Polyploidy

328. Heslop-Harrison JS. 2017. Polyploidy. In: Reference Module in Life Sciences, Elsevier, ISBN: 978-0-12- 809633-8, http://dx.doi.org/10.1016/B978-0-12-809633-8.06934-X (££$$€€) (see https://www.elsevier.com/solutions/sciencedirect/content/reference-modules for information about the series.)

Abstract
Polyploid organisms are eukaryotes that have more than two complete sets of chromosomes (one from each parent or ancestor) in somatic and germline cells of animals, fungi, and plants. Polyploidy of individual cells or cell types (endopolyploidy), arising from chromosome replication without cell division, is involved in the normal (eg, secretory cells) or abnormal (eg, many cancers) development of organisms. Polyploidy or “whole-genome duplication” is an important feature of genome evolution and speciation, and most lineages of plants and animals include rounds of such duplications in their evolutionary history. Many plant species, in particular, have both ancient whole-genome duplications and more recent polyploidy events in their ancestry. Polyploid individuals are found occasionally in all groups of eukaryotic organisms as a result of incorrect meiosis, fertilization, or cell division, although most spontaneously occurring animal polyploids are inviable. Polyploids can be generated experimentally by treatment with chemicals such as colchicine or by fusion of diploid nuclei. Many polyploids, particularly among plants, develop normally, and depending on the nature of the polyploidy may be sterile, or undergo meiosis that is indistinguishable from a normal diploid giving viable gametes.

Keywords
Amphidiploid; Autopolyploid; Eukaryotes; Tetraploid

FULL AUTHOR TEXT SUMMARY:

POLYPLOIDY

Amphipolyploid A species or hybrid having more than two sets of chromosomes that originate from more than one parental or ancestral species.

Autopolyploid A species or hybrid having more than two sets of chromosomes originating from the same parental or ancestral species.

Polyploid A species, individual organism, or cell having more than two sets of chromosomes (more than two genomes) in each cell nucleus.

Tetraploid A species or individual organism having four sets of chromosomes (four genomes or typically 4 times the basic haploid chromosome number of x) in each cell. A single cell may also be tetraploid.

Types of polyploidy and nomenclature

Polyploidy may occur by the number of chromosomes in a cell doubling because of a failure of chromosome sets to divide at mitosis, by fusion of nuclei from diploid cells, or by a failure of meiosis giving a 2n gamete, so the resulting embryo has at least one extra chromosome set. In presenting chromosome numbers or karyotype constitutions, the letter x is used to refer to the basic chromosome number of the ancestor of a polyploid. The diploid chromosome number, 2n, refers to the number of chromosomes in a cell of the individual normally producing the germ cells (the sporophyte): a non-polyploid, diploid organism as represented by most higher plants and animals would be described as 2n=2x with the number of chromosomes given. Polyploids still have 2n chromosomes, but more than two genomes, so a triploid with three genomes would be 3x; a tetraploid, 4x; a pentaploid, 5x; a hexaploid, 6x; an octaploid, 8x; or a dodecaploid, 12x. Many plant species are polyploid, and they can include multiple chromosome sets from one (autopolyploids) or more than one (allopolyploids) ancestral species. The group of species including wheat, rye, and barley (the grass tribe Triticeae) is a good example where many polyploid forms are known. The base chromosome number is x=7, found in the diploid species barley (Hordeum vulgare, 2n=2x=14), for example. The crop bread wheat, Triticum aestivum, is a hexaploid species with six sets each of seven chromosomes, and is designated as 2n=6x=42. A pentaploid with an additional chromosome (made perhaps by crossing a tetraploid with hexaploid wheat) would have a chromosome constitution of 2n=5x=35. Autotetraploids contain four sets of chromosomes from the same species of origin, and so they have double the chromosome number of their diploid ancestor. Sometimes, autopolyploids are classified in the same species as the diploid, and they may be fertile; there are morphologically similar diploid, 2n=2x=14, and tetraploid, 2n=4x=28, forms of the wall barley, Hordeum murinum. Allotetraploids contain four sets of chromosomes, but in contrast to autotetraploids, the four chromosome sets are derived from two distinct parental species (eg, in an intergeneric hybrid). Where the parental species are known, the allotetraploid species or individual can be described as amphidiploid or amphipolyploid. Allotetraploids include oilseed rape, Brassica napus, 2n=4x=38.

