Genetic relationships among wild and cultivated blackberries (Rubus caucasicus L.) based on amplified fragment length polymorphism markers

Abstract

Rubus is a large genus of flowering plants in the rose family, Rosaceae, subfamily Rosoideae. The blackberries, as well as various other Rubus species with mounding or rambling growth habits, are often called brambles. Little information is available on the genetic diversity of wild-grown blackberries. The objective of this study was to determine the genetic relationships among nine promising (high-yield capacity, free of pest and diseases, better fruit traits) wild blackberry (Rubus caucasicus L.) selections and the well-known cultivar, “Chester” by using amplified fragment length polymorphism (AFLP) markers. Genotypes were evaluated with three selective primer-enzyme combinations, producing a total of 223 AFLP fragments with 53% polymorphism ratio. Clustering of genotypes using unweighted pair-group method of arithmetic average cluster analysis clearly separated groups of wild blackberry genotypes while the variety “Chester” was clustered independently. Wild selections represented a distinct germplasm source on the basis of the estimated genetic distance among them. Genetic diversity data from this study will be helpful in using and exploiting the wild genetic material for breeding purposes as well as for further research.     

What's in a name; Genetic structure in Solanum section Petota studied using population-genetic tools

Background  

The taxonomy and systematic relationships among species of Solanum section Petota are complicated and the section seems overclassified. Many of the presumed (sub)species from South America are very similar and they are able to exchange genetic material. We applied a population genetic approach to evaluate support for subgroups within this material, using AFLP data. Our approach is based on the following assumptions: (i) accessions that may exchange genetic material can be analyzed as if they are part of one gene pool, and (ii) genetic differentiation among species is expected to be higher than within species.     

A generalised approach to the study and understanding of adaptive evolution

Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does the inheritance of molecular epigenetic changes fit into mainstream evolutionary theory? Is niche construction an evolutionary process? Is local adaptation via habitat choice also adaptive evolution? These examples suggest there is scope (and perhaps even a need) to broaden our views on evolution. We identify three aspects whose incorporation into a single framework would enable a more generalised approach to the understanding and study of adaptive evolution: (i) a broadened view of extended phenotypes; (ii) that traits can respond to each other; and (iii) that inheritance can be non-genetic. We use causal modelling to integrate these three aspects with established views on the variables and mechanisms that drive and allow for adaptive evolution. Our causal model identifies natural selection and non-genetic inheritance of adaptive parental responses as two complementary yet distinct and independent drivers of adaptive evolution. Both drivers are compatible with the Price equation; specifically, non-genetic inheritance of parental responses is captured by an often-neglected component of the Price equation. Our causal model is general and simplified, but can be adjusted flexibly in terms of variables and causal connections, depending on the research question and/or biological system. By revisiting the three examples given above, we show how to use it as a heuristic tool to clarify conceptual issues and to help design empirical research. In contrast to a gene-centric view defining evolution only in terms of genetic change, our generalised approach allows us to see evolution as a change in the whole causal structure, consisting not just of genetic but also of phenotypic and environmental variables.     

“It just becomes much more complicated”: Genetic counselors' views on genetics and prenatal testing

Many social scientists and commentators have expressed concerns about the acceleration of genetic medicine and testing in the last few decades. While there is a growing body of work on how patients and the lay public view the potential of genetic medicine, there remains relatively little social science research on the personal and professional views of master's-trained genetic counselors, a growing profession of clinicians who are often the key medical actors translating increasingly complex genetic information to patients. This study begins to fill in this lacuna by examining the perspectives of 26 genetic counselors in the USA on some of the central bioethical concerns raised by genetic testing, with a particular focus on prenatal testing. The study finds that while there is general enthusiasm for genetic medicine, and prenatal testing in particular, genetic counselors also have reflexive ambivalence, expressing both skepticism and concern about the usefulness and consequences of acquiring genetic information.     

