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

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.

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Pleiotropy of quantitative trait loci for organ weights and limb bone lengths in mice

Physiological Genomics ◽

10.1152/physiolgenomics.00018.2002 ◽

2002 ◽

Vol 10 (1) ◽

pp. 21-29 ◽

Cited By ~ 33

Author(s):

Larry J. Leamy ◽

Daniel Pomp ◽

E. J. Eisen ◽

James M. Cheverud

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genetic Basis ◽

Wild Strain ◽

Interval Mapping ◽

Antagonistic Pleiotropy ◽

Organ Weights ◽

Limb Bone ◽

Rapid Growth Rate ◽

Trait Loci

We investigated the genetic basis of several limb bone lengths and weights of organs in mice produced from a cross of the F1 between CAST/Ei (wild strain) and M16i (selected for rapid growth rate) back to M16i. From previous correlation studies, we hypothesized that quantitative trait loci (QTLs) would exhibit greater pleiotropy within than between the limb length and organ weight character sets. Using interval mapping procedures and significance testing at the chromosome-wise level, we discovered 14 putative QTLs affecting weight of the liver, spleen, heart, and/or kidney, 9 of which affected more than one organ; and 12 QTLs for limb lengths, all of which affected the length of two or more of the limb bones in these mice. As was hypothesized, most QTLs affected either organ weights or limb lengths independently of each other, although five QTLs were found that affected both sets of characters. The direction of the effect of these QTLs was almost always consistent within and between characters, with little evidence for antagonistic pleiotropy.

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Quantitative Trait Loci Responsible for Variation in Sexually Dimorphic Traits in Drosophila melanogaster

Genetics ◽

10.1093/genetics/163.2.771 ◽

2003 ◽

Vol 163 (2) ◽

pp. 771-787 ◽

Cited By ~ 5

Author(s):

Artyom Kopp ◽

Rita M Graze ◽

Shizhong Xu ◽

Sean B Carroll ◽

Sergey V Nuzhdin

Keyword(s):

Drosophila Melanogaster ◽

Genetic Variation ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genetic Basis ◽

Morphological Evolution ◽

Recombinant Inbred Lines ◽

Natural Populations ◽

Sexually Dimorphic ◽

Trait Loci

Abstract To understand the mechanisms of morphological evolution and species divergence, it is essential to elucidate the genetic basis of variation in natural populations. Sexually dimorphic characters, which evolve rapidly both within and among species, present attractive models for addressing these questions. In this report, we map quantitative trait loci (QTL) responsible for variation in sexually dimorphic traits (abdominal pigmentation and the number of ventral abdominal bristles and sex comb teeth) in a natural population of Drosophila melanogaster. To capture the pattern of genetic variation present in the wild, a panel of recombinant inbred lines was created from two heterozygous flies taken directly from nature. High-resolution mapping was made possible by cytological markers at the average density of one per 2 cM. We have used a new Bayesian algorithm that allows QTL mapping based on all markers simultaneously. With this approach, we were able to detect small-effect QTL that were not evident in single-marker analyses. Our results show that at least for some sexually dimorphic traits, a small number of QTL account for the majority of genetic variation. The three strongest QTL account for >60% of variation in the number of ventral abdominal bristles. Strikingly, a single QTL accounts for almost 60% of variation in female abdominal pigmentation. This QTL maps to the chromosomal region that Robertson et al. have found to affect female abdominal pigmentation in other populations of D. melanogaster. Using quantitative complementation tests, we demonstrate that this QTL is allelic to the bric a brac gene, whose expression has previously been shown to correlate with interspecific differences in pigmentation. Multiple bab alleles that confer distinct phenotypes appear to segregate in natural populations at appreciable frequencies, suggesting that intraspecific and interspecific variation in abdominal pigmentation may share a similar genetic basis.

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Interval Mapping of Quantitative Trait Loci Underlying Endosperm Traits with NC III and TTC Designs

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2008.01734 ◽

2009 ◽

Vol 34 (10) ◽

pp. 1734-1743

Author(s):

Xue-Feng WANG

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Interval Mapping ◽

Trait Loci

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On the Differences Between Maximum Likelihood and Regression Interval Mapping in the Analysis of Quantitative Trait Loci

Genetics ◽

10.1093/genetics/156.2.855 ◽

2000 ◽

Vol 156 (2) ◽

pp. 855-865 ◽

Cited By ~ 2

Author(s):

Chen-Hung Kao

Keyword(s):

