Localization of the mouse gene releasing sex-limited expression of Slp.

To probe genetic variation in the regulation of sexual dimorphism, we have characterized the mouse protein Slp, coded by the gene sex-limited protein (Slp). Slp expression in many strains is limited to males and is androgen-dependent. However, female expression is also observed in rare strains, due to nonlinked gene(s) termed regulator of sex-limitation (rsl). In this report we demonstrate that female expression of Slp results from homozygous recessive allele(s) at a single autosomal locus that maps to a 2.2-centimorgan interval on chromosome 13. This conclusion was supported by extensive genetic analyses including the use of polymorphic microsatellites to type numerous backcross progeny and a recombinant inbred series and to identify the congenic interval in three independently derived congenic strains. Four attractive candidate genes were identified by the localization of rsl. Interestingly, rsl was found not only to enable expression in females but to also increase expression in males. The findings suggest that the expression of Slp and perhaps other sexually dimorphic proteins is regulated by two pathways, one that is dependent upon rsl but not androgens and another that is rsl-independent but requires androgens.

Isolation and characterization of a pseudoautosomal region-specific genetic marker in C57BL/6 mice using genomic representational difference analysis.

Representational difference analysis was used to identify strain-specific differences in the pseudoautosomal region (PAR) of mouse X and Y chromosomes. One second generation (C57BL/6 x Mus spretus) x Mus spretus interspecific backcross male carrying the C57BL/6 (B6) PAR was used for tester DNA. DNA from five backcross males from the same generation that were M. spretus-type for the PAR was pooled for the driver. A cloned probe designated B6-38 was recovered that is B6-specific in Southern analysis. Analysis of genomic DNA from several inbred strains of laboratory mice and diverse Mus species and subspecies identified a characteristic Pst I pattern of fragment sizes that is present only in the C57BL family of strains. Hybridization was observed with sequences in DBA/2J and to a limited extent with Mus musculus (PWK strain) and Mus castaneus DNA. No hybridization was observed in DNA of different Mus species, M. spretus, M. hortulanus, and M. caroli. Genetic analyses of B6-38 was conducted using C57BL congenic males that carry M. spretus alleles for distal X chromosome loci and the PAR and outcrosses of heterozygous congenic females with M. spretus. These analyses demonstrated that the B6-38 sequences were inherited with both the X and Y chromosome. B6-38 sequences were genetically mapped as a locus within the PAR using two interspecific backcrosses. The locus defined by B6-38 is designated DXYRp1. Preliminary analyses of recombination between the distal X chromosome gene amelogenin (Amg) and the PAR loci for either TelXY or sex chromosome association (Sxa) suggest that the locus DXYRp1 maps to the distal portion of the PAR.

Sex and the single cell: meiosis in yeast.

Recent studies of Saccharomyces cerevisiae have significantly advanced our understanding of the molecular mechanisms of meiotic chromosome behavior. Structural components of the synaptonemal complex have been identified and studies of mutants defective in synapsis have provided insight into the role of the synaptonemal complex in homolog pairing, genetic recombination, crossover interference, and meiotic chromosome segregation. There is compelling evidence that most or all meiotic recombination events initiate with double-strand breaks. Several intermediates in the double-strand break repair pathway have been characterized and mutants blocked at different steps in the pathway have been identified. With the application of genetic, molecular, cytological, and biochemical methods in a single organism, we can expect an increasingly comprehensive and unified view of the meiotic process.

Genetic determinants of human hypertension.

Hypertension is a common trait of multifactorial determination imparting an increased risk of myocardial infarction, stroke, and end-stage renal disease. The primary determinants of hypertension, as well as the factors which determine specific morbid sequelae, remain unknown in the vast majority of subjects. Knowledge that a large fraction of the interindividual variation in this trait is genetically determined motivates the application of genetic approaches to the identification of these primary determinants. Success in this effort will afford insights into pathophysiology, permit preclinical identification of subjects with specific inherited susceptibility, and provide opportunities to tailor therapy to specific underlying abnormalities. To date, mutations in three genes have been implicated in the pathogenesis of human hypertension: mutations resulting in ectopic expression of aldosterone synthase enzymatic activity cause a mendelian form of hypertension known as glucocorticoid-remediable aldosteronism; mutations in the beta subunit of the amiloride-sensitive epithelial sodium channel cause constitutive activation of this channel and the mendelian form of hypertension known as Liddle syndrome; finally, common variants at the angiotensinogen locus have been implicated in the pathogenesis of essential hypertension in Caucasian subjects, although the nature of the functional variants and their mechanism of action remain uncertain. These early findings demonstrate the feasibility and utility of the application of genetic analysis to dissection of this trait.