On the role of chemical systems in the microphysical aspects of primary genetic mechanisms

It is pointed out that two fundamentally different views of primary genetic processes occur in the literature which are frequently confused. The first is a true communication-theoretic view, which regards the genetic apparatus as containing a real information-source and a transducer which converts that information to useful form. The second view is generally expressed as a template scheme based on the Watson-Crick model; it is shown that in this model there is actually no such thing as genetic information in a communication-theoretic sense. Both views are then discussed on the basis of microphysical principles developed in previous work of the author (Bull. Math. Biophysics,22, 227–255, 1960) in an attempt to find which approach is in closer accord with the biological facts. It is shown that, if the communication-theoretic view is correct, then the information-bearing object must act as a “catalyst,” but it is pointed out that the type of catalysis involved must be of a fundamentally different nature than that occurring in familiar enzyme-catalyzed reactions. On the basis of general considerations of irreversible changes in microphysical measuring systems, it is shown that any type of template must suffer a gradual and irreversible denaturation, which seems to make it unlikely that a template could play a primary role in fundamental genetic processes. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Contract AF 49(638)-917.     

The importance of reproductive strategies in population genetic approaches to conservation: an example from the marine angiosperm genus Zostera

Knowledge of the levels of genetic diversity maintained in natural populations can play a central role in conservation programmes, particularly in threatened habitats or species. Fluctuations in population size can lead to loss of variation and, consequently, increase the risk of extinction. We have examined whether such a genetic bottleneck has occurred in populations of two species in the seagrass genus Zostera, which are believed to have been affected by an outbreak of wasting disease at the start of the last century. A test for heterozygote excess at five nuclear microsatellite loci did not suggest the occurrence of a genetic bottleneck, but analysis of seven chloroplast microsatellite loci and sequence data from two regions did suggest a bottleneck in the chloroplast genome. Extremely low levels of between-population diversity suggest that all subpopulations can be treated as a single management unit for each species. Comparable levels of nuclear genetic diversity were found in the three populations of the primarily sexual Zostera marina var. angustifolia studied but a wider range of within-population diversity was found in Zostera noltii, which displays both sexual and vegetative reproductive strategies. This may be due to an increase in sexual recruitment due to localised fresh water inflow into the study site near to the most diverse population. Such populations should be prioritised as source material for any replanting or remediation due to natural or anthropogenic loss of Zostera beds in the area.     

Noninvasive methodology for the sampling and extraction of DNA from free‐ranging Atlantic spotted dolphins (Stenella frontalis)

Genetic sampling and molecular investigations are important parts of studying wild populations. However, collecting tissues from free‐ranging animals can be difficult or impractical. This study develops a sampling and extraction protocol for template DNA from faecal material collected in a marine environment from small cetaceans. DNA was extracted from faecal material of free‐ranging Atlantic spotted dolphins (Stenella frontalis) and subsequently tested for its suitability in molecular investigations by amplifying both mitochondrial and nuclear DNA. The resulting mitochondrial sequences were found to closely match known S. frontalis haplotypes. Three microsatellite loci were amplified and fall within the expected size range for cetaceans. Mother and calf families previously assigned by observation were genetically confirmed using both mitochondrial haplotype and allele sharing between the mother and offspring. The protocol effectively collects and extracts dolphin DNA from faecal samples and enables species identification as well as confirmation of genetic relatedness and should be considered as a noninvasive alternative to current protocols.     

The effects of polymorphisms in genes from the renin–angiotensin, bradykinin, and fibrinolytic systems on plasma t-PA and PAI-1 levels are dependent on environmental context

