Mapping genetic variants associated with Beta-adrenergic responses in inbred mice

β-blockers and β-agonists are primarily used to treat cardiovascular diseases. Inter-individual variability in response to both drug classes is well recognized, yet the identity and relative contribution of the genetic players involved are poorly understood. This work is the first genome-wide association study (GWAS) addressing the values and susceptibility of cardiovascular-related traits to a selective β(1)-blocker, Atenolol (ate), and a β-agonist, Isoproterenol (iso). The phenotypic dataset consisted of 27 highly heritable traits, each measured across 22 inbred mouse strains and four pharmacological conditions. The genotypic panel comprised 79922 informative SNPs of the mouse HapMap resource. Associations were mapped by Efficient Mixed Model Association (EMMA), a method that corrects for the population structure and genetic relatedness of the various strains. A total of 205 separate genome-wide scans were analyzed. The most significant hits include three candidate loci related to cardiac and body weight, three loci for electrocardiographic (ECG) values, two loci for the susceptibility of atrial weight index to iso, four loci for the susceptibility of systolic blood pressure (SBP) to perturbations of the β-adrenergic system, and one locus for the responsiveness of QTc (p<10(-8)). An additional 60 loci were suggestive for one or the other of the 27 traits, while 46 others were suggestive for one or the other drug effects (p<10(-6)). Most hits tagged unexpected regions, yet at least two loci for the susceptibility of SBP to β-adrenergic drugs pointed at members of the hypothalamic-pituitary-thyroid axis. Loci for cardiac-related traits were preferentially enriched in genes expressed in the heart, while 23% of the testable loci were replicated with datasets of the Mouse Phenome Database (MPD). Altogether these data and validation tests indicate that the mapped loci are relevant to the traits and responses studied.     

Polyandry by wood mice in natural populations

The microhabitat used by the garden dormouse Eliomys quercinus during its nocturnal activity was examined. Twenty-three variables describing habitat structure were measured at 100 trapping points. Logistic regression models were utilized to select the variables that discriminate between used and avoided trapping points and, in a series of pairwise contrasts, between trap sites used by different sexes, age classes and animals in different reproductive periods. Used sites were characterized by a higher (>40%) rock cover, a thicker shrub layer and a younger understory with trees of smaller trunk diameter. These variables describe areas with rockfalls from the upper slope, where trees were younger and smaller, the canopy closure reduced and the shrub layer more developed than in other parts of the forest. Dense shrubby vegetation provided protection from aerial predators and, in conjunction with rocks and stones, might have made hunting by birds and mammals more difficult. Garden dormice may also have been attracted by rocky areas acting as a heat source during the night. The selection of rocky areas was more important in the first months of the active period, when animals emerged from hibernation and started the mating season. At the end of summer, the animals used areas richer in herbs, where insects and other food resources were probably more abundant.     

Allelic expression changes in Medaka (Oryzias latipes) hybrids between inbred strains derived from genetically distant populations

Variations in allele expressions between genetically distant populations are one of the most important factors which affects their morphological and physiological variations. These variations are caused by natural mutations accumulated in their habitats. It has been reported that allelic expression differences in the hybrids of genetically distant populations are different from parental strains. In that case, there is a possibility that allelic expression changes lead to novel phenotypes in hybrids. Based on genomic information of the genetically distant populations, quantification and comparison of allelic expression changes make importance of regulatory sequences (cis-acting factors) or upstream regulatory factors (trans-acting modulators) for these changes clearer. In this study, we focused on two Medaka inbred strains, Hd-rR and HNI, derived from genetically distant populations and their hybrids. They are highly polymorphic and we can utilize whole-genome information. To analyze allelic expression changes, we established a method to quantify and compare allele-specific expressions of 11 genes between the parental strains and their reciprocal hybrids. In intestines of reciprocal hybrids, allelic expression was either similar or different in comparison with the parental strains. Total expressions in Hd-rR and HNI were tissue-dependent in the case of HPRT1, with high up-regulation of Hd-rR allele expression in liver. The proportion of genes with differential allelic expression in Medaka hybrids seems to be the same as that in other animals, despite the high SNP rate in the genomes of the two inbred strains. It is suggested that each tissue of the strain difference in trans-acting modulators is more important than polymorphisms in cis-regulatory sequences in producing the allelic expression changes in reciprocal hybrids.     

Recessive genetic variants affecting mating activity of males in natural populations ofDrosophila melanogaster

Mating activity of 115 wild males was compared with 88 homozygotes and 42 heterozygotes for their second chromosomes. Wild males, 48–96 hours old, inseminated on the average, 4.4±0.1 females per 24 hours. The hetero- and homozygotes for their second chromosomes (other chromosomes being randomly combined with those from the laboratory strain), inseminated on the average 2.8±0.2 and 2.0±0.2 females/24 h. respectively. There is no correlation between homozygotes and heterozygotes for the second chromosome and their wild ancestors which carried these chromosomes. Wild second chromosomes which in homozygous condition produced total sterility of their carriers, and some others which made for an unusually high activity in homozygous males, had on an average similar effects in wild carriers.This ariicle is warmly dedicated to Professor Theodosius Dobzhansky.     

