M J Kearsey

QTL Express mapping quantitative trait loci in simple and complex pedigrees

QTL Express is the first application for Quantitative Trait Locus (QTL) mapping in outbred populations with a web-based user interface. User input of three files containing a marker map, trait data and marker genotypes allows mapping of single or multiple QTL by the regression approach, with the option to perform permutation or bootstrap tests.

THE POWER OF THE CLASSICAL TWIN STUDY

SummaryA method based on the non-central chi-square distribution is developed for the calculation of sample sizes required to reject, with given probability, models of variation when they are “ wrong ”. The method is illustrated with reference to simple alternative models of variation in MZ and DZ twins reared together. Simulation of twin experiments finds the empirical power in good agreement with that predicted by the method. Tables are produced showing the sample sizes required for 95 per cent rejection at the 5 per cent level of inappropriate models of variation. For equivalent cases it is always found easier to reject an inappropriate simple genetical model of variation than an inappropriate simple environmental model. For several frequently encountered cases, more than 600 pairs of twins would be required to reject inappropriate alternative models. The optimum proportion of MZ and DZ twins in a sample will vary with the “true” model of variation but is most likely to be between two-thirds and one-half of DZ twin pairs.The possibility of detecting genetical non-additivity with the classical twin study is investigated by theoretical power calculations and simulation. In the absence of genotype-environment interactions, distributional skewness and mean-variance regression in DZ twins are found to be more powerful tests of directional dominance (or unequal gene frequencies) than the standard model fitting procedure and these tests may be worthwhile in future studies.

QTL analysis in plants; where are we now?

We have briefly reviewed the methods currently available for QTL analysis in segregating populations and summarized some of the conclusions arising from such analyses in plant populations. We show that the analytical methods locate QTL with poor precision (10–30 cM), unless the heritability of an individual QTL is high. Also the estimates of the QTL effects, particularly the dominance effects tend to be inflated because only large estimates are significant. Estimates of numbers of QTL per trait are generally low (<8) for individual trials. This may suggest that there are few QTL but probably reflects the power of the methods. There is no large correlation between the numbers of QTL found and the amount of the variation explained. Of those cases where dominance is measurable, dominance ratios are often ≲1, but seldom significantly greater. These latter cases need further analysis. Many QTL map close to candidate genes, and there is growing evidence from synteny studies of corresponding chromosome regions carrying similar QTL in different species. However, unreliability of QTL location may suggest false candidates.

Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome

Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.

QTL analysis: unreliability and bias in estimation procedures

Several statistical methods which employ multiple marker data are currently available for the analysis of quantitative trait loci (QTL) in experimental populations. Although comparable estimates of QTL location and effects have been obtained by these methods, using simulated and real data sets, their accuracy and reliability have not been extensively investigated. The present study specifically examines the merit of using F2 and doubled haploid populations for locating QTL and estimating their effects. Factors which may affect accuracy and reliability of QTL mapping, such as the number and position of the markers available, the accuracy of the marker locations and the size of the experimental population used, are considered. These aspects are evaluated for QTL of differing heritabilities and locations along the chromosome.A population of 300 F2 individuals and 150 doubled haploid lines gave estimates of QTL position and effect which were comparable, albeit extremely unreliable. Even for a QTL of high heritability (10%), the confidence interval was 35 cM. There was little increase in reliability to be obtained from using 300, rather than 200, F2 individuals and 100 doubled haploid lines gave similar results to 150. QTL estimates were not significantly improved either by using the expected, rather than the observed, marker positions or by using a dense map of markers rather than a sparse map. A QTL which was asymmetrically located in the linkage group resulted in inaccurate estimates of QTL position which were seriously biassed at low heritability of the QTL. In a population of 300 F2 individuals the bias increased from 4 cM to 20 cM, for a QTL with 10% and 2% heritability respectively.

