Male Locus Research Articles

Differences in Health Status Affect Susceptibility and Mapping of Genetic Loci for Atherosclerosis (Fatty Streak) in Inbred Mice

We observed differences in atherosclerosis susceptibility in mouse inbred strains over the years as the health status of our animal rooms increased. Therefore, we investigated the effect of animal room health status on atherosclerosis susceptibility in different strains. As these data can also be used for genome-wide association mapping, we performed a mapping study and compared our results with previously found quantitative trait loci for atherosclerosis in mouse and humans. Males and females from 48 inbred strains were housed in 2 animal rooms with different health status and given an atherogenic diet. We compared atherosclerosis susceptibility between animal rooms and between sexes and found that susceptibility is dependent on both health status and sex. Subsequently, the data were used for associations with loci on the mouse genome using 63 222 single nucleotide polymorphism. Three loci in males and 4 loci in females were identified using the data from the low-health status room. No significant associations were identified using the data from the high-health status room. Health status influences susceptibility to atherosclerosis and suggests that microbiological pressure plays an important role in the development of atherosclerosis in many strains. As we were only able to map susceptibility loci using the data from the lower health status room, we argue that susceptibility under these conditions is determined by a few key loci, whereas in the higher health status room different mechanisms might play a role in the differences in atherosclerosis susceptibility between strains and we did not have enough power to map the loci that are involved.

The influence of sex and estrous cycle on QTL for emotionality and ethanol consumption

The inbred rat strains Lewis (LEW) and Spontaneously Hypertensive Rats (SHR) differ with respect to several emotionality- and ethanol intake-related behaviors, one of which (inner locomotion in the open field; OF) is strongly influenced by a locus (Anxrr16) on chromosome (Chr) 4. We aimed to further investigate the influence of Chr 4 on these behaviors and to evaluate the role of the estrous cycle in QTL expression. LEW females and SHR males were intercrossed to produce F1 and F2 rats (96-97/sex), which were then tested in the OF, light-dark box (LDB), forced swimming test (FST), and an ethanol consumption procedure (ECP). In addition, another group of 96 F2 females were tested in the OF and LDB according to their estrous cycle phase. All animals were genotyped for microsatellite markers located on Chr 4 and two QTL analyses were performed. A factor analysis of the F2 population produced five factors reflecting different behavioral dimensions. QTL analysis revealed five significant loci in males, some of which with pleiotropic effects on behaviors measured in the OF, LDB, and ECP. The second QTL analysis revealed two significant loci in females in diestrous-proestrous and one in females in estrous-metestrous that influence behaviors in the OF and LDB. Results revealed that Anxrr16 and four other new QTL influence emotionality- and ethanol-related behaviors in male rats, whereas Anxrr16 attained suggestive levels only in females in diestrous-proestrous, which raises the need for taking into account factors related to the sex and estrous cycle in behavioral QTL analysis.

Computing power of quantitative trait locus association mapping for haploid loci

BackgroundStatistical power calculations are a critical part of any study design for gene mapping. Most calculations assume that the locus of interest is biallelic. However, there are common situations in human genetics such as X-linked loci in males where the locus is haploid. The purpose of this work is to mathematically derive the biometric model for haploid loci, and to compute power for QTL mapping when the loci are haploid.ResultsWe have derived the biometric model for power calculations for haploid loci and have developed software to perform these calculations. We have verified our calculations with independent mathematical methods.ConclusionOur results fill a need in power calculations for QTL mapping studies. Furthermore, failure to appropriately model haploid loci may cause underestimation of power.

Two loci on chromosome 9 control bile acid composition: evidence that a strong candidate gene, Cyp8b1, is not the culprit

An intercross between C57BL/6J and CASA/Rk mice was used to study the genetics of biliary bile acid composition. In parental strains, male C57BL/6J mice had significantly higher cholic acid (CA; 14%) and lower beta-muricholic acid (betaMC; 27%) than CASA/Rk mice, whereas females did not differ. However, quantitative trait locus analysis of F2 mice revealed no significant chromosome 9 loci in males but loci in females on chromosome 9 for percentage CA (%CA) at 72 centimorgan (cM) [logarithm of the odds (LOD) 5.89] and %betaMC at 54 cM (LOD 4.09). Chromosome 9 congenic and subcongenic strains representing CASA/Rk intervals 38-73 cM (9KK) and 68-73 cM (9DKK) on the C57BL/6J background were made. In 9KK and 9DKK males, %CA was increased and %betaMC was unchanged, whereas in 9KK but not 9DKK females, %CA was increased and %betaMC was decreased. Sterol 12alpha-hydroxylase (Cyp8b1) channels bile acid precursors into CA and maps at chromosome 9 (73 cM). However, there was no significant difference in Cyp8b1 mRNA or enzymatic activity between parental mice, parental-congenic-subcongenic mice, or high-low biliary %CA F2 mice. In summary, two chromosome 9 loci control sexually dimorphic effects on biliary bile acid composition: a distal (68-73 cM) major determinant in males, and a more proximal (38-68 cM) major determinant in females. In this intercross, Cyp8b1, a strong candidate, does not appear to be responsible.