Thrombosis is a key factor in the pathophysiology of cardiovascular disease. Important biochemical constituents of the fibrinolytic system, affecting thrombosis, include tissue-type plasminogen activator (t-PA) and plasminogen activator inhibitor-1 (PAI-1). Both t-PA and PAI-1 are determined by multiple genetic and environmental factors. We aimed to investigate whether the effects of polymorphism in genes from the renin–angiotensin, bradykinin, and fibrinolytic systems on t-PA or PAI-1 levels are dependent on environmental factors in a large population-based sample from the PREVEND study in Groningen, The Netherlands (n = 2,527). We found strong evidence (P ≤ 0.02) for interaction effects of polymorphisms from the bradykinin receptor (BDKRB2) gene and alcohol consumption on t-PA in females and males and on PAI-1 in males. Only suggestive evidence (P ≤ 0.10) was present for an interaction effect of the BDKRB2 gene and alcohol consumption on PAI-1 levels in females. Another consistent finding was evidence for an interaction between bradykinin receptor (BDKRB2) gene polymorphisms and body size as measured by body mass index and/or waist–hip-ratio. For each gender and for both t-PA and PAI-1 there was at least one BDKRB2–body size combination that exhibited suggestive (P ≤ 0.10), significant (P ≤ 0.04) and/or strong evidence (P ≤ 0.02) for interaction. In conclusion, the genetic architecture of t-PA and PAI-1 is dependent on the environmental context such as body size and alcohol use. The present study emphasizes the importance of including environmental factors in genetic analyses to fully comprehend the genetic architecture of a specific trait. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular ecology and biogeography of mangrove trees towards conceptual insights on gene flow and barriers: A review

In this review the most recent contributions to the field of molecular ecology and biogeography of mangrove trees are considered. Emphasis is on the obtained information of the different molecular marker methods used in mangrove genetics and on the potential to infer biogeographical patterns. Isozymes on average showed low or even no polymorphism in mangrove trees similar as known in seagrasses. The outcrossing Avicennia seems to be the most variable mangrove tree for isozymes. Both low amounts of interpretable allozymes and difficulties in maintaining the enzyme activity have reduced the number of successful studies during the isozyme era. Dominant marker methods (RAPD, AFLP and ISSR) were successful to demonstrate differences in amplified DNA products at large-scale geographical distances within Avicennia species and to estimate species relationships. Hybrid testing seldom revealed hybridization among tree species. The most promising markers (microsatellites or SSR) were only recently developed and will continue to provide evidence in future studies. SSR loci in Avicennia seem to show relatively low levels of polymorphism, though clearly demonstrating that populations located at the edge of the species range can be even more depauperated. Populations located more central in their native range and situated along the same coastline such as reported in Rhizophora, are expected to be only weakly differentiated due to increased levels of gene flow. Haplotypic chloroplast variants (PCR-RFLP) or sequences revealed strong genetic structuring between populations of Avicennia, Kandelia and Ceriops from different biogeographical oceanic regions. Recent views on long-distance dispersal and on gene flow across oceans as well as along the same coastline are discussed. A comparative analysis on genetic variables across species and regions indicated general trends in the partitioning of genetic variation. A conceptual map with a worldwide overview of those regions where high levels of gene flow were reported and of other regions that were considered as effective barriers, is presented. As an aim to increase the number of reliable comparisons of genetic variables across species or regions and to increase the relevance of mangrove genetics for local conservation issues, recommendations on the molecular markers and on the sampling design of individuals and populations are given within a conceptual context of evolutionary significant units.     

Sequential Designs for Genetic Epidemiological Linkage or Association Studies A Review of the Literature

Objectives. The cost of a genetic linkage or association study is largely determined by the number of individuals to be recruited, phenotyped, and genotyped. The efficiency can be increased by using a sequential procedure that reduces time and cost on average. Two strategies for sequential designs in genetic epidemiological studies can be distinguished: One approach is to increase the sample size sequentially and to conduct multiple significance tests on accumulating data. If significance or futility can be assumed with a certain probability, the study is stopped. Otherwise, it is carried on to the next stage. The second approach is to conduct early linkage analyses on a coarse marker grid, and to increase marker density in later stages. Interim analyses are performed to select interesting genomic areas for follow up. The aim of this article is to give a review on sequential procedures in the context of genetic linkage and association studies. Methods. A systematic literature search was performed in the Medline and the Linkage Bibliography databases. Articles were defined as relevant if a sequential design was proposed or applied in genetic linkage or association studies. Results. The majority of proposed study designs is developed to meet the demands of specific studies and lacks a theoretical foundation. A second group of procedures is based on simulation results and principally restricted to the specific simulated situations. Finally, some theoretically founded procedures have been proposed that are discussed in detail. Conclusions. Although interesting and promising procedures have been suggested, they still lack realizations for practical purposes. In addition, further developments are required to adapt sequential strategies for optimal use in genetic epidemiological studies.     

