scholarly journals In situ estimation of genetic variation of functional and ecological traits in Quercus petraea and Q.robur

2018 ◽  
Author(s):  
Hermine Alexandre ◽  
Laura Truffaut ◽  
Alexis Ducousso ◽  
Jean-Marc Louvet ◽  
Gérard Nepveu ◽  
...  
Keyword(s):  
Genetic Parameters ◽  
Genetic Relatedness ◽  
Genetic Correlations ◽  
Quercus Petraea ◽  
Ex Situ ◽  
Additive Variance ◽  
Adult Trees ◽  
Two Generations ◽  
Genomic Relatedness

AbstractBackgroundPredicting the evolutionary potential of natural tree populations requires the estimation of heritability and genetic correlations among traits on which selection acts, as differences in evolutionary success between species may rely on differences for these genetic parameters. In situ estimates are expected to be more accurate than measures done under controlled conditions which do not reflect the natural environmental variance.AimsThe aim of the current study was to estimate three genetic parameters (i.e. heritability, evolvability and genetic correlations) in a natural mixed oak stand composed of Quercus petraea and Quercus robur about 100 years old, for 58 traits of ecological and functional relevance (growth, reproduction, phenology, physiology, resilience, structure, morphology and defence).MethodsFirst we estimated genetic parameters directly in situ using realized genomic relatedness of adult trees and parentage relationships over two generations to estimate the traits additive variance. Secondly, we benefited from existing ex situ experiments (progeny tests and conservation collection) installed with the same populations, thus allowing comparisons of in situ heritability estimates with more traditional methods.ResultsHeritability and evolvability estimates obtained with different methods varied substantially and showed large confidence intervals, however we found that in situ were less precise than ex situ esti-mates, and assessments over two generations (with deeper relatedness) improved estimates of heritability while large sampling sizes are needed for accurate estimations. At the biological level, heritability values varied moderately across different ecological and functional categories of traits, and genetic correlations among traits were conserved over the two species.ConclusionWe identified limits for using realized genomic relatedness in natural stands to estimate the genetic variance, given the overall low variance of genetic relatedness and the rather low sampling sizes of currently used long term genetic plots in forestry. These limits can be overcome if larger sample sizes are considered, or if the approach is extended over the next generation.

scholarly journals Variability in genetic parameters among small populations

1977 ◽  
Vol 29 (3) ◽  
pp. 193-213 ◽  
Author(s):  
P. J. Avery ◽  
W. G. Hill
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Parameters ◽  
Additive Genetic Variance ◽  
Genetic Correlations ◽  
Small Populations ◽  
Base Population ◽  
Gene Frequencies ◽  
Additive Variance ◽  
Successive Generations ◽  
Additive Genes

SUMMARYFor a model in which quantitative traits are assumed to be determined solely by additive genes at many loci, formulae are developed for the variance among replicated small populations of size N, maintained without selection, of the additive genetic variance, heritability, genetic correlations and similar parameters. The base population is assumed to be in linkage equilibrium, but it is argued that most of the variation in the within-line additive variance (VAt at generation t) is due to linkage disequilibrium caused by sampling. If is the squared correlation of gene frequencies averaged over all pairs of loci at time t, the coefficient of variation (CV) of VAt equals , with similar formulae for other parameters.The formulae are evaluated for models of loci distributed uniformly along the chromosome but much of the disequilibrium is due to loci on different chromosomes. For unlinked loci CV(VAt) reaches √4/(3(N)), and for mammalian models, this value is not greatly exceeded. The variance in successive generations has a correlation of at least one-half due to the maintenance of linkage disequilibrium. The magnitude of this variance in parameters and their autocorrelation with time shows that accurate predictions cannot be made about genetic parameters in the base population from single replicate results.

scholarly journals Estimates of genetic parameters for physic nut traits based in the germplasm two years evaluation

2012 ◽  
Vol 42 (3) ◽  
pp. 429-435 ◽  
Author(s):  
Bruno Galvêas Laviola ◽  
Alexandre Alonso Alves ◽  
Fábio de Lima Gurgel ◽  
Tatiana Barbosa Rosado ◽  
Rodrigo Barros Rocha ◽  
...  
Keyword(s):  
Genetic Parameters ◽  
Genetic Correlations ◽  
Breeding Value ◽  
Physic Nut ◽  
Germplasm Bank ◽  
Additive Variance ◽  
True Breeding ◽  
Canopy Volume ◽  
Sib Families ◽  
True Breeding Value

