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Feature Papers in Genes & Environments
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Feature Papers in Genes & Environments

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Genes & Environments".

Deadline for manuscript submissions: closed (20 March 2023) | Viewed by 7753

Special Issue Editors

Dr. Jean Molinier

E-Mail Website
Guest Editor
Institut de Biologie Moleculaire des Plantes, Strasbourg, France
Interests: DNA repair; small RNA; genome-epigenome dynamics; abiotic stress
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Colleen Glyde Julian

E-Mail Website
Guest Editor
School of Medicine, University of Colorado, Denver, CO, USA
Interests: gene-environment interaction; human adaptation to hypoxia; developmental programming; genomics; epigenomics

Special Issue Information

Dear Colleagues,

Improved understanding of the interaction between genetic, epigenetic, and environmental factors holds great promise to provide deeper insight into the mechanisms underlying phenotypic variation and adaptive potential, each having important implications for biomedical research as well as deciphering the natural world around us. This Special Issue, entitled “Genes & Environments” will represent a collection of high-quality, original research or review articles focusing on recent advances in the study of gene-environment interaction, including but not limited to the molecular mechanisms by which genomes and environments interact, the phenotypic effects of gene-environment interaction, and novel analytical methods or approaches. We would like to invite submissions from Editorial Board Members of Genes to contribute pioneering papers reflecting the latest progress in their research fields, as well as invited papers from relevant experts, and encourage invitees to extend this opportunity to colleagues with expertise in relevant to “Genes & Environments”. With your contributions, we aim to represent our Section as an attractive open-access publishing platform for cutting-edge research related to gene-environment interaction.

Dr. Jean Molinier
Prof. Dr. Colleen Glyde Julian
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (4 papers)