Genetic and chaetal variation in Nais worms (Annelida,Clitellata, Naididae)

The genus Nais is a group of oligochaetous clitellates, common in eutrophic freshwater habitats. About 30 species are described. Species identification is based primarily on chaetal characters, which are often subtle, inconsistent, and even overlapping between nominal species. We investigated the correlation between genetic variation and chaetal morphology in this genus. Eighty‐one individuals from Europe, North America, and China were included in the study. Seventy‐five of these were preserved as vouchers. They were scrutinized with regard to chaetal morphology, and ten different morphotypes were identified. Three molecular markers, two mitochondrial (the COI gene and 16S rDNA) and one nuclear (the ITS region), were used to establish the genetic lineages in the material. Genetic variation was found to be largely congruent with chaetal character patterns. However, at least nine separately evolving lineages (all supported by mitochondrial as well as nuclear data) correspond to at most six nominal species. Four morphotypes/lineages are recognized as Nais barbata, Nais christinae, Nais elinguis, and Nais stolci, respectively, whereas five, or possibly more, lineages represent a morphological continuum covering the variation of the Nais communis/variabilis complex. Thus, cryptic speciation is revealed. Our results indicate that a taxonomic revision of the genus will be needed in the future.     

An insertion sequence unique to Frankia strain ArI5

At the genetic level, understanding of symbiotic nitrogen fixation by Frankia is limited to nif functions that are highly conserved among all organisms. The genetics and biochemistry of nodulation are largely unexplored because of a complete lack of genetic tools. In other bacteria, mobile genetic elements such as insertion sequences (IS) and transposons are commonly used to create mutations and insert new genetic material. We have characterized a 4 kbp segment of DNA from Frankia strain ArI5 that has the hallmarks of a mobile genetic element, inverted repeats flanking a gene encoding a transposase. There are at least six copies of this element in strain ArI5 but none in either strain CcI3 or CpI1. The inverted repeats are 17 nt long and separated by 2156 bp. Within that region are two, overlapping ORFs that each encode a transposase. RT-PCR analysis of RNA from Frankia ArI5 cells conclusively demonstrates the expression of one transposase gene and suggests that both may be transcribed. Numerous attempts to clone the intact IS in E. coli were unsuccessful suggesting that the element may be unstable in this context. A clone containing the complete IS was constructed in E. coli then modified by insertion of the kanamycin (KAN) resistance gene from Tn5. A fragment of DNA including the inverted repeats, transposase genes and KAN gene, was transferred to the suicide vector pJBSD1. The construct, pFRISK, was transformed into E. coli to search for transposition events.     

Genome fidelity during short- and long-term tissue culture and differentially cryostored meristems of silver birch (<Emphasis Type="Italic">Betula pendula</Emphasis>)

Clonal trueness of micropropagated or cryopreserved material is essential, especially with long-living tree species. In this study, the growth rate and morphology of regenerated silver birch (Betula pendula Roth) plants growing in the nursery were evaluated after different treatments: short-term (14 months) and long-term (70 months) tissue culture periods, cryostorage of in vivo buds and cryopreservation of in vitro shoot apices using four different slow cooling cryopreservation protocols with PGD (10% PEG, 10% glucose, 10% DMSO) as cryoprotectant. Genetic fidelity of the regenerated plants compared to the original donor trees was evaluated using RAPD assays together with chromosome analysis. The regenerated plants showed no genetic or phenotypic changes, and can thus be considered as reliable material for any research, breeding or silvicultural activities.     

