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.

Measures of association of genes at different loci (linkage disequilibrium) are widely used to determine whether the structure of natural populations is clonal or not, to map genes from population data, or to test for the homogeneity of response of molecular markers to background selection, for example. However, the usual definitions of parameters for gametic associations may not be suitable for all these purposes. In this paper, we derive the recursion equations for one- and two-locus identity probabilities in an infinite island model. We study the role of drift, gene flow, partial selfing and mutation model on the expected association of genes across loci. We define the ‘within-subpopulation identity disequilibrium’ as the difference between the joint two-locus probability of identity in state and the expected product of one-locus identity probabilities. We evaluate this parameter as a function of recombination rate, effective size, gene flow and selfing rate. Within-subpopulation identity disequilibrium attains maximum values for intermediate immigration rates, whatever the selfing rate. Moreover, identity disequilibrium may be very small, even for high selfing rates. We discuss the implications of these findings for the analysis of data from natural populations.

The yeast, Saccharomyces cerevisiae, was used as a model to investigate theories of ploidy evolution. Mutagenesis experiments using the alkylating agent EMS (ethane methyl sulphonate) were conducted to assess the relative importance that masking of deleterious mutations has on response to and recovery from DNA damage. In particular, we tested whether cells with higher ploidy levels have relatively higher fitnesses after mutagenesis, whether the advantages of masking are more pronounced in tetraploids than in diploids, and whether purging of mutations allows more rapid recovery of haploid cells than cells with higher ploidy levels. Separate experiments were performed on asexually propagating stationary phase cells using (1) prototrophic haploid (MATα) and diploid (MATa/α) strains and (2) isogenic haploid, diploid and tetraploid strains lacking a functional mating type locus. In both sets of experiments, haploids showed a more pronounced decrease in apparent growth rate than diploids, but both haploids and diploids appeared to recover very rapidly. Tetraploids did not show increased benefits of masking compared with diploids but volume measurements and FACScan analyses on the auxotrophic strains indicated that all treated tetraploid strains decreased in ploidy level and that some of the treated haploid lines increased in ploidy level. Results from these experiments confirm that while masking deleterious mutations provides an immediate advantage to higher ploidy levels in the presence of mutagens, selection is extremely efficient at removing induced mutations, leading growth rates to increase rapidly over time at all ploidy levels. Furthermore, ploidy level is itself a mutable trait in the presence of EMS, with both haploids and tetraploids often evolving towards diploidy (the ancestral state of S. cerevisiae) during the course of the experiment.

At the onset of metamorphosis in Drosophila melanogaster, the steroid hormone 20-OH ecdysone induces a small number of early and early-late puffs in the polytene chromosomes of the third-instar larval salivary gland whose activity is required for regulating the activity of a larger set of late puffs. Most of the corresponding early and early-late genes have been found to encode transcription factors that regulate a much larger set of late genes. In contrast, we describe here the identification of an ecdysone-regulated gene in the 62E early-late puff, denoted D-spinophilin, that encodes a protein similar to the mammalian protein spinophilin/neurabin II. The D-spinophilin protein is predicted to contain a highly conserved PP1-binding domain and adjacent PDZ domain, as well as a coiled-coil domain and SAM domain, and belongs to a family of related proteins from diverse organisms. Transcription of D-spinophilin is correlated with 62E puff activity during the early stages of metamorphosis and is ecdysone-dependent, making this the first member of this gene family shown to be regulated by a steroid hormone. Examination of the dynamic patterns of D-spinophilin expression during the early stages of metamorphosis are consistent with a role in central nervous system metamorphosis as well as a more general role in other tissues. As D-spinophilin appears to be the only member of this gene family in Drosophila, its study provides an excellent opportunity to elucidate the role of an important adaptor protein in a genetic model organism.