Sex-Specific Genetic Architecture of Whole Blood Serotonin Levels

Recently, a quantitative-trait locus (QTL) for whole blood serotonin level was identified in a genomewide linkage and association study in a founder population. Because serotonin level is a sexually dimorphic trait, in the present study, we evaluated the sex-specific genetic architecture of whole blood serotonin level in the same population. Here, we use an extended homozygosity-by-descent linkage method that is suitable for large complex pedigrees. Although both males and females have high broad heritability (H2=0.99), females have a higher additive component (h2=0.63 in females; h2=0.27 in males). Furthermore, the serotonin QTL on 17q that was identified previously in this population, integrin beta 3 (ITGB3), and a novel locus on 2q influence serotonin levels only in males, whereas linkage to a region on chromosome 6q is specific to females. Both sexes contribute to linkage signals on 12q and 16p. There were, overall, more associations meeting criteria for suggestive significance in males than in females, including those of ITGB3 and the serotonin transporter gene (5HTT). This analysis is consistent with heritable sexual dimorphism in whole blood serotonin levels resulting from the effects of a combination of sex-specific and sex-independent loci.

Genetic analysis of song dialect populations in Puget Sound white-crowned sparrows

The relationship between cultural variation and biological variation among natural populations has been the subject of both theoretical and empirical study. Zonotrichia leucophrys pugetensis is one of three subspecies of white-crowned sparrow known to form geographical song dialects. We investigated whether these dialects correspond to genetic differences among Z. l. pugetensis populations. We compared allele frequencies at four microsatellite loci in males from 11 sites spanning six dialects over the subspecies’ range in Oregon and Washington. Cluster analysis and genotype assignment tests indicated no tendency for sample sites within dialect areas to be genetically more similar than are sites from different dialect areas. AMOVA tests revealed high within-site variation and low but significant cross-site and cross-dialect-area variation. Finally, genetic distance between sites was not correlated with dialect differences when the effect of geographic distance was controlled statistically. We compare our finding of low genetic differentiation among Z. l. pugetensis dialect populations to results of previous studies on Z. l. nuttalli and Z. l. oriantha. Because genetic structuring appears weaker than cultural (song dialect) structure in this species, we discuss the behavioral mechanisms underlying dialect maintenance in the presence of apparent gene flow. Key words: birdsong, cultural evolution, geographic variation, microsatellites, Zonotrichia leucophrys pugetensis. [Behav Ecol 15:636–646 (2004)]

Chromosomal Variation, Segregation and Sex Determination in Hydrotaea Meridionalis (Diptera: Muscidae)

In addition to five pairs of euchromatic chromosomes common to all individuals, three different morphological types of heterochromatic chromosomes were found in Hydrotaea meridionalis: Two acrocentric chromosomes of different length and a smaller submetacentric chromosome that occur in different combinations. The most common type, the larger of the acrocentric chromosomes, occurred as a pair in 149 out of 197 larvae. Mother-offspring combinations revealed that the larvae progeny of several mothers carried morphologically only the common karyotype. Despite existing morphological variation in karyotypes the same karyotypes were found in male and female adult flies. This observation is interpreted by an autosomal sex-determining mechanism. As there was also found a sex-specific karyotype in males, a simple hypothesis to explain the observed distribution of karyotypes among sexes is suggested: one male locus located on one of the autosomes with a dominant heterogametic sex determination mechanism. Only in homozygous recessives for that locus is sex determined by the independent XX/XY sex-determining system.

Nucleotide variation at Msn and Alas2, two genes flanking the centromere of the X chromosome in humans.