Detection of polyploidy

Examination and counting of chromosome number by light microscopy is used to detect straightforward cases of polyploidy in cells or species: a multiple or sum of the number of chromosomes in related (diploid) species will be counted. Measurement of the DNA content of nuclei, finding a stepped series with increase in size equivalent to the size of the x, haploid, genome, is also used to measure ploidy. Other methods to test for polyploidy include construction of haploids that reach meiosis and show bivalent formation between the ancestral chromosome sets, or crossing of the polyploid to a suspected diploid ancestor; bivalents will pair between the ancestor and one genome in the polyploid (although chromosomes of an autopolyploid could pair with themselves leaving the suspected ancestral chromosomes as univalents). Molecular cytogenetic methods including in situ hybridization using species-specific repetitive DNA sequences or genomic DNA are proving valuable to analyze the constitution of allopolyploids. Duplications in the genome may involve ancestral polyploidy, but chromosomal aberration, aneuploidy, and sequence duplication can also occur; indeed, polyploids often tolerate aneuploidy well, and the occurrence of monosomic lines, where one chromosome is missing from a plant’s karyotype, is good evidence for polyploidy. With the wide application of DNA markers and sequencing methods, many whole-genome duplication and polyploid events that were not expected by scientists are being detected: dense molecular marker maps show the duplication of whole chromosome sets in species that were not previously considered as polyploids – the diploid Brassica mustards are of hexaploid origin (and thus, the cultivated B. napus (oilseed rape, canola) is a dodecaploid with originally 12 chromosome sets). Nevertheless, detection of polyploidy is often difficult because diploid relatives or ancestors no longer exist, and genetic mechanisms restore pseudodiploid behavior, involving strictly homologous chromosome pairing, so even amphidiploids may be fully fertile. Without such mechanisms, chromosomes will produce an assortment of pairing configurations, including trivalents and quadrivalents, which will not assort regularly to give balanced gametes. Where there is clear evidence of polyploidy in the ancestry, but it is both ancient and accompanied by diploid-like behavior, species may be referred to as having a palaeopolyploid origin.

Palaeopolyploidy in evolution

Polyploidy, involving the presence of multiple copies of identical or similar chromosome sets in one species, is an important feature of species evolution in the plant, animal, and fungal kingdoms. Polyploidy is widely considered as an enabling force in evolution. Because chromosome sets are duplicated in polyploids, heterozygosity may be fixed, and random mutation or factors modulating gene expression may be buffered (unlike a diploid), so new genes and gene functions may evolve, leaving the original function in the other chromosome set. More than 50% of plants are obvious polyploids, while detailed studies are showing that many other species are palaeopolyploids with repeated rounds of whole-genome duplication during evolution. Polyploidy, though, does not feature in the evolution of the other major plant group, gymnosperms, and very few recent polyploid gymnosperms have been discovered. In animals, polyploid species are well known among leeches, brine shrimp, and lizards, although many of these reproduce asexually as meiotic chromosome pairing is irregular. Detailed comparison of the gene content of chromosomes of animals combined with comparative analysis of chromosomes and genes in distantly related species is giving evidence of whole-genome duplication or palaeopolyploidy: in the evolutionary split of vertebrates from invertebrates, there are two rounds of polyploidy detected (one occurring after the split of the lampreys), with more recent whole-genome duplications in the Xenopus and fish lineages. In the fungi, there are examples of both autopolyploids (including asexually reproducing lines of the baker’s yeast Saccharomyces cerevisiae), allopolyploids and palaeopolyploids.

Origin of polyploidy

Polyploidy may occur spontaneously in cells, either because of abnormal divisions or as part of differentiation. Fertilization involving unreduced (2n) gametes is a frequent source of triploid and tetraploid organisms: a meiotic division fails or a polar body is not expelled, giving a 2n gamete. Fertilization by two male gametes may give triploids. In humans, triploid (2n=3x=69) and tetraploid conceptuses (2n=4x=92) (arising from both mechanisms) are found in as many as 20 and 6%, respectively, of spontaneous abortions. Polyploid cells and organisms can be made by treatment of cells with mitotic inhibitors (such as colchicine) which enable chromosome replication to occur without cell division.

