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PubMed1981

Trends in heterozygosity in the process of producing inbred strains of Japanese quail.

Trends in heterozygosity in the process of producing inbred strains of Japanese quail were examined through the characterization of protein polymorphisms based on gene freqencies of 7 polymorphic loci. The average heterozygosity (Ho) at generation 1 was 0.472 and it decreased with increasing inbreeding coefficient (F) to 0.214 at generation 5 when F was 0.594. In all generations, the observed heterozygosities of the surviving families tended to be higher than those of the families that did not survive. The frequency of heterozygotes of the Es-4 locus in surviving families was higher than that of the extinct families in each generation and the difference became conspicuous in generation 4. These results suggest that a heterozygote advantage of Es-4 locus is revealed by inbreeding.

Animals↗
PubMed2004

Habitat age, breeding system and kinship in the ant Formica fusca.

In polygyne ants (multiple queens per colony) factors that affect the distribution and survival of queens may play a key role in shaping the population-wide mating system and colony kin structure. The aim of this paper was to study the breeding system in two populations of different age in the facultatively polygyne ant Formica fusca. Both the observed numbers of queens, and the relatedness patterns among queens, workers and colony fathers were compared in two adjacent populations (ages 17 years and > 100 years) in Southern Finland. The results showed that both the mating system and colony kin structure differed between the study populations. In the old population the relatedness among workers, queens and colony fathers was high. The queens were also related to their mates, resulting in significant inbreeding in workers, but not in queens. Finally, the number of queens per colony fluctuated between years, suggesting queen turnover, and nest-mate queens shared their reproduction unequally (reproductive skew). In the younger population relatedness among queens and workers was lower than in the old population, and the colony fathers were unrelated. Furthermore, inbreeding was absent, and no conclusive evidence was found for reproductive skew among nest-mate queens. Finally, the number of queens per colony appeared more stable between years, although queen turnover occurred also in this population. The observed differences in dispersal and mating behaviour are discussed in the light of a potential connection between population age and habitat saturation.

Age Factors↗
PubMed2004

Size distribution and genetic structure in relation to clonal growth within a population of Magnolia tomentosa Thunb. (Magnoliaceae).

To establish a baseline for conservation of a threatened clonal tree, Magnolia tomentosa, we investigated size distribution and genetic structure within a population, using six microsatellite markers. Within the study site, 1044 living ramets (stems) were distinguished into 175 genets (individuals). The mean number of ramets per genet was 5.97, and 76% of all genets had multiple ramets. Genets, which apparently produced new ramets through sprouting and layering, were generally composed of several large ramets and many small ramets. Spatial autocorrelation analysis of microsatellite alleles revealed positive autocorrelation over short distances for both ramets and genets. The Moran's I-value of ramets in the shortest distance class was 3.8 times larger than that of genets, reflecting the effect of clonal growth. To analyse the size-class differences in genetic structure, the 175 genets were separated into two size classes, small and large. The correlogram for the small genets exhibited positive spatial autocorrelation in the shortest distance class, but this was not the case for the correlogram for the large genets, indicating that genetic structure is weakened or lost through self-thinning as the genets grow. The FIS value over all loci for the small genets was positive and deviated significantly from zero, while the corresponding value for the large genets was close to zero. The excess homozygotes in the small genets may be the result of genetic substructuring and/or inbreeding, and the reduction in homozygote frequency from the small to large genets may be because of loss of genetic structure and/or inbreeding depression.

Alleles↗
PubMed2005

Native breeds demonstrate high contributions to the molecular variation in northern European sheep.

Population contribution to genetic diversity can be estimated using neutral variation. However, population expansion or hybridization of diverged ancestries may weaken correlation between neutral and non-neutral variation. Microsatellite variation was studied at 25 loci in 20 native and 12 modern or imported northern European sheep breeds. Breed contributions to total gene diversity, allelic richness and mean allele-sharing distance between individuals were measured. Indications of changes in population size and admixtures of divergent ancestries were investigated and the extent of inbreeding was estimated. The northern European sheep demonstrated signs of reduction in effective population size. Many old, small populations made a substantial positive contribution to total molecular variation, but populations with several divergent major ancestries did not contribute substantially to molecular variation, with the exception of the Norwegian Rygja sheep. However, several diverged major ancestries may cause it to contribute less to non-neutral variation than expected from the microsatellite data. Breed uniqueness and within-breed variability generally had opposite effects on breed contributions to molecular diversity. The degree of inbreeding did not reflect the breed contribution to total gene diversity or allelic richness, but inbred populations increased the mean allele-sharing distance between individuals. Our study indicates breed conservation to be especially important in maintaining allelic variation in northern European sheep and supports the evolutionary importance of peripheral populations.

