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At least 595 records · Page 33Linked to original sources
PubMed2003

An apricot (Prunus armeniaca L.) F2 progeny linkage map based on SSR and AFLP markers, mapping plum pox virus resistance and self-incompatibility traits.

A genetic linkage map of apricot ( Prunus armeniaca L.) was constructed using AFLP and SSR markers. The map is based on an F(2) population (76 individuals) derived from self-pollination of an F(1) individual ('Lito') originated from a cross between 'Stark Early Orange' and 'Tyrinthos'. This family, designated as 'Lito' x 'Lito', segregated for two important agronomical traits: plum pox virus resistance (PPV) and self-incompatibility. A total of 211 markers (180 AFLPs, 29 SSRs and two agronomic traits) were assigned to 11 linkage groups covering 602 cM of the apricot genome. The average distance (cM/marker) between adjacent markers is 3.84 cM. The PPV resistance trait was mapped on linkage group G1 and the self-incompatibility trait was mapped on linkage group G6. Twenty two loci held in common with other Prunus maps allowed us to compare and establish homologies among the respective linkage groups.

Breeding↗
PubMed2005

An EM algorithm for mapping quantitative resistance loci.

Many disease resistance traits in plants have a polygenic background and the disease phenotypes are modified by environmental factors. As a consequence, the phenotypic values usually show a quantitative variation. The phenotypes of such disease traits, however, are often measured in discrete but ordered categories. These traits are called ordinal traits. In terms of disease resistance, they are called quantitative resistance traits, as opposed to qualitative resistance traits, and are controlled by the quantitative resistance loci (QRL). Classical quantitative trait locus mapping methods are not optimal for ordinal trait analysis because the assumption of normal distribution is violated. Methods for mapping binary trait loci are not suitable either because there are more than two categories in ordinal traits. We developed a maximum likelihood method to map these QRL. The method is implemented via a multicycle expectation-conditional-maximization (ECM) algorithm under the threshold model, where we can estimate both the QRL effects and the thresholds that link the disease liability and the categorical phenotype. The method is verified in simulated data under various combinations of the parameters. An SAS program is available to implement the multicycle ECM algorithm. The program can be downloaded from our website at www.statgen.ucr.edu.

Algorithms↗
PubMed2005

Linkage disequilibrium mapping of quantitative-trait Loci by selective genotyping.

The principles of linkage disequilibrium mapping of dichotomous diseases can be well applied to the mapping of quantitative-trait loci through the method of selective genotyping. In 1999, M. Slatkin considered a truncation selection (TS) approach. We propose in this report an extended TS approach and an extreme-rank-selection (ERS) approach. The properties of these selection approaches are studied analytically. By using a simulation study, we demonstrate that both the extended TS approach and the ERS approach provide remarkable improvements over Slatkin's original TS approach.

Genotype↗
PubMed1998

Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data.

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 locationwise (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.

Bayes Theorem↗
PubMed2003

Approaches to mapping genetically correlated complex traits.

Our Markov chain Monte Carlo (MCMC) methods were used in linkage analyses of the Framingham Heart Study data using all available pedigrees. Our goal was to detect and map loci associated with covariate-adjusted traits log triglyceride (lnTG) and high-density lipoprotein cholesterol (HDL) using multipoint LOD score analysis, Bayesian oligogenic linkage analysis and identity-by-descent (IBD) scoring methods. Each method used all marker data for all markers on a chromosome. Bayesian linkage analysis detected a linkage signal on chromosome 7 for lnTG and HDL, corroborating previously published results. However, these results were not replicated in a classical linkage analysis of the data or by using IBD scoring methods.We conclude that Bayesian linkage analysis provides a powerful paradigm for mapping trait loci but interpretation of the Bayesian linkage signals is subjective. In the absence of a LOD score method accommodating genetically complex traits and linkage heterogeneity, validation of these signals remains elusive.