Sex proportions of Haemoproteus blood parasites and local mate competition.

Recent genetic evidence suggests that parasitic protozoa often reproduce by "selfing," defined as sexual stages from a single, clonal lineage fertilizing each other. Selfing favors production of an excess of female over male progeny. We tested whether the proportion of male gametocytes of blood parasites of the genus Haemoproteus was affected by variables that could influence the probability of selfing. Proportions of male Haemoproteus gametocytes from 11 passerine host populations were not affected by the age of the parasites' avian hosts, date in season, sex of host, intensity of host's infection, or prevalence of parasites within host populations.

Molecular Genetic Basis of Opposite Gene by Environment Interactions in Reading Disability and Attention Deficit/Hyperactivity Disorder

The goal of this study is to better understand the genetic basis of Reading Disability (RD) and Attention Deficit Hyperactivity Disorder (ADHD) by examining molecular G x E interactions with parental education for each disorder. Research indicates that despite sharing genetic risk factors, RD and ADHD are influenced by different types of G x E interactions with parental education - a diathesis stress interaction in the case of ADHD and a bioecological interaction in RD. In order to resolve this apparent paradox, we conducted a preliminary study using behavioral genetic methods to test for G x E interactions in RD and the inattentive subtype of ADHD (ADHD-I) in the same sample of monozygotic and dizygotic Colorado Learning Disabilities Research Center same-sex twin pairs (DeFries et al., 1997), and our findings were consistent with the literature. We posited a genetic hypothesis for this opposite pattern of interactions, which suggests that only genes specific to each disorder enter into these opposite interactions, not the shared genes underlying their comorbidity. This study sought to further investigate this paradox using molecular genetics methods. We examined multiple candidate genes identified for RD or related language phenotypes and those identified for ADHD for G x E interactions with parental education. The specific aims of this study were as follows: 1) partition known risk alleles for RD and/or related language phenotypes and ADHD-I into those which are pleiotropic and non-pleiotropic by testing each risk allele for association with both RD and ADHD-I, 2) explore the main effects of parental education on both RD and ADHD-I, 3) address G-E correlations, and 4) conduct exploratory G x E interaction analyses in order to test the genetic hypothesis. Analyses suggested a number of pleiotropic genes that influence both RD and ADHD; however, results did not remain after correcting for multiple comparisons. Although exploratory G x E interaction findings were not significant after multiple comparison correction, results suggested a G x E interaction in the bioecological direction with KIAA0319, parental education, and ADHD-I. Given the limited power in the current study, replication of these findings with larger samples is necessary.

High throughput determination of sequence-function relationships in protein and RNA

Thesis (Ph.D.)--University of Washington, 2016-06

Fine-scale spatial genetic correlation analyses reveal strong female philopatry within a brush-tailed rock-wallaby colony in southeast Queensland

We combine spatial data on home ranges of individuals and microsatellite markers to examine patterns of fine-scale spatial genetic structure and dispersal within a brush-tailed rock-wallaby (Petrogale penicillata) colony at Hurdle Creek Valley, Queensland. Brush-tailed rock-wallabies were once abundant and widespread throughout the rocky terrain of southeastern Australia; however, populations are nearly extinct in the south of their range and in decline elsewhere. We use pairwise relatedness measures and a recent multilocus spatial autocorrelation analysis to test the hypotheses that in this species, within-colony dispersal is male-biased and that female philopatry results in spatial clusters of related females within the colony. We provide clear evidence for strong female philopatry and male-biased dispersal within this rock-wallaby colony. There was a strong, significant negative correlation between pairwise relatedness and geographical distance of individual females along only 800 m of cliff line. Spatial genetic autocorrelation analyses showed significant positive correlation for females in close proximity to each other and revealed a genetic neighbourhood size of only 600 m for females. Our study is the first to report on the fine-scale spatial genetic structure within a rock-wallaby colony and we provide the first robust evidence for strong female philopatry and spatial clustering of related females within this taxon. We discuss the ecological and conservation implications of our findings for rock-wallabies, as well as the importance of fine-scale spatial genetic patterns in studies of dispersal behaviour.

