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Mishra S, Duarte GT, Horemans N, Ruytinx J, Gudkov D, Danchenko M. Complexity of responses to ionizing radiation in plants, and the impact on interacting biotic factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171567. [PMID: 38460702 DOI: 10.1016/j.scitotenv.2024.171567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
In nature, plants are simultaneously exposed to different abiotic (e.g., heat, drought, and salinity) and biotic (e.g., bacteria, fungi, and insects) stresses. Climate change and anthropogenic pressure are expected to intensify the frequency of stress factors. Although plants are well equipped with unique and common defense systems protecting against stressors, they may compromise their growth and development for survival in such challenging environments. Ionizing radiation is a peculiar stress factor capable of causing clustered damage. Radionuclides are both naturally present on the planet and produced by human activities. Natural and artificial radioactivity affects plants on molecular, biochemical, cellular, physiological, populational, and transgenerational levels. Moreover, the fitness of pests, pathogens, and symbionts is concomitantly challenged in radiologically contaminated areas. Plant responses to artificial acute ionizing radiation exposure and laboratory-simulated or field chronic exposure are often discordant. Acute or chronic ionizing radiation exposure may occasionally prime the defense system of plants to better tolerate the biotic stress or could often exhaust their metabolic reserves, making plants more susceptible to pests and pathogens. Currently, these alternatives are only marginally explored. Our review summarizes the available literature on the responses of host plants, biotic factors, and their interaction to ionizing radiation exposure. Such systematic analysis contributes to improved risk assessment in radiologically contaminated areas.
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Affiliation(s)
- Shubhi Mishra
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia
| | - Gustavo Turqueto Duarte
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium
| | - Nele Horemans
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium; Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Joske Ruytinx
- Department of Bio-engineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dmitri Gudkov
- Institute of Hydrobiology, National Academy of Sciences of Ukraine, 04210 Kyiv, Ukraine
| | - Maksym Danchenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia.
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Gemeinholzer B, Rupp O, Becker A, Strickert M, Müller CM. Genotyping by sequencing and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.). Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1003057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The important worldwide forage crop red clover (Trifolium pratense L.) is widely cultivated as cattle feed and for soil improvement. Wild populations and landraces have great natural diversity that could be used to improve cultivated red clover. However, to date, there is still insufficient knowledge about the natural genetic and phenotypic diversity of the species. Here, we developed a low-cost complexity reduced mRNA analysis (mRNA-GBS) and compared the results with population genetic (GBS) and previously published mRNA-Seq data, to assess whether analysis of intraspecific variation within and between populations and transcriptome responses is possible simultaneously. The mRNA-GBS approach was successful. SNP analyses from the mRNA-GBS approach revealed comparable patterns to the GBS results, but due to site-specific multifactorial influences of environmental responses as well as conceptual and methodological limitations of mRNA-GBS, it was not possible to link transcriptome analyses with reduced complexity and sequencing depth to previously published greenhouse and field expression studies. Nevertheless, the use of short sequences upstream of the poly(A) tail of mRNA to reduce complexity are promising approaches that combine population genetics and expression profiling to analyze many individuals with trait differences simultaneously and cost-effectively, even in non-model species. Nevertheless, our study design across different regions in Germany was also challenging. The use of reduced complexity differential expression analyses most likely overlays site-specific patterns due to highly complex plant responses under natural conditions.
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Transposable Elements in the Revealing of Polymorphism-Based Differences in the Seeds of Flax Varieties Grown in Remediated Chernobyl Area. PLANTS 2022; 11:plants11192567. [PMID: 36235434 PMCID: PMC9571286 DOI: 10.3390/plants11192567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
The nuclear reactor accident in Chernobyl, Ukraine, resulted in effects both locally and farther away. Most of the contaminated areas were the agricultural fields and forests. Experimental fields were established near Chernobyl—radioactively contaminated fields localized 5 km from Chernobyl Nuclear Power Plant as well as the remediated soil that is localized directly in the Chernobyl town. Two flax varieties growing under chronic exposition to ionizing radiation were used for this study—the local Ukrainian variety Kyivskyi and a commercial variety Bethune. The screening of the length polymorphism generated by transposable elements insertions were performed. All known types of common flax transposon, retrotransposons and iPBS approach were used. In the iPBS multiplex analyze, for the Kyivskyi variety, a unique addition was found in the seeds from the radioactive contaminated field and for the Bethune variety, a total of five amplicon additions were obtained and one deletion. For the TRIM Cassandra fingerprints, two amplicon additions were generated in the seeds from radioactive contaminated fields for the Bethune variety. In summary, the obtained data represent the genetic diversity between control and irradiated subgroups of flax seeds from Chernobyl area and the presence of activated transposable elements due to the irradiation stress.
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Anderson D, Kaneko S, Harshman A, Okuda K, Takagi T, Chinn S, Beasley JC, Nanba K, Ishiniwa H, Hinton TG. Radiocesium accumulation and germline mutations in chronically exposed wild boar from Fukushima, with radiation doses to human consumers of contaminated meat. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119359. [PMID: 35487469 DOI: 10.1016/j.envpol.2022.119359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Genetic effects and radioactive contamination of large mammals, including wild boar (Sus scrofa), have been studied in Japan because of dispersal of radionuclides from the Fukushima Dai-ichi Nuclear Power Plant in 2011. Such studies have generally demonstrated a declining trend in measured radiocesium body burdens in wildlife. Estimating radiation exposure to wildlife is important to understand possible long-term impacts. Here, radiation exposure was evaluated in 307 wild boar inhabiting radioactively contaminated areas (50-8000 kBq m-2) in Fukushima Prefecture from 2016 to 2019, and genetic markers were examined to assess possible germline mutations caused by chronic radiation exposures to several generations of wild boar. Internal Cs activity concentrations in boar remained high in areas near the power plant with the highest concentration of 54 kBq kg-1 measured in 2019. Total dose rates to wild boar ranged from 0.02 to 36 μGy h-1, which was primarily attributed to external radiation exposure, and dose rates to the maximally exposed animals were above the generic no-effects benchmark of 10 μGy h-1. Using the estimated age of each animal, lifetime radiation doses ranged from <0.1 mGy to 700 mGy. Despite chronic exposures, the genetic analyses showed no significant accumulation of mutation events. Because wild boar is an occasional human dietary item in Japan, effective dose to humans from ingesting contaminated wild boar meat was calculated. Hypothetical consumption of contaminated wild boar meat from radioactively contaminated areas in Fukushima, at the per capita pork consumption rate (12.9 kg y-1), would result in an average effective annual dose of 0.9 mSv y-1, which is below the annual ingestion limit of 1 mSv y-1. Additionally, a consumption rate of about 1.4 kg y-1 of the most contaminated meat in this study would not exceed annual ingestion limits.
