scholarly journals Genotypic frequencies at equilibrium for polysomic inheritance under double-reduction

2019 ◽  
Author(s):  
Kang Huang ◽  
Tongcheng Wang ◽  
Derek W. Dunn ◽  
Pei Zhang ◽  
Xiaoxiao Cao ◽  
...  
Keyword(s):  
Selective Breeding ◽  
Numerical Solutions ◽  
Molecular Ecology ◽  
Double Reduction ◽  
Inbreeding Coefficients ◽  
Identical By Descent ◽  
Polysomic Inheritance ◽  
Standard Population ◽  
Multivalent Formation ◽  
Expected Values

AbstractPolyploids are organisms whose genomes consist of more than two complete sets of chromosomes. Both autopolyploids and allopolyploids may display polysomic inheritance. A peculiarity of polysomic inheritance is multivalent formation during meiosis resulting in double-reduction, which occurs when sister chromatid fragments are segregated into the same gamete. Double-reduction can result in gametes carrying identical-by-descent alleles and slightly increasing homozygosity. This will cause the genotypic frequencies to deviate from expected values and will thus bias the results of standard population genetic analytical methods used in molecular ecology and selective breeding. In this study, we extend existing double-reduction models to account for any even level of ploidy, and derive the symbolic expressions for genotypic frequencies via two methods. Inbreeding coefficients and heterozygosity under double-reduction and inbreeding are also calculated. Numerical solutions obtained by computer simulations are compared with analytical solutions predicted by the model to validate the model.

scholarly journals Rank-invariant estimation of inbreeding coefficients

Heredity ◽  
2021 ◽  
Author(s):  
Qian S. Zhang ◽  
Jérôme Goudet ◽  
Bruce S. Weir
Keyword(s):  
Genetic Data ◽  
Reference Population ◽  
Inbreeding Coefficient ◽  
Allele Sharing ◽  
Ancestral Allele ◽  
1000 Genomes ◽  
Inbreeding Coefficients ◽  
Identical By Descent ◽  
Invariant Estimation ◽  
The Individual

AbstractThe two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference population, but estimation from genetic data is not possible without data from the reference population. Most inbreeding estimators that make explicit use of sample allele frequencies as estimates of allele probabilities in the reference population are confounded by average kinships with other individuals. This means that the ranking of those estimates depends on the scope of the study sample and we show the variation in rankings for common estimators applied to different subdivisions of 1000 Genomes data. Allele-sharing estimators of within-population inbreeding relative to average kinship in a study sample, however, do have invariant rankings across all studies including those individuals. They are unbiased with a large number of SNPs. We discuss how allele sharing estimates are the relevant quantities for a range of empirical applications.

scholarly journals Assessment of Inbreeding Depression and Inbreeding Trend of Production Traits in Iraqi Holstein Cows

2019 ◽  
pp. 1-9
Author(s):  
Farzad Moradpour ◽  
Hana Hamidi
Keyword(s):  
Inbreeding Depression ◽  
Milk Fat ◽  
Fixed Effects ◽  
Continuous Variable ◽  
Inbreeding Coefficient ◽  
Holstein Cows ◽  
Production Traits ◽  
Inbreeding Coefficients ◽  
Identical By Descent ◽  
Related Individuals

Inbreeding is defined as the probability that two alleles at any locus are identical by descent and occur when related individuals are mated to each other. A total of 123427, 115810 and 88361 records of 412-d yields of milk, fat and protein of Iraqi Holstein cows were collected from 1995 to 2010 in 838 herds used to estimation the inbreeding depression and inbreeding trend. Pedigree records of Iraqi Holstein cow were used to assessment inbreeding coefficients and these coefficients ranged from 0 to 42%. Animal model was used to estimation inbreeding depression on traits. Fixed effects included in statistical model were herd – year, age at calving and inbreeding coefficient as continuous and discrete variable. When considering inbreeding as continuous variable in model, the inbreeding depression for 412-d yields of milk, fat and protein were -28.19, -0.98 and -0.88 kg per 1% increase in inbreeding in Iraqi Holsteins, respectively. In this group of animal that inbreeding coefficient was between 0 < F ≤ 5.34 inbreeding was not caused reduction in production traits. However, in group of animal that inbreeding coefficient was greater than 5.34, and inbreeding depression in production traits was observed. The result of this study confirms of inbreeding depression in Iraqi Holstein cows.

scholarly journals Genotypic Frequencies at Equilibrium for Polysomic Inheritance Under Double-Reduction

2019 ◽  
Vol 9 (5) ◽  
pp. 1693-1706 ◽  
Author(s):  
Kang Huang ◽  
Tongcheng Wang ◽  
Derek W. Dunn ◽  
Pei Zhang ◽  
Xiaoxiao Cao ◽  
...  
Keyword(s):  
Double Reduction ◽  
Polysomic Inheritance

scholarly journals Two-Locus Local Adaptation by Additive or Epistatic Gene Combinations in Autotetraploids Versus Diploids