Polyploidy in crop plants

The world’s four most important crops provide examples of the range of ploidy levels found in plants. Bread wheat is a hexaploid (2n=6x=42), derived as little as 30,000 years ago from a diploid species (2n=2x=14), Triticum tauschii, and a tetraploid, durum wheat (2n=4x=28), Triticum turgidum, itself derived from two diploid species Triticum monococcum and a species similar to Aegilops speltoides. The second most important crop, rice, is considered diploid, while molecular mapping data, the fertility of monosomic chromosome lines, cytogenetic comparisons with wild species, and some chromosome pairing data show that maize, the third most important crop, is a palaeotetraploid. Banana, another important crop, is cultivated as a triploid (2n=3x=33) to give sterile fruit with parthenocarpic development. A few “new” crops have been generated as synthetic hybrids: the wheat rye amphidiploid Triticale is widely grown in dry and colder areas of Canada and Poland. In horticulture, polyploids, whether species, natural, or artificial hybrids, are widely selected by breeders, not least because the fruit tends to be larger than that found in the diploid ancestor, as is found in strawberry and blueberry.

Polyploid cell types

Many normal individual plants and animals include polyploid cells with specialized functions, in particular those with secretory or nutritional functions. The reason why this endoreduplication of the genome (up to 1000 times or more, where the chromosomes replicate but there is no cell division) is needed for these functions is unclear. Examples include the mammalian placenta, salivary glands in some insects, or the tapetum surrounding the haploid pollen grains in plants. In many mammalian cancers, where cell division becomes unregulated, polyploid cells are also found, presumably as a consequence of decoupling of DNA replication and the cell cycle.

 

Relevant reading

Frawley LE, Orr-Weaver TL. 2015. Polyploidy. Current Biology 25 (9), R353–R358.

Heslop-Harrison JS. 2012. Genome evolution: Extinction, continuation or explosion? Current Opinion in Plant Biology 15 (2), 115–121.

Jiao Y, Wickett NJ, Ayyampalayam S. et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473 (7345), 97–100.

Renny-Byfield S, Wendel JF. 2014. Doubling down on genomes: Polyploidy and crop plants. American Journal of Botany 101 (10), 1711–1725.

FROM: Heslop-Harrison JS. 2017. Polyploidy. In: Reference Module in Life Sciences, Elsevier, ISBN: 978-0-12- 809633-8, http://dx.doi.org/10.1016/B978-0-12-809633-8.06934-X (££$$€€) (see https://www.elsevier.com/solutions/sciencedirect/content/reference-modules for information about the series.)

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Allowing pseudoscience into EU risk assessment processes is eroding public trust in science experts and in science as a whole- The bigger picture

Ducking Stool in the church of my home region, Leominster, Herefordshire, as used to try witches. (CC John Phillips geograph.org.uk)

Ducking Stool in the church of my home region, Leominster, Herefordshire, as used to try witches. (CC John Phillips geograph.org.uk)

329. Dietrich DR, Dekant W, Greim H, Heslop-Harrison P, Berry C, Boobis A, Hengstler JG, Sharpe R. 2016. Editorial: Allowing pseudoscience into EU risk assessment processes is eroding public trust in science experts and in science as a whole: The bigger picture. Chemico-Biological Interactions 257: 1-3. 21 July 2016.

http://dx.doi.org/10.1016/j.cbi.2016.07.023 ($$££€€). Author version pasted below. See also https://molcyt.org/2016/07/25/eu-safety-regulations-dont-mar-legislation-with-pseudoscience/ for associated correspondence in Nature.

It is time to end the influence of pseudoscience and pseudoscientists, including some self-appointed public advocacy groups, on European legislation. We advocate this not because of what the chemical industry may want or not want, but because it is the most credible, scientifically-sound and societally-beneficial solution, utilising well-defined and transparent processes of evidence gathering, weighing and risk assessment that should be at the core of decisions that support all legal procedures. This system is what has been developed, tried and tested in Europe over the years and is demonstrably protective of human health. Thus this surely should have been the aim of the European Commission in its decision on the criteria for EDCs in the regulation of biocides and pesticides.