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Affiliation(s)
- Donovan Anderson
- Institute of Radiation Emergency Medicine, Hirosaki University, Hirosaki, Aomori, Japan; Center for Research in Isotopes and Environmental Dynamics, University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Shingo Kaneko
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan
| | - Amber Harshman
- Environmental Protection Services Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kei Okuda
- Faculty of Human Environmental Studies, Hiroshima Shudo University, Hiroshima, Japan
| | - Toshihito Takagi
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan
| | - Sarah Chinn
- Savannah River Ecology Laboratory, Warnell School of Forestry and Natural Resources, University of Georgia, Aiken, SC, USA
| | - James C Beasley
- Savannah River Ecology Laboratory, Warnell School of Forestry and Natural Resources, University of Georgia, Aiken, SC, USA
| | - Kenji Nanba
- Institute of Environmental Radioactivity, Fukushima University, Fukushima City, Fukushima, Japan
| | - Hiroko Ishiniwa
- Institute of Environmental Radioactivity, Fukushima University, Fukushima City, Fukushima, Japan
| | - Thomas G Hinton
- Institute of Environmental Radioactivity, Fukushima University, Fukushima City, Fukushima, Japan; Centre for Environmental Radioactivity, Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
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Jopčík M, Libantová J, Lancíková V. Effect of chronic radiation on the flax (Linum usitatissimum L.) genome grown for six consecutive generations in the radioactive Chernobyl area. PHYSIOLOGIA PLANTARUM 2022; 174:e13745. [PMID: 35780328 DOI: 10.1111/ppl.13745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The growth of plants under chronic radiation stress in the Chernobyl area may cause changes in the genome of plants. To assess the extent of genetic and epigenetic changes in nuclear DNA, seeds of the annual crop flax (Linum usitatissimum L.) of the Kyivskyi variety, sown 21 years after the accident and grown for six generations in radioactive (RAD) and remediated (REM) fields were analysed. Flaxseed used for sowing first generation, which served as a reference (REF), was also analysed. The AFLP (Amplified Fragment Length Polymorphism) revealed a higher number of specific EcoRI-MseI loci (3.4-fold) in pooled flaxseed samples harvested from the RAD field compared with the REM field, indicating a link between the mutation process in the flax genome and the ongoing adaptation process. MSAP (Methylation-Sensitive Amplified Polymorphism) detecting EcoRI-MspI and EcoRI-HpaII loci in flax nuclear DNA genome showed no significant differences in methylation level, reaching about 33% in each of the groups studied. On the other hand, significant changes in the DNA methylation pattern of flaxseed samples harvested from the RAD field compared with controls were detected. Pairwise FST comparison revealed within both, EcoRI-MspI and transformed methylation-Sensitive data sets more than a 3-fold increase of genetic divergence in the RAD field compared with both controls. These results indicate that the nuclear genome of flax exposed to chronic radiation for six generations has more mutations and uses DNA methylation as one of the adaptation mechanisms for sustainability under adverse conditions.
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Affiliation(s)
- Martin Jopčík
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Nitra, Slovakia
| | - Jana Libantová
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Nitra, Slovakia
| | - Veronika Lancíková
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Nitra, Slovakia
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The Centre–Periphery Model, a Possible Explanation for the Distribution of Some Pinus spp. in the Sierra Madre Occidental, Mexico. FORESTS 2022. [DOI: 10.3390/f13020215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genetic diversity is key to survival of species. In evolutionary ecology, the general centre–periphery theory suggests that populations of species located at the margins of their distribution areas display less genetic diversity and greater genetic differentiation than populations from central areas. The aim of this study was to evaluate the genetic diversity and differentiation in six of the main pine species of the Sierra Madre Occidental (northern Mexico). The species considered were Pinus arizonica, P. cembroides, P. durangensis, Pinus engelmannii, P. herrerae and P. leiophylla, which occur at the margins and centre of the geographic distribution. We sampled needles from 2799 individuals belonging to 80 populations of the six species. We analysed amplified fragment length polymorphisms (AFLPs) to estimate diversity and rarity indexes, applied Principal Coordinate Analysis (PCoA), and used the Kruskal–Wallis test to detect genetic differences. Finally, we calculated Spearman’s correlation for association between variables. The general centre–periphery model only explained the traits in P. herrerae. The elevation gradient was an important factor that influenced genetic diversity. However, for elevation as partitioning criterion, most populations showed a central distribution. This information may be useful for establishing seed collections of priority individuals for maintenance in germplasm banks and their subsequent sustainable use.
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Goodman J, Brand J, Laptev G, Auld SKJR. Radiation‐mediated supply of genetic variation outweighs the effects of selection and drift in Chernobyl
Daphnia
populations. J Evol Biol 2022; 35:413-422. [PMID: 35048452 PMCID: PMC9303301 DOI: 10.1111/jeb.13983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Jessica Goodman
- Biological & Environmental Sciences University of Stirling Stirling United Kingdom
| | - June Brand
- Biological & Environmental Sciences University of Stirling Stirling United Kingdom
| | | | - Stuart K. J. R. Auld
- Biological & Environmental Sciences University of Stirling Stirling United Kingdom
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Sanín MJ, Zapata P, Pintaud JC, Galeano G, Bohórquez A, Tohme J, Hansen MM. Up and Down the Blind Alley: Population Divergence with Scant Gene Flow in an Endangered Tropical Lineage of Andean Palms (Ceroxylon quindiuense Clade: Ceroxyloideae). J Hered 2020; 108:288-298. [PMID: 28186241 DOI: 10.1093/jhered/esx006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/25/2017] [Indexed: 11/14/2022] Open
Abstract
Given the geographical complexity of the Andes, species distributions hold interesting information regarding the history of isolation and gene flow across geographic barriers and ecological gradients. Moreover, current threats to the region's enormous plant diversity pose an additional challenge to the understanding of these patterns. We explored the geographic structure of genetic diversity within the Ceroxylon quindiuense species complex (wax palms) at a regional scale, using a model-based approach to disentangle the historical mechanisms by which these species have dispersed over a range encompassing 17° of latitude in the tropical Andes. A total of 10 microsatellite loci were cross-amplified in 8 populations of the 3 species comprising the C. quindiuense complex. Analyses performed include estimates of molecular diversity and genetic structure, testing for genetic bottlenecks and an evaluation of the colonization scenario under approximate Bayesian computation. We showed that there was a geographical diversity gradient reflecting the orogenetic pattern of the northern Andes and its end at the cordilleras facing the Caribbean Sea. A general pattern of diversity suggests that the cordilleras of Colombia have served as historical recipients of gene flow occurring only scantly along the northern Andes. We provided evidence of important isolation between the largest populations of this complex, suggesting that both historical constraints to dispersal but also current anthropogenic effects might explain the high levels of population structuring. We provide a list of advisable measures for conservation stakeholders.
