Genetic diversity of the house mouse Mus musculus and geographic distribution of its subspecies-specific RAPD markers on the territory of Russia

Genetic diversity and geographic distribution of taxon-specific RAPD markers was examined in ten local populations of the house mouse Mus musculus (n = 42). The house mice were generally characterized by moderate genetic variation: polymorphism P99 = 60%, P95 = 32.57%; heterozygosity H = 0.12; the observed allele number n(a) = 1.6; the effective allele number n(e) = 1.18; the within-population differentiation Theta = 0.388; and Shannon index I = 0.19. The degree of genetic isolation of individual local populations was greatly variable. The genetic subdivision index G(st) varied from 0.162 to 0.770 at the gene flow of Nm = 2.58-0.149, while the among-population distances D(N) varied from 0.026 to 0.178. of the largest part of the genetic diversity was found among the populations (H(T) = 0.125), while the within-population diversity was twice lower (H(S) = 0.06). The samples examined were well discriminated relative to the sets of RAPD markers. The character distribution pattern provided conditional subdivision of the mice into the "western" and the "eastern" groups with the putative boarder along the Baikal Lake. The first group was characterized by the prevalence of the markers typical of M. m. musculus and M. m. domesticus. The second group was characterized by the prevalence of the markers typical of M. m. musculus, M. m. gansuensis, M. m. castaneus, M. m. domesticus, and m. m. wagneri. The genotype of the nominative subspecies M. m. musculus was background for all populations. In the populations examined some of earlier described subspecies-specific molecular markers were found at different frequencies, pointing to the involvement of several subspecies of M. musculus in the process of hybridization.     

Discovery of a new HBB haplotype <Emphasis Type="Italic">w2</Emphasis> in a wild-derived house mouse, <Emphasis Type="Italic">Mus musculus</Emphasis>

Genetic characterization of a wild-derived house mouse, Mus musculus, originally collected near Lake Balkhash in the Republic of Kazakhstan, was performed by examining protein polymorphisms and nucleotide sequences for the hemoglobin beta chain (HBB) subunits. Protein electrophoresis, which was performed on a cellulose-acetate plate, showed an independent mobility pattern representing a new, previously undiscovered haplotype. Neighbor-joining analyses of the HBB adult genes, i.e., HBB-T1 and HBB-T2, and the intergenic spacer region showed that the Lake Balkhash mouse possessed genomic components that were mixed from different haplotypes. Compared to the previously determined HBB haplotypes, d, p, and w1, the HBB-T1 gene and ca. 11 kb of the spacer region were most similar to the w1 haplotype; however, the remainder of the spacer region and the HBB-T2 gene were most similar to the d haplotype but may represent a still uncharacterized and divergent haplotype. The recombination event is predicted to have occurred 2.5 kb upstream of the HBB-T2 gene and may have occurred through intersubspecific hybridization between mice of the musculus subspecies group (with the w1 haplotype) and the castaneus subspecies group (with the d-like haplotype). Alternatively, an unknown subspecies group that is equidistantly divergent from each of these subspecies groups may have been involved. Our findings suggest reticulate evolution among the subspecies groups during the evolution of M. musculus.     

Duration discrimination in the mouse (<Emphasis Type="Italic">Mus musculus</Emphasis>)

Detection thresholds for an increment in duration of a 10-kHz pure tone were determined in the NMRI mouse using a Go/NoGo-procedure and the method of constant stimuli. Thresholds for reference durations of 50, 100 and 200 ms were obtained presenting the signals at a fixed level or at a level varying by ±3 dB. Thresholds were determined using signal-detection theory (d=1.0 or d=1.8) and the criterion of 50% correct responses. For a fixed level, the average Weber fraction T/T (criterion of d=1.8) significantly decreased from 1.18 or 1.23 at reference durations of 50 or 100 ms, respectively, to 0.97 at a reference duration of 200 ms. Thresholds were on average reduced by 46.8 or 55.4% for the threshold criteria d=1 or 50% correct responses, respectively. There was no effect of randomizing the level on the discrimination threshold. Duration discrimination in the NMRI mouse does not follow Webers law. The results are consistent with a mechanism summing up neural impulses over the duration of the stimulus. The psychoacoustic data are compared with results obtained by Brand et al. (J Acoust Soc Am 51:1291–1223, 2000) on the representation of acoustic signal duration in the mouse inferior colliculus.     