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Research

16 pages, 1025 KiB  
Article
Polymorphisms in Glutathione S-Transferase (GST) Genes Modify the Effect of Exposure to Maternal Smoking Metabolites in Pregnancy and Offspring DNA Methylation
by Parnian Kheirkhah Rahimabad, A. Daniel Jones, Hongmei Zhang, Su Chen, Yu Jiang, Susan Ewart, John W. Holloway, Hasan Arshad, Shakiba Eslamimehr, Robert Bruce and Wilfried Karmaus
Genes 2023, 14(8), 1644; https://doi.org/10.3390/genes14081644 - 18 Aug 2023
Viewed by 1490
Abstract
Maternal smoking in pregnancy (MSP) affects the offspring’s DNA methylation (DNAm). There is a lack of knowledge regarding individual differences in susceptibility to exposure to MSP. Glutathione S-transferase (GST) genes are involved in protection against harmful oxidants such as those found [...] Read more.
Maternal smoking in pregnancy (MSP) affects the offspring’s DNA methylation (DNAm). There is a lack of knowledge regarding individual differences in susceptibility to exposure to MSP. Glutathione S-transferase (GST) genes are involved in protection against harmful oxidants such as those found in cigarette smoke. This study aimed to test whether polymorphisms in GST genes influence the effect of MSP on offspring DNAm. Using data from the Isle of Wight birth cohort, we assessed the association of MSP and offspring DNAm in 493 mother-child dyads (251 male, 242 female) with the effect-modifying role of GST gene polymorphism (at rs506008, rs574344, rs12736389, rs3768490, rs1537234, and rs1695). MSP was assessed by levels of nicotine and its downstream metabolites (cotinine, norcotinine, and hydroxycotinine) in maternal sera. In males, associations of hydroxycotinine with DNAm at cg18473733, cg25949550, cg11647108, and cg01952185 and norcotinine with DNAm at cg09935388 were modified by GST gene polymorphisms (p-values < 0.05). In females, associations of hydroxycotinine with DNAm at cg12160087 and norcotinine with DNAm at cg18473733 were modified by GST gene polymorphisms (p-values < 0.05). Our study emphasizes the role of genetic polymorphism in GST genes in DNAm’s susceptibility to MSP. Full article
(This article belongs to the Special Issue Feature Papers in Genes & Environments)
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13 pages, 2667 KiB  
Article
Screening of Suitable Reference Genes for Immune Gene Expression Analysis Stimulated by Vibrio anguillarum and Copper Ions in Chinese Mitten Crab (Eriocheir sinensis)
by Fengyuan Yan, Hui Li, Xue Chen, Junjie Yu, Shengyan Su, Jianlin Li, Wei Ye and Yongkai Tang
Genes 2023, 14(5), 1099; https://doi.org/10.3390/genes14051099 - 17 May 2023
Viewed by 1519
Abstract
The reference gene expression is not always stable under different experimental conditions, and screening of suitable reference genes is a prerequisite in quantitative real-time polymerase chain reaction (qRT-PCR). In this study, we investigated gene selection, and the most stable reference gene for the [...] Read more.
The reference gene expression is not always stable under different experimental conditions, and screening of suitable reference genes is a prerequisite in quantitative real-time polymerase chain reaction (qRT-PCR). In this study, we investigated gene selection, and the most stable reference gene for the Chinese mitten crab (Eriocheir sinensis) was screened under the stimulation of Vibrio anguillarum and copper ions, respectively. Ten candidate reference genes were selected, including arginine kinase (AK), ubiquitin-conjugating enzyme E2b (UBE), glutathione S-transferase (GST), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1α (EF-1α), α-tubulin (α-TUB), heat shock protein 90 (HSP90), β-actin (β-ACTIN), elongation factor 2 (EF-2) and phosphoglucomutase 2 (PGM2). Expression levels of these reference genes were detected under the stimulation of V. anguillarum at different times (0 h, 6 h, 12 h, 24 h, 48 h and 72 h) and copper ions in different concentrations (11.08 mg/L, 2.77 mg/L, 0.69 mg/L and 0.17 mg/L). Four types of analytical software, namely geNorm, BestKeeper, NormFinder and Ref-Finder, were applied to evaluate the reference gene stability. The results showed that the stability of the 10 candidate reference genes was in the following order: AK > EF-1α > α-TUB > GAPDH > UBE > β-ACTIN > EF-2 > PGM2 > GST > HSP90 under V. anguillarum stimulation. It was GAPDH > β-ACTIN > α-TUB > PGM2 > EF-1α > EF-2 > AK > GST > UBE > HSP90 under copper ion stimulation. The expression of E. sinensis Peroxiredoxin4 (EsPrx4) was detected when the most stable and least stable internal reference genes were selected, respectively. The results showed that reference genes with different stability had great influence on the accurate results of the target gene expression. In the Chinese mitten crab (E. sinensis), AK and EF-1α were the most suitable reference genes under the stimulation of V. anguillarum. Under the stimulation of copper ions, GAPDH and β-ACTIN were the most suitable reference genes. This study provided important information for further research on immune genes in V. anguillarum or copper ion stimulation. Full article
(This article belongs to the Special Issue Feature Papers in Genes & Environments)
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15 pages, 1860 KiB  
Article
Variations in Growth and Photosynthetic Traits of Polyploid Poplar Hybrids and Clones in Northeast China