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Affiliation(s)
- María José Sanín
- From the Universidad CES, Calle 10 A No. 22 - 04Medellín, Colombia (Sanín); Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia (Galeano); Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia (Zapata, Bohórquez, and Tohme); Institut de Recherche pour le Développement IRD-CIRAD, TA A51/PS2, Montpellier cedex 5, France (Pintaud); and Department of Bioscience, Aarhus University, Aarhus, Denmark (Hansen)
| | - Patricia Zapata
- From the Universidad CES, Calle 10 A No. 22 - 04Medellín, Colombia (Sanín); Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia (Galeano); Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia (Zapata, Bohórquez, and Tohme); Institut de Recherche pour le Développement IRD-CIRAD, TA A51/PS2, Montpellier cedex 5, France (Pintaud); and Department of Bioscience, Aarhus University, Aarhus, Denmark (Hansen)
| | - Jean-Christophe Pintaud
- From the Universidad CES, Calle 10 A No. 22 - 04Medellín, Colombia (Sanín); Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia (Galeano); Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia (Zapata, Bohórquez, and Tohme); Institut de Recherche pour le Développement IRD-CIRAD, TA A51/PS2, Montpellier cedex 5, France (Pintaud); and Department of Bioscience, Aarhus University, Aarhus, Denmark (Hansen)
| | - Gloria Galeano
- From the Universidad CES, Calle 10 A No. 22 - 04Medellín, Colombia (Sanín); Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia (Galeano); Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia (Zapata, Bohórquez, and Tohme); Institut de Recherche pour le Développement IRD-CIRAD, TA A51/PS2, Montpellier cedex 5, France (Pintaud); and Department of Bioscience, Aarhus University, Aarhus, Denmark (Hansen)
| | - Adriana Bohórquez
- From the Universidad CES, Calle 10 A No. 22 - 04Medellín, Colombia (Sanín); Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia (Galeano); Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia (Zapata, Bohórquez, and Tohme); Institut de Recherche pour le Développement IRD-CIRAD, TA A51/PS2, Montpellier cedex 5, France (Pintaud); and Department of Bioscience, Aarhus University, Aarhus, Denmark (Hansen)
| | - Joseph Tohme
- From the Universidad CES, Calle 10 A No. 22 - 04Medellín, Colombia (Sanín); Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia (Galeano); Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia (Zapata, Bohórquez, and Tohme); Institut de Recherche pour le Développement IRD-CIRAD, TA A51/PS2, Montpellier cedex 5, France (Pintaud); and Department of Bioscience, Aarhus University, Aarhus, Denmark (Hansen)
| | - Michael Møller Hansen
- From the Universidad CES, Calle 10 A No. 22 - 04Medellín, Colombia (Sanín); Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia (Galeano); Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia (Zapata, Bohórquez, and Tohme); Institut de Recherche pour le Développement IRD-CIRAD, TA A51/PS2, Montpellier cedex 5, France (Pintaud); and Department of Bioscience, Aarhus University, Aarhus, Denmark (Hansen)
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Shimalina NS, Antonova EV, Pozolotina VN. Genetic polymorphism of Plantago major populations from the radioactive and chemical polluted areas. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 257:113607. [PMID: 31767232 DOI: 10.1016/j.envpol.2019.113607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/22/2019] [Accepted: 11/10/2019] [Indexed: 06/10/2023]
Abstract
The variability of nine microsatellite loci was studied for Plantago major L. populations from radioactive (East-Ural Radioactive Trace, EURT) and chemical (Karabash Copper Smelter, KCS) contaminated areas (Urals, Russia). The absorbed dose rates in the EURT area were 178-1455 times higher than background, and the indices of the total toxic load in the KCS area were 13-42 times higher than background values. In total, 65 alleles were identified in P. major populations, while the number of alleles per locus in the EURT and KCS samples was lower than in the background samples. The expected heterozygosity in all loci significantly exceeded the observed, indicating a high level of inbreeding. The largest number of rare alleles (11-21) was found in background samples, of which 3-7 alleles were private. In the technogenically disturbed zones, 8-11 rare alleles (1-2 private) were noted. The Bayesian analysis (K = 3) showed that no unique groups were found in any of the areas; descendants of all founders (pioneers) were represented in each population, but in different proportions. However, only 4.1% of the variability was distributed between local P. major populations (FST = 0.041) and 95.9% was concentrated within the samples. A pairwise comparison revealed genetic differentiation between all EURT samples. In the KCS area, there was no significant differentiation in pairs of samples that were at a distance of 3-4 km from each other. For samples from the KCS and background sites, the Mantel test showed a statistically significant relationship between geographical and genetic distances, therefore, the intensity of migration flows between these areas is high. For samples from the EURT and background areas, no such dependence was found. In both impact zones, P. major populations showed reduced genetic diversity. This article discusses the causes of this phenomenon.