The effects of habitat fragmentation due to forestry plantation establishment on the demography and genetic variation of a marsupial carnivore, Antechinus agilis

We conducted a demographic and genetic study to investigate the effects of fragmentation due to the establishment of an exotic softwood plantation on populations of a small marsupial carnivore, the agile antechinus (Antechinus agilis), and the factors influencing the persistence of those populations in the fragmented habitat. The first aspect of the study was a descriptive analysis of patch occupancy and population size, in which we found a patch occupancy rate of 70% among 23 sites in the fragmented habitat compared to 100% among 48 sites with the same habitat characteristics in unfragmented habitat. Mark-recapture analyses yielded most-likely population size estimates of between 3 and 85 among the 16 occupied patches in the fragmented habitat. Hierarchical partitioning and model selection were used to identify geographic and habitat-related characteristics that influence patch occupancy and population size. Patch occupancy was primarily influenced by geographic isolation and habitat quality (vegetation basal area). The variance in population size among occupied sites was influenced primarily by forest type (dominant Eucalyptus species) and, to a lesser extent, by patch area and topographic context (gully sites had larger populations). A comparison of the sex ratios between the samples from the two habitat contexts revealed a significant deficiency of males in the fragmented habitat. We hypothesise that this is due to male-biased dispersal in an environment with increased dispersal-associated mortality. The population size and sex ratio data were incorporated into a simulation study to estimate the proportion of genetic diversity that would have been lost over the known timescale since fragmentation if the patch populations had been totally isolated. The observed difference in genetic diversity (gene diversity and allelic richness at microsatellite and mitochondrial markers) between 16 fragmented and 12 unfragmented sites was extremely low and inconsistent with the isolation of the patch populations. Our results show that although the remnant habitat patches comprise approximately 2% of the study area, they can support non-isolated populations. However, the distribution of agile antechinus populations in the fragmented system is dependent on habitat quality and patch connectivity. (C) 2004 Elsevier Ltd. All rights reserved.

Genetic time-series analysis identifies a major QTL for in vivo alcohol metabolism not predicted by in vitro studies of structural protein polymorphism at the ADH1B or ADH1C loci

After ingestion of a standardized dose of ethanol, alcohol concentrations were assessed, over 3.5 hours from blood (six readings) and breath (10 readings) in a sample of 412 MZ and DZ twins who took part in an Alcohol Challenge Twin Study (ACTS). Nearly all participants were subsequently genotyped on two polymorphic SNPs in the ADH1B and ADH1C loci known to affect in vitro ADH activity. In the DZ pairs, 14 microsatellite markers covering a 20.5 cM region on chromosome 4 that includes the ADH gene family were assessed, Variation in the timed series of autocorrelated blood and breath alcohol readings was studied using a bivariate simplex design. The contribution of a quantitative trait locus (QTL) or QTL's linked to the ADH region was estimated via a mixture of likelihoods weighted by identity-by-descent probabilities. The effects of allelic substitution at the ADH1B and ADH1C loci were estimated in the means part of the model simultaneously with the effects sex and age. There was a major contribution to variance in alcohol metabolism due to a QTL which accounted for about 64% of the additive genetic covariation common to both blood and breath alcohol readings at the first time point. No effects of the ADH1B*47His or ADH1C*349Ile alleles on in vivo metabolism were observed, although these have been shown to have major effects in vitro. This implies that there is a major determinant of variation for in vivo alcohol metabolism in the ADH region that is not accounted for by these polymorphisms. Earlier analyses of these data suggested that alcohol metabolism is related to drinking behavior and imply that this QTL may be protective against alcohol dependence.

Genetic control of adventitious rooting on stem cuttings in two Pinus elliottii x P-caribaea hybrid families

Genetic control of adventitious rooting was characterised in two unrelated Pinus elliottii x P. caribaea families, an outbred F-1 (n = 287) and an inbred F-2 ( n = 357). Rooting percentage was assessed in three settings and root biomass was measured on a sub-set of clones ( n = 50) from each family in the third setting. On average, clones in the outbred F-1 had a higher rooting percentage (mean +/- SE; 59 +/- 1.9%) and biomass (mean +/- SD; 0.41 +/- 0.24 g) than clones in the inbred F-2 family ( mean +/- SE; 48 +/- 1.8% and mean +/- SD; 0.19 +/- 0.13 g). Genetic determination for rooting percentage was strong in both families, as indicated by high individual setting clonal repeatabilities ( e. g. Setting 3; outbred F-1 0.62 +/- 0.03 and inbred F-2 0.68 +/- 0.02 (H-2 +/- SE)) and the moderate-to-high genetic correlations amongst the three settings. For root biomass, clonal repeatabilities for both families were lower (outbred F-1 0.35 +/- 0.09 and inbred F-2 0.44 +/- 0.10 (H-2 +/- SE)). Weak positive genetic correlations between rooting percentage and root biomass in both families suggested a concomitant gain in root biomass would be insignificant when selecting solely on the more easily assessable rooting percentage.