The centromeric region of the X chromosome in humans experiences low rates of recombination over a considerable physical distance. In such a region, the effects of selection may extend to linked sites that are far away. To investigate the effects of this recombinational environment on patterns of nucleotide variability, we sequenced 4581 bp at Msn and 4697 bp at Alas2, two genes situated on either side of the X chromosome centromere, in a worldwide sample of 41 men, as well as in one common chimpanzee and one orangutan. To investigate patterns of linkage disequilibrium (LD) across the centromere, we also genotyped several informative sites from each gene in 120 men from sub-Saharan Africa. By studying X-linked loci in males, we were able to recover haplotypes and study long-range patterns of LD directly. Overall patterns of variability were remarkably similar at these two loci. Both loci exhibited (i) very low levels of nucleotide diversity (among the lowest seen in the human genome); (ii) a strong skew in the distribution of allele frequencies, with an excess of both very-low and very-high-frequency derived alleles in non-African populations; (iii) much less variation in the non-African than in the African samples; (iv) very high levels of population differentiation; and (v) complete LD among all sites within loci. We also observed significant LD between Msn and Alas2 in Africa, despite the fact that they are separated by approximately 10 Mb. These observations are difficult to reconcile with a simple demographic model but may be consistent with positive and/or purifying selection acting on loci within this large region of low recombination.

Bleomycin hydrolase and a genetic locus within the MHC affect risk for pulmonary fibrosis in mice.

Susceptibility to pulmonary fibrosis following environmental insults or cytotoxic cancer therapies has a genetic component. In mouse strains differing in susceptibility to bleomycin-induced lung fibrosis, we show highly significant linkage to only two loci. The first locus on chromosome 17 in the major histocompatibility complex (MHC), LOD = 17.4, named Blmpf1, is highly significant in both males and females, and accounts for approximately 20% of the phenotypic variance. We confirmed the presence of Blmpf1 in MHC congenic mice and narrowed the region to 2.7 cM in a reduced MHC congenic strain. The second locus on chromosome 11, LOD = 5.6, named Blmpf2, is significant in males only. A model including an interaction between Blmpf1 and Blmpf2 best fit the data in males. We confirmed Blmpf2 in a chromosome substitution strain, C57BL/6J-11(C3H), and found that its presence reduces the severity of fibrosis. Functional studies of bleomycin hydrolase activity indicate that this enzyme modulates bleomycin-induced pulmonary fibrosis, suggesting that it may be a candidate gene for Blmpf2. The data suggest sex-specific models of susceptibility to bleomycin-induced lung fibrosis, with an interaction between Blmpf2 and Blmpf1 for the more susceptible males and Blmpf1 as the major locus in females. A putative mechanism for the interaction between the two loci in males is that bleomycin hydrolase functions as an MHC class I epitope-processing protease.

Modulation of multiple experimental arthritis models by collagen-induced arthritis quantitative trait loci isolated in congenic rat lines: different effects of non-major histocompatibility complex quantitative trait loci in males and females.

Collagen-induced arthritis (CIA) is a model of inflammatory arthritis with many similarities to rheumatoid arthritis (RA). We previously mapped in F(2) offspring of CIA-susceptible DA and CIA-resistant F344 rats, 5 quantitative trait loci (QTLs) for which F344 alleles were associated with reduced CIA severity. In the present study, we sought to characterize the independent arthritis-modulating effects of these 5 QTLs. CIA-regulatory regions were transferred from the F344 genome to the DA background or vice versa by repeated backcrossing. The arthritis-modulating effects of the transferred alleles were determined by comparing the severity of experimentally induced arthritis in congenic rats with that in DA rats. Congenic lines with either the F344 major histocompatibility complex (MHC) on the DA background or the DA MHC on the F344 background were resistant to CIA, confirming both MHC and non-MHC contributions to the genetic regulation of CIA. F344 alleles at the Cia3 and Cia5 regions of chromosomes 4 and 10 reduced CIA severity relative to that observed in DA rats. F344 Cia4 and Cia6 regions of chromosomes 7 and 8 failed to significantly alter CIA severity. Arthritis-modifying effects of Cia4 and Cia6 were, however, detected in pristane-induced and/or Freund's incomplete adjuvant oil-induced arthritis. The arthritis-modifying effects of the non-MHC CIA-regulatory loci differed in males and females. These congenic lines confirmed the existence and location of genes that regulate the severity of experimental arthritis in rats. Mechanisms responsible for the sex-specificity of individual arthritis-regulatory loci may explain some of the sex differences observed in RA and other autoimmune diseases in humans.

High-throughput variation detection and genotyping using microarrays.