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Affiliation(s)
- Nadezhda S Shimalina
- Laboratory of Population Radiobiology, Institute of Plant & Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta str. 202, Ekaterinburg, 620144, Russia
| | - Elena V Antonova
- Laboratory of Population Radiobiology, Institute of Plant & Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta str. 202, Ekaterinburg, 620144, Russia.
| | - Vera N Pozolotina
- Laboratory of Population Radiobiology, Institute of Plant & Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta str. 202, Ekaterinburg, 620144, Russia
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Mousseau TA, Møller AP. Plants in the Light of Ionizing Radiation: What Have We Learned From Chernobyl, Fukushima, and Other "Hot" Places? FRONTIERS IN PLANT SCIENCE 2020; 11:552. [PMID: 32457784 PMCID: PMC7227407 DOI: 10.3389/fpls.2020.00552] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/14/2020] [Indexed: 05/13/2023]
Abstract
Perhaps the main factor determining success of space travel will be the ability to control effects of ionizing radiation for humans, but also for other living organisms. Manned space travel will require the cultivation of food plants under conditions of prolonged exposure to ionizing radiation. Although there is a significant literature concerning the effects of acute high dose rate exposures on plant genetics, growth, and development, much less is known concerning the effects of chronic low dose irradiation especially those related to the impacts of the high energy protons and heavy ions that are encountered in the space environment. Here, we make the argument that in situ studies of the effects of radionuclides at nuclear accident sites (e.g., Chernobyl and Fukushima), atomic bomb test sites, and areas of naturally high radiation levels, could provide insights concerning the mechanisms of radiation effects on living systems that cannot be assessed short of conducting research in space, which is not yet feasible for large scale, long term, multigenerational experiments. In this article we review the literature concerning the effects of chronic low-dose rate radiation exposure from studies conducted in Chernobyl, Fukushima, and other regions of the world with high ambient radiation levels (parts of India in particular). In general, mutation rates and other measures of genetic damage are considerably elevated, pollen and seed viability are reduced, growth rates are slower, and the frequency of developmental abnormalities is increased, although there is considerable variation among taxa for these effects. In addition, there are interactions between radiation and other environmental stressors (e.g., temperature, drought, heavy metals) that may play important roles in determining susceptibility to radiation induced stress.
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Affiliation(s)
- Timothy A. Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
- SURA/LASSO/NASA, ISS Utilization and Life Sciences Division, Kennedy Space Center, Cape Canaveral, FL, United States
- *Correspondence: Timothy A. Mousseau,
| | - Anders Pape Møller
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
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11
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Fuller N, Ford AT, Lerebours A, Gudkov DI, Nagorskaya LL, Smith JT. Chronic radiation exposure at Chernobyl shows no effect on genetic diversity in the freshwater crustacean, Asellus aquaticus thirty years on. Ecol Evol 2019; 9:10135-10144. [PMID: 31624541 PMCID: PMC6787803 DOI: 10.1002/ece3.5478] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022] Open
Abstract
Analysis of genetic diversity represents a fundamental component of ecological risk assessments in contaminated environments. Many studies have assessed the genetic implications of chronic radiation exposure at Chernobyl, generally recording an elevated genetic diversity and mutation rate in rodents, plants, and birds inhabiting contaminated areas. Only limited studies have considered genetic diversity in aquatic biota at Chernobyl, despite the large number of freshwater systems where elevated dose rates will persist for many years. Consequently, the present study aimed to assess the effects of chronic radiation exposure on genetic diversity in the freshwater crustacean, Asellus aquaticus, using a genome-wide SNP approach (Genotyping-by-sequencing). It was hypothesized that genetic diversity in A. aquaticus would be positively correlated with dose rate. A. aquaticus was collected from six lakes in Belarus and the Ukraine ranging in dose rate from 0.064 to 27.1 µGy/hr. Genotyping-by-sequencing analysis was performed on 74 individuals. A significant relationship between geographical distance and genetic differentiation confirmed the Isolation-by-Distance model. Conversely, no significant relationship between dose rate and genetic differentiation suggested no effect of the contamination gradient on genetic differentiation between populations. No significant relationship between five measures of genetic diversity and dose rate was recorded, suggesting that radiation exposure has not significantly influenced genetic diversity in A. aquaticus at Chernobyl. This is the first study to adopt a genome-wide SNP approach to assess the impacts of environmental radiation exposure on biota. These findings are fundamental to understanding the long-term success of aquatic populations in contaminated environments at Chernobyl and Fukushima.
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Affiliation(s)
- Neil Fuller
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Alex T. Ford
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Adélaïde Lerebours
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Dmitri I. Gudkov
- Department of Freshwater RadioecologyInstitute of HydrobiologyKievUkraine
| | - Liubov L. Nagorskaya
- Applied Science Center for Bioresources of the National Academy of Sciences of BelarusMinskBelarus
| | - Jim T. Smith
- School of Earth & Environmental SciencesUniversity of PortsmouthPortsmouthUK
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Horemans N, Spurgeon DJ, Lecomte-Pradines C, Saenen E, Bradshaw C, Oughton D, Rasnaca I, Kamstra JH, Adam-Guillermin C. Current evidence for a role of epigenetic mechanisms in response to ionizing radiation in an ecotoxicological context. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 251:469-483. [PMID: 31103007 DOI: 10.1016/j.envpol.2019.04.125] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/14/2019] [Accepted: 04/27/2019] [Indexed: 05/22/2023]
Abstract
The issue of potential long-term or hereditary effects for both humans and wildlife exposed to low doses (or dose rates) of ionising radiation is a major concern. Chronic exposure to ionising radiation, defined as an exposure over a large fraction of the organism's lifespan or even over several generations, can possibly have consequences in the progeny. Recent work has begun to show that epigenetics plays an important role in adaptation of organisms challenged to environmental stimulae. Changes to so-called epigenetic marks such as histone modifications, DNA methylation and non-coding RNAs result in altered transcriptomes and proteomes, without directly changing the DNA sequence. Moreover, some of these environmentally-induced epigenetic changes tend to persist over generations, and thus, epigenetic modifications are regarded as the conduits for environmental influence on the genome. Here, we review the current knowledge of possible involvement of epigenetics in the cascade of responses resulting from environmental exposure to ionising radiation. In addition, from a comparison of lab and field obtained data, we investigate evidence on radiation-induced changes in the epigenome and in particular the total or locus specific levels of DNA methylation. The challenges for future research and possible use of changes as an early warning (biomarker) of radiosensitivity and individual exposure is discussed. Such a biomarker could be used to detect and better understand the mechanisms of toxic action and inter/intra-species susceptibility to radiation within an environmental risk assessment and management context.