Long terminal repeat retrotransposons of <Emphasis Type="Italic">Mus musculus</Emphasis>

Background

Long terminal repeat (LTR) retrotransposons make up a large fraction of the typical mammalian genome. They comprise about 8% of the human genome and approximately 10% of the mouse genome. On account of their abundance, LTR retrotransposons are believed to hold major significance for genome structure and function. Recent advances in genome sequencing of a variety of model organisms has provided an unprecedented opportunity to evaluate better the diversity of LTR retrotransposons resident in eukaryotic genomes.

Results

Using a new data-mining program, LTR_STRUC, in conjunction with conventional techniques, we have mined the GenBank mouse (Mus musculus) database and the more complete Ensembl mouse dataset for LTR retrotransposons. We report here that the M. musculus genome contains at least 21 separate families of LTR retrotransposons; 13 of these families are described here for the first time.

Conclusions

All families of mouse LTR retrotransposons are members of the gypsy-like superfamily of retroviral-like elements. Several different families of unrelated non-autonomous elements were identified, suggesting that the evolution of non-autonomy may be a common event. High sequence similarity between several LTR retrotransposons identified in this study and those found in distantly-related species suggests that horizontal transfer has been a significant factor in the evolution of mouse LTR retrotransposons.

     

An <Emphasis Type="Italic">en masse</Emphasis> phenotype and function prediction system for <Emphasis Type="Italic">Mus musculus</Emphasis>

Background:

Individual researchers are struggling to keep up with the accelerating emergence of high-throughput biological data, and to extract information that relates to their specific questions. Integration of accumulated evidence should permit researchers to form fewer - and more accurate - hypotheses for further study through experimentation.

Results:

Here a method previously used to predict Gene Ontology (GO) terms for Saccharomyces cerevisiae (Tian et al.: Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 2008, 9(Suppl 1):S7) is applied to predict GO terms and phenotypes for 21,603 Mus musculus genes, using a diverse collection of integrated data sources (including expression, interaction, and sequence-based data). This combined 'guilt-by-profiling' and 'guilt-by-association' approach optimizes the combination of two inference methodologies. Predictions at all levels of confidence are evaluated by examining genes not used in training, and top predictions are examined manually using available literature and knowledge base resources.

Conclusion:

We assigned a confidence score to each gene/term combination. The results provided high prediction performance, with nearly every GO term achieving greater than 40% precision at 1% recall. Among the 36 novel predictions for GO terms and 40 for phenotypes that were studied manually, >80% and >40%, respectively, were identified as accurate. We also illustrate that a combination of 'guilt-by-profiling' and 'guilt-by-association' outperforms either approach alone in their application to M. musculus.

     

Activity of error-prone DNA polymerase iota in different periods of house mouse <Emphasis Type="Italic">Mus musculus</Emphasis> ontogeny

Analysis of incorrect activity of error-prone DNA polymerase iota in M. musculus ontogeny demonstrated considerable changes in its activity, which peaks in most organs during prenatal development and decreases in the adult body. We propose that the capacity of error-prone DNA polymerases to synthesize on damaged DNA regions is critical for the realization of rapidly changing genetic program in mammalian embryogenesis, which relieves the replication block and prevents cell death.     

Genetic diversity in <Emphasis Type="Italic">in vitro</Emphasis>-conserved germplasm of <Emphasis Type="Italic">Curcuma</Emphasis> L. as revealed by RAPD markers

A set of 30 accessions of five Curcuma species-C. latifolia, C. malabarica, C. manga and C. raktakanta and 13 morphotypes (identified on the basis of morphological markers) of C. longa conserved in the In Vitro Genebank at National Bureau of Plant Genetic Resources, New Delhi, were subjected to RAPD analysis. Of the 200 RAPD primers screened, 21 polymorphic primers were selected for further study. Mean genetic similarities based on Jaccard’s similarity coefficient ranged from 0.18 to 0.86 in accessions of cultivated species, i.e., C. longa and from 0.25 to 0.86 in wild species. The dendrogram derived from the RAPD data corroborated the morphological classification of the morphotypes. The efficiency of individual RAPD primers was also compared; primers OPC-20, OPO-06, OPC-01 and OPL-03 were adjudged highly informative in discriminating the germplasm of Curcuma.     

