The geographical scale of genetic structure in a continuous population is highly dependent on its breeding system and dispersion capabilities, and this knowledge is important for the study of population dynamics as well as for conservation purposes. In the present study, spatial autocorrelation statistics and intersimple sequence repeat (ISSR) markers were used to describe the genetic structure of a natural population of a prominent aromatic plant, Lippia origanoides, native to the Chicamocha Canyon in northeastern Colombia. For this purpose, individuals were sampled from two localities within the Chicamocha Canyon, where the species is abundant and continuously distributed. Cluster (principal coordinate analysis (PCO) and unweighted pair group method using arithmetic averages (UPGMA)), analysis of molecular variance (AMOVA) and Bayesian analyses revealed a low level of genetic differentiation among the two localities, suggesting that they belong to a single population. Genetic diversity levels in this population, described as the percentage of polymorphic loci (P=86·21%) and quantified using Shannon's diversity index (I=0·453) and the average panmictic heterozygosity (HB=0·484), were shown to be comparable to or higher than that in other plant species with allogamous breeding systems and to other related Verbenaceae species. Fine-scale autocorrelation analyses showed a pattern consistent with the classical model of isolation by distance with moderate but significant levels of local spatial structure. Our results suggest that sampling individuals at distances greater than ~1·2 km may result in the collection of different genotypes, which could help preserve the levels of genetic diversity in a propagation programme. The causes of this spatial pattern are currently unknown and could be influenced by many contemporary factors such as restricted seed dispersal and/or short-distance pollen movement, among others.

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.

In the Brassicaceae plant family, which includes the Arabidopsis and Brassica genera, self-incompatibility (SI) is controlled by genes at the S locus. Using experimental crosses, we studied the pattern of inheritance of S-locus alleles in the wild species Brassica cretica. Four full-sib families were established and unequal segregation of alleles at the SRK SI gene was found in one family. The segregation distortion acted in favour of a recessive (class II) allele and was best explained by some form of gametic-level selection. Our findings are discussed in the light of theoretical predictions of differential accumulation of deleterious mutations among S-locus alleles.

Microsatellites or simple sequence repeats (SSRs) are co-dominant molecular markers. When we used fluorescent SSR markers to construct a linkage map for the female heterogametic silkworm (Bombyx mori, ZW), we found that some loci did not segregate in a Mendelian ratio of 1:1 in a backcross population. These loci segregated in a 3:1 ratio of single bands compared with double bands. Further examination of band patterns indicated that three types of SSR bands were present: two homozygotes and one heterozygote. In the beginning, we considered to discard these markers. By scoring male and female F1 individuals, we confirmed that these loci were located on the Z chromosome. Using the sex-linked visible mutation sch (K05) and its wild-type (C108), we constructed an F1 male backcross (BC1M) mapping population. The combination of sch backcross and SSR data enabled us to map the SSR markers to the Z chromosome. By adjusting input parameters based on these data, we were able to use Mapmaker software to construct a linkage map. This strategy takes advantage of co-dominant markers for positional cloning of genes on the Z chromosome. We localized sch to the Z chromosome relative to six SSR markers and one PCR marker, covering a total of 76·1 cM. The sch mutation is an important sex-linked visible mutation widely used in breeding of commercial silkworms (e.g. male silkworm selection rearing). Localization of the sch gene may prove helpful in cloning the gene and developing strains for marker-assisted selection in silkworm breeding.

We have previously shown that laboratory populations of the olive fruitfly Bactrocera oleae come to equilibrium with allele frequencies at the 6-phosphogluconate dehydrogenase (6-PGD) locus markedly different from those of wild populations. In this study, we present new evidence from perturbation experiments in support of the notion that the locus is under selective pressure under laboratory conditions. Eleven populations were started with frequencies at the 6-PGD locus different from the laboratory equilibrium. Over 12 generations, the populations showed a return to the previous equilibrium, indicating a direct and powerful selection pressure on the naturally occurring allozymes of this locus. That is, a marked increase of the F allele followed by a compensatory decrease of allele I. Populations were set up to minimize the effects of associative overdominance, and we discuss the possible influence of this factor. Nucleotide sequence for the 6-PGD F and I alleles revealed two missense mutations at positions 501 and 730 leading to different amino acids among the two alleles.