Author text:

  1. Dietrich DR, Dekant W, Greim H, Heslop-Harrison P, Berry C, Boobis A, Hengstler JG, Sharpe R. 2016.Editorial: Allowing pseudoscience into EU risk assessment processes is eroding public trust in science experts and in science as a whole: The bigger picture. Chemico-Biological Interactions 257: 1-3. 21 July 2016. http://dx.doi.org/10.1016/j.cbi.2016.07.023

Allowing pseudoscience into EU risk assessment processes is eroding public trust in science experts and in science as a whole: The bigger picture

Daniel R. Dietrich*, Wolfgang Dekant Helmut Greim Pat Heslop-Harrison Sir Colin Berry, Alan Boobis, Jan Hengstler and Richard Sharpe

doi:10.1016/j.cbi.2016.07.023

Imagine we are beamed back into the 12th century and are staying overnight at a country tavern. We by our clothes met with both curiosity and hostility from the tavern regulars. In the middle of the night we are roughly wakened by the owner and some of his men and directly accused of having stolen from one of the regulars after first poisoning him. Despite our protests and the lack of any reasonable proof we are accused of being thieves and murderers and are subjected to trial by ordeal to prove our innocence.

The trial takes the form of having our hands and feet tied and being thrown into the river; if we sink and drown we are obviously guilty, however if we float God has recognized our innocence and lets us live (judicium Dei). To a scientist, it seems likely we would drown.

Thankfully, over the past 800 years the development of the judicial system has brought us to the point where an accused is considered innocent until proven guilty. Whether the context is Criminal, where a “beyond reasonable doubt” standard of proof is required, or Civil, where the “balance of probability” is the standard, the burden of proof lies with the accusing party, but in either case is based on objective evidence.

If we were in the tavern now, it would be necessary for the accuser (or his legal representative) to prove, beyond reasonable doubt in this case, that we had poisoned the man and stolen the goods from him. In practice, the onus of the demonstration of proof on the accuser is not restricted to criminal cases but applies to many legal procedures in democracies.

Unfortunately Europe, in the application of its legislation relating to chemicals, is in danger of falling back into the medieval approach. The most recent example is the advocacy group- [1], media- and NGO- [2] driven move to have glyphosate banned, despite solid evidence and multiple expert assessments [3], [4] and [5] that this herbicide is without risk to consumers and is the herbicide with the least negative environmental and health impact. The “public” is being misled by pseudoscientists to believe that the compound is highly dangerous to humans and the environment, a claim that runs counter to the evidence and to expert (critical) assessment of that evidence. The media are rife with quotes from poorly informed and often scientifically less well-informed politicians and others who had analysed their water, urine, beer, and vegetables and reported trace amounts of glyphosate, four-thousand-fold below potentially harmful levels for humans [6]. Under this onslaught of misinformation, decision-makers may prefer to disregard evidence-based data that contradict a precautionary viewpoint.

In a similarly misleading vein, there have been seemingly endless discussions about “endocrine disrupters” and their postulated human health effects, based on association studies. For these to be causal, they require us to accept that extremely low-level exposures cause effects in humans, whereas most of the experimental data indicate such exposures are without effect. Most recently, the debate on “endocrine disruptors” has shifted focus to the concept that doses of these compounds below their ‘no-observed-effect level’ (in animal and in vitro studies) can cause adverse effects (so-called non-monotonic dose-response curves) [7], even though the evidence that endocrine systems can be perturbed in this way just does not exist; indeed, there is ample human data on abnormally low hormone exposures that tell us this is not how such systems work. However, this detailed evidence is being ignored and the most prominent proponents of endocrine disruption-mediated human health effects are now using this to argue that hazard identification alone is necessary for regulatory purposes [7]. However, hazard characterization, including potency evaluation, and exposure assessment are the principles on which the protection of humans from adverse effects of environmental chemicals is undertaken, and has proved to be very effective. This is also the consensus approach recommended for endocrine disrupters [8]. This is a logical path that demands detailed evidence gathering and weighing of the science that then forms the basis of the information on which the legal process is based. Do we want to throw this trusted and tried process away?