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Affiliation(s)
- Nele Horemans
- Belgian Nuclear Research Centre, Boeretang 200, B-2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Agoralaan, 3590, Diepenbeek, Belgium.
| | - David J Spurgeon
- Centre for Ecology and Hydrology, MacLean Building, Benson Lane, Wallingford, Oxon, OX10 8BB, UK
| | - Catherine Lecomte-Pradines
- Institut de Radioprotection et de Sûreté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul Lez Durance, France
| | - Eline Saenen
- Belgian Nuclear Research Centre, Boeretang 200, B-2400, Mol, Belgium
| | - Clare Bradshaw
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Deborah Oughton
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences, 1430, Aas, Norway
| | - Ilze Rasnaca
- Centre for Ecology and Hydrology, MacLean Building, Benson Lane, Wallingford, Oxon, OX10 8BB, UK
| | - Jorke H Kamstra
- Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Christelle Adam-Guillermin
- Institut de Radioprotection et de Sûreté Nucléaire, PSE-SANTE, Cadarache, Saint Paul Lez Durance, France
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Morillo C. AC, Morillo C. Y, Leguizamo M. MF. Caracterización morfológica y molecular de Oxalis tuberosa Mol. en el departamento de Boyacá. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2019. [DOI: 10.15446/rev.colomb.biote.v21n1.57356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Dentro de los tubérculos andinos de mayor importancia, después de la papa, se encuentra la ibia (Oxalis tuberosa Mol.) ya que constituye un alimento básico para las comunidades andinas. Boyacá es uno de los departamentos de Colombia, en donde todavía existe la tradición de cultivar y consumir tubérculos andinos como los cubios, ullucus y rubas o ibias, sin embargo están amanezados por la erosión genética. No existen estudios sobre estos recursos fitogenéticos en Boyacá, por lo cual el objetivo de esta investigación fue colectar y caracterizar morfológica y molecularmente materiales de ibias en este departamento. El análisis morfológico mostro que las características más discriminantes fueron: color de los tallos aéreos, pigmentación de las axilas, color del follaje, color de la flor, color del pedúnculo y pedicelo, color predominante de la superficie del tubérculo, color secundario de la superficie del tubérculo, color predominante y secundario de la pulpa, distribución del color secundario de la pulpa y forma de los tubérculos. El análisis de similitud diferenció a los materiales en dos grandes grupos, de acuerdo principalmente a características morfológicas como el color y hábito de floración. El valor de hetorocigosidad promedio para la población total fue de 0.39 el cual se considera alto al compararse con otros estudios de diversidad genética en ibias. El análisis de varianza molecular (AMOVA) y el Fst (coeficiente de diferenciación genética) muestran que existe una alta variabilidad genética entre los materiales de ibias evaluados la cual debe ser conservada y aprovechada dentro de futuros programas de mejoramiento.
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Pfeiffer VW, Ford BM, Housset J, McCombs A, Blanco‐Pastor JL, Gouin N, Manel S, Bertin A. Partitioning genetic and species diversity refines our understanding of species-genetic diversity relationships. Ecol Evol 2018; 8:12351-12364. [PMID: 30619550 PMCID: PMC6308885 DOI: 10.1002/ece3.4530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/27/2018] [Accepted: 08/03/2018] [Indexed: 12/24/2022] Open
Abstract
Disentangling the origin of species-genetic diversity correlations (SGDCs) is a challenging task that provides insight into the way that neutral and adaptive processes influence diversity at multiple levels. Genetic and species diversity are comprised by components that respond differently to the same ecological processes. Thus, it can be useful to partition species and genetic diversity into their different components to infer the mechanisms behind SGDCs. In this study, we applied such an approach using a high-elevation Andean wetland system, where previous evidence identified neutral processes as major determinants of the strong and positive covariation between plant species richness and AFLP genetic diversity of the common sedge Carex gayana. To tease apart putative neutral and non-neutral genetic variation of C. gayana, we identified loci putatively under selection from a dataset of 1,709 SNPs produced using restriction site-associated DNA sequencing (RAD-seq). Significant and positive relationships between local estimates of genetic and species diversities (α-SGDCs) were only found with the putatively neutral loci datasets and with species richness, confirming that neutral processes were primarily driving the correlations and that the involved processes differentially influenced local species diversity components (i.e., richness and evenness). In contrast, SGDCs based on genetic and community dissimilarities (β-SGDCs) were only significant with the putative non-neutral datasets. This suggests that selective processes influencing C. gayana genetic diversity were involved in the detected correlations. Together, our results demonstrate that analyzing distinct components of genetic and species diversity simultaneously is useful to determine the mechanisms behind species-genetic diversity relationships.
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Affiliation(s)
- Vera Wilder Pfeiffer
- Nelson Institute for Environmental ScienceUniversity of Wisconsin – MadisonMadisonWisconsin
| | - Brett Michael Ford
- Department of BiologyUniversity of British ColumbiaKelownaBritish ColumbiaCanada
| | - Johann Housset
- Alcina ForetsMontpellierFrance
- Centre d’étude de la forêtUniversité du Québec à MontréalMontréalQuebecCanada
| | - Audrey McCombs
- Department of Statistics, Ecology and Evolutionary Biology ProgramIowa State UniversityAmesIowa
| | | | - Nicolas Gouin
- Departamento de BiologíaFacultad de CienciasUniversidad de La SerenaLa SerenaChile
- Centro de Estudios Avanzados en Zonas ÁridasLa SerenaChile
- Instituto de Investigación Multidisciplinar en Ciencia y TecnologíaUniversidad de La SerenaLa SerenaChile
| | - Stéphanie Manel
- EPHEPSL Research UniversityCNRSUM, SupAgro, IRDINRAUMR 5175 CEFEMontpellierFrance
| | - Angéline Bertin
- Departamento de BiologíaFacultad de CienciasUniversidad de La SerenaLa SerenaChile
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Volkova PY, Geras'kin SA, Horemans N, Makarenko ES, Saenen E, Duarte GT, Nauts R, Bondarenko VS, Jacobs G, Voorspoels S, Kudin M. Chronic radiation exposure as an ecological factor: Hypermethylation and genetic differentiation in irradiated Scots pine populations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 232:105-112. [PMID: 28931465 DOI: 10.1016/j.envpol.2017.08.123] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/14/2017] [Accepted: 08/24/2017] [Indexed: 05/18/2023]
Abstract
Genetic and epigenetic changes were investigated in chronically irradiated Scots pine (Pinus sylvestris L.) populations from territories that were heavily contaminated by radionuclides as result of the Chernobyl Nuclear Power Plant accident. In comparison to the reference site, the genetic diversity revealed by electrophoretic mobility of AFLPs was found to be significantly higher at the radioactively contaminated areas. In addition, the genome of pine trees was significantly hypermethylated at 4 of the 7 affected sites.