In spite of increasingly widespread interest in planting physic nut, breeding efforts are still in its infancy. In that context, an important resource recently established aiming future breeding efforts was the assembly of a germplasm bank with near 200 accessions. The objective of this study was to estimate genetic parameters, repeatibility coefficients and genetic correlation between seven traits, measured in 110 accessions (half sib families) of this germplasm bank in different stages of development. The results show that higher relative values of additive variance were only found for yield and height, and the existence of low environmental variation (either of temporary or permanent nature) among plots within blocks. Given the high repeatibility values found for all traits, on average three measurements are necessary to predict, accurately and efficiently, the true breeding value of an individual. Based on the results of genetic correlations, breeding effort should initially be use track trees with increased stem diameter, elevated number of branches and canopy volume so as to increase the chances of finding an exceptionally highly productive tree.

scholarly journals Genetska struktura populacija hrasta kitnjaka (Quercus petraea (Matt.) Lieblein) u Bosni i Hercegovini na temelju analize izoenzimskih biljega

2016 ◽  
Vol 140 (3-4) ◽  
pp. 127-135
Author(s):  
Dalibor Ballian
Keyword(s):  
Quercus Petraea ◽  
Ex Situ

Hrast kitnjak [Quercus petraea (Matt.) Lieblein] jedna je od najvažnijih vrsta šumskog drveća u Bosni i Hercegovini, iako je sadašnja struktura šuma hrasta kitnjaka vrlo slaba. Razlog tomu treba tražiti u jakom povijesnom utjecaju čovjeka na tu vrstu, brojne neplanske i nestručne sječe i slabo razvijen sustav gospodarenja ovom vrijednom vrstom. U uvjetima Bosne i Hercegovine kitnjak se nalazi na 333 000 ha, u malim čistim i većinom mješovitim sastojinama s grabom i ponekad bukvom. Kroz ovo istraživanje želimo odgovoriti na sljedeća pitanja: kakva je genetska struktura odabranih populacija hrasta kitnjaka u Bosni i Hercegovini, te kakvo je značenje poznavanja genetičke strukture u procesima obnove? Analizirali smo 17 prirodnih populacija hrasta kitnjaka uz uporabu 11 enzimskih sustava s 14 genskih lokusa i registrirali 82 alela. Registriran je velik polimorfizam, a samo je kod genskog lokusa sorbitol registriran potpuni monomorfizam, dok je kod genskog lokusa Pgi – A dobiven polimorfizam samo u jednoj populaciji. Prosječan broj alela za istraživane populacije kretao se od 1,7143 do 3,1429, a efektivni broj od 1.1089 do 1.2585. Stvarna i teorijska heterozigotnost najniža je bila u populaciji Gračanica s 0,0947, dok je najveća bila u populaciji Bugojno s 0,1869. Fiksacijski indeks u svim populacijama je bio negativan, što ukazuje na dobru stabilnost istraživanih populacija te da su slabi ili izostaju procesi inbridinga u populacijama. Najveće genetske udaljenosti u odnosu na ostale pokazala je populacija Tešanj. Rezultati diferencijacije pokazuju male vrijednosti, što ukazuje na kratko vrijeme od njihovog razdvajanja te prisut­nost toka gena i malog gubitka prilagodbenog potencijala. Dobiveni rezultati omogućuju preporuku potrebnih mjera za očuvanje genetskih izvora metodama in situ i ex situ te obnovu i uporabu reprodukcijskog materijala hrasta kitnjaka u Bosni i Hercegovini.

scholarly journals Inferring phenotypic plasticity and local adaptation to climate across tree species ranges using forest inventory data

2019 ◽  
Author(s):  
Thibaut Fréjaville ◽  
Bruno Fady ◽  
Antoine Kremer ◽  
Alexis Ducousso ◽  
Marta Benito Garzón
Keyword(s):  
Phenotypic Plasticity ◽  
Local Adaptation ◽  
Forest Inventory ◽  
Abies Alba ◽  
Tree Height ◽  
Quercus Petraea ◽  
National Forest Inventory ◽  
Ex Situ ◽  
Distribution Ranges

