scholarly journals Genetic variance and fixation probabilities at quantitative trait loci in mutation-selection balance

1991 ◽  
Vol 58 (2) ◽  
pp. 139-144 ◽  
Author(s):  
Peter D. Keightley
Keyword(s):  
Quantitative Trait Loci ◽  
Mutation Rate ◽  
Quantitative Trait ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Fixation Rate ◽  
Trait Loci ◽  
Fixation Probabilities

SummaryGenetic variance and fixation probabilities are evaluated for a model of a quantitative trait at a balance between mutation, selection and drift in which many alleles can segregate at each locus. If the distribution of effects of new mutant alleles is such that mutations are unconditionally deleterious, as might be the case in natural populations, genetic variance maintained is proportional to the number of mutations occurring in the genome per generation, but is independent of the number of loci at which they appear. If selectively advantageous alleles can occur these tend to interfere to a greater extent with each others' fixation and increasing mutation rate leads to a decrease in the genetic variance as a fraction of the variance maintained in the absence of selection. Fixation probabilities of new mutant alleles approach that for neutral alleles with increasing mutation rate at a locus irrespective of their effects on fitness. The additive genetic variance contributed by the locus may appear to be ‘decoupled’ from the fixation rate of mutant alleles.

scholarly journals A Genome Scan for Quantitative Trait Loci in a Wild Population of Red Deer (Cervus elaphus)

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1863-1873 ◽  
Author(s):  
J Slate ◽  
P M Visscher ◽  
S MacGregor ◽  
D Stevens ◽  
M L Tate ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Cervus Elaphus ◽  
Quantitative Trait ◽  
Red Deer ◽  
Wild Population ◽  
Additive Genetic Variance ◽  
Model Organisms ◽  
A Genome ◽  
Trait Loci ◽  
In The Wild

Abstract Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.

scholarly journals Footprints in time: comparative quantitative trait loci mapping of the pitcher-plant mosquito, Wyeomyia smithii

2012 ◽  
Vol 279 (1747) ◽  
pp. 4551-4558 ◽  
Author(s):  
William E. Bradshaw ◽  
Kevin J. Emerson ◽  
Julian M. Catchen ◽  
William A. Cresko ◽  
Christina M. Holzapfel
Keyword(s):  
Quantitative Trait Loci ◽  
Adaptive Evolution ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Natural Populations ◽  
Cumulative Effect ◽  
Single Species ◽  
Interval Mapping ◽  
Photoperiodic Response ◽  
Trait Loci

Identifying regions of the genome contributing to phenotypic evolution often involves genetic mapping of quantitative traits. The focus then turns to identifying regions of ‘major’ effect, overlooking the observation that traits of ecological or evolutionary relevance usually involve many genes whose individual effects are small but whose cumulative effect is large. Herein, we use the power of fully interfertile natural populations of a single species of mosquito to develop three quantitative trait loci (QTL) maps: one between two post-glacially diverged populations and two between a more ancient and a post-glacial population. All demonstrate that photoperiodic response is genetically a highly complex trait. Furthermore, we show that marker regressions identify apparently ‘non-significant’ regions of the genome not identified by composite interval mapping, that the perception of the genetic basis of adaptive evolution is crucially dependent upon genetic background and that the genetic basis for adaptive evolution of photoperiodic response is highly variable within contemporary populations as well as between anciently diverged populations.

scholarly journals Mapping Quantitative Trait Loci Using Naturally Occurring Genetic Variance Among Commercial Inbred Lines of Maize (Zea maysL.)

Genetics ◽  
2005 ◽  
Vol 169 (4) ◽  
pp. 2267-2275 ◽  
Author(s):  
Yuan-Ming Zhang ◽  
Yongcai Mao ◽  
Chongqing Xie ◽  
Howie Smith ◽  
Lang Luo ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Genetic Variance ◽  
Inbred Lines ◽  
Naturally Occurring ◽  
Trait Loci

Modeling Epistasis of Quantitative Trait Loci Using Cockerham's Model

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1243-1261 ◽  
Author(s):  
Chen-Hung Kao ◽  
Zhao-Bang Zeng
Keyword(s):  
Quantitative Trait Loci ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Genetic Variance ◽  
Genetic Model ◽  
Linkage Equilibrium ◽  
Gene Effects ◽  
Multiple Loci ◽  
Trait Loci ◽  
Orthogonal Property

AbstractWe use the orthogonal contrast scales proposed by Cockerham to construct a genetic model, called Cockerham's model, for studying epistasis between genes. The properties of Cockerham's model in modeling and mapping epistatic genes under linkage equilibrium and disequilibrium are investigated and discussed. Because of its orthogonal property, Cockerham's model has several advantages in partitioning genetic variance into components, interpreting and estimating gene effects, and application to quantitative trait loci (QTL) mapping when compared to other models, and thus it can facilitate the study of epistasis between genes and be readily used in QTL mapping. The issues of QTL mapping with epistasis are also addressed. Real and simulated examples are used to illustrate Cockerham's model, compare different models, and map for epistatic QTL. Finally, we extend Cockerham's model to multiple loci and discuss its applications to QTL mapping.

