identify the variants involved in hypercholesterolemia among Malays and to determine the association between genetic and non-genetic risk factors. This nested case–control study included [...] Read more.
Hypercholesterolemia was prevalent in 44.9% of The Malaysian Cohort participants, of which 51% were Malay. This study aimed to identify the variants involved in hypercholesterolemia among Malays and to determine the association between genetic and non-genetic risk factors. This nested case–control study included 25 Malay participants with the highest low-density lipoprotein cholesterol (LDL-C, >4.9 mmol/L) and total cholesterol (TC, >7.5 mmol/L) and 25 participants with the lowest LDL-C/TC. Genomic DNA was extracted, and whole-exome sequencing was performed using the Ion ProtonTM system. All variants were annotated, filtered, and cross-referenced against publicly available databases. Forty-five selected variants were genotyped in 677 TMC Malay participants using the MassARRAY® System. The association between genetic and non-genetic risk factors was determined using logistic regression analysis. Age, fasting blood glucose, tobacco use, and family history of hyperlipidemia were significantly associated with hypercholesterolemia. Participants with the novel OSBPL7 (oxysterol-binding protein-like 7) c.651_652del variant had 17 times higher odds for hypercholesterolemia. Type 2 diabetes patients on medication and those with PCSK9 (proprotein convertase subtilisin/kexin type 9) rs151193009 had low odds for hypercholesterolemia. Genetic predisposition can interact with non-genetic factors to increase hypercholesterolemia risk in Malaysian Malays. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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7 pages, 1039 KiB  
Case Report
Live Birth of a Healthy Child in a Couple with Identical mtDNA Carrying a Pathogenic c.471_477delTTTAAAAinsG Variant in the MOCS2 Gene
by Maria Tofilo 1,2, Natalia Voronova 1, Leila Nigmatullina 1,2,3, Elena Kuznetsova 3, Valeria Timonina 4, Bogdan Efimenko 5, Oybek Turgunkhujaev 6,7, Svetlana Avdeichik 2,3, Muhammad Ansar 8,9, Konstantin Popadin 4,5,10, Anastasia Kirillova 1,3,* and Ilya Mazunin 1,*
1 Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
2 Medical Genomics, 170100 Tver, Russia
3 Fomin Clinics, 119192 Moscow, Russia
4 School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
5 Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia
6 Neurology Department, Semeynaya Clinic, 121059 Moscow, Russia
7 A.I. Burnazyan Federal Medical and Biophysical Center, 123098 Moscow, Russia
8 Department of Ophthalmology, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, University of Lausanne, 1015 Lausanne, Switzerland
9 Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi 74200, Pakistan
10 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
Genes 2023, 14(3), 720; https://doi.org/10.3390/genes14030720 - 15 Mar 2023
Viewed by 2108
Abstract
Molybdenum cofactor deficiency type B (MOCODB; #252160) is an autosomal recessive metabolic disorder that has only been described in 37 affected patients. In this report, we describe the presence of an in-frame homozygous variant (c.471_477delTTTAAAAinsG) in the MOCS2 gene in an affected child, [...] Read more.
Molybdenum cofactor deficiency type B (MOCODB; #252160) is an autosomal recessive metabolic disorder that has only been described in 37 affected patients. In this report, we describe the presence of an in-frame homozygous variant (c.471_477delTTTAAAAinsG) in the MOCS2 gene in an affected child, diagnosed with Ohtahara syndrome according to the clinical manifestations. The analysis of the three-dimensional structure of the protein and the amino acid substitutions suggested the pathogenicity of this mutation. To prevent transmitting this mutation to the next generation, we used preimplantation genetic testing for the monogenic disorders (PGT-M) protocol to select MOCS2 gene mutant-free embryos for transfer in an in vitro fertilization (IVF) program. As a result, a healthy child was born. Interestingly, both parents of the proband shared an identical mitochondrial (mt) DNA control region, assuming their close relationship and thus suggesting that both copies of the nuclear rare variant c.471_477delTTTAAAAinsG may have been transmitted from the same female ancestor. Our estimation of the a priori probability of meeting individuals with the same mtDNA haplotype confirms the assumption of a possible distant maternal relationship among the proband’s direct relatives. Full article
(This article belongs to the Special Issue Next Generation Sequencing in Clinical Diagnostics)
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13 pages, 2243 KiB  
Article
Marker Assisted Introgression of Resistance Genes and Phenotypic Evaluation Enabled Identification of Durable and Broad-Spectrum Blast Resistance in Elite Rice Cultivar, CO 51
by Thiyagarajan Thulasinathan 1, Bharathi Ayyenar 1, Rohit Kambale 1, Sudha Manickam 1, Gopalakrishnan Chellappan 2, Priyanka Shanmugavel 1, Manikanda B. Narayanan 1, Manonmani Swaminathan 2 and Raveendran Muthurajan 1,*
1 Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
2 Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India
Genes 2023, 14(3), 719; https://doi.org/10.3390/genes14030719 - 15 Mar 2023
Cited by 12 | Viewed by 3060
Abstract
Across the globe, rice cultivation is seriously affected by blast disease, caused by Magnaporthe oryzae. This disease has caused heavy yield loss to farmers over the past few years. In this background, the most affordable and eco-friendly strategy is to introgress blast-resistant [...] Read more.
