scholarly journals Facial shape and allometry quantitative trait locus intervals in the Diversity Outbred mouse are enriched for known skeletal and facial development genes

2019 ◽  
Author(s):  
David C. Katz ◽  
J. David Aponte ◽  
Wei Liu ◽  
Rebecca M. Green ◽  
Jessica M. Mayeux ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Complex Traits ◽  
Complex Structure ◽  
Three Dimensional ◽  
Allelic Diversity ◽  
Experimental Population ◽  
Facial Shape ◽  
Diversity Outbred ◽  
Facial Development ◽  
Skeletal Diversity

AbstractThe biology of how faces are built and come to differ from one another is complex. Discovering the genes that contribute to differences in facial morphology is one key to untangling this complexity, with important implications for medicine and evolutionary biology. This study maps quantitative trait loci (QTL) for skeletal facial shape using Diversity Outbred (DO) mice. The DO is a randomly outcrossed population with high heterozygosity that captures the allelic diversity of eight inbred mouse lines from three subspecies. The study uses a sample of 1147 DO animals (the largest sample yet employed for a shape QTL study in mouse), each characterized by 22 three-dimensional landmarks, 56,885 autosomal and X-chromosome markers, and sex and age classifiers. We identified 37 facial shape QTL across 20 shape principal components (PCs) using a mixed effects regression that accounts for kinship among observations. The QTL include some previously identified intervals as well as new regions that expand the list of potential targets for future experimental study. Three QTL characterized shape associations with size (allometry). Median support interval size was 3.5 Mb. Narrowing additional analysis to QTL for the five largest magnitude shape PCs, we found significant overrepresentation of genes with known roles in growth, skeletal development, and sensory organ development. For most intervals, one or more of these genes lies within 0.25 Mb of the QTL’s peak. QTL effect sizes were small, with none explaining more than 0.5% of facial shape variation. Thus, our results are consistent with a model of facial diversity that is influenced by key genes in skeletal and facial development and, simultaneously, is highly polygenic.Author SummaryThe mammalian face is a complex structure serving many functions. We studied the genetic basis for facial skeletal diversity in a large sample of mice from an experimental population designed for the study of complex traits. We quantified the contribution of genetic variation to variation in three-dimensional facial shape across more than 55,000 genetic markers spread throughout the mouse genome. We found 37 genetic regions which are very likely to contribute to differences in facial shape. We then conducted a more detailed analysis of the genetic regions associated with the most variable aspects of facial shape. For these regions, a disproportionately large number of genes are known to be important to growth and to skeletal and facial development. The magnitude of these genetic contributions to differences in facial shape are consistently small. Our results therefore support the notion that facial skeletal diversity is influenced by many genes of small effect, but that some of these small effects may be related to genes that are fundamental to skeletal and facial development.

scholarly journals Facial shape and allometry quantitative trait locus intervals in the Diversity Outbred mouse are enriched for known skeletal and facial development genes

PLoS ONE ◽  
2020 ◽  
Vol 15 (6) ◽  
pp. e0233377
Author(s):  
David C. Katz ◽  
J. David Aponte ◽  
Wei Liu ◽  
Rebecca M. Green ◽  
Jessica M. Mayeux ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Facial Shape ◽  
Diversity Outbred ◽  
Outbred Mouse ◽  
Trait Locus ◽  
Facial Development

scholarly journals Modeling Allelic Diversity of Multi-parent Mapping Populations Affects Detection of Quantitative Trait Loci

2021 ◽  
Author(s):  
Sarah Odell ◽  
Asher I Hudson ◽  
Sébastien Praud ◽  
Pierre Dubreuil ◽  
Marie-Helene Tixier ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Qtl Mapping ◽  
Flowering Time ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Association Studies ◽  
Allelic Diversity ◽  
Genome Wide Association Studies ◽  
Trait Loci ◽  
Mapping Populations

The search for quantitative trait loci (QTL) that explain complex traits such as yield and flowering time has been ongoing in all crops. Methods such as bi-parental QTL mapping and genome-wide association studies (GWAS) each have their own advantages and limitations. Multi-parent advanced generation intercross (MAGIC) populations contain more recombination events and genetic diversity than bi-parental mapping populations and reduce the confounding effect of population structure that is an issue in association mapping populations. Here we discuss the results of using a MAGIC population of doubled haploid (DH) maize lines created from 16 diverse founders to perform QTL mapping. We compare three models that assume bi-allelic, founder, and ancestral haplotype allelic states for QTL. The three methods have different power to detect QTL for a variety of agronomic traits. Although the founder approach finds the most QTL, there are also QTL unique to each method, suggesting that each model has advantages for traits with different genetic architectures. A closer look at a well-characterized flowering time QTL, qDTA8, which contains vgt1, suggests a potential epistatic interaction and highlights the strengths and weaknesses of each method. Overall, our results reinforce the importance of considering different approaches to analyzing genotypic datasets, and show the limitations of binary SNP data for identifying multi-allelic QTL.

scholarly journals Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits

2014 ◽  
Author(s):  
Darren Kessner ◽  
John Novembre
Keyword(s):  
Quantitative Trait Loci ◽  
Artificial Selection ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Quantitative Traits ◽  
Extreme Values ◽  
Massively Parallel Sequencing ◽  
Experimental Population ◽  
Selection Experiments ◽  
Trait Loci