High-density genetic mapping for coffee leaf rust resistance

Coffee leaf rust caused by the fungus Hemileia vastatrix causes considerable economic losses for coffee producers. Although agrochemical products can provide sufficient disease control, the use of resistant cultivars is a safer alternative. This resistance may be constrained by one or a few genetic factors, mainly those found in material originating from interspecific hybrids. In this study, the genetic analysis of an F ₂ population consisting of 224 plants derived from a crossing of Híbrido de Timor UFV 427-15 (resistant) with Catuaí Amarelo IAC 30 (susceptible) showed that a dominant gene confers the resistance of coffee to race II of H. vastatrix. From a genetic map saturated with 25 amplified fragment length polymorphism (AFLP) markers linked to the resistance gene, we developed a high-density genetic map with six sequence-characterized amplified region (SCAR) markers delimiting a chromosomal region of 9.45 cM and flanking the dominant gene at 0.7 and 0.9 cM. This is the first saturated and high-density genetic map obtained from this region containing the resistance gene. The results of this study are of great importance for the introduction of molecular markers for marker-assisted selection; they will also facilitate studies related to the cloning, structure, and function of race-specific genes involved in the resistance of coffee trees to H. vastatrix.     

The flowering locus Hr colocalizes with a major QTL affecting winter frost tolerance in Pisum sativum L.

An understanding of the genetic determinism of frost tolerance is a prerequisite for the development of frost tolerant cultivars for cold northern areas. In legumes, it is not known to which extent vernalization requirement or photoperiod responsiveness are necessary for the development of frost tolerance. In pea (Pisum sativum L.) however, the flowering locus Hr is suspected to influence winter frost tolerance by delaying floral initiation until after the main winter freezing periods have passed. The objective of this study was to dissect the genetic determinism of frost tolerance in pea by QTL analysis and to assess the genetic linkage between winter frost tolerance and the Hr locus. A population of 164 recombinant inbred lines (RILs), derived from the cross Champagne x Terese was evaluated both in the greenhouse and in field conditions to characterize the photoperiod response from which the allele at the Hr locus was inferred. In addition, the population was also assessed for winter frost tolerance in 11 field conditions. Six QTL were detected, among which three were consistent among the different experimental conditions, confirming an oligogenic determinism of frost tolerance in pea. The Hr locus was found to be the peak marker for the highest explanatory QTL of this study. This result supports the hypothesis of the prominent part played by the photoperiod responsiveness in the determinism of frost tolerance for this species. The consistency of three QTL makes these positions interesting targets for marker-assisted selection. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The spatial genetic structure of the White‐banded Tanager (Aves,Passeriformes) in fragmented Neotropical savannas suggests two evolutionarily significant units

Understanding the genetic structure of a species is crucial for evolutionary biology research and species conservation. The objectives of this study were to investigate the genetic structure of Neothraupis fasciata in Brazilian savannas and to assess genetic differentiation of its disjunct population in the Amazonian savannas of the state of Amapá. Population genetic structure was assessed in relation to isolation by distance and landscape variables connected with habitat heterogeneity. The influences of factors, such as habitat fragmentation and core–periphery distribution, on genetic diversity were also examined. Data were derived from a set of microsatellite loci of adult individuals from nine localities: eight distributed across the Cerrado and one in the disjunct Amazonian savanna of Amapá. Analysis revealed moderate genetic diversity and moderate population genetic structure, with at least two genetic clusters, one of which is represented exclusively by the disjunct Amapá population. The genetic structure found is not the result of significant influences by geographical distance, habitat heterogeneity, or the core–periphery effect, nor by intense biome fragmentation due to anthropic action. The disjunct Amapá population exhibited a moderate level of genetic differentiation compared to the Cerrado population, suggesting that both can be considered distinct evolutionarily significant units for conservation purposes. Abstract in Portuguese is available with online material.     