Across the globe, rice cultivation is seriously affected by blast disease, caused by Magnaporthe oryzae. This disease has caused heavy yield loss to farmers over the past few years. In this background, the most affordable and eco-friendly strategy is to introgress blast-resistant genes from donors into elite rice cultivars. However, it is not only challenging to evolve such resistance lines using conventional breeding approaches, but also a time-consuming process. Therefore, the marker-assisted introduction of resistance genes has been proposed as a rapid strategy to develop durable and broad-spectrum resistance in rice cultivars. The current study highlights the successful introgression of a blast resistance gene, i.e., Pi9, into CO 51, an elite rice cultivar which already has another resistance gene named Pi54. The presence of two blast resistance genes in the advanced backcross breeding materials (BC2F2:3) was confirmed in this study through a foreground selection method using functional markers such as NBS4 and Pi54MAS. The selected positive introgressed lines were further genotyped for background selection with 55 SSR markers that are specific to CO 51. Consequently, both Pi9 as well as Pi54 pyramided lines, with 82.7% to 88.1% of the recurrent parent genome recovery, were identified and the selected lines were evaluated under hotspot. The analysis outcomes found that both the lines possessed a high level of resistance against blast disease during the seedling stage itself. In addition to this, it was also noticed that the advanced breeding rice lines that carry Pi9 + Pi54 were effective in nature and exhibited a higher degree of resistance against blast disease compared to the lines that were introgressed with a single blast resistance gene. Thus, the current study demonstrates a rapid and a successful introgression and pyramiding of two blast resistance genes, with the help of markers, into a susceptible yet high-yielding elite rice cultivar within a short period of time. Those gene pyramided rice lines can be employed as donors to introgress the blast-resistant genes in other popular susceptible cultivars. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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14 pages, 494 KiB  
Article
Association of NEF2L2 Rs35652124 Polymorphism with Nrf2 Induction and Genotoxic Stress Biomarkers in Autism
by Lev N. Porokhovnik 1, Vladimir M. Pisarev 2,*, Anastasia G. Chumachenko 2, Julia M. Chudakova 1, Elizaveta S. Ershova 1, Natalia N. Veiko 1, Natalia L. Gorbachevskaya 3, Uliana A. Mamokhina 4, Alexander B. Sorokin 4,5, Anna Ya. Basova 6, Mikhail S. Lapshin 6, Vera L. Izhevskaya 1 and Svetlana V. Kostyuk 1
1 Research Centre for Medical Genetics, 1 Moskvorechie Street, 115478 Moscow, Russia
2 Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 25 Petrovka Street, 107031 Moscow, Russia
3 Mental Health Research Center, 34 Kashirskoe highway, 115478 Moscow, Russia
4 Federal Resource Center for Organization of Comprehensive Support to Children with Autism Spectrum Disorders, 29 Sretenka Street, 127051 Moscow, Russia
5 Haskins Laboratories, 300 George Street, New Haven, CT 06511, USA
6 G.E. Sukhareva Research and Practical Center of Children and Adolescents Mental Health, 21A Fifth Donskoy Drive, 119334 Moscow, Russia
Genes 2023, 14(3), 718; https://doi.org/10.3390/genes14030718 - 15 Mar 2023
Cited by 6 | Viewed by 2625
Abstract
Increased oxidative/genotoxic stress is known to impact the pathophysiology of ASD (autism spectrum disorder). Clinical studies, however, reported limited, heterogeneous but promising responses to treatment with antioxidant remedies. We determined whether the functional polymorphism of the Nrf2 gene, master regulator of anti-oxidant adaptive [...] Read more.