by Luping Jiang, Xiangzhu Xu, Qun Cai, Rui Han, Mulualem Tigabu, Tingbo Jiang and Xiyang Zhao
Genes 2022, 13(11), 2161; https://doi.org/10.3390/genes13112161 - 19 Nov 2022
Cited by 4 | Viewed by 2199
Abstract
To evaluate differences among 19 different ploidy hybrid poplar clones grown in northeast China, 21 traits related to growth traits and photosynthetic characteristics were detected and analyzed. Abundant phenotypic variations exist among and within populations, and these variations are the basis of forest [...] Read more.
To evaluate differences among 19 different ploidy hybrid poplar clones grown in northeast China, 21 traits related to growth traits and photosynthetic characteristics were detected and analyzed. Abundant phenotypic variations exist among and within populations, and these variations are the basis of forest tree genetic improvements. In this research, variance analysis showed that the traits except the net photosynthesis rate among the different ploidies and all the other traits exhibited significant differences among the ploidies or clones (p < 0.01). Estimation of phenotypic coefficients of variation, genotypic coefficients of variation, and repeatability is important for selecting superior materials. The larger the value, the greater the potential for material selection improvement. The repeatability of the different traits ranged from 0.88 to 0.99. The phenotypic and genotypic coefficients of variation of all the investigated traits ranged from 6.88% to 57.40% and from 4.85% to 42.89%, respectively. Correlation analysis showed that there were significant positive correlations between tree height, diameter, and volume. Transpiration rate, intercellular carbon dioxide concentration, and stomatal conductance were significantly positively correlated with each other but negatively correlated with instantaneous water use efficiency. Growth traits were weakly correlated with photosynthetic indexes. The rank correlation coefficient showed that most of the growth indicators reached a significant correlation level among different years (0.40–0.98), except 1-year-old tree height with 4-year-old tree height and 1-year-old ground diameter with 3-year-old tree height, which indicated the potential possibility for early selection of elite clones. Principal analysis results showed that the contribution rate of the first principal component was 46.606%, and 2-year-old tree height, 2-year-old ground diameter, 3-year-old tree height, 3-year-old ground diameter, 3-year-old diameter at breast height, 3-year-old volume, 4-year-old tree height, 4-year-old ground diameter, 4-year-old diameter at breast height, and 4-year-old volume showed higher vector values than other traits. With the method of multiple-trait comprehensive evaluation to evaluate clones, SX3.1, SY3.1, and XY4.2 were selected as elite clones, and the genetic gains of height, basal diameter, diameter at breast height, and volume of selected clones ranged from 12.85% to 64.87% in the fourth growth year. The results showed fundamental information for selecting superior poplar clones, which might provide new materials for the regeneration and improvement of forests in Northeast China. Full article
(This article belongs to the Special Issue Feature Papers in Genes & Environments)
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12 pages, 1953 KiB  
Article
Reference Gene Selection for qPCR Analysis in Schima superba under Abiotic Stress
by Jun Yao, Gang Zhu, Dongcheng Liang, Boxiang He, Yingli Wang, Yanling Cai and Qian Zhang
Genes 2022, 13(10), 1887; https://doi.org/10.3390/genes13101887 - 18 Oct 2022
Cited by 9 | Viewed by 1905
Abstract
Quantitative real-time PCR (qPCR) is an indispensable technique for gene expression analysis in modern molecular biology. The selection and evaluation of suitable reference genes is a prerequisite for accurate gene expression analysis. Schimasuperba is a valuable tree species that is environmentally adaptable [...] Read more.
Quantitative real-time PCR (qPCR) is an indispensable technique for gene expression analysis in modern molecular biology. The selection and evaluation of suitable reference genes is a prerequisite for accurate gene expression analysis. Schimasuperba is a valuable tree species that is environmentally adaptable and highly fire-resistant. In this study, 12 candidate reference genes were selected to check their stability of gene expression in different tissues under abiotic stresses: cold stress, salt stress, and drought stress by ΔCt, geNorm, NormFinder, BestKeeper, and RefFinder. The results indicated that AP-2 was the most stably expressed overall and for the cold stress and drought stress. eIF-5α gene expression was the most stable under the salt stress treatment, while UBQ expression was the most stable across mature leaves, shoots, stems, and roots. In contrast, UBC20, GAPDH, and TUB were the least stably expressed genes tested. This study delivers valid reference genes in S. superba under the different experimental conditions, providing an important resource for the subsequent elucidation of the abiotic stress adaptation mechanisms and genes with biological importance. Full article
(This article belongs to the Special Issue Feature Papers in Genes & Environments)
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