Animals↗
PubMed2007

High levels of variation despite genetic fragmentation in populations of the endangered mountain pygmy-possum, Burramys parvus, in alpine Australia.

In endangered mammals, levels of genetic variation are often low and this is accompanied by genetic divergence among populations. The mountain pygmy-possum (Burramys parvus) is an endangered marsupial restricted to the alpine region of Victoria and New South Wales, Australia. By scoring variation at eight microsatellite loci, we found that B. parvus populations exhibit high levels of genetic divergence and fall into three distinct groups from the northern, central and southern areas of the distribution of this species, consistent with previous assessments of mitochondrial DNA variation. F(ST) values between populations from these regions ranged from 0.19 to 0.54. Within the central area, there was further genetic fragmentation, and a linear association between genetic and geographical distance. This pattern is likely to reflect limited dispersal across barriers despite the fact that individual B. parvus can move several kilometres. Levels of genetic variation within populations were high with the exception of a southern population where there was evidence of inbreeding. From a conservation perspective, all three areas where B. parvus are found should be considered as separate gene pools; management of populations within these areas needs to take into account the low gene flow between populations, as well as threats posed by roads, resorts and other developments in the alpine region. The low genetic variability and inbreeding in the southern population is of particular concern given the high levels of variability in other B. parvus populations.

Animals↗
PubMed2005

A measure of the within-chromosome synergistic epistasis for Drosophila viability.

In order to detect possible synergistic epistasis for viability in Drosophila melanogaster we assayed the relative viability of chromosomes II in: (i) panmixia, (ii) forced total homozygosity, and (iii) homozygosity for, on the average, half of their loci. As these genotypes were constructed using exactly the same set of chromosomes in the three cases, the design allows us to estimate the inbreeding depression rate at two different inbreeding levels in the absence of purging natural selection. Overall, no consistent synergistic epistasis was found. However, there was a small fraction of chromosomes whose severely deleterious effect when homozygous was almost significantly larger than expected from their viability when homozygous for half of their loci. This suggests occasional but important synergistic epistasis, which might confer evolutionary advantage to recombination in tightly linked genomes. Nevertheless, such epistasis is unlikely to be an evolutionary advantage driving the evolution of sexual anisogamous reproduction, as its contribution to overall viability is small when compared with the two-fold cost of anisogamy.

Analysis of Variance↗
PubMed2005

The distribution of genetic founder contributions within and among selection and control lines of an experiment with laying hens.

Pedigree analysis was used to monitor genetic dynamics in retrospect in two identically selected lines (S1, S2) and a control (CL) of laying hens, originating from a common base. The pedigree of the last generation animals had nine generations of ancestors the members of the first known generation of ancestors were taken as founders. In each generation and in all lines one son was randomly chosen from each of 20 sires. Selection of females was randomly one daughter from each of 80 dams in CL and the best 80 according to a complex criterion in S1 and S2. The experiment included seven generations of selection. After three generations 51.6, 51.5 and 95.5% of the female founders of the base generation remained in S1, S2 and CL, respectively. The corresponding figures for the founder males were 67.7, 65.1 and 96.2%. These fractions did not change much in the following generations. On average 88.5, 87.1 and 78.8% of the remaining founders of the last generation were present in the pedigree of a last generation animal in S1, S2 and CL, respectively. The average genetic contribution of a founder male to the genome of the last generation was 1.22, 1.25 and 1.04% in S1, S2 and CL, respectively. The corresponding female contributions were 0.64, 0.60 and 0.49%, respectively. The most important founders of S1 and S2, which contributed 90% of the genome of their own line, contributed 80% of the genome of the other line and 73% of the one of CL in both cases. The most important founders of CL contributed 82% to the genomes of S1 and S2. The numbers of founder genome equivalents, were 9.8, 10.3 and 12.2 for S1, S2 and CL in the last generation and indicate a considerable loss of founder alleles in all lines. Effective population sizes calculated from average rate of inbreeding obtained from pedigrees were 91.1, 98.3 and 122.5 for S1, S2 and CL, respectively. Using the squared founder contributions for this purpose resulted in effective sizes of 0.966, 0.941 and 0.959 of the former values for S1, S2 and CL, respectively. Mating only animals with four different grand sires reduced inbreeding compared with random mating over the duration of the experiment. The effectiveness of this scheme was, however, strongly reduced in the last generation.

Animals↗
PubMed1998

NER rat strain: a new type of genetic model in epilepsy research.