Increased oxidative/genotoxic stress is known to impact the pathophysiology of ASD (autism spectrum disorder). Clinical studies, however, reported limited, heterogeneous but promising responses to treatment with antioxidant remedies. We determined whether the functional polymorphism of the Nrf2 gene, master regulator of anti-oxidant adaptive reactions to genotoxic stress, links to the genotoxic stress responses and to an in vitro effect of a NRF2 inductor in ASD children. Oxidative stress biomarkers, adaptive responses to genotoxic/oxidative stress, levels of master antioxidant regulator Nrf2 and its active form pNrf2 before and after inducing by dimethyl fumarate (DMF), and promotor rs35652124 polymorphism of NFE2L2 gene encoding Nrf2 were studied in children with ASD (n = 179). Controls included healthy adults (n = 101). Adaptive responses to genotoxicity as indicated by H2AX and cytoprotection by NRF2 contents positively correlated in ASD children with a Spearman coefficient of R = 0.479 in T+, but not CC genotypes. ASD children with NRF2 rs35652124 CC genotype demonstrated significantly higher H2AX content (0.652 vs. 0.499 in T+) and pNrf2 induction by DMF, lowered 8-oxo-dG concentration in plasma and higher cfDNA/plasma nuclease activity ratio. Our pilot findings suggest that in ASD children the NEF2L2 rs35652124 polymorphism impacts adaptive responses that may potentially link to ASD severity. Our data warrant further studies to reveal the potential for NEF2L2 genotype-specific and age-dependent repurposing of DMF and/or other NRF2-inducing drugs. Full article
(This article belongs to the Special Issue Genetics of Complex Human Disease)
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14 pages, 1406 KiB  
Article
Mutational Spectrum of the ABCA12 Gene and Genotype–Phenotype Correlation in a Cohort of 64 Patients with Autosomal Recessive Congenital Ichthyosis
by Alrun Hotz 1,2,3, Julia Kopp 1, Emmanuelle Bourrat 4, Vinzenz Oji 3,5, Kira Süßmuth 5, Katalin Komlosi 1,2,3, Bakar Bouadjar 6, Iliana Tantcheva-Poór 7, Maritta Hellström Pigg 8, Regina C. Betz 9, Kathrin Giehl 3,10, Fiona Schedel 5, Lisa Weibel 11, Solveig Schulz 12, Dora V. Stölzl 13, Gianluca Tadini 3,14, Emine Demiral 15, Karin Berggard 16, Andreas D. Zimmer 1, Svenja Alter 1,2,3 and Judith Fischer 1,2,3,*add Show full author list remove Hide full author list
1 Institute of Human Genetics, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
2 Center for Cornification Disorders, Freiburg Center for Rare Diseases, Medical Center, University of Freiburg, 79106 Freiburg, Germany
3 European Reference Networks (ERN Skin), 75015 Paris, France
4 Department of Dermatology, Reference Center for Rare Skin Diseases MAGEC, Saint Louis Hospital AP-HP, 75015 Paris, France
5 Department of Dermatology and Venereology, Muenster University Medical Center, 48149 Muenster, Germany
6 Department of Dermatology, CHU of Bab-El-Oued Algiers, Algiers 16008, Algeria
7 Department of Dermatology and Venereology, Faculty of Medicine and University Hospital, University of Cologne, 50937 Cologne, Germany
8 Clinical Genetics, Karolinska University Hospital, 171 64 Solna, Sweden
9 Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, 53127 Bonn, Germany
10 Department of Dermatology, Venerology und Allergology, University Hospital of Munich, 80337 Munich, Germany
11 Pediatric Skin Center, Dermatology Department, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
12 Synlab Medical Practice for Human Genetics Jena, 07747 Jena, Germany
13 Center for Inflammatory Skin Diseases, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
14 Pediatric Dermatology Unit, Department of Pathophysiology and Transplantation, Fondazione IRCCS Ca’ Granda—Ospedale Maggiore Policlinico, University of Milan, 20122 Milan, Italy
15 Department of Medical Genetics, Inonu University School of Medicine, 44280 Malatya, Turkey
16 Department of Dermatology and Venereology, Skåne University Hospital, 221 85 Lund, Sweden
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Genes 2023, 14(3), 717; https://doi.org/10.3390/genes14030717 - 15 Mar 2023
Cited by 13 | Viewed by 7147
Abstract
Autosomal recessive congenital ichthyosis (ARCI) is a non-syndromic congenital disorder of cornification characterized by abnormal scaling of the skin. The three major phenotypes are lamellar ichthyosis, congenital ichthyosiform erythroderma, and harlequin ichthyosis. ARCI is caused by biallelic mutations in ABCA12, ALOX12B, [...] Read more.
