Changing environments and genetic variation: inbreeding does not compromise short-term physiological responses

Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.2109 ◽

2019 ◽

Vol 286 (1915) ◽

pp. 20192109 ◽

Cited By ~ 1

Author(s):

James Buckley ◽

Rónán Daly ◽

Christina A. Cobbold ◽

Karl Burgess ◽

Barbara K. Mable

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Physiological Responses ◽

Flowering Phenology ◽

Mating Strategies ◽

Relative Fitness ◽

Evolutionary Potential ◽

Short Term ◽

Arabidopsis Lyrata ◽

Physiological Capacity

Selfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce their long-term evolutionary potential. However, appropriate short-term plastic responses to new environmental conditions might not require high levels of standing genetic variation. In this study, we tested whether mating system variation among populations, and associated changes in genetic variability, affected short-term responses to environmental challenges. We compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a perennial plant, Arabidopsis lyrata , under constant growth chamber conditions and an outdoor common garden environment outside its native range. We found no effect of inbreeding on survival, flowering phenology or short-term physiological responses. Specifically, naturally occurring inbreeding had no significant effects on the plasticity of metabolome profiles, using either multivariate approaches or analysis of variation in individual metabolites, with inbreeding populations showing similar physiological responses to outbreeding populations over time in both growing environments. We conclude that low genetic diversity in naturally inbred populations may not always compromise fitness or short-term physiological capacity to respond to environmental change, which could help to explain the global success of selfing mating strategies.

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Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1707492115 ◽

2018 ◽

Vol 115 (4) ◽

pp. 816-821 ◽

Cited By ~ 23

Author(s):

Benjamin Laenen ◽

Andrew Tedder ◽

Michael D. Nowak ◽

Per Toräng ◽

Jörg Wunder ◽

...

Keyword(s):

Genetic Diversity ◽

Mating System ◽

Purifying Selection ◽

Mating Strategies ◽

Genomic Variation ◽

The Arctic ◽

Mixed Mating ◽

Genome Wide ◽

Arabis Alpina ◽

The Impact

Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina. We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina. These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.

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Understanding photothermal interactions will help expand production range and increase genetic diversity of lentil (Lens culinaris Medik.)

10.1101/2020.07.18.207761 ◽

2020 ◽

Cited By ~ 1

Author(s):

Derek M. Wright ◽

Sandesh Neupane ◽

Taryn Heidecker ◽

Teketel A. Haile ◽

Clarice J. Coyne ◽

...

Keyword(s):

Genetic Diversity ◽

Lens Culinaris ◽

Photoperiod Sensitivity ◽

Future Climate Change ◽

Climate Change Scenarios ◽

List Type ◽

Exotic Germplasm ◽

Breeding Programs ◽

Wide Range ◽

Production Areas

SummaryLentil (Lens culinaris Medik.) is cultivated under a wide range of environmental conditions, which led to diverse phenological adaptations and resulted in a decrease in genetic variability within breeding programs due to reluctance in using genotypes from other environments.We phenotyped 324 genotypes across nine locations over three years to assess their phenological response to the environment of major lentil production regions and to predict days from sowing to flowering (DTF) using a photothermal model.DTF was highly influenced by the environment and is sufficient to explain adaptation. We were able to predict DTF reliably in most environments using a simple photothermal model, however, in certain site-years, results suggest there may be additional environmental factors at play. Hierarchical clustering of principal components revealed the presence of eight groups based on the responses of DTF to contrasting environments. These groups are associated with the coefficients of the photothermal model and revealed differences in temperature and photoperiod sensitivity.Expanding genetic diversity is critical to the success of a breeding program; understanding adaptation will facilitate the use of exotic germplasm. Future climate change scenarios will result in increase temperature and/or shifts in production areas, we can use the photothermal model to identify genotypes most likely to succeed in these new environments.

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Inter simple sequence repeats (ISSRs): Neglected DNA markers for molecular dissection of Plasmodium species in long-tailed Macaque (Macaca fascicularis)

10.7287/peerj.preprints.1253v1 ◽

2015 ◽

Cited By ~ 1

Author(s):

Parastoo Khajeaian ◽

Soon Guan Tan ◽

Alireza Valdiani ◽

Christina Seok Yien Yong ◽

Mohammad Zareian Jahromi ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variation ◽

Macaca Fascicularis ◽

High Efficiency ◽

Plasmodium Species ◽

Issr Markers ◽

Malaria Vectors ◽

Wide Range ◽

Simple Sequence

Understanding the genetic variation of the Plasmodium parasites could play an important role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR) markers have successfully been tested for investigating the genetic diversity of malaria vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic variation of Plasmodium species, as well. To illustrate the genetic diversity of two infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium cynomolgi, infected and uninfected monkey blood samples were separately collected on filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of three clusters. However, the most significant result of the cluster analysis was revealing the high efficiency of ISSR markers in the discrimination of the two Plasmodium species from each other. The cluster analysis showed a wide range of genetic diversity among both Plasmodium and the long-tailed Macaque accessions. The principal component analysis (PCA) also confirmed the cluster analysis results.