A new set of BXD recombinant inbred lines from advanced intercross populations in mice

Background  

Recombinant inbred (RI) strains are an important resource for mapping complex traits in many species. While large RI panels are available for Arabidopsis, maize, C. elegans, and Drosophila, mouse RI panels typically consist of fewer than 30 lines. This is a severe constraint on the power and precision of mapping efforts and greatly hampers analysis of epistatic interactions.     

Allelic diversity of high-molecular-weight glutenin protein subunits in natural populations of Dasypyrum villosum (L.) Candargy

Dasypyrum villosum (L.) Candargy (2n=14, V genome) is a wild, allogamous, diploid grass species that is a potential genetic resource for wheat improvement. The diversity of high-molecular-weight (HMW) glutenin subunits of the seed storage proteins of this species was examined in populations sampled in their natural habitats in Italy and Yugoslavia where the species is widely distributed. The results of selfed progeny tests confirmed that the allelic variation of HMW-glutenin subunits in D. villosum is controlled by a single locus (Glu-V1). Fourteen alleles at Glu-V1 were found among 982 individuals representing 12 populations from Italy and two from Yugoslavia, with a mean of seven alleles per population. Among the 14 Glu-V1 alleles, one produced no HMW-glutenin subunits, ten coded for a single subunit, and three for two subunits. The mobilities of all the subunits in SDS-PAGE gels were greater than that of reference subunit 7 of Triticum aestivum cv Chinese Spring. Eight of the alleles were relatively abundant (mean frequency over all populations ranged from 0.08 to 0.17) and distributed widely among the 14 populations (8 to 14); five of the alleles were rare (0.003 to 0.021) and found in only 1 to 5 populations. The frequencies of two alleles could not be individually estimated because of the similar electrophoretic mobility of their subunits. The multiple-allelic diversity at Glu-V1 was high (H_e ranged from 0.700 to 0.857) but similar from population to population. Overall, about 7% of the total allelic variation was distributed among populations (G_st=0.072), and more than 90% within populations. Whether the allelic variation at Glu-V1 is subject to natural selection is unknown, but the discovery of the homozygous null Glu-V1 alleles in the present study may be useful in pursuing this question. The multiple-allelic diversity in Glu-V1 presents the plant breeder with an opportunity to evaluate and select the most useful alleles for transfer to wheat. The importance of an evaluation genetic diversity in a wild species before interspecific gene transfers are attempted is well illustrated in this study.     

Allelic variation at the VHa locus in natural populations of rabbit (Oryctolagus cuniculus, L.)

The large interallelic distances between the three rabbit Ig V(H)a lineages, a1, a2 and a3, suggest that the persistence time of the V(H)a polymorphism could amount to 50 million years, which is much longer than that of MHC polymorphisms. Rabbit originated in the Iberian Peninsula where two subspecies coexist, one of which is confined to Southwestern Iberia (Oryctolagus cuniculus algirus). We studied the V(H) loci in the original species range to obtain a better understanding of the evolutionary history of this unusual polymorphism. Serological surveys revealed that sera from the subspecies algirus, when tested with V(H)a locus-specific alloantisera, showed either cross-reactivity ("a-positive" variants) or no reaction at all ("a-blank"). Using RT-PCR, we determined 120 sequences of rearranged V(H) genes expressed in seven algirus rabbits that were typed as either a-positive or a-blank. The data show that the V(H) genes transcribed in a-positive rabbits are closely related to the V(H)1 alleles of domestic rabbits. In contrast, a-blank rabbits were found to preferentially use V(H) genes that, although clearly related to the known V(H)a genes, define a new major allotypic lineage, designated a4. The a4 sequences have hallmark rabbit V(H)a residues together with a number of unprecedented amino acid changes in framework region 2 and 3. The net protein distances between the V(H)a4 and the V(H)a1, a2, and a3 lineages were 20, 29, and 21% respectively. We conclude that at least four distantly related lineages of the rabbit V(H)a locus exist, one of which seems to be endemic in the Iberian range.     

Isolation and genetic characterization of alcohol dehydrogenase thermostability variants occurring in natural populations of Drosophila melanogaster

Drosophila melanogaster collected from natural populations were examined fo thermostability variants within electrophoretic mobility classes of two enzymes. In alcohol dehydrogenases, two discrete forms of the "slow" allozyme and three discrete forms of the "fast" allozyme were revealed by postelectrophoretic treatments ranging from 15 sec at 40 C to 40 sec at 43 C. All variants have been mapped to within 0.7 unit of the Adh locus. Results of a geographic survey indicate that two alleles giving rise to fast-moderate and slow-moderate allozymes are common everywhere; other variants have a collective frequency ranging from 0% to 7%. In a test of the possibility that the rare Adh alleles could be generated by intragenic recombination between the two common alleles, electrophoresis and heat treatment of progeny recombinant for flanking markers of Adh revealed no new allozymes. Among 27 stocks containing slow alpha-glycerophosphate dehydrogenase allozymes and 109 fast stocks, heat treatments revealed no additional variation.     