Mapping QTL controlling yield and yield components in a spring barley (Hordeum vulgare L.) cross using marker regression

An RFLP map constructed from 99 doubled haploid lines of a cross between two spring barley varieties (Blenheim × Kym) was used to localize quantitative trait loci (QTL) controlling grain yield and yield components by marker regression and single-marker analysis. Trials were conducted over three years. Genotype-by-year interaction was detected for plant grain weight and ear grain weight so they were analysed separately for each year. None was detected for thousand-grain weight and ear grain number so data were pooled over years. A total of eleven QTL were detected for plant grain weight over two years and fourteen for ear grain weight over three years. Seven QTL were detected for plot yield. The locus with the largest effect was on chromosome 2(2H)L and accounted for 19% of the variation in the progeny. Eight QTL were detected for thousand-grain weight and five for ear grain number. Many of the QTL detected were in comparable positions in each year. Yield and yield components were only partly correlated. Comparisons based on common RFLP markers showed that some QTL were found in positions similar to those identified in other studies. For a number of QTL the identification of linked markers provided suitable opportunities for marker-assisted selection and improvement of barley and reference markers with which to analyse the homoeologous chromosome regions of wheat and other cereals.

Expression quantitative trait loci analysis in plants

An expression Quantitative Trait Locus or eQTL is a chromosomal region that accounts for a proportion of the variation in abundance of a mRNA transcript observed between individuals in a genetic mapping population. A single gene can have one or multiple eQTLs. Large scale mRNA profiling technologies advanced genome-wide eQTL mapping in a diverse range of organisms allowing thousands of eQTLs to be detected in a single experiment. When combined with classical or trait QTLs, correlation analyses can directly suggest candidates for genes underlying these traits. Furthermore, eQTL mapping data enables genetic regulatory networks to be modelled and potentially provide a better understanding of the underlying phenotypic variation. The mRNA profiling data sets can also be used to infer the chromosomal positions of thousands of genes, an outcome that is particularly valuable for species with unsequenced genomes where the chromosomal location of the majority of genes remains unknown. In this review we focus on eQTL studies in plants, addressing conceptual and technical aspects that include experimental design, genetic polymorphism prediction and candidate gene identification.

Biometrical analysis of a random mating population: A comparison of five experimental designs

Biometrical analysis of a random mating population: A comparison of five experimental designs

Genetics of quantitative traits in Arabidopsis thaliana

The genetic control of 22 quantitative traits, including developmental rates and sizes, was examined in generations of Arabidopsis thaliana derived from the cross between the ecotypes, Columbia (Col) and Landsberg erecta (Ler). The data were obtained from three sets of families raised in the same trial: the 16 basic generations, that is, parents, F1s, F2s, backcrosses, recombinant inbred lines (RILs) and a triple test cross (TTC), the latter produced by crossing the RILs to Col, Ler and their F1. The data were analysed by two approaches. The first (approach A) involved traditional generation mean and variance component analysis and the second (B), based around the RILs and TTC families, involved marker-based QTL analysis.From (A), genetic differences between Col and Ler were detected for all traits with moderate heritabilities. Height at flowering was the only trait to show heterosis. Dominance was partial to complete for all height traits, and there was no overdominance but there was strong evidence for directional dominance. For most other traits, dominance was ambidirectional and incomplete, with average dominance ratios of around 80%. Epistasis, particularly of the duplicate type that opposes dominance, was a common feature of all traits. The presence of epistasis must imply multiple QTL for all traits.The QTL analysis located 38 significant effects in four regions of chromosomes I, II, IV and V, but not III. QTL affecting rosette size and leaf number were identified in all four regions, with days to maturity on chromosomes IV and V. The only QTL for height was located at the expected position of the erecta gene (chromosome II; 50u2009cM), but the additive and dominance effects of this single QTL did not adequately explain the generation means. The possible involvement of other interacting height QTL is discussed.

Maximum likelihood estimation of linkage between a marker gene and a quantitative locus

A maximum likelihood approach is developed for estimating the recombination fraction in a segregating population (F2), between a marker gene and a locus affecting a quantitative trait as well as estimating the means and variances of the three genotypes of the quantitative trait. The experimental results from computer simulations show that even with experimental sizes of 500, estimates of the parameters can be obtained by aid of the codominant marker gene as long as the heritability of the quantitative trait in question is not less than 0·10. However at low heritabilities the variances of estimates are very large.