Relying on hazard identification alone relieves the “accusing party” of the burden of proof (i.e. obtaining the evidence) and allows for endless new allegations of potential effects on human health, for which evidence is not required – it is simply assumed to be present. We don’t think that any of us would like our doctors to use similar approaches for looking after our health; no, doctors want evidence of what is wrong so that they can target it specifically to restore normal health. The consequences of doing otherwise can be fatal [9]. What about the wider implications of a hazard-based approach? Will we ban cars or aeroplanes because they are clearly hazardous, or oxygen and water because they are hazardous to human health? In this regard, the putative hazard has now changed; now endocrine disrupters are being advocated as a prime cause for obesity and type II diabetes [10]. How credible is this? We know that obesity and type II diabetes can often be corrected by reducing appetite, food intake and additional exercise, difficult though this may be, but what evidence is there that reducing exposure to so-called endocrine-disrupting ‘obesogens’ can reduce the incidence of obesity and type II diabetes? There is no such evidence, yet we are asked to believe that ‘obesogens’ are an important human health risk and because of this should be the major focus of future research and regulation efforts in this area [11]. Like medieval justice, the accusing (scaremongering) party never faces the consequences of their accusations or allegations. On the contrary, the accusing party will benefit from the uncertainty introduced. However, any damages incurred, whether these be to human health, through unintended consequences, society or the economy [12], are common good and not the responsibility of the accusing party.

These trends are testimony to the apparent movement to overturn the use of verifiable facts and evidence-based risk assessment in regulation and politics. Further, they undermine the concept of burden of proof, central to our judicial systems, developed over the past centuries. Indeed, arguably, undue emphasis on hazard identification alone has already found its way into some EU chemicals legislation, ignoring more informative weight of evidence and risk assessment approaches, based on sound science, that have served society well over the years. Indeed, it is not merely chemical risk assessment that is currently at stake, it is science as a whole. Reports of the lack of reproducibility of published scientific findings [13] and public disagreement among scientists (and pseudoscientists) on the dangers of compounds, despite good evidence to the contrary, erodes public trust in scientists, and science as a whole – few without scientific training realize that science progresses by the detection of, and subsequent elimination of, errors. This is why acting on findings in isolation, all too common an occurrence today, is an unsound strategy. Perhaps equally important, failure of decision makers to recognise this, leads to unnecessarily restrictive and potentially damaging regulation.

Arguments such as those we voice above are now routinely attacked, sometimes with blatant disregard for the facts and scientific evidence provided, on the basis that ‘this is what the chemical industry wants, so these authors must be speaking on behalf of that industry’ or worse ‘these scientist must be paid by industry, thus are corrupt and therefore trivialize hazards’ [14], [15] and [16]. This is not the case! But such unwarranted accusations of conflicts of interest in the absence of robust scientific evidence to support their assertions [17] and [18], have become the mode du jour in such disputes [19]. In some cases, this has resulted in conflict of interest policies that could lead to an overall lack of scientific balance among the group of experts considered not to be thus conflicted. A number of NGO’s have an interest in maintaining public concerns about specific issues, and indeed may rely on such concerns for charitable donations. Hence, there is a strong motivation to disregard data that contradicts a precautionary point of view. Regrettably, some scientists appear to put the need to obtain research funding above the objective appraisal of the evidence. Unlike potential financial bias, these possible conflicts of interest [19] are rarely considered in such debates. But these attitudes can distort opinions provided to organisations such as EFSA, WHO, WHO/IARC, EPA and others. The consequence is that scientific argument and weight of evidence that might disagree with the initial allegation or accusation, can be undermined. This process damages the credibility of governmental organizations and the well-developed processes that are the very foundations of our society and our well-being. Simply following the discussion on the alleged effects of MMR vaccine on autism provides ample evidence of this [20].

For sure, the chemical industry has every interest in protecting its products and profits, and will lobby to this effect. However, to ensure longevity of their products and to avoid litigation, industry is as interested in an evidence-based approach to risk assessment as we are, and collecting the evidence is a huge and expensive task that industry has to undertake, as is mandated by the regulating authorities, to justify the safety of its products. Is it sensible to say “No” to such evidence and instead to assume that if a chemical is hazardous it should be banned, irrespective of how low the concentrations are that we, the public, are exposed to? In essence, we would be saying that an evidence-based approach is not as good as a presumptive approach based on no evidence. This is to throw away scientific principles and good practice and to replace it with something akin to witchcraft.

It is time to end the influence of pseudoscience and pseudoscientists, including some self-appointed public advocacy groups, on European legislation. We advocate this not because of what the chemical industry may want or not want, but because it is the most credible, scientifically-sound and societally-beneficial solution, utilising well-defined and transparent processes of evidence gathering, weighing and risk assessment that should be at the core of decisions that support all legal procedures. This system is what has been developed, tried and tested in Europe over the years and is demonstrably protective of human health. Thus this surely should have been the aim of the European Commission in its decision on the criteria for EDCs in the regulation of biocides and pesticides [21].