Allelic variants of human calcitonin receptor in the Japanese population

Evidence from cDNA cloning has shown that calcitonin receptors (CTRs) have seven potential transmembrane domains. In this study, structural analysis of CTRs from ten cultured human tumor cell lines and 117 human blood samples demonstrated allelic variants at the 1377th nucleotide in intracellular domain 4, expressing either proline or leucine as the 463rd amino acid. It was found that the variant with proline at this site was the more prevalent type of CTR among the Japanese population. Received: 21 June 1996     

Allelic spectrum of the natural variation in CRP

With the recent completion of the International HapMap Project, many tools are in hand for genetic association studies seeking to test the common variant/common disease hypothesis. In contrast, very few tools and resources are in place for genotype–phenotype studies hypothesizing that rare variation has a large impact on the phenotype of interest. To create these tools for rare variant/common disease studies, much interest is being generated towards investing in re-sequencing either large sample sizes of random chromosomes or smaller sample sizes of patients with extreme phenotypes. As a case study for rare variant discovery in random chromosomes, we have re-sequenced ~1,000 chromosomes representing diverse populations for the gene C-reactive protein (CRP). CRP is an important gene in the fields of cardiovascular and inflammation genetics, and its size (~2 kb) makes it particularly amenable medical or deep re-sequencing. With these data, we explore several issues related to the present-day candidate gene association study including the benefits of complete SNP discovery, the effects of tagSNP selection across diverse populations, and completeness of dbSNP for CRP. Also, we show that while deep re-sequencing uncovers potentially medically relevant coding SNPs, these SNPs are fleetingly rare when genotyped in a population-based survey of 7,000 Americans (NHANES III). Collectively, these data suggest that several different types re-sequencing and genotyping approaches may be required to fully understand the complete spectrum of alleles that impact human phenotypes.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Allelic variants of hereditary prions: The bimodularity principle

Modern biology requires modern genetic concepts equally valid for all discovered mechanisms of inheritance, either “canonical” (mediated by DNA sequences) or epigenetic. Applying basic genetic terms such as “gene” and “allele” to protein hereditary factors is one of the necessary steps toward these concepts. The basic idea that different variants of the same prion protein can be considered as alleles has been previously proposed by Chernoff and Tuite. In this paper, the notion of prion allele is further developed. We propose the idea that any prion allele is a bimodular hereditary system that depends on a certain DNA sequence (DNA determinant) and a certain epigenetic mark (epigenetic determinant). Alteration of any of these 2 determinants may lead to establishment of a new prion allele. The bimodularity principle is valid not only for hereditary prions; it seems to be universal for any epigenetic hereditary factor.     

Further definition of the Ly-5 system

Ly-5 is expressed by cells of the hematopoietic branch of development. Further serological analysis of the Ly-5 system, aided by Ly-5 monoclonal antibodies and by two Ly-5 congenic mouse strains, reveals two new Ly-5 alloantigens, Ly-5. 3 and Ly-5.4. The data define three thymocyte phenotypes, Ly-5.1,3, Ly-5.2,4, and Ly-5.2,3, and three corresponding genotypes, Ly-5 ^a, Ly-5 ^b, and Ly-5 ^c, respectively. Ly-5 ^ais by far the most common allele. The Ly-5 ^callele is found only in the ST/bJ strain, a finding that accords with the presently unique pattern of restriction fragments previously observed in Southern blotting of ST/bJ DNA with an Ly-5 cDNA probe. Present serological and biochemical data favor the interpretation that the compound Ly-5 phenotype of thymocytes is attributable to two separate Ly-5 molecular isoforms that exhibit a discrete difference in protein composition, bear different Ly-5 antigens, and are produced jointly by thymocytes, unlike other Ly-5 isoforms previously shown to distinguish different hematopoietic cell lineages.     

Nucleotide variation in wild and inbred mice

The house mouse is a well-established model organism, particularly for studying the genetics of complex traits. However, most studies of mice use classical inbred strains, whose genomes derive from multiple species. Relatively little is known about the distribution of genetic variation among these species or how variation among strains relates to variation in the wild. We sequenced intronic regions of five X-linked loci in large samples of wild Mus domesticus and M. musculus, and we found low levels of nucleotide diversity in both species. We compared these data to published data from short portions of six X-linked and 18 autosomal loci in wild mice. We estimate that M. domesticus and M. musculus diverged <500,000 years ago. Consistent with this recent divergence, some gene genealogies were reciprocally monophyletic between these species, while others were paraphyletic or polyphyletic. In general, the X chromosome was more differentiated than the autosomes. We resequenced classical inbred strains for all 29 loci and found that inbred strains contain only a small amount of the genetic variation seen in wild mice. Notably, the X chromosome contains proportionately less variation among inbred strains than do the autosomes. Moreover, variation among inbred strains derives from differences between species as well as from differences within species, and these proportions differ in different genomic regions. Wild mice thus provide a reservoir of additional genetic variation that may be useful for mapping studies. Together these results suggest that wild mice will be a valuable complement to laboratory strains for studying the genetics of complex traits.