2019 ◽  
Vol 110 (7) ◽  
pp. 866-879 ◽  
Author(s):  
Navid Mostafaee ◽  
Cortland K Griswold
Keyword(s):  
Local Adaptation ◽  
Genetic Basis ◽  
Double Reduction ◽  
Epistatic Interactions ◽  
Gametic Disequilibrium ◽  
Theoretical Comparison ◽  
Interesting Difference ◽  
Ideal Situation ◽  
Multivalent Formation ◽  
High Selection

Abstract In this article, we present a theoretical comparison of local adaptation between diploid and autotetraploid populations when fitness is determined by either additive or epistatic interactions between alleles at 2 loci. A continent-island model of local adaptation is derived, with 1-way migration from the continent to the island and distinct genotypes adaptive on the continent versus the island. The meiotic component of the model accounts for multivalent formation and the processes of chromosomal gametic disequilibrium and double reduction, which are unique to autotetraploids. Both the adaptability and efficiency of adaptation are investigated, where adaptability asks whether a population adapts and efficiency is the rate of adaptation. With an additive genetic basis to fitness, diploids experience better adaptability and efficiency than autotetraploids. With epistasis, our results indicate a limited parameter space in which autotetraploids have greater adaptability than diploids, but results indicate an interesting difference between adaptability and efficiency of adaptation. Oftentimes, diploids exhibit greater adaptability whereas autotetraploids exhibit greater efficiency of adaptation. These findings provide evidence for the advantage of epistasis within autotetraploids when efficiency of adaptation is of interest. Although autotetraploids are more efficient, under the same conditions and at equilibrium, diploid populations often have higher mean local fitness. Overall, the most ideal situation for autotetraploid local adaptation compared to diploids is when epistasis is strong, mutation is weak, recombination is high, selection is strong, deleterious selection is additive, chromosomal gametic disequilibrium is present, and double reduction is absent.

Quantitative Diameter Measurements of Chromatin and TMV Fibers in the Freeze-Dried State

1988 ◽  
Vol 46 ◽  
pp. 170-171
Author(s):  
B. D. Athey ◽  
A. L. Stout ◽  
M. F. Smith ◽  
J. P. Langmore
Keyword(s):  
Reliable Method ◽  
Fiber Diameter ◽  
Quantitative Agreement ◽  
One Dimension ◽  
Fiber Axis ◽  
Two Dimensional ◽  
Fiber Density ◽  
Variable Diameter ◽  
Freeze Dried ◽  
Expected Values

Although there is general agreement that Inactive chromosome fibers consist of helically packed nucleosomes, the pattern of packing is still undetermined. Only one of the proposed models, the crossed-linker model, predicts a variable diameter dependent on the length of DNA between nucleosomes. Measurements of the fiber diameter of negatively-stained and frozen- hydrated- chromatin from Thyone sperm (87bp linker) and Necturus erythrocytes (48bp linker) have been previously reported from this laboratory. We now introduce a more reliable method of measuring the diameters of electron images of fibrous objects. The procedure uses a modified version of the computer program TOTAL, which takes a two-dimensional projection of the fiber density (represented by the micrograph itself) and projects it down the fiber axis onto one dimension. We illustrate this method using high contrast, in-focus STEM images of TMV and chromatin from Thyone and Necturus. The measured diameters are in quantitative agreement with the expected values for the crossed-linker model for chromatin structure

Atomic Imaging of Crystals using Large-Angle Electron Scattering in STEM

1990 ◽  
Vol 48 (1) ◽  
pp. 74-75
Author(s):  
D.E. Jesson ◽  
S. J. Pennycook
Keyword(s):  
Wave Function ◽  
Electron Scattering ◽  
Numerical Solutions ◽  
Large Angle ◽  
Real Space ◽  
High Angle ◽  
Analytical Treatment ◽  
Order Zero ◽  
Experimental Conditions ◽  
Ewald Sphere

It is well known that conventional atomic resolution electron microscopy is a coherent imaging process best interpreted in reciprocal space using contrast transfer function theory. This is because the equivalent real space interpretation involving a convolution between the exit face wave function and the instrumental response is difficult to visualize. Furthermore, the crystal wave function is not simply related to the projected crystal potential, except under a very restrictive set of experimental conditions, making image simulation an essential part of image interpretation. In this paper we present a different conceptual approach to the atomic imaging of crystals based on incoherent imaging theory. Using a real-space analysis of electron scattering to a high-angle annular detector, it is shown how the STEM imaging process can be partitioned into components parallel and perpendicular to the relevant low index zone-axis.It has become customary to describe STEM imaging using the analytical treatment developed by Cowley. However, the convenient assumption of a phase object (which neglects the curvature of the Ewald sphere) fails rapidly for large scattering angles, even in very thin crystals. Thus, to avoid unpredictive numerical solutions, it would seem more appropriate to apply pseudo-kinematic theory to the treatment of the weak high angle signal. Diffraction to medium order zero-layer reflections is most important compared with thermal diffuse scattering in very thin crystals (<5nm). The electron wave function ψ(R,z) at a depth z and transverse coordinate R due to a phase aberrated surface probe function P(R-RO) located at RO is then well described by the channeling approximation;

Genetic Prehistory in Selective Breeding: A Prelude to Mendel

2003 ◽  
Vol 77 (4) ◽  
pp. 619-620
Author(s):  
Philip L. Frana
Keyword(s):  
Selective Breeding
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