The extent of intra-individual and intra-species heterogeneity in the nuclear rDNA internal transcribed spacer (ITS) was investigated among the ‘Asiatic Vigna’ species (subgenus Ceratotropis). High intra- and inter-individual ITS polymorphism was observed among Vigna radiata accessions, where multiple ITS length variants ranging from ~700 to ~770 bp were detected on PCR amplification. Subsequent analysis revealed that the variants are ‘heteroduplex ITS fragments’ generated during the PCR process. Analysis of ITS from wild and cultivated forms of ten Vigna species from subgenus Ceratotropis revealed substantial intra-species divergence in four species: Vigna umbellata, Vigna trilobata, V. radiata and Vigna minima. However, no other species analysed showed intra-individual ITS heterogeneity as observed in V. radiata. The results demonstrate differential evolution of ITS sequence among wild and cultivated forms of V. radiata. Evidence indicates that intra-species hybridization and a slow ‘molecular drive’ are responsible for this phenomenon. Sequence analysis of 5·8S, ITS1 and ITS2 and secondary-structure analysis of ITS regions indicate that the ITS variants do not belong to pseudogenic rDNA repeat units. Further, reverse transcriptase-PCR (RT-PCR) analysis showed that rDNA repeat units harbouring certain intra-individual ITS variants were transcriptionally inactive, indicating the regulation of these loci by epigenetic gene silencing. The V. radiata ITS variants, when analysed together, did not cause any phylogenetic errors at the species level.

Population genetics theory predicts that differences in breeding systems should be an important factor in the dynamics of selfish genetic elements, because of different intensities of selection on both hosts and elements. We examined population frequencies of transposable elements (TEs) in natural populations of the self-fertilizing nematode Caenorhabditis elegans and its outcrossing relative Caenorhabditis remanei. We identified a Tc1-like class of elements in the C. remanei genome with homology to the terminal inverted repeats of the C. elegans Tc1 transposon, which we name mTcre1. We measured levels of insertion polymorphism for all 32 Tc1 elements present in the genome sequence of the C. elegans N2 strain, and 16 mTcre1 elements from the genome sequence of the C. remanei PB4641 strain. We show that transposons are less polymorphic and segregate at higher frequencies in C. elegans compared with C. remanei. Estimates of the intensity of selection based on the population frequencies of polymorphic elements suggest that transposons are selectively neutral in C. elegans, but subject to purifying selection in C. remanei. These results are consistent with a reduced efficacy of natural selection against TEs in selfing populations, but may in part be explained by non-equilibrium TE dynamics.

Alleles of many genes in the house mouse (Mus musculus domesticus) t complex influence embryonic development, male transmission ratio, male fertility and other traits. Homozygous t lethal alleles cause prenatal lethality, whereas male t semilethal homozygotes and males heterozygous for two complementing t lethal haplotypes are sterile. Without a mechanism maintaining these deleterious genes, t lethals and t semilethals should be eliminated by selection. The mechanism for maintaining them is transmission ratio distortion (TRD), which is said to occur when a t/+ male sires a significantly greater proportion of fetuses carrying his t haplotype (80–100%) than his wild-type chromosome 17. To understand how this selfish DNA functions in trapped populations, the objectives of this study were to examine the structure of t haplotypes in Colorado field populations and to determine transmission ratios in these populations. The data presented here indicate two possible causes for lower than expected transmission ratios in field populations: (1) single-sire fertilization by sperm from mosaic t males may lack all t haplotype genes causing high TRD. (2) t-bearing sperm fertilizing multiple-sire litters are diluted by+sperm from males having the most common genotype (+/+).

To study the effect of genetic background on the Fmr1 knockout mutation in mice, we compared the acoustic startle response (ASR) of male fragile X knockout mice bred in three different genetic backgrounds, including C57BL/6J (C57BL/6J×129P2/OlaHsd) F1 and F2 intercross. ASR is used as a behavioural tool to assess the neuronal basis of behavioural plasticity. For each background studied, fragile X knockouts clearly differed in ASR from their control littermates. C57BL/6J knockouts showed an increase in ASR in response to the lowest stimulus of 90 dB and a decrease in ASR in response to the highest stimulus of 110 dB when compared with control mice, whereas knockouts of the F1 generation showed significantly lower ASRs for all the three stimulus intensities used when compared with control littermates. These data demonstrate that the expression of the fragile X phenotype in ASR of fragile X knockout mice may be influenced by the presence of 129 genes in the genetic background and that modifier genes may influence the fragile X phenotype. Surprisingly, and in contrast with knockouts of the F1 generation that showed a decreased ASR, knockouts of the F2 generation showed a significantly increased ASR compared with their control littermates. This is especially remarkable as both F1 and F2 mice consist of 50% of the genetic material from each of the parental strains C57BL/6J and 129P2/OlaHsd strain. Thus, the different distribution of the genetic background seems to be responsible for the difference in ASR between F1 and F2. This opposite ASR in the F1 and F2 generations is unique in behavioural studies and has, to our knowledge, not been previously reported.

We propose an empirical Bayes method based on the extreme value theory (EVT) (BE) for the analysis of data from spotted microarrays where the interest of the investigator (e.g. to identify up-regulated gene markers of a disease) or the design of the experiment (e.g. in certain ‘wild-type versus mutant’ experiments) limits identification of differentially expressed genes to those regulated in a single direction (either up or down). In such experiments, unlike in genome-wide microarrays, analysis is restricted to the tail of the distribution (extremes) of all the genes in the genome. The EVT provides a platform to account for this extreme behaviour, and is therefore a natural candidate for inference about differential expression. We compared the performance of the developed BE method with two other empirical Bayes methods on two real ‘wild-type versus mutant’ datasets where a single direction of regulation was expected due to experimental design, and in a simulation study. The BE method appears to have a better fit to the real data. In the analysis of simulated data, the BE method showed better accuracy and precision while being robust to different characteristics of microarray experiments. The BE method, therefore, seems promising and useful for inference about differential expression in microarrays where either only up- or down-regulated genes are relevant or expected.

Dominance is an important source of variation in complex traits. Here, we have carried out the first thorough investigation of quantitative trait locus (QTL) detection using variance component (VC) models extended to incorporate both additive and dominant QTL effects. Simulation results showed that the empirical distribution of the test statistic when testing for dominant QTL effects did not behave in accordance with existing theoretical expectations and varied with pedigree structure. Extensive simulations were carried out to assess accuracy of estimates, type 1 error and statistical power in two-generation human-, poultry- and pig-type pedigrees each with 1900 progeny in small-, medium- and large-sized families, respectively. The distribution of the likelihood-ratio test statistic was heavily dependent on family structure, with empirical thresholds lower for human pedigrees. Power to detect QTL was high (0·84–1·0) in pig and poultry scenarios for dominance effects accounting for >7% of phenotypic variance but much lower (0·42) in human-type pedigrees. Maternal or common environment effects can be partially confounded with dominance and must be fitted in the QTL model. Including dominance in the QTL model did not affect power to detect additive QTL effects. Also, detection of spurious dominance QTL effects only occurred when maternal effects were not included in the QTL model. When dominance effects were present in the data but not in the analysis model, this resulted in spurious detection of additive QTL or inflated estimates of additive QTL effects. The study demonstrates that dominance can be included routinely in QTL analysis of general pedigrees; however, optimal power is dependent on selection of the appropriate thresholds for pedigree structure.