scholarly journals Flour yield QTLs in three Australian doubled haploid wheat populations

2006 ◽  
Vol 57 (10) ◽  
pp. 1115 ◽  
Author(s):  
A. Lehmensiek ◽  
P. J. Eckermann ◽  
A. P. Verbyla ◽  
R. Appels ◽  
M. W. Sutherland ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Doubled Haploid ◽  
Quantitative Trait ◽  
Genetic Variance ◽  
Trial Data ◽  
Trait Loci ◽  
Flour Yield ◽  
Similar Location ◽  
Yield Character

Flour yield quantitative trait loci (QTLs) were identified in 3 Australian doubled haploid populations, Sunco × Tasman, CD87 × Katepwa, and Cranbrook × Halberd. Trial data from 3 to 4 sites or years were available for each population. QTLs were identified on chromosomes 2BS, 4B, 5AL, and 6BL in the Sunco × Tasman population, on chromosomes 4B, 5AS, and 6DL in the CD87 × Katepwa population, and on chromosomes 4DS, 5DS, and 7AS in the Cranbrook × Halberd population. In the Sunco × Tasman cross the highest genetic variance was detected with the QTL on chromosome 2B (31.3%), in the CD87 × Katepwa cross with the QTL on chromosome 4B (23.8%), and in the Cranbrook × Halberd cross with the QTL on chromosome 5D (18%). Only one QTL occurred in a similar location in more than one population, indicating the complexity of the flour yield character across different backgrounds.

A Haplotype-Based Algorithm for Multilocus Linkage Disequilibrium Mapping of Quantitative Trait Loci With Epistasis

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1533-1548 ◽  
Author(s):  
Xiang-Yang Lou ◽  
George Casella ◽  
Ramon C Littell ◽  
Mark C K Yang ◽  
Julie A Johnson ◽  
...  
Keyword(s):  
Parameter Estimation ◽  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Association Studies ◽  
Natural Populations ◽  
Evolutionary Relationship ◽  
Linkage Disequilibrium Mapping ◽  
Trait Loci

AbstractFor tightly linked loci, cosegregation may lead to nonrandom associations between alleles in a population. Because of its evolutionary relationship with linkage, this phenomenon is called linkage disequilibrium. Today, linkage disequilibrium-based mapping has become a major focus of recent genome research into mapping complex traits. In this article, we present a new statistical method for mapping quantitative trait loci (QTL) of additive, dominant, and epistatic effects in equilibrium natural populations. Our method is based on haplotype analysis of multilocus linkage disequilibrium and exhibits two significant advantages over current disequilibrium mapping methods. First, we have derived closed-form solutions for estimating the marker-QTL haplotype frequencies within the maximum-likelihood framework implemented by the EM algorithm. The allele frequencies of putative QTL and their linkage disequilibria with the markers are estimated by solving a system of regular equations. This procedure has significantly improved the computational efficiency and the precision of parameter estimation. Second, our method can detect marker-QTL disequilibria of different orders and QTL epistatic interactions of various kinds on the basis of a multilocus analysis. This can not only enhance the precision of parameter estimation, but also make it possible to perform whole-genome association studies. We carried out extensive simulation studies to examine the robustness and statistical performance of our method. The application of the new method was validated using a case study from humans, in which we successfully detected significant QTL affecting human body heights. Finally, we discuss the implications of our method for genome projects and its extension to a broader circumstance. The computer program for the method proposed in this article is available at the webpage http://www.ifasstat.ufl.edu/genome/~LD.

Mapping epigenetic quantitative trait loci (QTL) altering a developmental trajectory

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 28-33 ◽  
Author(s):  
Rongling Wu ◽  
Chang-Xing Ma ◽  
Jun Zhu ◽  
George Casella
Keyword(s):  
Genetic Variation ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Genetic Variance ◽  
Genetic Model ◽  
Epigenetic Modification ◽  
Growth Trait ◽  
Developmental Trajectory ◽  
Growth Trajectory ◽  
Trait Loci

Genetic variation in a quantitative trait that changes with age is important to both evolutionary biologists and breeders. A traditional analysis of the dynamics of genetic variation is based on the genetic variance–covariance matrix among different ages estimated from a quantitative genetic model. Such an analysis, however, cannot reveal the mechanistic basis of the genetic variation for a growth trait during ontogeny. Age-specific genetic variance at time t conditional on the causal genetic effect at time t – 1 implies the generation of episodes of new genetic variation arising during the interval t – 1 to t. In the present paper, the conditional genetic variance estimated from Zhu's (1995) conditional model was partitioned into its underlying individual quantitative trait loci (QTL) using molecular markers in an F2 progeny of poplars (Populus trichocarpa and Populus deltoides). These QTL, defined as epigenetic QTL, govern the alterations of growth trajectory in a population. Three epigenetic QTL were detected to contribute significantly to variation in growth trajectory during the period from the establishment year to the subsequent year in the field. It is suggested that the activation and expression of epigenetic QTL are influenced by the developmental status of trees and the environment in which they are grown.Key words: epigenetic modification, development, marker, poplar, QTL.

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