Autosomal recessive congenital ichthyosis (ARCI) is a non-syndromic congenital disorder of cornification characterized by abnormal scaling of the skin. The three major phenotypes are lamellar ichthyosis, congenital ichthyosiform erythroderma, and harlequin ichthyosis. ARCI is caused by biallelic mutations in ABCA12, ALOX12B, ALOXE3, CERS3, CYP4F22, NIPAL4, PNPLA1, SDR9C7, SULT2B1, and TGM1. The most severe form of ARCI, harlequin ichthyosis, is caused by mutations in ABCA12. Mutations in this gene can also lead to congenital ichthyosiform erythroderma or lamellar ichthyosis. We present a large cohort of 64 patients affected with ARCI carrying biallelic mutations in ABCA12. Our study comprises 34 novel mutations in ABCA12, expanding the mutational spectrum of ABCA12-associated ARCI up to 217 mutations. Within these we found the possible mutational hotspots c.4541G>A, p.(Arg1514His) and c.4139A>G, p.(Asn1380Ser). A correlation of the phenotype with the effect of the genetic mutation on protein function is demonstrated. Loss-of-function mutations on both alleles generally result in harlequin ichthyosis, whereas biallelic missense mutations mainly lead to CIE or LI. Full article
(This article belongs to the Special Issue Feature Papers in Human Genomics and Genetic Diseases 2023)
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17 pages, 942 KiB  
Article
Exploring the Lifetime Effect of Children on Wellbeing Using Two-Sample Mendelian Randomisation
by Benjamin Woolf 1,2,3,*, Hannah M. Sallis 2,4,† and Marcus R. Munafò 1,2,†
1 School of Psychological Science, University of Bristol, Bristol BS8 1TU, UK
2 MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
3 MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 1TN, UK
4 Centre for Academic Mental Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
These authors contributed equally to this work.
Genes 2023, 14(3), 716; https://doi.org/10.3390/genes14030716 - 14 Mar 2023
Cited by 3 | Viewed by 2935
Abstract
Background: Observational research implies a negative effect of having children on wellbeing. Objectives: To provide Mendelian randomisation evidence of the effect of having children on parental wellbeing. Design: Two-sample Mendelian randomisation. Setting: Non-clinical European ancestry participants. Participants: We used the UK Biobank (460,654 [...] Read more.
Background: Observational research implies a negative effect of having children on wellbeing. Objectives: To provide Mendelian randomisation evidence of the effect of having children on parental wellbeing. Design: Two-sample Mendelian randomisation. Setting: Non-clinical European ancestry participants. Participants: We used the UK Biobank (460,654 male and female European ancestry participants) as a source of genotype-exposure associations, the Social Science Genetics Consortia (SSGAC) (298,420 male and female European ancestry participants), and the Within-Family Consortia (effective sample of 22,656 male and female European ancestry participants) as sources of genotype-outcome associations. Interventions: The lifetime effect of an increase in the genetic liability to having children. Primary and secondary outcome measures: The primary analysis was an inverse variance weighed analysis of subjective wellbeing measured in the 2016 SSGAC Genome Wide Association Study (GWAS). Secondary outcomes included pleiotropy robust estimators applied in the SSGAC and an analysis using the Within-Family consortia GWAS. Results: We did not find strong evidence of a negative (standard deviation) change in wellbeing (β = 0.153 (95% CI: −0.210 to 0.516) per child parented. Secondary outcomes were generally slightly deflated (e.g., −0.049 [95% CI: −0.533 to 0.435] for the Within-Family Consortia and 0.090 [95% CI: −0.167 to 0.347] for weighted median), implying the presence of some residual confounding and pleiotropy. Conclusions: Contrary to the existing literature, our results are not compatible with a measurable negative effect of number of children on the average wellbeing of a parent over their life course. However, we were unable to explore non-linearities, interactions, or time-varying effects. Full article
(This article belongs to the Special Issue Statistical Methods for Genetic Epidemiology)
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20 pages, 1252 KiB  
Review
Telomere Length Changes in Cancer: Insights on Carcinogenesis and Potential for Non-Invasive Diagnostic Strategies
by Zuzana Holesova 1, Lucia Krasnicanova 2, Rami Saade 2, Ondrej Pös 1,3, Jaroslav Budis 1,3,4, Juraj Gazdarica 1,4,5, Vanda Repiska 2,6 and Tomas Szemes 1,3,5,*
1 Geneton s.r.o., 84104 Bratislava, Slovakia
2 Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
3 Comenius University Science Park, Comenius University, 84104 Bratislava, Slovakia
4 Slovak Centre of Scientific and Technical Information, 81104 Bratislava, Slovakia
5 Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 84205 Bratislava, Slovakia
6 Medirex Group Academy, n.o., 94905 Nitra, Slovakia
Genes 2023, 14(3), 715; https://doi.org/10.3390/genes14030715 - 14 Mar 2023
Cited by 20 | Viewed by 6893
Abstract
Telomere dynamics play a crucial role in the maintenance of chromosome integrity; changes in telomere length may thus contribute to the development of various diseases including cancer. Understanding the role of telomeric DNA in carcinogenesis and detecting the presence of cell-free telomeric DNA [...] Read more.