The genetic dissection of complex traits may ultimately require a large number of SNPs to be genotyped in multiple individuals who exhibit phenotypic variation in a trait of interest. Microarray technology can enable rapid genotyping of variation specific to study samples. To facilitate their use, we have developed an automated statistical method (ABACUS) to analyze microarray hybridization data and applied this method to Affymetrix Variation Detection Arrays (VDAs). ABACUS provides a quality score to individual genotypes, allowing investigators to focus their attention on sites that give accurate information. We have applied ABACUS to an experiment encompassing 32 autosomal and eight X-linked genomic regions, each consisting of approximately 50 kb of unique sequence spanning a 100-kb region, in 40 humans. At sufficiently high-quality scores, we are able to read approximately 80% of all sites. To assess the accuracy of SNP detection, 108 of 108 SNPs have been experimentally confirmed; an additional 371 SNPs have been confirmed electronically. To access the accuracy of diploid genotypes at segregating autosomal sites, we confirmed 1515 of 1515 homozygous calls, and 420 of 423 (99.29%) heterozygotes. In replicate experiments, consisting of independent amplification of identical samples followed by hybridization to distinct microarrays of the same design, genotyping is highly repeatable. In an autosomal replicate experiment, 813,295 of 813,295 genotypes are called identically (including 351 heterozygotes); at an X-linked locus in males (haploid), 841,236 of 841,236 sites are called identically.

The evolution of chromosomal sex determination and dosage compensation

In many species, sex is determined by a system based on X and Y chromosomes, the latter having lost much of their genetic activity. Y chromosomes have evolved independently many times, and the associated change in gene dosage in the heterogametic (XY) sex is often compensated for by regulatory mechanisms which ensure equal amounts of gene products of X-linked loci in males and females. There have recently been substantial advances in our knowledge of the molecular biology and genetics of sex chromosomes and dosage compensation, and in our understanding of the population genetic processes which are involved in their evolution.

Positive correlation between the occurrence of chromosome breakage and the induction of point mutations associated with male recombination 31.1 MRF system of hybrid dysgenesis in Drosophila melanogaster

One of the weak singed ( sn w) mutations, induced by the 31.1 MRF in the X-chromosome of a laboratory strain, is highly unstable, often changing to either a strong expression ( sn st) or reverting to wild type ( sn +). The present study shows that the X-chromosome carrying the ( sn w) mutation and the X-chromosome carrying one of the sn st alleles derived from the sn w mutation generate different frequencies of deletions associated with the w locus. Moreover, they produce different frequencies of mutations associated with the w locus in males after the reintroduction of the 31.1 MRF second chromosome. The occurrece of the deletions and the induction of the mutations are positively correlated and increase when flies are raised at a higher temperature. These data indicate that the induction of the w mutations follows the generation of chromosome breaks in the w locus. The break-points of the recovered deletions occurred in specific sites in the 3C subdivision. Furthermore both sn w and sn st X-chromosomes induce different frequencies of non-disjunction in females depending on the culture temperature and the genetic background. The present data also show that the 23.5 MRF second chromosome which exhibits specific differences in its activities from the 31.1 MRF is unable to induce w mutations. This fact supports our previous indications that the 31.1 MRF and the 23.5 MRF are not identical.

Dosage compensation of the sex-linked enzyme phosphoglucomutase in the orthoptera

Sex-linkage of phosphoglucomutase (PGM) is widespread in the Orthoptera. For each of three species studied (representing the two suborders), the specific activity of PGM in males (the heterogametic sex) is almost identical to that in females, providing direct evidence that the difference in gene dose of a sex-linked locus in males and females is compensated in the Orthoptera. The Orthoptera is only the third group for which compensation has been demonstrated. Dosage compensation has been investigated in three orders of insects: it is present in Orthoptera and Diptera but absent in Lepidoptera. It is postulated that dosage compensation arose or was present in related archopteran ancestors and has been secondarily lost in Lepidoptera, possibly in association with female heterogamety in this group.

A test of nonrandom segregation.

Within a family, associations between a disease and a marker locus are often inferred when affected offspring share marker alleles more often than is expected by chance. Generally, this is due to nonrandom parental transmission of marker alleles and specifically could be due to linkage, epistatic gene action, or segregation distortion at the marker locus. In this paper, we discuss the statistical properties of a general test of nonrandom segregation of a marker gene. The exact probability distribution of the test under the null hypothesis of random segregation is derived, as is the distribution under the alternative hypothesis of genetic linkage. We compute the mean and variance of these distributions as a means of judging the adequacy of random segregation to explain disease-marker data but also provide a method for computing the exact significance value under the null hypothesis. These methods have been utilized for studying HLA segregation in families with tuberculoid leprosy. On the assumption that this type of leprosy is autosomal recessive, we find evidence that a gene controlling susceptibility to infection by Mycobacterium leprae resides on human chromosome 6, approximately 13 map units away from the HLA locus in males.