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Inter simple sequence repeats (ISSRs): Neglected DNA markers for molecular dissection of Plasmodium species in long-tailed Macaque (Macaca fascicularis)

10.7287/peerj.preprints.1253 ◽

2015 ◽

Author(s):

Parastoo Khajeaian ◽

Soon Guan Tan ◽

Alireza Valdiani ◽

Christina Seok Yien Yong ◽

Mohammad Zareian Jahromi ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variation ◽

Macaca Fascicularis ◽

High Efficiency ◽

Plasmodium Species ◽

Issr Markers ◽

Malaria Vectors ◽

Wide Range ◽

Simple Sequence

Understanding the genetic variation of the Plasmodium parasites could play an important role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR) markers have successfully been tested for investigating the genetic diversity of malaria vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic variation of Plasmodium species, as well. To illustrate the genetic diversity of two infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium cynomolgi, infected and uninfected monkey blood samples were separately collected on filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of three clusters. However, the most significant result of the cluster analysis was revealing the high efficiency of ISSR markers in the discrimination of the two Plasmodium species from each other. The cluster analysis showed a wide range of genetic diversity among both Plasmodium and the long-tailed Macaque accessions. The principal component analysis (PCA) also confirmed the cluster analysis results.

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Diversity of Morphological Traits and Glucosinolate Composition in Backcross Progenies of Brassica Rapa L. × Eruca Vesicaria (L.) Cav. Hybrids

10.21203/rs.3.rs-1163106/v1 ◽

2021 ◽

Author(s):

Aiko Kaminishi ◽

Fumika Miyohashi ◽

Nobuhiro Kita

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Brassica Rapa ◽

Morphological Traits ◽

Leaf Shape ◽

Morphological Characteristics ◽

Regeneration Potential ◽

Wide Range

Abstract Breeding at both interspecific and intergeneric levels is an effective method for expanding genetic variation of cruciferous crops; however, few commercially accepted varieties have been released because of difficulties in generating fertile progenies. We employed backcross strategy to introduce Eruca vesicaria-specific characteristics into Brassica rapa and successfully obtained four BC1F1 lines that showed a wide range of diversity of morphological traits and glucosinolate (GSL) composition. Thus, leaf shape, anthocyanin coloration, glucoraphanin content, and red petal veins were found to be inherited mainly from E. vesicaria, though most of the morphological characteristics and GSL composition were inherited from intergeneric F1 plants. Since all BC1F1 lines showed post-fertilization barriers, backcrossing with B. rapa was performed and BC2F1 progenies were successfully obtained, which showed diverse morphological characteristics and GSL composition as well as higher regeneration potential. These results suggest that widening of genetic diversity of B. rapa can be achieved through successive reciprocal backcrossing of B. rapa × E. vesicaria hybrids with B. rapa.

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Genetic Diversity Among Some Rice Genotypes with Different Drought Tolerance based on SSR Markers

Cercetari Agronomice in Moldova ◽

10.1515/cerce-2016-0024 ◽

2016 ◽

Vol 49 (3) ◽

pp. 39-50 ◽

Cited By ~ 3

Author(s):

H.A. Freeg ◽

G.B. Anis ◽

A.A. Abo-Shousha ◽

A.N. El-Banna ◽

A. El-Sabagh

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Drought Tolerance ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Allelic Diversity ◽

Similarity Coefficients ◽

Wide Range ◽

Single Marker ◽

Rice Genotypes

Abstract Rice is the most important food crop for the developing world. Hence, identifying rice genotypes to drought tolerance for using as donors in breeding is one of the most important challenges for rice research. Therefore, Molecular markers are useful tools to determine genetic diversity and identifying rice genotypes to drought tolerance. In the present study, A number of 41 rice genotypes with different drought tolerance from different geographic locations were evaluated for genetic diversity by using 15 SSR markers. A total of 68 alleles were detected of which 61(89.79%) were polymorphic. The number of alleles detected by a single marker varied from 2 to 8 alleles with an average of 4.71 alleles per locus. The polymorphic information content (PIC) values ranged from 0.07 (RM219) to 0.80 (RM263) with an average of 0.52. Genetic similarity coefficients of pair wise comparisons were estimated on the basis of the polymorphic microsatelite loci ranged from 0.23 to 0.91 indicating a wide range of genetic variation present among the studied genotypes. It was determined that the primers RM20A, RM302, RM212 and RM286 could be useful for selecting drought tolerant lines through MAS approach. The most significant application of these identified major QTLs for drought tolerance is to collect those favorable alleles into elite local line through marker assisted breeding. The results indicated the ability of SSR markers to identify the allelic diversity and genetic variation among the studied rice genotypes. These results recommended for using this material in future breeding programs to provide important source of genetic diversity for drought tolerance in rice.