Quantitative Trait Loci ◽

Maximum Likelihood ◽

Qtl Mapping ◽

Quantitative Trait ◽

Mean Squared Error ◽

Interval Mapping ◽

Size Difference ◽

Ratio Test ◽

Trait Loci ◽

Variance Explained

AbstractThe differences between maximum-likelihood (ML) and regression (REG) interval mapping in the analysis of quantitative trait loci (QTL) are investigated analytically and numerically by simulation. The analytical investigation is based on the comparison of the solution sets of the ML and REG methods in the estimation of QTL parameters. Their differences are found to relate to the similarity between the conditional posterior and conditional probabilities of QTL genotypes and depend on several factors, such as the proportion of variance explained by QTL, relative QTL position in an interval, interval size, difference between the sizes of QTL, epistasis, and linkage between QTL. The differences in mean squared error (MSE) of the estimates, likelihood-ratio test (LRT) statistics in testing parameters, and power of QTL detection between the two methods become larger as (1) the proportion of variance explained by QTL becomes higher, (2) the QTL locations are positioned toward the middle of intervals, (3) the QTL are located in wider marker intervals, (4) epistasis between QTL is stronger, (5) the difference between QTL effects becomes larger, and (6) the positions of QTL get closer in QTL mapping. The REG method is biased in the estimation of the proportion of variance explained by QTL, and it may have a serious problem in detecting closely linked QTL when compared to the ML method. In general, the differences between the two methods may be minor, but can be significant when QTL interact or are closely linked. The ML method tends to be more powerful and to give estimates with smaller MSEs and larger LRT statistics. This implies that ML interval mapping can be more accurate, precise, and powerful than REG interval mapping. The REG method is faster in computation, especially when the number of QTL considered in the model is large. Recognizing the factors affecting the differences between REG and ML interval mapping can help an efficient strategy, using both methods in QTL mapping to be outlined.

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Time-Related Mapping of Quantitative Trait Loci Underlying Tiller Number in Rice

Genetics ◽

10.1093/genetics/151.1.297 ◽

1999 ◽

Vol 151 (1) ◽

pp. 297-303 ◽

Cited By ~ 3

Author(s):

Wei-Ren Wu ◽

Wei-Ming Li ◽

Ding-Zhong Tang ◽

Hao-Ran Lu ◽

A J Worland

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Composite Interval Mapping ◽

Interval Mapping ◽

Tiller Number ◽

Multiple Trait ◽

Phenotypic Data ◽

Recombinant Inbred Population ◽

Trait Loci ◽

Final Observation

Abstract Using time-related phenotypic data, methods of composite interval mapping and multiple-trait composite interval mapping based on least squares were applied to map quantitative trait loci (QTL) underlying the development of tiller number in rice. A recombinant inbred population and a corresponding saturated molecular marker linkage map were constructed for the study. Tiller number was recorded every 4 or 5 days for a total of seven times starting at 20 days after sowing. Five QTL were detected on chromosomes 1, 3, and 5. These QTL explained more than half of the genetic variance at the final observation. All the QTL displayed an S-shaped expression curve. Three QTL reached their highest expression rates during active tillering stage, while the other two QTL achieved this either before or after the active tillering stage.

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Quantitative Trait Loci for Susceptibility to Tapeworm Infection in the Red Flour Beetle

Genetics ◽

10.1093/genetics/165.3.1307 ◽

2003 ◽

Vol 165 (3) ◽

pp. 1307-1315

Author(s):

Daibin Zhong ◽

Aditi Pai ◽

Guiyun Yan

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genetic Basis ◽

Life Cycles ◽

Red Flour Beetle ◽

Phenotypic Variance ◽

Flour Beetle ◽

Trait Loci ◽

Host Ecology ◽

Tapeworm Infection

Abstract Parasites have profound effects on host ecology and evolution, and the effects of parasites on host ecology are often influenced by the magnitude of host susceptibility to parasites. Many parasites have complex life cycles that require intermediate hosts for their transmission, but little is known about the genetic basis of the intermediate host's susceptibility to these parasites. This study examined the genetic basis of susceptibility to a tapeworm (Hymenolepis diminuta) in the red flour beetle (Tribolium castaneum) that serves as an intermediate host in its transmission. Quantitative trait loci (QTL) mapping experiments were conducted with two independent segregating populations using amplified fragment length polymorphism (AFLP) markers and randomly amplified polymorphic DNA (RAPD) markers. A total of five QTL that significantly affected beetle susceptibility were identified in the two reciprocal crosses. Two common QTL on linkage groups 3 and 6 were identified in both crosses with similar effects on the phenotype, and three QTL were unique to each cross. In one cross, the three main QTL accounted for 29% of the total phenotypic variance and digenic epistasis explained 39% of the variance. In the second cross, the four main QTL explained 62% of the variance and digenic epistasis accounted for only 5% of the variance. The actions of these QTL were either overdominance or underdominance. Our results suggest that the polygenic nature of beetle susceptibility to the parasites and epistasis are important genetic mechanisms for the maintenance of variation within or among beetle strains in susceptibility to tapeworm infection.

