Biomedical subjects

C A Hackett

Publications and source records attributed to C A Hackett.

13 recordsLinked to original sources

PubMed2001

Multi-trait QTL mapping in barley using multivariate regression.

Many studies of QTL locations record several different traits on the same population, but most analyses look at this information on a trait-by-trait basis. In this paper we show how the regression approach to QTL mapping of Haley & Knott (1992) may be extended to a multi-trait analysis via multivariate regression, easily programmed in statistical packages. A procedure for identifying QTL locations using forward selection and bootstrapping is proposed. The method is applied to examine the locations for QTLs for six yield characters (the number of fertile stems, the grain number of the main stem, the main stem grain weight, the single plant yield, the plot yield and the thousand grain weight) in a doubled haploid population of spring barley. Several chromosomal locations with effects on more than one trait are found. The method is also suitable for examining a single trait measured in different years or environments, and is used here to examine data on heading date, a highly heritable trait, and plot yield, a trait with moderate heritability and showing QTL-environment interactions.

Chromosome Mapping↗

PubMed2001

A comment on Xie and Xu: 'mapping quantitative trait loci in tetraploid species'.

Xie & Xu (2000) present a model for mapping quantitative trait loci in an autotetraploid population. However, one aspect of their model, namely gamete formation, does not properly represent the biological process in autotetraploid species. This paper gives a more realistic formulation for this part of the model, and discusses the consequences for multipoint mapping.

Breeding↗

PubMed2001

Construction of a genetic linkage map in tetraploid species using molecular markers.

This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular markers scored on two parents and their full-sib progeny. The steps of the analysis are as follows: identification of parental genotypes from the parental and offspring phenotypes; testing for independent segregation of markers; partition of markers into linkage groups using cluster analysis; maximum-likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstructing their linkage phases. The information from different marker configurations about the recombination frequency is examined and found to vary considerably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applied to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato.

Algorithms↗

PubMed2001

Interval mapping of quantitative trait loci in autotetraploid species.

This article presents a method for QTL interval mapping in autotetraploid species for a full-sib family derived by crossing two parents. For each offspring, the marker information on each chromosome is used to identify possible configurations of chromosomes inherited from the two parents and the locations of crossovers on these chromosomes. A branch and bound algorithm is used to identify configurations with the minimum number of crossovers. From these configurations, the conditional probability of each possible QTL genotype for a series of positions along the chromosome can be estimated. An iterative weighted regression is then used to relate the trait values to the QTL genotype probabilities. A simulation study is performed to assess this approach and to investigate the effects of the proportion of codominant to dominant markers, the heritability, and the population size. We conclude that the method successfully locates QTL and estimates their parameters accurately, and we discuss different modes of action of the QTL that may be modeled.

Algorithms↗

PubMed2000

Construction of a genetic linkage map for Camellia sinensis (tea).

Genetic maps are a vital tool in cultivar improvement programmes for woody perennial tree crops such as tea (Camellia sinensis). A population thought to be derived from two known, noninbred parents was scored for RAPD and AFLP markers, in order to develop a linkage map. However, a very high proportion of the markers exhibited unexpected segregation ratios in the light of their configurations in the parents, and an exploratory statistical analysis revealed patterns in the marker scores which can most easily be explained by the hypothesis of three male parents contributing pollen to this cross. We discuss the evidence for this and the subsequent analysis required to assemble the markers from the female parent into the first linkage map for tea. The map has 15 linkage groups of three or more markers, agreeing with the haploid chromosome number of tea. The statistical methods that revealed the subpopulations are easy to apply routinely, and may prove a useful diagnostic tool for the analysis of noninbred mapping populations.

Chromosome Mapping↗

PubMed2000

Phenotypic responses of wild barley to experimentally imposed water stress.

Responses to water stress within a population of wild barley from Tabigha, Israel, were examined. The population's distribution spans two soil types: Terra Rossa (TR) and Basalt (B). Seeds were collected from plants along a 100 m transect; 24 genotypes were sampled from TR and 28 from B. Due to different soil water-holding capacities, plants growing on TR naturally experience more intense drought than plants growing on B. In a glasshouse experiment, water was withheld from plants for two periods (10 d and 14 d) after flag leaf emergence. A total of 15 agronomic, morphological, developmental, and fertility related traits were examined by analysis of variance (ANOVA). Ten of these traits were significantly affected by the treatment. A high degree of phenotypic variation was found in the population with significant genotypextreatment and soil typextreatment interactions. Principal component analysis (PCA) was performed using combined control and stress treatment data sets. The first three principal components (pc) explained 88.8% of the variation existing in the population with pc1 (47.9%) comprising yield-related and morphological traits, pc2 (22.9%) developmental characteristics and pc3 (18.0%) fertility-related traits. The relative performance of individual genotypes was determined and water stress tolerant genotypes identified. TR genotypes were significantly less affected by the imposed water stress than B genotypes. Moreover, TR genotypes showed accelerated development under water deficit conditions. Data indicate that specific genotypes demonstrating differential responses may be useful for comparative physiological studies, and that TR genotypes exhibiting yield stability may have value for breeding barley better adapted to drought.

Adaptation, Physiological↗

PubMed1999

Approximate standard errors in semiparametric models.