Cholesterol, HDL↗
PubMed2004

Nonparametric estimation of the effects of quantitative trait loci.

Interval mapping of quantitative trait loci from breeding experiments plays an important role in understanding the mechanisms of disease, both in humans and other organisms. Standard approaches to estimation involve parametric assumptions for the component distributions and may be sensitive to model misspecification. Some nonparametric tests have been studied. However, nonparametric estimation of the phenotypic distributions has not been considered in the genetics literature, even though such methods might provide essential nonparametric summaries for comparing different loci. We develop a sufficient condition for identifiability of the phenotypic distributions. Simple nonparametric estimators for the distributions are proposed for uncensored and right censored data. They have a closed form and their small and large sample properties are readily established. Their practical utility as numerical summaries which complement nonparametric tests is demonstrated on two recent genetics examples.

Animals↗
PubMed2004

Yield response to water deficit in an upland rice mapping population: associations among traits and genetic markers.

A population of recombinant inbred rice lines from a cross between the upland japonica cultivar Azucena and the upland indica cultivar Bala was evaluated in a series of upland field experiments. Water stress was imposed during the reproductive stage by managed irrigation during the dry season, while control treatments were maintained in aerobic, well-irrigated conditions. Water deficit resulted in a yield reduction of 17 to 50%. The genetic correlation between stress and control yields was quite high when stress was mild, and the heritability of yield was similar in stress and control treatments across both years of this study. Genetic correlations between secondary traits such as leaf rolling and drying and yield under stress varied from high (leaf drying) to insignificant (leaf rolling). Lines with superior yield tended to have fewer panicles and larger grain size than the high-yielding parent, Bala, even though the panicle number was positively correlated with yield and the thousand-grain weight was not associated with yield for the population as a whole. Analysis of quantitative trait loci (QTLs) for yield and yield components allowed the identification of 31 regions associated with growth or yield components. Superior alleles came from either parent. Several of the regions identified had also been reported for root mass at depth or maximum root length in this population in other studies made under controlled environments, and for leaf drying (LD) in field studies. However, the direction of the effect of QTLs was not consistent, which indicates that there was not necessarily a causal relationship between these secondary traits and performance. We conclude that mapping populations can provide novel insights on the actual relationships between yield components and secondary traits in stress and control environments and can allow identification of significant QTLs for yield components under drought stress.

Biomass↗
PubMed2003

Dimension reduction for mapping mRNA abundance as quantitative traits.

The advent of sophisticated genomic techniques for gene mapping and microarray analysis has provided opportunities to map mRNA abundance to quantitative trait loci (QTL) throughout the genome. Unfortunately, simple mapping of each individual mRNA trait on the scale of a typical microarray experiment is computationally intensive, subject to high sample variance, and therefore underpowered. However, this problem can be addressed by capitalizing on correlation among the large number of mRNA traits. We present a method to reduce the dimensionality for mapping gene expression data as quantitative traits. We used a blind method, principal components, and a sighted method, hierarchical clustering seeded by disease relevant traits, to define new traits composed of a small collection of promising mRNAs. We validated the principle of our approach by mapping the expression levels of metabolism genes in a population of F(2)-ob/ob mice derived from the BTBR and C57BL/6J strains. We found that lipogenic and gluconeogenic mRNAs, which are known targets of insulin action, were closely associated with the insulin trait. Multiple interval mapping and Bayesian interval mapping of this new trait revealed significant linkages to chromosome regions that were contained in loci associated with type 2 diabetes in this same mouse sample. As a further statistical refinement, we show that principal component analysis also effectively reduced dimensions for mapping phenotypes composed of mRNA abundances.

Animals↗
PubMed1995

Strategies for mapping and identifying quantitative trait loci specifying behavioral responses to alcohol.