High rates of mildly deleterious mutation could cause the extinction of small populations, reduce neutral genetic variation and provide an evolutionary advantage for sex. In the first attempts to estimate the rate of mildly deleterious mutation, Mukai and Ohnishi allowed spontaneous mutations to accumulate on D. melanogaster second chromosomes shielded from recombination and selection. Viability of the shielded chromosomes appeared to decline rapidly, implying a deleterious mutation rate on the order of one per zygote per generation. These results have been challenged, however; at issue is whether Mukai and Ohnishi may have confounded viability declines caused by mutation with declines resulting from environmental changes or other extraneous factors. Here, using a method not sensitive to non-mutational viability changes, I reanalyse the previous mutation-accumulation (MA) experiments, and report the results of a new one. I show that in each of four experiments, including Mukai's two experiments, viability declines due to mildly deleterious mutations were rapid. The results give no support for the view that Mukai overestimated the declines. Although there is substantial variation in estimates of genomic mutation rates from the experiments, this variation is probably due to some combination of sampling error, strain differences and differences in assay conditions, rather than to failure to distinguish mutational and non-mutational viability changes.

We examined the genetic architecture of four fitness-related traits (reproductive success, ovariole number, body size and early fecundity) in a panel of 98 Oregon-R × 2b3 recombinant inbred lines (RILs). Highly significant genetic variation was observed in this population for female, but not male, reproductive success. The cross-sex genetic correlation for reproductive success was 0·20, which is not significantly different from zero. There was significant genetic variation segregating in this cross for ovariole number, but not for body size or early fecundity. The RILs were genotyped for cytological insertion sites of roo transposable elements, yielding 76 informative markers with an average spacing of 3·2 cM. Quantitative trait loci (QTL) affecting female reproductive success and ovariole number were mapped using a composite interval mapping procedure. QTL for female reproductive success were located at the tip of the X chromosome between markers at cytological locations 1B and 3E; and on the left arm of chromosome 2 in the 30D–38A cytological region. Ovariole number QTL mapped to cytological intervals 62D–69D and 98A–98E, both on the third chromosome. The regions harbouring QTL for female reproductive success and ovariole number were also identified as QTL for longevity in previous studies with these lines.

These studies centre on the ‘Barcelona’ karyotypic race of the western house mouse (Mus musculus domesticus), first described by Adolph & Klein (1981). This is one of many races within M. m. domesticus characterized by metacentric chromosomes that have originated by repeated Robertsonian fusions, with perhaps further modification by whole-arm reciprocal translocations. Data on 111 mice from 20 sites show that the race is centred 24 km to the west of Barcelona city and has a homozygous metacentric karyotype of 2n = 28 (3·8, 4·14, 5·15, 6·10, 9·11, 12·13). The race has a small range, and mice with the standard 40-acrocentric karyotype were caught only 30 km from the race centre. Throughout the area of occurrence of metacentrics there is polymorphism (i.e. presence of acrocentrics in the population), although all six metacentrics approach fixation close to the race centre. Thus, there is a hybrid zone between the Barcelona and standard races. The centres and widths of all clines (except 3·8) were determined. Likelihood ratio tests showed that most of the cline centres differed significantly in position (i.e. the clines were staggered) and the clines for metacentrics 6·10 and 9·11 were significantly narrower than those for 4·14, 5·15 and 12·13. Overall, the clines tended to be wider the further they were from the race centre. There are various possible explanations for this hybrid zone structure and further data are needed to distinguish between them.

The possibility of using linkage disequilibrium mapping in natural plant populations was assessed. In studying linkage disequilibrium among 137 mapped AFLP markers in four populations of sea beet (Beta vulgaris ssp. maritima (L.) Arcang.) it was shown that tightly linked loci could be detected by screening for associations. It was hypothesized that the short distances spanned by linkage disequilibrium enable markers that are very tightly linked to a target gene to be identified. The hypothesis was tested by whole-genome screening of AFLP markers for association with the gene for the annual growth habit, the B gene, in a sample of 106 sea beets. Despite the dominant nature of AFLP, two markers showing significant linkage disequilibrium with the B gene were detected. The results indicate the potential use of linkage disequilibrium for gene mapping in natural plant populations.

A method is proposed to infer genetic parameters within a cohort, using data from all individuals in an experiment. An application is the study of changes in additive genetic variance over generations, employing data from all generations. Inferences about the genetic variance in a given generation are based on its marginal posterior distribution, estimated via Markov chain Monte Carlo methods. As defined, the additive genetic variance within the group is directly related to the amount of selection response to be expected if parents are chosen within the group. Results from a simulated selection experiment are used to illustrate properties of the method. Four sets of data are analysed: directional selection with and without environmental trend, and random selection, with and without environmental trend. In all cases, posterior credibility intervals of size 95% assign relatively high density to values of the additive genetic variance and heritability in the neighbourhood of the true values. Properties and generalizations of the method are discussed.