ABSTRACTAimTo test whether adaptive and plastic trait responses to climate across species distribution ranges can be untangled using field observations, under the rationale that, in natural forest tree populations, long-term climate shapes local adaptation while recent climate change drives phenotypic plasticity.LocationEurope.Time period1901-2014.TaxaSilver fir (Abies alba Mill.) and sessile oak (Quercus petraea (Matt.) Liebl.).MethodsWe estimated the variation of individual tree height as a function of long-term and short-term climates to tease apart local adaptation, plasticity and their interaction, using mixed-effect models calibrated with National Forest Inventory data (in-situ models). To validate our approach, we tested the ability of in-situ models to predict independently tree height observations in common gardens where local adaptation to climate of populations and their plasticity can be measured and separated. In-situ model predictions of tree height variation among provenances (populations of different geographical origin) and among planting sites were compared to observations in common gardens and to predictions from a similar model calibrated using common garden data (ex-situ model).ResultsIn Q. petraea, we found high correlations between in-situ and ex-situ model predictions of provenance and plasticity effects and their interaction on tree height (r > 0.80). We showed that the in-situ models significantly predicted tree height variation among provenances and sites for Abies alba and Quercus petraea. Spatial predictions of phenotypic plasticity across species distribution ranges indicate decreasing tree height in populations of warmer climates in response to recent anthropogenic climate warming.Main conclusionsOur modelling approach using National Forest Inventory observations provides a new perspective for understanding patterns of intraspecific trait variation across species ranges. Its application is particularly interesting for species for which common garden experiments do not exist or do not cover the entire climatic range of the species.

scholarly journals 33 Genetic parameters for reproductive traits in purebred and crossbred swine

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 11-11
Author(s):  
Luke M Kramer ◽  
Ania Wolc ◽  
Hadi Esfandyari ◽  
Dinesh Thekkoot ◽  
Chunyan Zhang ◽  
...  
Keyword(s):  
Genetic Parameters ◽  
Genetic Correlations ◽  
Reproductive Traits ◽  
Single Step ◽  
Allele Frequencies ◽  
Superior Performance ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Additive Variance ◽  
Breeding Programs

Abstract For swine breeding programs, testing and selection programs are located in nucleus units that are generally managed differently and with higher health levels than commercial herds where descendants of nucleus animals are expected to perform. This approach assumes that superior animals selected in nucleus herds will have progeny with superior performance at the commercial level. There is clear evidence that this may not be true for all traits of economic importance and thus methods including data collected at the commercial level may increase accuracy of selection at the nucleus level. This study’s goal was to estimate genetic parameters for five reproductive traits between two purebred maternal nucleus populations and their commercial F1 offspring: Total Number Born, Number Born Alive, Number Born Alive > 1kg, Number Weaned, and Litter Weight. Estimates were based on single-step GBLUP in the BLUPF90 programs by utilizing any two combinations of a purebred and the F1 population, and by using all three populations jointly. The genomic relationship matrix between the three populations was generated by using within-population allele frequencies for relationships within a population, and across-population allele frequencies for relationships of the F1 with the purebred animals. The two purebred populations were assumed to be genetically unrelated. The use of two versus three populations did not impact estimates of heritability, additive variance, or genetic correlations. Heritabilities ranged from 0.02 to 0.09 for the F1, from 0.07 to 0.18 for Landrace, and from 0.07 to 0.21 for Yorkshire. Genetic correlations between the same traits in F1 and Landrace ranged from 0.22 to 0.93, and from 0.31 to 0.84 for F1 and Yorkshire. This range of genetic correlations indicates that the use of crossbred information can aid in the selection of purebreds for commercial crossbred performance for some traits. Funded by Genome Canada Genomic Applications Partnerships Program.