Genetic diversity assessment in Portugal accessions of <Emphasis Type="Italic">Olea europaea</Emphasis> by RAPD markers

Eighty seven olive (Olea europaea ssp. sativa L.) cultivar accessions from Portugal were characterized by means of randomly amplified polymorphic DNA (RAPD) markers. Of the 11 arbitrary 10-mer primers tested a total of 92 polymorphic bands were obtained, representing 87.6 % of the total amplification products. Twenty nine different genotypes were clearly discriminated. Differences were not found among the amplification profiles from different individuals of the same cultivar. All the genotypes could be identified by the combination of three primers: OPR-1, OPK-14 and OPA-1, seven genotype-specific markers being detected. Genetic relationships were estimated by the unweighted pair-group method with arithmetic averaging (UPGMA). The genetic analysis of the results showed a gradual distance between the various cultivars, making it difficult to identify well-differentiated phylogenetic groups, although two clusters were distinguishable with 35 % similarity, in addition to three independent branches with lower similarity: Galega, Tentilheira and Redondal. The dendrogram reflect some relationships for most of the cultivars according to the use of the fruit and ecological adaptation.     

Comparative genome mapping of the deer mouse (<Emphasis Type="Italic">Peromyscus maniculatus</Emphasis>) reveals greater similarity to rat (<Emphasis Type="Italic">Rattus norvegicus</Emphasis>) than to the lab mouse (<Emphasis Type="Italic">Mus musculus</Emphasis>)

Background  

Deer mice (Peromyscus maniculatus) and congeneric species are the most common North American mammals. They represent an emerging system for the genetic analyses of the physiological and behavioral bases of habitat adaptation. Phylogenetic evidence suggests a much more ancient divergence of Peromyscus from laboratory mice (Mus) and rats (Rattus) than that separating latter two. Nevertheless, early karyotypic analyses of the three groups suggest Peromyscus to be exhibit greater similarities with Rattus than with Mus.     

Assessment of genetic diversity in <Emphasis Type="Italic">Trigonella foenum-graecum</Emphasis> and <Emphasis Type="Italic">Trigonella caerulea</Emphasis>using ISSR and RAPD markers

Background  

Various species of genus Trigonella are important from medical and culinary aspect. Among these, Trigonella foenum-graecum is commonly grown as a vegetable. This anti-diabetic herb can lower blood glucose and cholesterol levels. Another species, Trigonella caerulea is used as food in the form of young seedlings. This herb is also used in cheese making. However, little is known about the genetic variation present in these species. In this report we describe the use of ISSR and RAPD markers to study genetic diversity in both, Trigonella foenum-graecum and Trigonella caerulea.     

<Emphasis Type="Italic">Ty</Emphasis>1<Emphasis Type="Italic">/copia</Emphasis>- and <Emphasis Type="Italic">Ty</Emphasis>3<Emphasis Type="Italic">/gypsy</Emphasis>-like DNA sequences in <Emphasis Type="Italic">Helianthus </Emphasis>species

Two repeated DNA sequences isolated from a partial genomic DNA library of Helianthus annuus, p HaS13 and p HaS211, were shown to represent portions of the int gene of a Ty3 /gypsy retroelement and of the RNase-Hgene of a Ty1 /copia retroelement, respectively. Southern blotting patterns obtained by hybridizing the two probes to BglII- or DraI-digested genomic DNA from different Helianthus species showed p HaS13 and p HaS211 were parts of dispersed repeats at least 8 and 7 kb in length, respectively, that were conserved in all species studied. Comparable hybridization patterns were obtained in all species with p HaS13. By contrast, the patterns obtained by hybridizing p HaS211 clearly differentiated annual species from perennials. The frequencies of p HaS13- and p HaS211-related sequences in different species were 4.3x10(4)-1.3x10(5) copies and 9.9x10(2)-8.1x10(3) copies per picogram of DNA, respectively. The frequency of p HaS13-related sequences varied widely within annual species, while no significant difference was observed among perennial species. Conversely, the frequency variation of p HaS211-related sequences was as large within annual species as within perennials. Sequences of both families were found to be dispersed along the length of all chromosomes in all species studied. However, Ty3 /gypsy-like sequences were localized preferentially at the centromeric regions, whereas Ty1/ copia-like sequences were less represented or absent around the centromeres and plentiful at the chromosome ends. These findings suggest that the two sequence families played a role in Helianthusgenome evolution and species divergence, evolved independently in the same genomic backgrounds and in annual or perennial species, and acquired different possible functions in the host genomes.     