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Affiliation(s)
- P Yu Volkova
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation.
| | - S A Geras'kin
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation
| | - N Horemans
- Belgian Nuclear Research Centre SCK•CEN, Biosphere Impact Studies, Boeretang 200, 2400, Mol, Belgium
| | - E S Makarenko
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation
| | - E Saenen
- Belgian Nuclear Research Centre SCK•CEN, Biosphere Impact Studies, Boeretang 200, 2400, Mol, Belgium
| | - G T Duarte
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation
| | - R Nauts
- Belgian Nuclear Research Centre SCK•CEN, Biosphere Impact Studies, Boeretang 200, 2400, Mol, Belgium
| | - V S Bondarenko
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation
| | - G Jacobs
- Flemish Institute for Technological Research (VITO NV), Boeretang 200, 2400 Mol, Belgium
| | - S Voorspoels
- Flemish Institute for Technological Research (VITO NV), Boeretang 200, 2400 Mol, Belgium
| | - M Kudin
- Polessye State Radiation Ecological Reserve, 247618, Belarus
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Roberts DG, Forrest CN, Denham AJ, Ayre DJ. Clonality disguises the vulnerability of a threatened arid zone Acacia. Ecol Evol 2017; 7:9451-9460. [PMID: 29187981 PMCID: PMC5696425 DOI: 10.1002/ece3.3246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 05/28/2017] [Accepted: 05/30/2017] [Indexed: 11/09/2022] Open
Abstract
Long-lived, widespread plant species are expected to be genetically diverse, reflecting the interaction between large population sizes, overlapping generations, and gene flow. Such species are thought to be resilient to disturbance, but may carry an extinction debt due to reproductive failure. Genetic studies of Australian arid zone plant species suggest an unusually high frequency of asexuality, polyploidy, or both. A preliminary AFLP genetic study implied that the naturally fragmented arid zone tree, Acacia carneorum, is almost entirely dependent on asexual reproduction through suckering, and stands may have lacked genetic diversity and interconnection even prior to the onset of European pastoralism. Here we surveyed microsatellite genetic variation in 20 stands to test for variation in life histories and further assessed the conservation status of the species by comparing genetic diversity within protected stands in National Parks and disturbed range lands. Using herbarium records, we estimate that 219 stands are extant, all of which occur in the arid zone, west of the Darling River in southeastern Australia. With two exceptions, all surveyed stands comprised only one multilocus genet and at least eight were putatively polyploid. Although some stands comprise thousands of stems, our findings imply that the species as a whole may represent ~240 distinct genetic individuals, many of which are polyploid, and most are separated by >10 km of unsuitable habitat. With only 34% of stands (and therefore genets) occurring within conservation reserves, A. carneorum may be at much greater risk of extinction than inferred from on-ground census data. Land managers should prioritize on-ground preservation of the genotypes within existing reserves, protecting both vegetative suckers and seedlings from herbivory. Importantly, three stands are known to set viable seed and should be used to generate genetically diverse germ-plasm for ex situ conservation, population augmentation, or translocation.
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Affiliation(s)
- David G Roberts
- School of Biological Sciences and Centre for Sustainable Ecosystem Services University of Wollongong Wollongong NSW Australia.,Present address: Centre of Excellence in Natural Resource Management The University of Western Australia Albany WA Australia
| | - Cairo N Forrest
- School of Biological Sciences and Centre for Sustainable Ecosystem Services University of Wollongong Wollongong NSW Australia
| | - Andrew J Denham
- School of Biological Sciences and Centre for Sustainable Ecosystem Services University of Wollongong Wollongong NSW Australia.,New South Wales Office of Environment and Heritage Hurstville NSW Australia
| | - David J Ayre
- School of Biological Sciences and Centre for Sustainable Ecosystem Services University of Wollongong Wollongong NSW Australia
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Danchenko M, Klubicova K, Krivohizha MV, Berezhna VV, Sakada VI, Hajduch M, Rashydov NM. Systems biology is an efficient tool for investigation of low-dose chronic irradiation influence on plants in the Chernobyl zone. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716060050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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18
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Yemets AI, Blume RY, Sorochinsky BV. Adaptation of the gymnosperms to the conditions of irradiation in the Chernobyl zone: from morphological abnormalities to the molecular genetic consequences. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716060086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Tsuda Y, Chen J, Stocks M, Källman T, Sønstebø JH, Parducci L, Semerikov V, Sperisen C, Politov D, Ronkainen T, Väliranta M, Vendramin GG, Tollefsrud MM, Lascoux M. The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west? Mol Ecol 2016; 25:2773-89. [PMID: 27087633 DOI: 10.1111/mec.13654] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/23/2016] [Accepted: 04/09/2016] [Indexed: 01/17/2023]
Abstract
Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive structure plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.
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Affiliation(s)
- Yoshiaki Tsuda
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.,CNR, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Michael Stocks
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Thomas Källman
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | | | - Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Vladimir Semerikov
- Urals Division of the Russian Academy of Sciences, Institute of Plant and Animal Ecology, 8 Marta Str., 202, 620144, Ekaterinburg, Russia
| | - Christoph Sperisen
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, CH-8903, Birmendsdorf, Switzerland
| | - Dmitry Politov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin str. 3, 119991, Moscow, Russia
| | - Tiina Ronkainen
- Environmental Change Research Unit (ECRU), Department of Environmental Sciences, University of Helsinki, PO Box 65, FI-00014, Helsinki, Finland
| | - Minna Väliranta
- Environmental Change Research Unit (ECRU), Department of Environmental Sciences, University of Helsinki, PO Box 65, FI-00014, Helsinki, Finland
| | - Giovanni Giuseppe Vendramin
- CNR, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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Ávila-Flores IJ, Hernández-Díaz JC, González-Elizondo MS, Prieto-Ruíz JÁ, Wehenkel C. Degree of Hybridization in Seed Stands of Pinus engelmannii Carr. In the Sierra Madre Occidental, Durango, Mexico. PLoS One 2016; 11:e0152651. [PMID: 27064490 PMCID: PMC4827862 DOI: 10.1371/journal.pone.0152651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 03/17/2016] [Indexed: 11/24/2022] Open
Abstract
Hybridization is an important evolutionary force, because interspecific gene transfer can introduce more new genetic material than is directly generated by mutations. Pinus engelmannii Carr. is one of the nine most common pine species in the pine-oak forest ecoregion in the state of Durango, Mexico. This species is widely harvested for lumber and is also used in reforestation programmes. Interspecific hybrids between P.engelmannii and Pinus arizonica Engelm. have been detected by morphological analysis. The presence of hybrids in P. engelmannii seed stands may affect seed quality and reforestation success. Therefore, the goals of this research were to identify introgressive hybridization between P. engelmannii and other pine species in eight seed stands of this species in Durango, Mexico, and to examine how hybrid proportion is related to mean genetic dissimilarity between trees in these stands, using Amplified Fragment Length Polymorphism (AFLP) markers and morphological traits. Differences in the average current annual increment of putative hybrids and pure trees were also tested for statistical significance. Morphological and genetic analyses of 280 adult trees were carried out. Putative hybrids were found in all the seed stands studied. The hybrids did not differ from the pure trees in vigour or robustness. All stands with putative P. engelmannii hybrids detected by both AFLPs and morphological traits showed the highest average values of the Tanimoto distance, which indicates: i) more heterogeneous genetic material, ii) higher genetic variation and therefore iii) the higher evolutionary potential of these stands, and iv) that the morphological differentiation (hybrid/not hybrid) is strongly associated with the Tanimoto distance per stand. We conclude that natural pairwise hybrids are very common in the studied stands. Both morphological and molecular approaches are necessary to confirm the genetic identity of forest reproductive material.