References

[1] A.T.W.I Action, Protect Our Health, Stop Monsanto (2016)

[2] P.A.N. Europe Environmental NGOs Press Charges Against Monsanto German government institute and European Food Safety Authority (2016)

[3] J. FAO/WHO Pesticide residues in food 2016 J. FAO/WHO (Ed.), Special Session of the Joint FAO/WHO Meeting on Pesticide Residues, JMPR FAO/WHO (2016), p. 123

[4] B.f. Risikobewertung The BfR Has Finalised its Draft Report for the Re-evaluation of Glyphosate BfR, Berlin (2015)

[5] E.F.S. Authority Conclusion on the peer review of the pesticide risk assessment of the active substance glyphosate EFSA J., 13 (2015), pp. 4302–4408

[6] B.f. Risikobewertung Glyphosate in Urine – Concentrations Are Far below the Range Indicating a Potential Health Hazard Opinion No. 014/2013Berlin (2013)

[7] E. News Society Leaders Help Inform International EDC Regulations (2016)

[8] R. Solecki, A. Kortenkamp, Å. Bergman, I. Chahoud, G.H. Degen, D.R. Dietrich, H. Greim, H. Håkansson, U. Hass, T. Husoy, M. Jacobs, S. Jobling, A. Mantovani, P. Marx-Stoelting, A. Piersma, R. Slama, R. Stahlmann, M. van den Berg, R.T. Zoeller, A.R. Boobis Scientific principles for the identification of endocrine disrupting chemicals – a consensus statement Environ. Health Perspect. (2016) (in press)

[9] P. Posadzki, A. Alotaibi, E. Ernst Adverse effects of homeopathy: a systematic review of published case reports and case series. Int. J. Clin. Pract., 66 (2012), pp. 1178–1188

[10] J. Legler, T. Fletcher, E. Govarts, M. Porta, B. Blumberg, J.J. Heindel, L. Trasande Obesity, diabetes, and associated costs of exposure to endocrine-disrupting chemicals in the European Union J. Clin. Endocrinol. Metab., 100 (2015), pp. 1278–1288

[11] J.J. Heindel et al. Parma consensus statement on metabolic disruptors Environ. Health, 14 (2015), p. 54 http://dx.doi.org/10.1186/s12940-015-0042-7

[12] D.R. Dietrich, W. Dekant, H. Greim, P. Heslop-Harrison, C. Berry, A. Boobis, J. Hengstler, R.M. Sharpe Don’t mar legislation with pseudoscience. Nature, 535 (2016), p. 355

[13] M. Baker 1,500 scientists lift the lid on reproducibility. Nature, 533 (2016), pp. 452–454

[14] J. Garwood Do toxic editors trivialise hidden hazards? Lab. Times, 3 (2014), pp. 39–42

[15] S. Horel A Toxic Affair: Season Finale Corporate Europe Observatory (2016)

[16] S. Horel, B. Bienkowsi Special Report: Scientists Critical of EU Chemical Policy Have Industry Ties (2013) Environmental Health News

[17] R. Slama, J.P. Bourguignon, B. Demeneix, R. Ivell, G. Panzica, A. Kortenkamp, T. Zoeller Scientific issues relevant to setting regulatory criteria to identify endocrine disrupting substances in the European Union Environ. Health Perspect. (2016) http://dx.doi.org/10.1289/EHP217

[18] P. Grandjean, D. Ozonoff Transparency and translation of science in a modern world Environ. Health, 12 (2013), p. 70

[19] D.R. Dietrich, J.G. Hengstler Conflict of interest statements: current dilemma and a possible way forward Arch. Toxicol. (2016) http://dx.doi.org/10.1007/s00204-016-1783-y

[20] P. Hobson-West ‘Trusting blindly can be the biggest risk of all’: organised resistance to childhood vaccination in the UK Sociol. Health Illn., 29 (2007), pp. 198–215

[21] E. Commission Press Release 15.06.2016: Commission Presents Scientific Criteria to Identify Endocrine Disruptors in the Pesticides and Biocides Areas European Commission, Bruxelles (2016)

*Corresponding author.