Effect of the estrus cycle stage on sensitivity to pheromone 2,5-dimethylpyrazine in the house mouse <Emphasis Type="Italic">Mus musculus</Emphasis>

Frequency of cytogenetic disturbances was estimated in mitotically dividing bone marrow cells of CBA strain female mice after 24-h long action of pheromone 2,5-dimethylpyrazine (2,5-DMP). The stage of estrus cycle of each animal was taken into acount at the moment of the end of the pheromone action. The analysis was performed using the anatelophase method that allows evaluating frequencies of various types of disturbances—bridges, fragments, delayed chromosomes. The spontaneous level of the mitotic disturbances revealed by the anatelophase method in animals of the control group amounts to 5.4%. Action of pheromone 2,5-dimethylpyrazine induced the mitosis disturbances detected in the dividing bone marrow cells at the anaphase-telophase stage in the females at the di-+ postestrus stage. The corresponding frequency of disturbances after the pheromone action was equal to 9.2%. In the female in estrus, the mitotic disturbance level amounted 6.7%, which not differed statistically significantly from control. It is suggested that differences in female mouse hormonal state at different estrus cycle stages affect sensitivity to olfactory signals. Mechanisms of the revealed effect and significance of the differences in sensitivity to pheromone for reproductive processes are discussed.     

Genetic diversity of <Emphasis Type="Italic">avenin-like b</Emphasis> genes in <Emphasis Type="Italic">Aegilops tauschii</Emphasis> Coss

Avenin-like storage proteins influence the rheological properties and processing quality in common wheat, and the discovery of new alleles will benefit wheat quality improvement. In this study, 13 avenin-like b alleles (TaALPb7D-A–M) were discovered in 108 Aegilops tauschii Coss. accessions. Ten alleles were reported for the first time, while the remaining three alleles were the same as alleles in other species. A total of 15 nucleotide changes were detected in the 13 alleles, resulting in only 11 amino acid changes because of synonymous mutations. Alleles TaALPb7D-E, TaALPb7D-G, and TaALPb7D-J encoded the same protein. These polymorphic sites existed in the N-terminus, Repetitive region (Left), Repetitive region (Right) and C-terminus domains, with no polymorphisms in the signal peptide sequence nor in those encoding the 18 conserved cysteine residues. Phylogenetic analysis divided the TaALPb7Ds into four clades. The Ae. tauschii alleles were distributed in all four clades, while the alleles derived from common wheat, TaALPb7D-G and TaALPb7D-C, belonged to clade III and IV, respectively. Alleles TaALPb7D-G and TaALPb7D-C were the most widely distributed, being present in nine and six countries, respectively. Iran and Turkey exhibited the highest genetic diversity with respect to TaALPb7D alleles, accessions from these countries carrying seven and six alleles, respectively, which implied that these countries were the centers of origin of the avenin-like b gene. The new alleles discovered and the phylogenetic analysis of avenin-like b genes will provide breeding materials and a theoretical basis for wheat quality improvement.     

Genetic diversity of <Emphasis Type="Italic">Magnolia ashei</Emphasis> characterized by SSR markers

The Ashe magnolia (Magnolia ashei) is a deciduous small tree most noted for its large 1–2 foot long leaves and fragrant creamy white flowers. Although the species is adapted to and used in landscapes in many parts of the U.S., it is endemic only to Northwest Florida where it is limited to ten counties growing on undisturbed bluffs and ravine banks. The populations are highly fragmented and are threatened by degradation of habitat, leading the species to be listed as endangered in the state of Florida. SSR markers were developed to determine the genetic diversity of wild populations of M. ashei in order to guide long-term conservation strategies. 18 marker loci identified a total of 82 alleles that were used to characterize allelic diversity of M. ashei from 11 wild populations, 14 cultivated sources, five accessions of M. macrophylla, and three interspecific hybrids. Results indicated a higher than expected level of heterozygosity within populations, and a clear distinction between Eastern and Western populations; conservation efforts should therefore focus on maintaining these distinct groups in corresponding ex situ seed orchards to counteract pressures due to overcollection, pollution, and loss of habitat due to development. Clustering of individuals was similar using several analytical methods, indicating that despite relatively small sample sizes, our analysis is a valid reflection of the diversity among and relationships between these populations.     