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Affiliation(s)
- Israel Jaime Ávila-Flores
- Doctorado Institucional en Ciencias Agropecuarias y Forestales, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
| | - José Ciro Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
| | - Maria Socorro González-Elizondo
- CIIDIR Unidad Durango, Instituto Politécnico Nacional, Sigma 119 Fracc, 20 de Noviembre II, Durango, Durango, México, C.P., 34220
| | - José Ángel Prieto-Ruíz
- Facultad de Ciencias Forestales, Universidad Juárez del Estado de Durango, Blv. Durango y Ave, Papaloapan s/n. Col. Valle del Sur, Durango, Durango, México, C.P., 34120
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
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Feng X, Liu J, Gong X. Species Delimitation of the Cycas segmentifida Complex (Cycadaceae) Resolved by Phylogenetic and Distance Analyses of Molecular Data. FRONTIERS IN PLANT SCIENCE 2016; 7:134. [PMID: 26913044 PMCID: PMC4753401 DOI: 10.3389/fpls.2016.00134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/25/2016] [Indexed: 06/02/2023]
Abstract
The Cycas segmentifida complex consists of eight species whose distributions overlap in a narrow region in Southwest China. These eight taxa are also morphologically similar and are difficult to be distinguished. Consequently, their taxonomic status has been a matter of discussion in recent years. To study this species complex, we sequenced four plastid intergenic spacers (cpDNA), three nuclear genes and genotyped 12 microsatellites for the eight taxa from 19 different localities. DNA sequences were analyzed using Maximum Likelihood (ML) method and Bayesian Inference (BI), and microsatellites were analyzed using the Neighbor-joining (NJ) and structure inference methods. Results of cpDNA, nuclear gene GTP and microsatellites all rejected the hypotheses that this complex consisted of eight taxa or one distinct lineage (species) but two previously described species were adopted: Cycas guizhouensis K. M. Lan et R. F. Zou and Cycas segmentifida D. Y. Wang et C. Y. Deng. Cycas longlinensis H. T. Chang et Y. C. Zhong was included in C. guizhouensis and the other five taxa were included in C. segmentifida. Our species delimitation inferred from molecular data largely corresponds to morphological differentiation. However, the other two nuclear genes were unable to resolve species boundaries for this complex independently. This study offered evidences from different genomes for dealing with the species boundaries and taxonomical treatment of the C. segmentifida complex in an integrated perspective.
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Affiliation(s)
- Xiuyan Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
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22
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Applying Effective Population Size Estimates of Kandelia obovata Sheue, Liu and Yong to Conservation and Restoration Management. FORESTS 2015. [DOI: 10.3390/f6051439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Ranade SS, Ganea LS, Razzak AM, García Gil MR. Fungal Infection Increases the Rate of Somatic Mutation in Scots Pine (Pinus sylvestris L.). J Hered 2015; 106:386-94. [PMID: 25890976 DOI: 10.1093/jhered/esv017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/16/2015] [Indexed: 11/13/2022] Open
Abstract
Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8×10(-3) mutations per locus), as compared to the controls (2.0×10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (χ(2) = 12.9883, df = 1, P = 0.0003134).
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Affiliation(s)
- Sonali Sachin Ranade
- From the Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, SE 901-83 Umeå, Sweden (Ranade, Ganea, Razzak, and García Gil)
| | - Laura-Stefana Ganea
- From the Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, SE 901-83 Umeå, Sweden (Ranade, Ganea, Razzak, and García Gil)
| | - Abdur M Razzak
- From the Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, SE 901-83 Umeå, Sweden (Ranade, Ganea, Razzak, and García Gil)
| | - M R García Gil
- From the Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, SE 901-83 Umeå, Sweden (Ranade, Ganea, Razzak, and García Gil).
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Gong YQ, Zhan QQ, Nguyen KS, Nguyen HT, Wang YH, Gong X. The historical demography and genetic variation of the endangered Cycas multipinnata (Cycadaceae) in the red river region, examined by chloroplast DNA sequences and microsatellite markers. PLoS One 2015; 10:e0117719. [PMID: 25689828 PMCID: PMC4331093 DOI: 10.1371/journal.pone.0117719] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/26/2014] [Indexed: 11/18/2022] Open
Abstract
Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA) sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU). In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species.
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Affiliation(s)
- Yi-Qing Gong
- Plant Science Institute, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Qing Zhan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Khang Sinh Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Cau Giay District, Ha Noi, Vietnam
| | - Hiep Tien Nguyen
- Center for Plant Conservation, Cau Giay District, Ha Noi, Vietnam
| | - Yue-Hua Wang
- Plant Science Institute, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Simental-Rodríguez SL, Quiñones-Pérez CZ, Moya D, Hernández-Tecles E, López-Sánchez CA, Wehenkel C. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico. PLoS One 2014; 9:e111623. [PMID: 25375134 PMCID: PMC4222919 DOI: 10.1371/journal.pone.0111623] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/02/2014] [Indexed: 11/18/2022] Open
Abstract
Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between genetic variants and species diversity may be crucial in shaping tree communities.