Telomere dynamics play a crucial role in the maintenance of chromosome integrity; changes in telomere length may thus contribute to the development of various diseases including cancer. Understanding the role of telomeric DNA in carcinogenesis and detecting the presence of cell-free telomeric DNA (cf-telDNA) in body fluids offer a potential biomarker for novel cancer screening and diagnostic strategies. Liquid biopsy is becoming increasingly popular due to its undeniable benefits over conventional invasive methods. However, the organization and function of cf-telDNA in the extracellular milieu are understudied. This paper provides a review based on 3,398,017 cancer patients, patients with other conditions, and control individuals with the aim to shed more light on the inconsistent nature of telomere lengthening/shortening in oncological contexts. To gain a better understanding of biological factors (e.g., telomerase activation, alternative lengthening of telomeres) affecting telomere homeostasis across different types of cancer, we summarize mechanisms responsible for telomere length maintenance. In conclusion, we compare tissue- and liquid biopsy-based approaches in cancer assessment and provide a brief outlook on the methodology used for telomere length evaluation, highlighting the advances of state-of-the-art approaches in the field. Full article
(This article belongs to the Special Issue DNA Damage and Repair at the Crossroad with Telomeres)
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16 pages, 2248 KiB  
Article
An Investigation into Compound Likelihood Ratios for Forensic DNA Mixtures
by Richard Wivell 1,*, Hannah Kelly 1, Jason Kokoszka 2, Jace Daniels 2, Laura Dickson 3, John Buckleton 1,4 and Jo-Anne Bright 1
1 Institute of Environmental Science and Research Limited, Private Bag 92012, Auckland, New Zealand
2 Alabama Department of Forensic Sciences, 1 Forensic Drive, Mobile, AL 36617, USA
3 Washoe County Sherriff’s Office, Forensic Science Division, 911 Parr Blvd, Reno, NV 89512, USA
4 Department of Statistics, University of Auckland, Private Bag 92019, Auckland, New Zealand
Genes 2023, 14(3), 714; https://doi.org/10.3390/genes14030714 - 14 Mar 2023
Cited by 1 | Viewed by 2915
Abstract
Simple propositions are defined as those with one POI and the remaining contributors unknown under Hp and all unknown contributors under Ha. Conditional propositions are defined as those with one POI, one or more assumed contributors, and the remaining contributors [...] Read more.
Simple propositions are defined as those with one POI and the remaining contributors unknown under Hp and all unknown contributors under Ha. Conditional propositions are defined as those with one POI, one or more assumed contributors, and the remaining contributors (if any) unknown under Hp, and the assumed contributor(s) and N unknown contributors under Ha. In this study, compound propositions are those with multiple POI and the remaining contributors unknown under Hp and all unknown contributors under Ha. We study the performance of these three proposition sets on thirty-two samples (two laboratories × four NOCs × four mixtures) consisting of four mixtures, each with N = 2, N = 3, N = 4, and N = 5 contributors using the probabilistic genotyping software, STRmix™. In this study, it was found that conditional propositions have a much higher ability to differentiate true from false donors than simple propositions. Compound propositions can misstate the weight of evidence given the propositions strongly in either direction. Full article
(This article belongs to the Special Issue Forensic DNA Mixture Interpretation and Probabilistic Genotyping)
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