A possible smoking susceptibility locus on chromosome 11p12: Evidence from sex-limitation linkage analyses in a sample of Australian twin families

Many twin studies have identified sex differences in the influence of genetic and environmental factors on smoking behaviors. We explore the evidence for sex differences for smoking initiation and cigarette consumption in a sample of Australian twin families, and extend these models to incorporate sex differences in linkage analyses for these traits. We further examine the impact of including or excluding non-smokers in genetic analyses of tobacco consumption. Accounting for sex differences improved linkage results in some instances. We identified one region suggestive of linkage on chromosome 11p12. This locus, as well as another region identified on chromosome 6p12, replicates regions identified in previous studies.

Age determination in individual wild-caught Drosophila serrata using pteridine concentration

Fluorescence spectrophotometry can reliably detect levels of the pteridine 6-biopterin in the heads of individual Drosophila serrata Malloch 1927. Pteridine content in both laboratory and field captured flies is typically a level of magnitude higher than the minimally detectable level (mean(lab)=0.54 units, mean(field)=0.44 units, minimum detectable level=0.01 units) and can be used to predict individual age in laboratory populations with high certainty (r(2)=57%). Laboratory studies of individuals of known age ( from 1 to 48 days old) indicate that while pteridine level increases linearly with age, they also increase in a linear manner with rearing temperature and ambient light levels, but are independent of sex. As expected, the longevity of laboratory-reared males ( at least 48 days) is higher than the range of predicted ages of wild-caught males based on individual pteridine levels (40 days). However, the predictive equation based on pteridine level alone suggested that a number of wild-caught males were less than 0 days old, and the 95% confidence for these predictions based on the inverse regression broad. The age of the oldest wild-caught male is to fall within the range of 2 to 50 days. The effects of temperature and light intensity determined in laboratory study (effect sizes omega(2)=14.3 and respectively) suggests that the calibration of the prediction equation for field populations would significantly improved when combined with fine scaled studies of habitat temperature and light conditions. ability to determine relative age in individual wild-caught D. serrata presents great opportunities for a variety evolutionary studies on the dynamics of populations.

Determining the effective dimensionality of the genetic variance-covariance matrix

Determining the dimensionality of G provides an important perspective on the genetic basis of a multivariate suite of traits. Since the introduction of Fisher's geometric model, the number of genetically independent traits underlying a set of functionally related phenotypic traits has been recognized as an important factor influencing the response to selection. Here, we show how the effective dimensionality of G can be established, using a method for the determination of the dimensionality of the effect space from a multivariate general linear model introduced by AMEMIYA (1985). We compare this approach with two other available methods, factor-analytic modeling and bootstrapping, using a half-sib experiment that estimated G for eight cuticular hydrocarbons of Drosophila serrata. In our example, eight pheromone traits were shown to be adequately represented by only two underlying genetic dimensions by Amemiya's approach and factor-analytic modeling of the covariance structure at the sire level. In, contrast, bootstrapping identified four dimensions with significant genetic variance. A simulation study indicated that while the performance of Amemiya's method was more sensitive to power constraints, it performed as well or better than factor-analytic modeling in correctly identifying the original genetic dimensions at moderate to high levels of heritability. The bootstrap approach consistently overestimated the number of dimensions in all cases and performed less well than Amemiya's method at subspace recovery.

Genetic and Cultural Transmission of Smoking Initiation: An Extended Twin Kinship Model

Background Considerable evidence from twin and adoption studies indicates that genetic and shared environmental factors play a significant role in the initiation of smoking behavior. Although twin and adoption designs are powerful to detect genetic and environmental influences, they do not provide information on the processes of assortative mating and parent–offspring transmission and their contribution to the variability explained by genetic and/or environmental factors. Methods We examined the role of genetic and environmental factors for smoking initiation using an extended kinship design. This design allows the simultaneous testing of additive and non-additive genetic, shared and individual-specific environmental factors, as well as sex differences in the expression of genes and environment in the presence of assortative mating and combined genetic and cultural transmission. A dichotomous lifetime smoking measure was obtained from twins and relatives in the Virginia 30,000 sample. Results Results demonstrate that both genetic and environmental factors play a significant role in the liability to smoking initiation. Major influences on individual differences appeared to be additive genetic and unique environmental effects, with smaller contributions from assortative mating, shared sibling environment, twin environment, cultural transmission and resulting genotype–environment covariance. The finding of negative cultural transmission without dominance led us to investigate more closely two possible mechanisms for the lower parent–offspring correlations compared to the sibling and DZ twin correlations in subsets of the data: (i) age × gene interaction, and (ii) social homogamy. Neither mechanism provided a significantly better explanation of the data, although age regression was significant. Conclusions This study showed significant heritability, partly due to assortment, and significant effects of primarily non-parental shared environment on smoking initiation.