Multiple sex-determining factors have been found in natural populations of the housefly, Musca domestica. Their distribution seems to follow a geographical cline. The ‘standard’ system, with a male-determining factor, M, located on the Y chromosome, prevails at higher latitudes and altitudes. At lower latitudes and altitudes M factors have also been found on any of the five autosomes. Such populations often also harbour a dominant autosomal factor, FD, which induces female development even in the presence of several M factors. Autosomal M factors were first observed some 50 years ago. It has been hypothesized that following their initial appearance, they are spreading northwards, replacing the standard XY system, but this has never been systematically investigated. To scrutinize this hypothesis, we here compare the current distribution of autosomal M factors in continental Europe, on a transect running from Germany to southern Italy, with the distribution reported 25 years ago. Additionally, we analysed the frequencies of the FD factor, which has not been done before for European populations. In contrast to earlier predictions, we do not find a clear change in the distribution of sex-determining factors: as 25 years ago, only the standard XY system is present in the north, while autosomal M factors and the FD factor are prevalent in Italy. We discuss possible causes for this apparently stable polymorphism.

Phylogenetic relationships in the USDA Vigna germplasm collection are somewhat unclear and their genetic diversity has not been measured empirically. To reveal interspecific phylogenetic relationships and assess their genetic diversity, 48 accessions representing 12 Vigna species were selected, and 30 gene-derived markers from legumes were employed. Some high-quality amplicons were sequenced. Indels (insertion/deletions) were discovered from the sequence alignments that were specific identifiers for some Vigna species. With regard to revealing polymorphisms, intron-spanning markers were more effective than exon-derived markers. These gene-derived markers were more successful in revealing interspecific polymorphisms than intraspecific polymorphisms at both the DNA fragment and sequence levels. Two different dendrograms were generated from DNA fragment data and sequence data, respectively. The results from these two dendrograms supported each other and showed similar phylogenetic relationships among the Vigna species investigated. The accessions clustered into four main groups and 13 subgroups. Each subgroup represents a subgenus or a species. Phylogenetic analysis revealed that an accession might be misclassified in our collection. The putative misclassified accession was further supported by seed morphology. Limited intraspecific genetic diversity was revealed by these gene-derived markers and/or sequences. The USDA Vigna germplasm collection currently consists of multiple species with many accessions further classified into specific subspecies, but very few subspecies of the total subspecies available exist within the collection. Based on our results, more attention should be paid to the subspecies, wild forms and/or botanical varieties for future curation in order to expand the genetic diversity of Vigna germplasm in the USDA collection.

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.

Previously we performed a 1012-generation mutation accumulation (MA) study in yeast and found that a surprisingly large proportion of fitness-altering mutations were beneficial. To verify this result and assess the impact of sampling error in our previous study, we have continued the MA experiment for an additional 1050 cell generations and re-estimated mutation parameters. After correcting for biases due to selection, we estimate that 13% of the mutations accumulated during this study are beneficial. We conclude that the high proportions of beneficial mutations observed in this and our previous study cannot be explained by sampling error. We also estimate the genome-wide mutation rate to be 13·7×10−5 mutations per haploid genome per cell generation and the absolute value of the average heterozygous effect of a mutation to be 7·3%.

There is limited experimental information about the genetic basis of micro-environmental variance (VE) (developmental stability) and environmental correlations. This study, by using a population of maize recombinant inbred lines (RIL) and simple sequence repeat (SSR) polymorphic markers, aims at the following: firstly, to quantify the genetic component of the VE or developmental stability for four traits in maize and the environmental correlation between these traits, and secondly, to identify quantitative trait loci (QTLs) that influence these quantities. We found that, when estimating variances and correlations and testing their homogeneity, estimates and tests are needed that are not highly dependent on normality assumptions. There was significant variation among the RILs in VE and in the environmental correlation for some of the traits, implying genetic heterogeneity in the VE and environmental correlations. The genetic coefficient of variation of the environmental variance () was estimated to be 20%, which is lower than estimates obtained for other species. A few genomic regions involved in the stability of one trait or two traits were detected, and these did not have an important influence on the mean of the trait. One region that could be associated with the environmental correlations between traits was also detected.