<Emphasis Type="Italic">Agrobacterium</Emphasis><Emphasis Type="Italic">tumefaciens</Emphasis>-mediated transformation of callus cells of <Emphasis Type="Italic">Crataegus</Emphasis><Emphasis Type="Italic">aronia</Emphasis>

A genetic transformation system has been developed for callus cells of Crataegus aronia using Agrobacterium tumefaciens. Callus culture was established from internodal stem segments incubated on Murashige and Skoog (MS) medium supplemented with 5 mg l⁻¹ Indole-3-butyric acid (IBA) and 0.5 mg l⁻¹ 6-benzyladenine (BA). In order to optimize the callus culture system with respect to callus growth and coloration, different types and concentrations of plant growth regulators were tested. Results indicated that the best average fresh weight of red colored callus was obtained on MS medium supplemented with 2 mg l⁻¹ 2,4-dichlorophenoxyacetic acid (2,4-D) and 1.5 mg l⁻¹ kinetin (Kin) (callus maintenance medium). Callus cells were co-cultivated with Agrobacterium harboring the binary plasmid pCAMBIA1302 carrying the mgfp5 and hygromycin phosphotransferase (hptII) genes conferring green fluorescent protein (GFP) activity and hygromycin resistance, respectively. Putative transgenic calli were obtained 4 weeks after incubation of the co-cultivated explants onto maintenance medium supplemented with 50 mg l⁻¹ hygromycin. Molecular analysis confirmed the integration of the transgenes in transformed callus. To our knowledge, this is the first time to report an Agrobacterium-mediated transformation system in Crataegus aronia.     

Revision of the <Emphasis Type="Italic">Serrulati</Emphasis> species of <Emphasis Type="Italic">Penstemon</Emphasis> section <Emphasis Type="Italic">Saccanthera</Emphasis> subsection <Emphasis Type="Italic">Serrulati</Emphasis>

A revision of Penstemon sect. Saccanthera subsect. Serrulati includes a new species (P. salmonensis), a new variety (P. triphyllus var. infernalis), and the elevation of a subspecies to species (P. curtiflorus), bringing the total number of species to eight, which are keyed and described, complete with nomenclature and type citations.     

<Emphasis Type="Italic">Galleria</Emphasis><Emphasis Type="Italic">mellonella</Emphasis> are Resistant to <Emphasis Type="Italic">Pneumocystis</Emphasis><Emphasis Type="Italic">murina</Emphasis> Infection

Studying Pneumocystis has proven to be a challenge from the perspective of propagating a significant amount of the pathogen in a facile manner. The study of several fungal pathogens has been aided by the use of invertebrate model hosts. Our efforts to infect the invertebrate larvae Galleria mellonella with Pneumocystis proved futile since P. murina neither caused disease nor was able to proliferate within G. mellonella. It did, however, show that the pathogen could be rapidly cleared from the host.     

Genetic diversity of <Emphasis Type="Italic">Pistacia khinjuk</Emphasis> Stocks. using RAPD markers and leaf morphological characters

The aim of this research was to study the genetic diversity of Pistacia khinjuk Stocks. and also to reveal the genetic relationships. Leaf morphological characters of 16 genotypes together with Randomly Amplified Polymorphic DNA (RAPD) marker data were used for this purpose. Leaf morphological characters were used for factor analysis, which determined four main factors. Grouping of genotypes by these factors was performed by Ward’s method. Fifteen primers produced a total of 146 fragments, with an average of 9.73 fragments per primer, of which 129 were polymorphic. The unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard’s similarity coefficient matrix. According to RAPD data, genotypes were separated into three groups. The first contained the genotypes with round leaflets. Genotypes with three lanceolate leaflets were located in the second and third groups, respectively. This study revealed that high diversity exists among genotypes of P. khinjuk, like in P. vera. Also it could be postulated that genotypes of P. khinjuk with oblique and lanceolate leaflets are probably descendents of the genotypes with acuminate and roundish leaflets.