We consider semiparametric models with p regressor terms and q smooth terms. We obtain an explicit expression for the estimate of the regression coefficients given by the back-fitting algorithm. The calculation of the standard errors of these estimates based on this expression is a considerable computational exercise. We present an alternative, approximate method of calculation that is less demanding. With smoothing splines, the method is exact, while with loess, it gives good estimates of standard errors. We assess the adequacy of our approximation and of another approximation with the help of two examples.

Agriculture↗

PubMed1998

Linkage analysis in tetraploid potato and association of markers with quantitative resistance to late blight (Phytophthora infestans).

We have constructed a partial linkage map in tetraploid potato which integrates simplex, duplex and double-simplex AFLP markers. The map consists of 231 maternal and 106 paternal markers with total map lengths of 990.9 cM and 484.6 cM. The longer of the two cumulative map lengths represents approximately 25% coverage of the genome. In tetraploids, much of the polymorphism between parental clones is masked by 'dosage' which significantly reduces the number of individual markers that can be scored in a population. Consequently, the major advantage of using AFLPs--their high multiplex ratio--is reduced to the point where the use of alternative multi-allelic marker types would be significantly more efficient. The segregation data and map information have been used in a QTL analysis of late blight resistance, and a multi-allelic locus at the proximal end of chromosome VIII has been identified which contributes significantly to the expression of resistance. No late blight resistance genes or QTLs have previously been mapped to this location.

Chromosome Mapping↗

PubMed1997

On predicting improvement and relapse in generalized anxiety disorder following psychotherapy.

This paper concerns an investigation of outcome predictors in a clinical trial of psychological therapies for generalized anxiety disorder. A variety of information of potential predictive value was obtained at three stages of patient contact: the initial referral, a screening interview and early sessions of therapy. Three measures of the clinical significance of change over a 12-month follow-up period were used to construct a composite measure which categorized outcome in terms of sustained improvement, relapse and no consistent change. Logistic regression was used to examine the validity of predictors identified in previous research and the relative importance of data obtained from the three different stages. Seventy-one per cent of patients were correctly classified as improved or not from initial data with a significant increase in accuracy with information from the screening interview (77 per cent) and early sessions (82 per cent). Patients who relapsed or not were predicted with considerable accuracy from initial data (90 per cent) and there was no significant increase in predictive power with additional information. The most powerful and robust predictors were: type of treatment received, marital status, marital tension and complexity of clinical presentation in terms of axis 1 co-morbidity. A conceptual framework for prediction is outlined.

Adolescent↗

PubMed1995

Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers.

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.

Base Sequence↗

PubMed1995

Genetic mapping of quantitative trait loci for traits with ordinal distributions.

Statistical methods for mapping quantitative trait loci relative to genetic markers are now well established for continuous traits with normal distributions. However, many traits of economic importance are recorded on a discrete, ordinal scale. Here we describe a model developed for the analysis of ordinal traits, such as degree of difficulty in calving or categories of plant disease resistance. The model estimates the distance from the quantitative trait locus to neighbouring genetic markers, and also genetic parameters, either as gene effects on an underlying continuous scale or as probabilities of the observed categories. The model is tested on simulated data and is compared with an analysis based on mixtures of normal distributions. The ordinal model is found to estimate the parameters more accurately, especially when the number of categories is small or when only one linked marker is available.

Animal Husbandry↗

PubMed1993

Identification of RAPD markers linked to a Rhynchosporium secalis resistance locus in barley using near-isogenic lines and bulked segregant analysis.

Three hundred random sequence 10-mer primers were used to screen a pair of near-isogenic lines of barley and their donor parent for markers linked to genes conferring resistance to Rhynchosporium secalis. One primer was identified which reproducibly generated a product, SC10-65-H400, from the donor parent and the Rhynchosporium-resistant near-isogenic line but not from the recurrent parent. Segregation analysis on a barley doubled haploid population and examination of a further three near-isogenic lines, their donor and recurrent parents confirmed that this marker was linked to the Rhynchosporium resistance locus (Rh) on chromosome 3L. The presence or absence of SC10-65-H400 was subsequently used along with the resistance phenotype to identify two groups of individuals in the doubled haploid population which possessed alternative alleles at both loci and defined a genetic interval between these two markers. Based on that information two bulked DNA samples were constructed by combining equal amounts of DNA from five individuals from each group. The two bulks and doubled haploid parental lines were screened with 700 10-mer primers. Seven products were identified which were present in the 'resistant' bulk and parent and were absent in the susceptible samples. Segregation analysis established their association with Rh. In addition co-segregation of the linked markers with a set of chromosome arm specific RFLPs confirmed the location of the Rh locus on the long arm of barley chromosome 3.

Base Sequence↗

PubMed1992

The use of Taylor's power law to describe the aggregated distribution of gastro-intestinal nematodes of sheep.

The distribution of gastro-intestinal nematodes collected from lambs was investigated using the Taylor's power law index of aggregation beta, which is known to be independent of the mean population size. For 12 out of the 15 nematode species investigated the estimate of beta was not significantly different from 2.0. For these species a logarithmic transformation would stabilize the variance of the distributions prior to further statistical analysis. The remaining species had values of beta which were significantly lower than 2.0. For these species a variance-stabilizing transformation is given by z = x1-beta/2.

Animals↗