Most responses to alcohol in both humans and animals are heritable, and this genetic sensitivity to ethanol is determined by multiple genes. However, the number of genes, their identities, and just how they determine susceptibility to the actions of alcohol are unknown. Herein, we describe a multistage strategy for mapping quantitative trait loci (QTLs) using recombinant inbred strains and F2 mice. Precise mapping of the chromosome positions of these QTLs should increase our understanding of the genetic causes for individual differences in behavioral sensitivity to alcohol by (1) identifying genomic markers associated with sensitivity to alcohol, (2) allowing the genes specifying behavior to be cloned by position, and (3) elucidating "candidate" genes demonstrating linkage to markers associated with behavioral responses to alcohol. Syntenic conservation between the mouse and human genomes should facilitate the eventual mapping and cloning of human homologs of these QTLs. Ultimately, cloning of these genes may allow the development of gene therapies or other therapeutic interventions for management or prevention of alcoholism and alcohol abuse.

Alcohol Drinking↗
PubMed2004

Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana.

Genetic analysis of natural variation in ecotypes of Arabidopsis thaliana can facilitate the discovery of new genes or of allelic variants of previously identified genes controlling physiological processes in plants. We mapped quantitative trait loci (QTL) for light response in recombinant inbred lines (RILs) derived from the Columbia and Kashmir accessions via two methods: composite interval mapping and eXtreme array mapping (XAM). After measuring seedling hypocotyl lengths in blue, red, far-red, and white light, and in darkness, eight QTL were identified by composite interval mapping and five localized near photoreceptor loci. Two QTL in blue light were associated with CRY1 and CRY2, two in red light were near PHYB and PHYC, and one in far-red light localized near PHYA. The RED2 and RED5 QTL were verified in segregating lines. XAM was tested for the identification of QTL in red light with pools of RILs selected for extreme phenotypes. Thousands of single feature polymorphisms detected by differential DNA hybridized to high-density oligo-nucleotide arrays were used to estimate allele frequency differences between the pools. The RED2 QTL was identified clearly; differences exceeded a threshold of significance determined by simulations. The sensitivities of XAM to population type and size and genetic models were also determined by simulation analysis.

Arabidopsis↗
PubMed2004

QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima.

International rice export markets are increasing demands for rapid improvements in grain quality characteristics. The African rice Oryza glaberrima is a new potential source of genes that will enhance the eating, cooking, and milling properties of the rice grain. The objective of this research was to identify and characterize quantitative trait loci (QTLs) among 312 doubled haploid lines derived from the BC3F1 of an interspecific cross of O. sativa x O. glaberrima. Genetic material was planted in replicated plots and evaluated for ten grain quality traits in 2001 in Colombia. A linkage map was constructed with 100 polymorphic microsatellite markers using the mapdisto software program to adjust for segregation distortion. Transgressive segregation was observed for all traits. Interval and composite interval analyses identified 27 QTLs for nine characters located on 11/12 chromosomes. The chromosomal positions of QTLs for percentage amylose, alkali-spreading score, and percentage protein were in agreement with data reported by others, whereas QTL markers for percentage head rice, percentage milled rice, percentage protein, and percentage brown rice were different in our mapping population. Five major QTLs were found to be associated with improved percentage rice bran, percentage amylose, and alkali-spreading score. Seven QTLs for improved percentage rice bran, percentage milled rice, alkali-spreading score, percentage protein, and grain length/width ratio were derived from the O. glaberrima accession. Three new QTLs for percentage rice bran are reported here for the first time. Results from this study suggest that the African rice might be a valuable new source for introgression and improvement of several traits that affect quality traits demanded by the different rice export markets.

Chromosome Mapping↗
PubMed2001

Map-based cloning of quantitative trait loci: progress and prospects.