Triploid oysters were induced using cytochalasin B upon retention of either the first (meiosis I triploids) or the second (meiosis II triploids) polar body in embryos from a single cohort derived from mixed parentage. Allozyme and microsatellite assays enabled the confirmation of both parentage and triploidy status in each oyster. Comparison of meiosis I triploids, meiosis II triploids and diploid siblings established that improved physiological performance in triploids was associated with increased allelic variation, rather than with the quantitative dosage effects of ploidy status. An unidentified maternal influence also interacted with genotype. Among full sibs, allelic variation measured as multi-locus enzyme heterozygosity accounted for up to 42% of the variance in physiological performance; significant positive influences were identified upon feeding rate, absorption efficiency, net energy balance and growth efficiency (= net energy balance ÷ energy absorbed). Whilst allelic variation was greater in both meiosis I and meiosis II triploids than in diploid siblings, both allelic variation and net energy balance were highest in triploids induced at meiosis I. This suggests that it may be preferable to induce triploidy by blocking meiosis I, rather than meiosis II as has traditionally been undertaken during commercial breeding programmes.

Four large (n > 1000) populations of Drosophila melanogaster, derived from control populations maintained on a 3 week discrete generation cycle, were subjected to selection for fast development and early reproduction. Egg to eclosion survivorship and development time and dry weight at eclosion were monitored every 10 generations. Over 70 generations of selection, development time in the selected populations decreased by approximately 36 h relative to controls, a 20% decline. The difference in male and female development time was also reduced in the selected populations. Flies from the selected populations were increasingly lighter at eclosion than controls, with the reduction in dry weight at eclosion over 70 generations of selection being approximately 45% in males and 39% in females. Larval growth rate (dry weight at eclosion/development time) was also reduced in the selected lines over 70 generations, relative to controls, by approximately 32% in males and 24% in females. However, part of this relative reduction was due to an increase in growth rate of the controls populations, presumably an expression of adaptation to conditions in our laboratory. After 50 generations of selection had elapsed, a considerable and increasing pre-adult viability cost to faster development became apparent, with viability in the selected populations being about 22% less than that of controls at generation 70 of selection.

The evolution of a quantitative trait subject to stabilizing selection and immigration, with the immigrants deviating from the local optimum, is considered under a number of different models of the underlying genetic basis of the trait. By comparing exact predictions under the infinitesimal model obtained using numerical methods with predictions of a simplified approximate model based on ignoring linkage disequilibrium, the increase in the expressed genetic variance as a result of linkage disequilibrium generated by migration is shown to be relatively small and negligible, provided that the genetic variance relative to the squared deviation of immigrants from the local optimum is sufficiently large or selection and migration is sufficiently weak. Deviation from normality is shown to be less important by comparing predictions of the infinitesimal model with a model presupposing normality. For a more realistic symmetric model, involving a finite number of loci only, no linkage and equal effects and frequencies across loci, additional changes in the genetic variance arise as a result of changes in underlying allele frequencies. Again, provided that the genetic variance relative to the squared deviation of the immigrants from the local optimum is small, the difference between the predictions of infinitesimal and the symmetric model are small unless the number of loci is very small. However, if the genetic variance relative to the squared deviation of the immigrants from the local optimum is large, or if selection and migration are strong, both linkage disequilibrium and changes in the genetic variance as a result of changes in underlying allele frequencies become important.

We study genetic variation in phenotypic plasticity maintained by a balance between mutation and weak stabilizing selection. We consider linear reaction norms allowing for spatial and/or temporal variation in the environments of development and selection. We show that the overall genetic variation maintained does not depend on whether the trait is plastic or not. The genetic variances in height and slope of a linear reaction norm, and their covariance, are predicted to decrease with the variation in the environment. Non-pleiotropic loci influencing either height or slope are expected to decrease the genetic variance in slope relative to that in height. Decrease in the ratio of genetic variance in slope to genetic variance in height with increasing variation in the environment presents a test for the presence of loci that only influence the slope, and not the height. We use data on Drosophila to test the theory. In seven of eight pair-wise comparisons genetic variation in reaction norm is higher in a less variable environment than in a more variable environment, which is in accord with the model's predictions.

Volume 76, number 2, October 2000

Page 166, column 1,

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