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Affiliation(s)
| | | | - Daniel Moya
- Higher Technical School of Agricultural and Forestry Engineering, Universidad Castilla-La Mancha, Albacete, Spain
| | - Enrique Hernández-Tecles
- Higher Technical School of Agricultural and Forestry Engineering, Universidad Castilla-La Mancha, Albacete, Spain
| | | | - Christian Wehenkel
- Forestry and Wood Industry Institute, Universidad Juárez del Estado de Durango, Durango, Mexico
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26
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Stefani F, Rusconi M, Valsecchi S, Marziali L. Evolutionary ecotoxicology of perfluoralkyl substances (PFASs) inferred from multigenerational exposure: a case study with Chironomus riparius (Diptera, Chironomidae). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 156:41-51. [PMID: 25146235 DOI: 10.1016/j.aquatox.2014.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 07/17/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
A multigeneration toxicity test on Chironomus riparius was performed with the aim of investigating the evolutionary consequences of exposure to perfluoralkyl substances (perfluorooctane sulfonic acid, PFOS; perfluorooctanoic acid, PFOA; perfluorobutane sulfonate, PFBS). Six-hundred larvae were bred per treatment and per generation until emergence and egg deposition under a nominal concentration of 10μg/L of contaminants. Newborn larvae were used to start the next generation. Evolution of genetic variability was evaluated along a total of 10 consecutive generations based on 5 microsatellite loci. Analysis of life-history traits (survival, sex ratio and reproduction) was also carried out. Rapid genetic variability reduction was observed in all treatments, including controls, across generations due to the test conditions. Nevertheless, an increased mutation rate determined a stronger conservation of genetic variability in PFOS and, at minor extent, in PFBS exposed populations compared to controls. No significant effects were induced by exposure to PFOA. Direct mutagenicity or induced stress conditions may be at the base of increased mutation rate, indicating the potential risk of mutational load caused by exposure to PFOS and PFBS. The test provided the opportunity to evaluate the use of approximate Bayesian computation (ABC) and coalescent approaches in evolutionary ecotoxicology. A weak performance was evidenced for ABC, either in terms of bias or dispersion of effective population sizes and of estimates of mutation rate. On the contrary, coalescent simulations proved the sensitivity of traditional genetic endpoints (i.e. heterozygosity and number of alleles) to the alteration of mutation rate, but not to erosion of genetic effective size.
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Affiliation(s)
- F Stefani
- Water Research Institute-National Research Council (IRSA-CNR), via del Mulino 19, Brugherio, MB, Italy.
| | - M Rusconi
- Water Research Institute-National Research Council (IRSA-CNR), via del Mulino 19, Brugherio, MB, Italy.
| | - S Valsecchi
- Water Research Institute-National Research Council (IRSA-CNR), via del Mulino 19, Brugherio, MB, Italy.
| | - L Marziali
- Water Research Institute-National Research Council (IRSA-CNR), via del Mulino 19, Brugherio, MB, Italy.
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Mothersill C, Smith R, Lariviere D, Seymour C. Chronic exposure by ingestion of environmentally relevant doses of (226)Ra leads to transient growth perturbations in fathead minnow (Pimephales promelas, Rafinesque, 1820). Int J Radiat Biol 2013; 89:950-64. [PMID: 23724911 DOI: 10.3109/09553002.2013.809817] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PURPOSE To assess the impact of environmentally relevant levels of ingested (226)Ra on a common freshwater fish species. METHODS Fathead minnow (Pimephales promelas, Rafinesque) were obtained at the first feeding stage and established on a commercial fish food diet containing (226)Ra in the activity range 10 mBq/g(-1), -10,000 mBq/g(-1). They remained on this diet for 24 months and were sampled invasively at 1,6,18 and 24 months to assess growth, biochemical indices and accumulated dose and non-invasively also at 12 and 15 months to assess growth. RESULTS Fish fed 10 and 100 mBq/g(-1) diet showed a small transitory deregulation of growth at 6 and 12 months. Fish fed higher activities showed less significant or insignificant effects. There was a trend at 18 months which was stronger at 24 months for the population distribution to change in all of the (226)Ra fed groups so that smaller fish were smaller and bigger fish were bigger than the controls. There were also significant differences in the ratios of protein:DNA at 24 months which were seen as a trend but were not significant at earlier time points. CONCLUSIONS Fish fed a radium diet for 2 years show a small and transitory growth dysregulation at 6 and 12 months. The effects predominate at the lower activities suggesting hormetic or homeostatic adjustments. There was no effect on growth of exposure to the high activities (226)Ra. This suggests that radium does not have a serious impact on the ecology of the system and the level of radium that would be transferred to humans is very low. The results may be important in the assessment of long-term environmental impacts of (226)Ra exposure.
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Affiliation(s)
- Carmel Mothersill
- Department of Medical Physics and Applied Radiation Sciences, McMaster University , Hamilton, Ontario
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Klubicová K, Danchenko M, Skultety L, Berezhna VV, Uvackova L, Rashydov NM, Hajduch M. Soybeans grown in the Chernobyl area produce fertile seeds that have increased heavy metal resistance and modified carbon metabolism. PLoS One 2012; 7:e48169. [PMID: 23110204 PMCID: PMC3482187 DOI: 10.1371/journal.pone.0048169] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 09/21/2012] [Indexed: 11/19/2022] Open
Abstract
Plants grow and reproduce in the radioactive Chernobyl area, however there has been no comprehensive characterization of these activities. Herein we report that life in this radioactive environment has led to alteration of the developing soybean seed proteome in a specific way that resulted in the production of fertile seeds with low levels of oil and β-conglycinin seed storage proteins. Soybean seeds were harvested at four, five, and six weeks after flowering, and at maturity from plants grown in either non-radioactive or radioactive plots in the Chernobyl area. The abundance of 211 proteins was determined. The results confirmed previous data indicating that alterations in the proteome include adaptation to heavy metal stress and mobilization of seed storage proteins. The results also suggest that there have been adjustments to carbon metabolism in the cytoplasm and plastids, increased activity of the tricarboxylic acid cycle, and decreased condensation of malonyl-acyl carrier protein during fatty acid biosynthesis.
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Affiliation(s)
- Katarína Klubicová
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Maksym Danchenko
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, Kyiv, Ukraine
| | - Ludovit Skultety
- Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
- Center for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Valentyna V. Berezhna
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, Kyiv, Ukraine
| | - Lubica Uvackova
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Namik M. Rashydov
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, Kyiv, Ukraine
| | - Martin Hajduch
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Nitra, Slovak Republic
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