Daniel R. Dietrich Human and Environmental Toxicology, University of Konstanz, 78457 Konstanz, Germany

Wolfgang Dekant Department of Toxicology, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany

Helmut Greim Technical University of Munich, Hohenbachernstr. 15-17, 85354 Freising-Weihenstephan, Germany

Pat Heslop-Harrison Department of Genetics, University Road, University of Leicester, LE1 7RH, United Kingdom

Sir Colin Berry Queen Mary – Pathology, Queen Mary, London, London E1 4NS, United Kingdom

Alan Boobis Department of Medicine, Hammersmith Campus, Imperial College London, London W12 0NN, United Kingdom

Jan Hengstler Department of Toxicology, IfADo, Ardeystrasse 67, 44139 Dortmund, Germany

Richard Sharpe MRC Centre for Reproductive Health, 47 Little France Crescent, University of Edinburgh, Edinburgh EH16 4TJ United Kingdom

Available online 21 July 2016

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EU safety regulations – Dont mar legislation with pseudoscience

328. Dietrich DR, Dekant W, Greim H, Heslop-Harrison P, Berry C, Boobis A, Hengstler JG, Sharpe R. 2016. EU safety regulations: Don’t mar legislation with pseudoscience. Nature 535: 355 (21 July 2016) doi:10.1038/535355c

We are concerned that some of the European Union’s processes for setting safety regulations for chemicals are being influenced by media and pseudoscience scaremongering. Pseudoscience has no place in such decisions, which should be based purely on well-defined and transparent evidence.

For example, endocrine disruptors are being blamed for obesity and type 2 diabetes (J. Legler et al. J. Clin. Endocrinol. Metab. 100, 12781288; 2015) despite the absence of supporting evidence for this, and despite food and sugar over-consumption being established as a proven cause. As a consequence, the European Commission’s criteria for regulating endocrine-disrupting compounds as a threat to human health are based on correlational, not causal, studies (see go.nature.com/29rjlik).

Conflicts of interest can contribute to the problem, beyond the commercial motivation of industry. Some non-governmental organizations might need to maintain public concerns to boost charitable donations. Decision-makers might prefer to disregard evidence-based data that contradict a precautionary viewpoint. And some scientists put securing research funds above objective appraisal of the evidence.

Acting on hazard identification alone relieves the scaremongering party of the burden of proof, when harm is simply assumed. As a result, regulations can become unnecessarily restrictive. They may even be damaging, for example if an agricultural ban were to be imposed on triazole fungicides because of their endocrine-disrupting potential. The risk to humans at such levels of exposure would be negligible (J. E. Chambers et al. Crit. Rev. Toxicol. 44, 176210; 2014). It makes no sense to override such evidence with a blanket ban on potentially hazardous chemicals that ignores the public’s demonstrable low level of exposure.

http://www.nature.com/nature/journal/v535/n7612/extref/535355c-s1.pdf

 

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Molecular Cytogenetics Group – an infographic of what we do

Infographic: what we do in the Molecular Cytogenetics Research Group

Infographic: what we do in the Molecular Cytogenetics Research Group

Infographic: what we do in the Molecular Cytogenetics Research Group

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Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance

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324. Ali N, Heslop-Harrison JS, Ahmad H, Graybosch RA, Hein GL, Schwarzacher T. 2016. Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance. Heredity (2016) 117, 114–123; published online 1 June 2016 doi:10.1038/hdy.2016.36

Author version: N_Ali_et al 2016 Multiple Alien Introgressions in Wheat

Publisher site: http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy201636a.pdf