AbstractEvolve and resequence studies combine artificial selection experiments with massively parallel sequencing technology to study the genetic basis for complex traits. In these experiments, individuals are selected for extreme values of a trait, causing alleles at quantitative trait loci (QTLs) to increase or decrease in frequency in the experimental population. We present a new analysis of the power of artificial selection experiments to detect and localize quantitative trait loci. This analysis uses a simulation framework that explicitly models whole genomes of individuals, quantitative traits, and selection based on individual trait values. We find that explicitly modeling QTL provides produces qualitatively different insights than considering independent loci with constant selection coefficients. Specifically, we observe how interference between QTLs under selection impacts the trajectories and lengthens the fixation times of selected alleles. We also show that a substantial portion of the genetic variance of the trait (50–100%) can be explained by detected QTLs in as little as 20 generations of selection, depending on the trait architecture and experimental design. Furthermore, we show that power depends crucially on the opportunity for recombination during the experiment. Finally, we show that an increase in power is obtained by leveraging founder haplotype information to obtain allele frequency estimates.

scholarly journals Mapping of Quantitative Trait Loci Controlling Adaptive Traits in Coastal Douglas Fir. III. Quantitative Trait Loci-by-Environment Interactions

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1489-1506
Author(s):  
Kathleen D Jermstad ◽  
Daniel L Bassoni ◽  
Keith S Jech ◽  
Gary A Ritchie ◽  
Nicholas C Wheeler ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Moisture Stress ◽  
Interval Mapping ◽  
Douglas Fir ◽  
Adaptive Traits ◽  
Growth Cessation ◽  
Trait Loci ◽  
Growth Initiation

Abstract Quantitative trait loci (QTL) were mapped in the woody perennial Douglas fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) for complex traits controlling the timing of growth initiation and growth cessation. QTL were estimated under controlled environmental conditions to identify QTL interactions with photoperiod, moisture stress, winter chilling, and spring temperatures. A three-generation mapping population of 460 cloned progeny was used for genetic mapping and phenotypic evaluations. An all-marker interval mapping method was used for scanning the genome for the presence of QTL and single-factor ANOVA was used for estimating QTL-by-environment interactions. A modest number of QTL were detected per trait, with individual QTL explaining up to 9.5% of the phenotypic variation. Two QTL-by-treatment interactions were found for growth initiation, whereas several QTL-by-treatment interactions were detected among growth cessation traits. This is the first report of QTL interactions with specific environmental signals in forest trees and will assist in the identification of candidate genes controlling these important adaptive traits in perennial plants.

Ab Initio Determination of a New Complex Structure (55 Non-Hydrogen Atoms) from Synchrotron Powder Data: An Uncommon Nickel Succinate, Ni7(C4H4O4)4(OH)6(H2O)3•7H2O

2004 ◽  
Vol 443-444 ◽  
pp. 333-336
Author(s):  
N. Guillou ◽  
C. Livage ◽  
W. van Beek ◽  
G. Férey
Keyword(s):  
Ab Initio ◽  
Complex Structure ◽  
Three Dimensional ◽  
Free Water ◽  
Hydrogen Atoms ◽  
Monoclinic System ◽  
Synchrotron Powder Diffraction ◽  
Chloride Hexahydrate ◽  
Autogenous Pressure

Ni7(C4H4O4)4(OH)6(H2O)3. 7H2O, a new layered nickel(II) succinate, was prepared hydrothermally (180°C, 48 h, autogenous pressure) from a 1:1.5:4.1:120 mixture of nickel (II) chloride hexahydrate, succinic acid, potassium hydroxide and water. It crystallizes in the monoclinic system (space group P21/c, Z = 4) with the following parameters a = 7.8597(1) Å, b = 18.8154(3)Å, c = 23.4377(4) Å,ϐ = 92.0288(9)°, and V = 3463.9(2) Å3. Its structure, which contains 55 non-hydrogen atoms, was solved ab initio from synchrotron powder diffraction data. It can be described from hybrid organic-inorganic layers, constructed from nickel oxide corrugated chains. These chains are built up from NiO6hexameric units connected via a seventh octahedron. Half of the succinates decorate the chains, and the others connect them to form the layers. The three dimensional arrangement is ensured by hydrogen bonds directly between two adjacent layers and via free water molecules.

Swirl Flow Investigations on the Enhancement of Heat Transfer Processes in Cyclone Cooling Ducts

2012 ◽  
Author(s):  
Florian Wassermann ◽  
Sven Grundmann ◽  
Michael Kloss ◽  
Heinz-Peter Schiffer
Keyword(s):  
Heat Transfer ◽  
Mass Transfer ◽  
Complex Structure ◽  
Three Dimensional ◽  
Swirl Flow ◽  
Flow Structures ◽  
Stable Complex ◽  
Reynolds Analogy ◽  
Transfer Processes ◽  
Cooling Ducts

Cyclone cooling is a promising method to enhance heat-transfer processes in future internal turbine-blade leading-edge cooling-ducts. The basic component of such cooling channels is the swirl generator, which induces a swirling movement of the coolant. The angular momentum generates stable, complex and three-dimensional flow structures of helical shape with alternating axial flow directions. Full three-dimensional and three-component velocity measurements using magnetic resonance velocimetry (3D3C-MRV) were conducted, with the aim to understand the complex structure of pipe flows with strong swirl. In order to mimic the effect of different installation concepts of the cyclone-cooling ducts an idealized bend-duct swirl-tube configuration with variable exit orifices has been investigated. Pronounced helical flow structures and distinct velocity zones could be found in this swirl flow. One substantial result is the identification of stationary helix-shaped streaks of high axial velocity in the direct vicinity of the wall. These findings are in good agreement with mass-transfer measurements that also show helix-shaped structures with increased mass transfer at the inner surface of the tube. According to the Reynolds analogy between heat and mass transfer, augmented heat-transfer processes in these areas are to be expected.

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