The hobo-related sequences (hRSs) were considered as degenerate and inactive elements until recently, when one mobilizable copy was described. Using this sequence as the initial seed to search for homologous sequences in 12 available Drosophila genomes, in addition to searching for these sequences by PCR and Southern blot in nine other species, we found homologous sequences in every species of the Drosophila melanogaster species subgroup. Some evidence suggests that these non-autonomous sequences were kept mobilizable for at least 0·4 million years. Also, some very short sequences with miniature inverted-repeat transposable element (MITE) characteristics were found among these hRSs. These hRSs and their ‘MITE-like’ counterparts could provide a good example of the steps proposed in models that describe the MITEs origin.

Non-random mating in plant populations can be influenced by numerous reproductive and demographic factors, including floral morphology and inter-plant distance. Here, we investigate patterns of outcrossed mating through male function in Narcissus triandrus, a tristylous, bee-pollinated wild daffodil from the Iberian Peninsula, to test pollen transfer models which predict that floral morphology promotes asymmetrical mating and biased morph ratios. Unlike other tristylous species, N. triandrus has an incompatibility system that permits intra-morph mating and long-level rather than mid-level stamens in the L-morph. Incomplete sex-organ reciprocity should result in significant intra-morph mating in the L-morph. We measured mating patterns in two L-biased populations – dimorphic (two style morphs) and trimorphic (three style morphs) – using multilocus genotyping and maximum-likelihood-based paternity analysis. We also examined the spatial distribution of style morphs and neutral markers to investigate the potential consequence of spatially restricted mating on morph ratios. As predicted, we detected significant amounts of intra-morph mating in the L-morph in both populations. Pollen transfer coefficients generally supported predictions based on the Darwinian hypothesis that anthers and stigmas of equivalent level promote pollinator-mediated cross-pollination in heterostylous populations. There was evidence of significant spatial aggregation of both style morphs and neutral markers in populations of N. triandrus, probably as a result of restricted pollen and seed dispersal. Our results provide empirical support for theoretical models of pollen transfer, which indicate that the commonly observed L-biased morph ratios in Narcissus species result from significant intra-morph mating in the L-morph because of its atypical floral morphology.

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 (+/+).

The accumulation of seed mass in soybean is affected by both genotype and environment. The aim of the present study was to measure additive, epistatic and quantitative trait locus (QTL)×environment (QE) interaction effects of QTLs on the development of 100-seed weight in a population of 143 F5 derived recombinant inbred lines (RILs) developed from the cross between the soybean cultivars ‘Charleston’ and ‘Dong Nong 594’. Broad-sense heritability of 100-seed weight from 30 days (30D) to 80D stages was 0·58, 0·52, 0·62, 0·60, 0·66 and 0·57, respectively. A total of 17 QTLs with conditional additive (a) effect and/or conditional additive×environment interaction (ae) effect at specific stages were identified in ten linkage groups by conditional mapping. Of them, only 4 QTLs had significant a effect or ae effect at different stages of seed development. Among QTLs with significant a effect, five acted positively and six acted negatively on seed development. A total of 35 epistatic pairwise QTLs of 100-seed weight were identified by conditional mapping at different developmental stages. Five pairs of QTL showed the additive×additive epistatic (aa) effect and 16 QTLs showed the aa×environment interaction (aae) effect at the different developmental stages. QTLs with aa effect as well with their environmental interaction effect appeared to vary at different developmental stages. Overall, the results indicated that 100-seed weight in soybean is under developmental, genetic and environmental control.