Map-based cloning has been considered problematic for isolating quantitative trait loci (QTLs) due to the confounding phenotypic effects of environment and other QTLs. However, five recent studies, all in plants, have succeeded in cloning QTLs using map-based methods. We review the important features of these studies and evaluate the prospects for broader application of the techniques. Successful map-based cloning requires that QTLs represent single genes that can be isolated in near-isogenic lines, and that genotypes can be unambiguously inferred by progeny testing. In plants or animals for which map-based cloning of genes with discrete phenotypes is feasible, the modified procedures required for QTLs should not be limiting in most cases. The choice between map-based cloning and alternative methods will depend on details of the species and traits being studied.

Arabidopsis↗
PubMed2000

[Study of mapping QTLs for milk traits on the German dairy cattle].

A total of 1,130 bulls belonging to 20 half-sib families of German dairy cattle were genotyped for 229 microsatellite markers on 30 chromosomes. The data were used in an attempt to map quantitative trait loci applying regression as multiple-marker regression. For association analysis with a granddaughter design, the estimated breeding values for 3 milk traits were used: milk production, fat production and protein production. The empirical values of significance thresholds were determined by using a permutation test on the experimental data. Several significant QTLs were found on some chromosomes, especially on the chromosome 14. The results give a strong support for the experiments of Coppieters et al. and Ron et al.

Animals↗
PubMed1999

Disequilibrium mapping of a quantitative-trait locus in an expanding population.

Linkage disequilibrium (LD) mapping can be successful if there is strong nonrandom association between marker alleles and an allele affecting a trait of interest. The principles of LD mapping of dichotomous traits are well understood, but less is known about LD mapping of a quantitative-trait locus (QTL). It is shown in this report that selective genotyping can increase the power to detect and map a rare allele of large effect at a QTL. Two statistical tests of the association between an allele and a quantitative character are proposed. These tests are approximately independent, so information from them can be combined. Analytic theory is developed to show that these two tests are effective in detecting the presence of a low-frequency allele with a relatively large effect on the character when the QTL is either already a candidate locus or closely linked to a marker locus that is in strong LD with the QTL. The latter situation is expected in a rapidly growing population in which the allele of large effect was present initially in one copy. Therefore, the proposed tests are useful under the same conditions as those for successful LD mapping of a dichotomous trait or disease. Simulations show that, for detection of the presence of a QTL, these tests are more powerful than a simple t-test. The tests also provide a basis for defining a measure of association, gamma, between a low-frequency allele at a putative QTL and a low-frequency allele at a marker locus.

Genetics, Population↗
PubMed1995

Mapping and manipulating quantitative traits in maize.

Maize has been used effectively as a model organism in the development and evaluation of molecular markers for the identification, mapping and manipulation of major genes affecting the expression of quantitative traits in plants. Although quantitative geneticists have recognized the possibility of major loci, the general dogma had emerged that quantitative traits were controlled by many loci, each with a small effect. This interpretation sent a quantitative traits because it would be essentially impossible to isolate a gene responsible for the trait. Recent results from numerous mapping studies have shown that quantitative traits are controlled by, at least some, factors with major effects, and have given credibility to the conclusion that major loci exist and that one might be able to study them. Positive results from marker-facilitated selection and introgression studies have further strengthened this conclusion.

Chromosome Mapping↗
PubMed2001

A score-statistic approach for the mapping of quantitative-trait loci with sibships of arbitrary size.

The Haseman-Elston method is widely used for the mapping of quantitative-trait loci. However, this method does not use all the information in the data, because it only considers the sib-pair trait-value difference. In addition, the Haseman-Elston method was developed for independent sib pairs; its generalization to nonindependent sib pairs is not straightforward. Here we introduce a score test statistic derived from a normal likelihood based on multiplex sibship data, conditional on identical-by-descent sharing statuses. This score test is asymptotically equivalent to the corresponding likelihood-ratio test, but it is much easier to implement. Because the proposed test uses all of the trait values, it makes more efficient use of the data than does the Haseman-Elston method. The proposed test is naturally applicable to sibships of arbitrary size. The finite-sample properties of the proposed score statistic are evaluated via simulations.

Chromosome Mapping↗