An in situ and ex situ TEM study of the formation of thin cobalt silicide films by molecular beam epitaxy on the silicon (100) surface

1988 ◽  
Vol 46 ◽  
pp. 884-885
Author(s):  
D. Loretto ◽  
J. M. Gibson ◽  
S. M. Yalisove ◽  
R. T. Tung
Keyword(s):  
Molecular Beam Epitaxy ◽  
Molecular Beam ◽  
Defect Density ◽  
High Vacuum ◽  
Ultra High Vacuum ◽  
Ex Situ ◽  
Metal Base ◽  
In Situ Experiments ◽  
Potential Applications

The cobalt disilicide/silicon system has potential applications as a metal-base and as a permeable-base transistor. Although thin, low defect density, films of CoSi2 on Si(111) have been successfully grown, there are reasons to believe that Si(100)/CoSi2 may be better suited to the transmission of electrons at the silicon/silicide interface than Si(111)/CoSi2. A TEM study of the formation of CoSi2 on Si(100) is therefore being conducted. We have previously reported TEM observations on Si(111)/CoSi2 grown both in situ, in an ultra high vacuum (UHV) TEM and ex situ, in a conventional Molecular Beam Epitaxy system.The procedures used for the MBE growth have been described elsewhere. In situ experiments were performed in a JEOL 200CX electron microscope, extensively modified to give a vacuum of better than 10-9 T in the specimen region and the capacity to do in situ sample heating and deposition. Cobalt was deposited onto clean Si(100) samples by thermal evaporation from cobalt-coated Ta filaments.

The use of transmission and analytical electron microscopy in studying reactions and phase transformations in thin film

1993 ◽  
Vol 51 ◽  
pp. 842-843
Author(s):  
K. Barmak
Keyword(s):  
Thin Film ◽  
Thin Films ◽  
Phase Transformations ◽  
Analytical Electron Microscopy ◽  
Ex Situ ◽  
Multilayer Thin Films ◽  
Absolute Concentration ◽  
Analytical Electron ◽  
Deposition Step

Generally, processing of thin films involves several annealing steps in addition to the deposition step. During the annealing steps, diffusion, transformations and reactions take place. In this paper, examples of the use of TEM and AEM for ex situ and in situ studies of reactions and phase transformations in thin films will be presented.The ex situ studies were carried out on Nb/Al multilayer thin films annealed to different stages of reaction. Figure 1 shows a multilayer with dNb = 383 and dAl = 117 nm annealed at 750°C for 4 hours. As can be seen in the micrograph, there are four phases, Nb/Nb3-xAl/Nb2-xAl/NbAl3, present in the film at this stage of the reaction. The composition of each of the four regions marked 1-4 was obtained by EDX analysis. The absolute concentration in each region could not be determined due to the lack of thickness and geometry parameters that were required to make the necessary absorption and fluorescence corrections.

Transmission Electron Microscopy of Epitaxial silicides grown by ultra high vacuum deposition

1989 ◽  
Vol 47 ◽  
pp. 462-463
Author(s):  
D. Loretto ◽  
J. M. Gibson ◽  
S. M. Yalisove
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Electron Diffraction ◽  
High Vacuum ◽  
High Energy ◽  
Energy Electron ◽  
Ultra High Vacuum ◽  
Ex Situ ◽  
Transmission Electron

The silicides CoSi2 and NiSi2 are both metallic with the fee flourite structure and lattice constants which are close to silicon (1.2% and 0.6% smaller at room temperature respectively) Consequently epitaxial cobalt and nickel disilicide can be grown on silicon. If these layers are formed by ultra high vacuum (UHV) deposition (also known as molecular beam epitaxy or MBE) their thickness can be controlled to within a few monolayers. Such ultrathin metal/silicon systems have many potential applications: for example electronic devices based on ballistic transport. They also provide a model system to study the properties of heterointerfaces. In this work we will discuss results obtained using in situ and ex situ transmission electron microscopy (TEM).In situ TEM is suited to the study of MBE growth for several reasons. It offers high spatial resolution and the ability to penetrate many monolayers of material. This is in contrast to the techniques which are usually employed for in situ measurements in MBE, for example low energy electron diffraction (LEED) and reflection high energy electron diffraction (RHEED), which are both sensitive to only a few monolayers at the surface.