The nature and extent of long-distance seed dispersal are currently poorly understood, largely due to the inherent difficulty in detecting such a phenomenon. Genetic methods provide one of the few general approaches that offer the potential to accurately address this issue. Phenotypic and allozymic approaches were applied to characterize inter-population seed dispersal of the sea rocket (Cakile maritima, Brassicaceae), a glabrous and succulent annual herb. Genetic variation was assessed on 360 individuals sampled from nine populations. Genetic diversity across populations was high, 37% of which was represented by Qst and 16% by Fst. When genetic distances were used to construct the UPGMA dendrogram, populations were clustered into three groups at the 90% similarity level. The pattern of clustering can be explained by examining the direction of sea currents around Tunisian coasts. We have shown in this study that C. maritima seeds can survive up to 4 months immersion in sea water and up to 1 year of floating in sea water; therefore, seed dispersal between populations is possible both in terms of seed survival and current patterns.

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv oryzae (Xoo) is one of the major constraints to productivity in South-East Asia. The strategy of using major genes, singly or in combination, continues to be the most effective approach for BB management. Currently, more than two dozen genes have been designated but not all the known genes are effective against all the prevalent pathotypes. The challenge, therefore, is to continue to expand the gene pool of effective and potentially durable resistance genes. Wild species constitute an important reservoir of the resistance genes including BB. An accession of Oryza nivara (IRGC 81825) was found to be resistant to all the seven Xoo pathotypes prevalent in northern states of India. Inheritance and mapping of resistance in O. nivara was studied by using F2, BC2F2, BC3F1 and BC3F2 progenies of the cross involving Oryza sativa cv PR114 and the O. nivara acc. 81825 using the most virulent Xoo pathotype. Genetic analysis of the segregating progenies revealed that the BB resistance in O. nivara was conditioned by a single dominant gene. Bulked segregant analysis (BSA) of F2 population using 191 polymorphic SSR markers identified a ∼35 centiMorgans (cM) chromosomal region on 4L, bracketed by RM317 and RM562, to be associated with BB resistance. Screening of BC3F1 and BC2F2 progenies and their genotyping with more than 30 polymorphic SSR markers in the region, covering Bacterial artificial chromosome (BAC) clone OSJNBb0085C12, led to mapping of the resistance gene between the STS markers based on annotated genes LOC_Os04g53060 and LOC_Os04g53120, which is ∼38·4 kb. Since none of the known Xa genes, which are mapped on chromosome 4L, are effective against the Xoo pathotypes tested, the BB resistance gene identified and transferred from O. nivara is novel and is tentatively designated as Xa30(t). Homozygous resistant BC3F3 progenies with smallest introgression region have been identified.

In the housefly, Musca domestica L., sex is usually determined by a dominant factor, M, located on the Y chromosome. However, there are ‘autosomal male’ (AM) populations in which the M factor is located on one or more of the five autosomes (I–V) or on X. We examined changes in the frequency of AM and YM males in North Carolina populations of houseflies after 4 years in the laboratory (NC Lab 02:06) and after 4 or 5 years in the field (NC 2006 and NC 2007). In 2002, 77·7% of the male houseflies were III/III;XYM, 20% were IIIM/III;XX, and 2·3% were IIIM/III;XYM. After 4 years in the laboratory, IIIM/III males disappeared and 17·4% of the males were XMYM. Conversely, 4 years later, the field population was relatively unchanged from 2002. Thus, there was a strong selection against IIIM/III males in the laboratory, but not in the field. Field-collected flies from 2007 indicated a slight increase in the frequency of XYM males and a slight decrease in the frequency of IIIM/III males (relative to 2002 and 2006), suggesting that the relative frequency of XYM and IIIM/III can vary slightly over time in field populations. The detection of XMYM males in 2007 offered the opportunity to evaluate the frequency of the female-determining FD factor, which was found to be present in both the laboratory and field populations, but frequencies varied greatly. The present study represents the first report of FD in houseflies from North America. The significance of these results, relative to observed clines in AM versus YM males, is discussed.

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.