Synthetic polymers and their potential as genetic materials

DNA and RNA are the only known natural genetic materials. Systematic modification of each of their chemical building blocks (nucleobase, sugar, and phosphate) has enabled the study of the key properties that make those nucleic acids genetic materials. All three moieties contribute to replication and, significantly, all three moieties can be replaced by synthetic analogs without loss of function. Synthetic nucleic acid polymers capable of storing and propagating information not only expand the central dogma, but also highlight that DNA and RNA are not unique chemical solutions for genetic information storage. By considering replication as a question of information transfer, we propose that any polymer that can be replicated could serve as a genetic material. Editor's suggested further reading in BioEssays Xenobiology: A new form of life as the ultimate biosafety tool Abstract     

Cellular “bauplans”: Evolving unicellular forms by means of Julia sets and Pickover biomorphs

The universe of cellular forms has received scarce attention by mainstream neo-Darwinian views. The possibility that a fundamental trait of biological order may consist upon, or be guided by, developmental processes not completely amenable to natural selection was more akin to previous epochs of biological thought, i.e. the “bauplan” discussion. Thirty years ago, however, Lynn and Tucker studied the biological mechanisms responsible for defining organelles position inside cells. The fact that differentiated structures performing a specific function within the eukaryotic cell (i.e. mitochondrion, vacuole, or chloroplast) were occupying specific positions in the protoplasm was the observational and experimental support of the ‘morphogenetic field’ notion at the cellular level. In the present paper we study the morphogenetic field evolution yielding from an initial population of undifferentiated cells to diversified unicellular organisms as well as specialized eukaryotic cell types. The cells are represented as Julia sets and Pickover biomorphs, simulating the effect of Darwinian natural selection with a simple genetic algorithm. The morphogenetic field “defines” the locations where cells are differentiated or sub-cellular components (or organelles) become organized. It may be realized by different possibilities, one of them by diffusing chemicals along the Turing model. We found that Pickover cells show a higher diversity of size and form than those populations evolved as Julia sets. Another novelty is the way that cellular organelles and cell nucleus fill in the cell, always in dependence on the previous cell definition as Julia set or Pickover biomorph. Our findings support the existence of specific attractors representing the functional and stable form of a differentiated cell—genuine cellular bauplans. The configuration of the morphogenetic field is “attracted” towards one or another attractor depending on the environmental influences as modeled by a particular fitness function. The model promotes the classical discussions of D’Arcy Thompson and the more recent views of Waddington, Goodwin and others that consider organisms as dynamical systems that evolve through a ‘master plan’ of transformations, amenable to natural selection. Intriguingly, the model also connects with current developments on mechanobiology, highlighting the informational–developmental role that cytoskeletons may play.     

A series of mutable alleles of the white locus in Drosophila melanogaster

Summary The origin and phenotypes of a number of zeste mutant stocks with mutable white loci are described. Each newly arising form was lighter in eye color than the mutant it originated from. In each case the lighter pigmentation is believed to be due to an increase in genetic material in the proximal region of the white locus, the increase supposedly being the result of unequal crossing over. Some of the mutations which arose in the mutable stocks are reversions. They occurred in males as well as in homo- and heterozygous females. The reversions are believed to be due to a decrease in genetic material in the proximal region of the white locus. The decrease is assumed to be the result of intrachromosomal recombination. At least some of these events took place premeiotically. New mutants which originate frequently from mutable stocks are stable. In addition to the structure of the mutable white locus there is probably at least one still unknown factor which affects its mutability since the frequency of mutations arising in the mutable stocks decreases over the years.     

Eukaryotic checkpoints are absent in the cell division cycle ofEntamoeba histolytica

Fidelity in transmission of genetic characters is ensured by the faithful duplication of the genome, followed by equal segregation of the genetic material in the progeny. Thus, alternation of DNA duplication (S-phase) and chromosome segregation during the M-phase are hallmarks of most well studied eukaryotes. Several rounds of genome reduplication before chromosome segregation upsets this cycle and leads to polyploidy. Polyploidy is often witnessed in cells prior to differentiation, in embryonic cells or in diseases such as cancer. Studies on the protozoan parasite,Entamoeba histolytica suggest that in its proliferative phase, this organism may accumulate polyploid cells. It has also been shown that although this organism contains sequence homologs of genes which are known to control the cell cycle of most eukaryotes, these genes may be structurally altered and their equivalent function yet to be demonstrated in amoeba. The available information suggests that surveillance mechanisms or ‘checkpoints’ which are known to regulate the eukaryotic cell cycle may be absent or altered inE. histolytica.