Atomic Layer Deposition of LiF and Lithium Ion Conducting (AlF3)(LiF)x Alloys Using Trimethylaluminum, Lithium Hexamethyldisilazide and Hydrogen Fluoride

2017 ◽  
Author(s):  
Younghee Lee ◽  
Daniela M. Piper ◽  
Andrew S. Cavanagh ◽  
Matthias J. Young ◽  
Se-Hee Lee ◽  
...  
Keyword(s):  
Lithium Ion ◽  
Atomic Layer ◽  
Mass Gain ◽  
Alloy Film ◽  
Ex Situ ◽  
X Ray ◽  
Layer Deposition ◽  
Ion Conducting ◽  
Good Agreement

<div>Atomic layer deposition (ALD) of LiF and lithium ion conducting (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloys was developed using trimethylaluminum, lithium hexamethyldisilazide (LiHMDS) and hydrogen fluoride derived from HF-pyridine solution. ALD of LiF was studied using in situ quartz crystal microbalance (QCM) and in situ quadrupole mass spectrometer (QMS) at reaction temperatures between 125°C and 250°C. A mass gain per cycle of 12 ng/(cm<sup>2</sup> cycle) was obtained from QCM measurements at 150°C and decreased at higher temperatures. QMS detected FSi(CH<sub>3</sub>)<sub>3</sub> as a reaction byproduct instead of HMDS at 150°C. LiF ALD showed self-limiting behavior. Ex situ measurements using X-ray reflectivity (XRR) and spectroscopic ellipsometry (SE) showed a growth rate of 0.5-0.6 Å/cycle, in good agreement with the in situ QCM measurements.</div><div>ALD of lithium ion conducting (AlF3)(LiF)x alloys was also demonstrated using in situ QCM and in situ QMS at reaction temperatures at 150°C A mass gain per sequence of 22 ng/(cm<sup>2</sup> cycle) was obtained from QCM measurements at 150°C. Ex situ measurements using XRR and SE showed a linear growth rate of 0.9 Å/sequence, in good agreement with the in situ QCM measurements. Stoichiometry between AlF<sub>3</sub> and LiF by QCM experiment was calculated to 1:2.8. XPS showed LiF film consist of lithium and fluorine. XPS also showed (AlF<sub>3</sub>)(LiF)x alloy consists of aluminum, lithium and fluorine. Carbon, oxygen, and nitrogen impurities were both below the detection limit of XPS. Grazing incidence X-ray diffraction (GIXRD) observed that LiF and (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloy film have crystalline structures. Inductively coupled plasma mass spectrometry (ICP-MS) and ionic chromatography revealed atomic ratio of Li:F=1:1.1 and Al:Li:F=1:2.7: 5.4 for (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloy film. These atomic ratios were consistent with the calculation from QCM experiments. Finally, lithium ion conductivity (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloy film was measured as σ = 7.5 × 10<sup>-6</sup> S/cm.</div>

A New Method of Wafer Level Plan View TEM Sample Preparation by DualBeam

2008 ◽  
Author(s):  
Hyoung H. Kang ◽  
Michael A. Gribelyuk ◽  
Oliver D. Patterson ◽  
Steven B. Herschbein ◽  
Corey Senowitz
Keyword(s):  
Sample Preparation ◽  
Ex Situ ◽  
Wafer Level ◽  
Cross Sectional ◽  
Plan View ◽  
Manufacturing Line ◽  
Transmission Electron ◽  
Thin Lamella ◽  
Preparation Techniques

Abstract Cross-sectional style transmission electron microscopy (TEM) sample preparation techniques by DualBeam (SEM/FIB) systems are widely used in both laboratory and manufacturing lines with either in-situ or ex-situ lift out methods. By contrast, however, the plan view TEM sample has only been prepared in the laboratory environment, and only after breaking the wafer. This paper introduces a novel methodology for in-line, plan view TEM sample preparation at the 300mm wafer level that does not require breaking the wafer. It also presents the benefit of the technique on electrically short defects. The methodology of thin lamella TEM sample preparation for plan view work in two different tool configurations is also presented. The detailed procedure of thin lamella sample preparation is also described. In-line, full wafer plan view (S)TEM provides a quick turn around solution for defect analysis in the manufacturing line.

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