Pyramiding of alien-derived Wheat streak mosaic virus (WSMV) resistance and resistance enhancing genes in wheat is a cost-effective and environmentally safe strategy for disease control. PCR-based markers and cytogenetic analysis with genomic in situ hybridization were applied to identify alien chromatin in four genetically diverse populations of wheat (Triticum aestivum) lines incorporating chromosome segments from Thinopyrum intermedium and Secale cereale (rye). Out of twenty experimental lines, ten carried Th. intermedium chromatin as T4DL*4Ai#2S translocations, while, unexpectedly, seven lines were positive for alien chromatin (Th. intermedium or rye) on chromosome 1B. The newly described rye 1RS chromatin, transmitted from early in the pedigree, was associated with enhanced WSMV-resistance. Under field conditions, the 1RS chromatin alone showed some resistance, while together with the Th. intermedium 4Ai#2S offered superior resistance to that demonstrated by the known resistant cultivar Mace. Most alien-wheat lines carry whole chromosome arms, and it is notable that these lines showed intra-arm recombination within the 1BS arm. The translocation breakpoints between 1BS and alien chromatin fell in three categories: 1) at or near to the centromere, 2) intercalary between markers UL-Thin5 and Xgwm1130, and 3) towards the telomere between Xgwm0911 and Xbarc194. Labelled genomic Th. intermedium DNA hybridized to the rye 1RS chromatin under high stringency conditions, indicating the presence of shared tandem repeats among the cereals. The novel small alien fragments may explain the difficulty in developing well-adapted lines carrying Wsm1 despite improved tolerance to the virus. The results will facilitate directed chromosome engineering producing agronomically desirable WSMV-resistant germplasm.

KEYWORDS

Fluorescent in situ hybridization, molecular markers, wheat, Thinopyrum intermedium, rye, Wheat streak mosaic virus

 

Author version: N_Ali_et al 2016 Multiple Alien Introgressions in Wheat

Publisher site: http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy201636a.pdf

 

 

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Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida flowers: sequenced by a consortium including the MolCyt,.com lab

Petunia hybrida flowers: sequenced by a consortium including the MolCyt.com lab

325b. Bombarely, Moser M, Amrad A, Bao M, Bapaume L, Barry CS,  Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D’Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus S, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C. 2016. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants 2: article number 16074.

http://dx.doi.org/10.1038/nplants.2016.74

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n=14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization, the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee- to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral color patterns and pollination systems. The high quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.

 

See also related / supplementary manuscript from Molecular Cytogenetics lab.

 

 

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Analysis of Petunia vein clearing virus (PVCV) sequences, retroelements and tandem repeats in Petunia axillaris N and P. inflata S6

PetuniaNaturePVCVchromosomes.jpg325a. Schwarzacher T, Heslop-Harrison JS, Richert-Pöggeler KR. 2016. Analysis of Petunia vein clearing virus (PVCV) sequences, retroelements and tandem repeats in Petunia axillaris N and P. inflata S6. Supplementary manuscript 2. Nature Plants 2: article number 16074.

Link to manuscript: Petunia_PVCV_Repeats_SchwarzacherEtAl2016

Within the genome sequence assemblies of P. axillaris (PaxiN) and P. inflata (PinfS6) and unassembled reads, we analysed the occurrence of endogenous Petunia vein clearing virus (PVCV) sequences, other endogenous pararetrovirus (EPRV) sequences, LTR-retroelements, and tandem repeats. Petunia genomes show substantial diversity in their pararetroviral sequences as revealed in searches using the polymerase motif. Homologies to two genera of Caulimoviridae, Petu- and Florendoviruses, with more than 60% amino acid identity, were present in both species. Almost complete PVCV copies, fragments, and degenerate copies, sometimes in tandem arrays, were found. PVCV motifs were more frequent in P. axillaris, with the results seen in the assemblies confirmed by in situ hybridization of PVCV fragments to metaphase chromosomes indicating that P. axillaris is likely a more permissive host for EPRVs. LTR-retroelements are localised near centromeres; about 6500 full length elements were found in the PinfS6 assembly while 4500 were in PaxiN. Apart from rDNA, microsatellites and telomeric sequences, no highly abundant tandem repeats were identified in the assembly or raw reads. Repeat cluster analysis indicates that LTR-retroelements are associated with simple sequence repeats and low complexity DNA families and that repeats within Petunia are very diverse, with none having amplified to form a major proportion of the genome. The repeat landscape of Petunia is different from other species of Solanaceae, in particular the x=12 crown group including Solanum and Nicotiana, with a relative low proportion of total repeats for a genome size of 1.4Gb, x=7, and a high degree of genome plasticity.

Link to manuscript: Petunia_PVCV_Repeats_SchwarzacherEtAl2016

Supplementary manuscript 2 from

325b. Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS,  Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D’Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus S, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C. 2016. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants 2: article number 16074. doi:10.1038/nplants.2016.74

http://dx.doi.org/10.1038/nplants.2016.74

 

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