Chromatin structure and transcriptional activity of an X-linked heat shock gene in drosophila pseudoobscura.

Nuclease digestion of isolated nuclei was used to test whether differential chromatin structure exists for a dosage-compensated heat shock gene in Drosophila pseudoobscura. No differences were observed in nuclease sensitivity at this locus in males and females, either under heat shock or non-heat shock conditions, using micrococcal nuclease or DNase I. Although the higher level of nuclease sensitivity characterized by the induced state was removed when nuclei were prepared in high salt (0.45 M sodium chloride), this procedure did not reveal covert differences in X-linked chromatin structure between males and females. However, a clear difference was observed in the nuclease sensitivity at low level (uninduced) and high level (heat-induced) expression of the X-linked heat shock gene, suggesting that the same gene transcribed at two steady state rates can have different chromatin structures.

Bar reversion and hybrid dysgenesis inDrosophila melanogaster:reversion in males and in inversions

SUMMARYThe effect of the P-M system of hybrid dysgenesis inDrosophila melanogasteron unequal crossing-over was studied using the Bar duplication. This system of dysgenesis had no demonstrable effect on the rate of Bar reversion. In the course of the study it was found that there was a greatly reduced rate of reversion in two homozygous inversion stocks. Further, one revertant was found which may result from unequal crossing over at the Bar locus in males.

CYTOGENETIC ANALYSIS OF PSEUDOLINKAGE OF LDH LOCI IN THE TELEOST GENUS SALVELINUS

Cytological and genetic analyses provide evidence that spontaneous centric fusion and fission can account for curious patterns of pseudolinkage of two LDH loci in males of brook trout (Salvelinus fontinalis) and in the F(1), F(2) and backcross generations of lake trout (S. namaycush) x brook trout hybrids. Intraindividual polymorphisms for acrocentric and metacentric chromosomes in somatic and gonadal tissue of these fish have been related to the proposed polyploid evolution in Salmonidae.

The mutagenic effectiveness of fast neutrons in male and female mice

Previous work has shown that protracted doses of fast neutrons induce high frequencies of specific locus mutations and of reciprocal translocations in mouse spermatogonia. However, they are mutagenically very ineffective when the dictyate oocyte is the stage at risk. The mutagenic response of similar germ-cell stages in the 2 sexes, namely the mitotically dividing primordial spermatogonia and oogonia with their precursors, has now been compared following irradiation for 1 week before the 12th day of embryonic life with a mean dose of 108.5 rad fast neutrons +20.5 R γ-contamination. The large clusters of specific locus mutations found in both series show conclusively t that mutations can be readily induced in female early embryonic germ cells as well as in male. Cluster size was used to estimate the mean number of germ cell at risk, from which mutation frequencies were calculated. These were 5.3·10 −5 per locus in males and 6.4·10 −5 per locus in females, from which induced mutation rates of 42·10 −8 and 58.10 −8 per rad respectively can be calculated. If dose attenuation is allowed for, higher figures are obtained. Those given are somewhat lower than the rate after protracted fast neutron irradiation of spermatogonia in the adult (109·10 −8 per rad) but higher than the mutation rates after low linear-energy transfer irradiation of spermatogonia and much higher than frequencies after protracted irradiation of dictyate oocytes. Air-dried preparations from testicular cell suspensions of 20 males irradiated as embryos were scored for presence of multivalent configurations indicating translocations. 2 had high and 2 had low frequencies of translocations; in addition, 1 mouse proved to be XYY and another had a clone of XO cells. The overall translocation frequency was 1.2%, which is lower than would be expected with irradiation of adult spermatogonia. It is concluded that the intrinsic radiosensitivity of male and female genetic material is similar in mice and that in the male these early embryonic stages are not much less sensitive than spermatogonia in the adult. It seems likely that the immature dictyate oocyte is the only germ-cell stage in the female from which mutations cannot be recovered.

Variation in crossing-over between two autosomal loci in males of Culex pipiens

To determine the cause of variation in frequency of crossing-over between two loci on chromosome II of Culex pipiens, males were allowed to inseminate several females. It was found that crossing-over was more common in some males than it was in others. There was also a good deal of variation in frequency of crossing-over among progenies sired by a single male, but it is not clear whether this variation is large enough to be significant.