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Genetic diversity and population structure of the endangered endemic species Paeonia decomposita from China and implications for its conservation

10.1101/860734 ◽

2019 ◽

Author(s):

Shi-Quan Wang

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Distance ◽

Significant Positive Correlation ◽

Isolation By Distance ◽

List Type ◽

Positive Correlation ◽

Conservation Measures ◽

Distance Model

AbstractPaeonia decomposita, endemic to China, has important ornamental, medicinal and economic value and is regarded as a threatened endangered plant. The genetic diversity and structure have seldom been described. A conservation management plan is not currently available. In present study, 16 pairs of SSR primers were used to evaluate genetic diversity and population structure. A total of 122 alleles were obtained with a mean of 7.625 alleles per locus. The expected heterozygosity (He) varied from 0.043 to 0.901 (mean 0.492). Moderate genetic diversity (He=0.405) among populations were revealed, with Danba identified as the center of genetic diversity. Mantel tests revealed a significant positive correlation between geographic and genetic distance among populations (r=0.592, P=0.0001), demonstrating consistency with the isolation by distance model. Analysis of molecular variance (AMOVA) results indicated that the principal genetic variation existed within populations (73.48%) rather than among populations (26.52%). Bayesian structure analysis and principal coordinate analysis (PCoA) supported classification of the populations into three clusters. Based on the level of observed genetic diversity, three management unints were proposed as conservation measures. The results will be beneficial for the conservation and exploitation of the species, providing a theoretical basis for further research on its evolution and phylogeography.HightlightsGenetic diversity among populations was moderate in Paeonia decompositaThere is significant positive correlation between geographic and genetic distance among populations, consistent with the isolation by distance modelPrincipal genetic variation existed within populations rather than among populations.The populations divided into three clusters.Three management unints were proposed as conservation measures.

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Comparison of Deterministic and Linear Cosine Spatial Filtering of Transmission Electron Micrographs

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100096230 ◽

1972 ◽

Vol 30 ◽

pp. 596-597

Author(s):

David A. Ansley

Keyword(s):

Spherical Aberration ◽

Focal Length ◽

Chromatic Aberration ◽

Spatial Filter ◽

Operating Conditions ◽

Objective Lens ◽

List Type ◽

Spatial Filters ◽

Transmission Electron ◽

Wide Range

The coherence of the electron flux of a transmission electron microscope (TEM) limits the direct application of deconvolution techniques which have been used successfully on unmanned spacecraft programs. The theory assumes noncoherent illumination. Deconvolution of a TEM micrograph will, therefore, in general produce spurious detail rather than improved resolution.A primary goal of our research is to study the performance of several types of linear spatial filters as a function of specimen contrast, phase, and coherence. We have, therefore, developed a one-dimensional analysis and plotting program to simulate a wide 'range of operating conditions of the TEM, including adjustment of the:(1) Specimen amplitude, phase, and separation(2) Illumination wavelength, half-angle, and tilt(3) Objective lens focal length and aperture width(4) Spherical aberration, defocus, and chromatic aberration focus shift(5) Detector gamma, additive, and multiplicative noise constants(6) Type of spatial filter: linear cosine, linear sine, or deterministic

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Triply-periodic nanostructures in surfactant, block copolymer, and biomembrane systems, and simulation of TEMs

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100150253 ◽

1993 ◽

Vol 51 ◽

pp. 884-885

Author(s):

David M. Anderson ◽

Tomas Landh

Keyword(s):

Liquid Crystalline ◽

Diblock Copolymers ◽

Cubic Phase ◽

List Type ◽

Interpenetrating Networks ◽

Triply Periodic ◽

Wide Range ◽

Bicontinuous Cubic ◽

Phase Liquid ◽

Dividing Surface

First discovered in surfactant-water liquid crystalline systems, so-called ‘bicontinuous cubic phases’ have the property that hydropnilic and lipophilic microdomains form interpenetrating networks conforming to cubic lattices on the scale of nanometers. Later these same structures were found in star diblock copolymers, where the simultaneous continuity of elastomeric and glassy domains gives rise to unique physical properties. Today it is well-established that the symmetry and topology of such a morphology are accurately described by one of several triply-periodic minimal surfaces, and that the interface between hydrophilic and hydrophobic, or immiscible polymer, domains is described by a triply-periodic surface of constant, nonzero mean curvature. One example of such a dividing surface is shown in figure 5.The study of these structures has become of increasing importance in the past five years for two reasons:1)Bicontinuous cubic phase liquid crystals are now being polymerized to create microporous materials with monodispersed pores and readily functionalizable porewalls; figure 3 shows a TEM from a polymerized surfactant / methylmethacrylate / water cubic phase; and2)Compelling evidence has been found that these same morphologies describe biomembrane systems in a wide range of cells.

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