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Quantitative Trait Loci Affecting Differences in Floral Morphology Between Two Species of Monkeyflower (Mimulus)

Genetics ◽

10.1093/genetics/149.1.367 ◽

1998 ◽

Vol 149 (1) ◽

pp. 367-382 ◽

Cited By ~ 11

Author(s):

H D Bradshaw ◽

Kevin G Otto ◽

Barbara E Frewen ◽

John K McKay ◽

Douglas W Schemske

Keyword(s):

Quantitative Trait Loci ◽

Reproductive Isolation ◽

Quantitative Trait ◽

Floral Morphology ◽

Cumulative Effect ◽

Sympatric Species ◽

Accurate Estimate ◽

Phenotypic Variance ◽

Trait Loci ◽

Morphological Differences

Abstract Conspicuous differences in floral morphology are partly responsible for reproductive isolation between two sympatric species of monkeyflower because of their effect on visitation of the flowers by different pollinators. Mimulus lewisii flowers are visited primarily by bumblebees, whereas M. cardinalis flowers are visited mostly by hummingbirds. The genetic control of 12 morphological differences between the flowers of M. lewisii and M. cardinalis was explored in a large linkage mapping population of F2 plants (n = 465) to provide an accurate estimate of the number and magnitude of effect of quantitative trait loci (QTLs) governing each character. Between one and six QTLs were identified for each trait. Most (9/12) traits appear to be controlled in part by at least one major QTL explaining ≥25% of the total phenotypic variance. This implies that either single genes of individually large effect or linked clusters of genes with a large cumulative effect can play a role in the evolution of reproductive isolation and speciation.

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Bayesian Mapping of Multiple Quantitative Trait Loci From Incomplete Inbred Line Cross Data

Genetics ◽

10.1093/genetics/148.3.1373 ◽

1998 ◽

Vol 148 (3) ◽

pp. 1373-1388

Author(s):

Mikko J Sillanpää ◽

Elja Arjas

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Composite Interval Mapping ◽

Backcross Progeny ◽

Random Variable ◽

Interval Mapping ◽

Mapping Method ◽

Structure Mapping ◽

Standard Interval ◽

Trait Loci

Abstract A novel fine structure mapping method for quantitative traits is presented. It is based on Bayesian modeling and inference, treating the number of quantitative trait loci (QTLs) as an unobserved random variable and using ideas similar to composite interval mapping to account for the effects of QTLs in other chromosomes. The method is introduced for inbred lines and it can be applied also in situations involving frequent missing genotypes. We propose that two new probabilistic measures be used to summarize the results from the statistical analysis: (1) the (posterior) QTL-intensity, for estimating the number of QTLs in a chromosome and for localizing them into some particular chromosomal regions, and (2) the location wise (posterior) distributions of the phenotypic effects of the QTLs. Both these measures will be viewed as functions of the putative QTL locus, over the marker range in the linkage group. The method is tested and compared with standard interval and composite interval mapping techniques by using simulated backcross progeny data. It is implemented as a software package. Its initial version is freely available for research purposes under the name Multimapper at URL http://www.rni.helsinki.fi/~mjs.

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A Rank-Based Nonparametric Method for Mapping Quantitative Trait Loci in Outbred Half-Sib Pedigrees: Application to Milk Production in a Granddaughter Design

Genetics ◽

10.1093/genetics/149.3.1547 ◽

1998 ◽

Vol 149 (3) ◽

pp. 1547-1555 ◽

Cited By ~ 2

Author(s):

Wouter Coppieters ◽

Alexandre Kvasz ◽

Frédéric Farnir ◽

Juan-Jose Arranz ◽

Bernard Grisart ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Real Data ◽

Interval Mapping ◽

Mapping Method ◽

Residual Variance ◽

Data Set ◽

Wilcoxon Rank Sum Test ◽

Holstein Friesian ◽

Trait Loci

Abstract We describe the development of a multipoint nonparametric quantitative trait loci mapping method based on the Wilcoxon rank-sum test applicable to outbred half-sib pedigrees. The method has been evaluated on a simulated dataset and its efficiency compared with interval mapping by using regression. It was shown that the rank-based approach is slightly inferior to regression when the residual variance is homoscedastic normal; however, in three out of four other scenarios envisaged, i.e., residual variance heteroscedastic normal, homoscedastic skewed, and homoscedastic positively kurtosed, the latter outperforms the former one. Both methods were applied to a real data set analyzing the effect of bovine chromosome 6 on milk yield and composition by using a 125-cM map comprising 15 microsatellites and a granddaughter design counting 1158 Holstein-Friesian sires.

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

Genetics ◽

10.1093/genetics/165.3.1489 ◽

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.

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