PURPOSE: We characterized and evaluated as an animal model of epilepsy NER, a new epileptic rat strain, which was developed by inbreeding rats with spontaneous tonic-clonic seizures in a stock of Crj:Wistar. METHODS: Animals were monitored through the inbreeding course, and video-EEGs were recorded selectively. External seizure-provoking stimuli were applied to NER and to a control parental strain. F1, F2, and backcross progenies were produced between NER and a nonepileptic unrelated strain. Pathologic study included hematoxylin-and-eosin (HE), Klüver-Barrera's, modified Bodian silver, and neo-Timm's staining. RESULTS: After the F9 generation, 94%-98% of NER exhibited spontaneous tonic-clonic convulsions, beginning with neck and forelimb clonus, wild jumping/running, opisthotonic posturing, and evolving to tonic, then clonic convulsion, followed by postictal flaccidity. Most seizure onsets occurred between 2-4 months of age, and the incidence was 0.45 +/- 0.21 seizures in 12 h. Ictal cortical and hippocampal EEGs were characterized by high-voltage spikes followed by diffuse spike-and-wave or polyspike-and-wave complexes. NER revealed seizure susceptibility to pentylenetetrazol, tossing, and transcorneal electroshock, but not to tactile, photic, or acoustic stimuli, or to transauricular electroshock. Mating experiments revealed that 0% (0/46) of the animals in F1, 25.5% (13/51) in F2, and 63.6% (56/88) in backcross progenies exhibited spontaneous tonic-clonic convulsions without sex difference. For all these epileptic traits, no pathologic changes were demonstrated in the CNS. CONCLUSIONS: NER frequently exhibited spontaneous convulsions, controlled by a major autosomal recessive gene for epilepsy, that are comparable to generalized tonic-clonic seizures in humans. This can serve as a new genetic model in epilepsy research.

Animals↗
PubMed2001

Genetic selection for high and low alcohol consumption in a limited-access paradigm.

BACKGROUND: Several rat lines have been bred for their differences in alcohol consumption based on a continuous-access paradigm in which alcohol solution is available 24 hr/day. The limited-access paradigm (LAP), in which access to alcohol solution is restricted to a short period per day, however, has been used extensively to investigate the neurochemical mechanisms underlying alcohol consumption. There is evidence of possible differences in genetic determination of alcohol drinking in a continuous- versus limited-access condition. For these reasons, selective breeding for high- and low-alcohol consumption (HARF and LARF, respectively) based on a LAP was conducted. METHODS: N/Nih rats were used as the breeding stock. A within-family breeding procedure was used to develop HARF and LARF lines with 10 families per line. Access to alcohol solution was restricted to 20 min/day. Alcohol was provided as 3%, 6% and 12% w/v solutions. Average intake of alcohol during the 12% phase was used as the selection criterion. Inbreeding began in the seventh generation. RESULTS: After the sixth generation of selection, rats from the HARF line consumed an average of 1.2 g/kg, whereas rats from the LARF line consumed an average of 0.6 g/kg of alcohol during the 20-min access period. Alcohol consumption remained stable over the next eight generations of inbreeding. In the continuous-access-drinking paradigm, the HARF and LARF rats consumed an average of 5.5 to 7.0 g/kg and 1.0 to 2.0 g/kg of alcohol per day respectively. An estimated heritability of 0.25 was obtained. CONCLUSIONS: These findings indicate that alcohol drinking in the LAP is influenced by genetic factors. Differences in alcohol drinking in the LAP also generalize to continuous access drinking. These rat lines will be very useful for investigations into the genetic and neurochemical mechanisms underlying alcohol drinking.

Alcohol Drinking↗
PubMed2003

Impact of genetic manipulation on the fitness of Anopheles stephensi mosquitoes.

Genetic modification of mosquitoes offers exciting possibilities for controlling malaria, but success will depend on how transformation affects the fitness of modified insects. The expression of an exogenous gene, the mutations caused by its insertion, and inbreeding while transformed lines are established can all lead to reductions in fitness. Factors influencing fitness were investigated in cage experiments with four lines of transgenic Anopheles stephensi, a vector species of human malaria. The results indicate direct costs of the introduced transgene in at least three out of the four lines, as well as an apparent cost of the inbreeding involved in making transgenic homozygotes.

Animals↗
PubMed2000

Identification of quantitative trait loci for serum cholesterol levels in stroke-prone spontaneously hypertensive rats.

The stroke-prone spontaneously hypertensive rat (SHRSP) has been reported to show significantly lower levels of serum total cholesterol than the normotensive control strain Wistar-Kyoto rat (WKY). Because selective inbreeding was conducted for stroke proneness, this concomitantly inherited characteristic of SHRSP may play some pathophysiological role in stroke. We evaluated the genetic determinants of the cholesterol trait by estimating heritability and subsequently by undertaking a genome-wide screen with 161 genetic markers in F(2) progeny involving SHRSP and WKY (104 male and 106 female rats). Three quantitative trait loci (QTLs) were detected on rat chromosomes 5, 7, and 15. Markers from the linked region on chromosome 15 indicated significant evidence of linkage with a maximal log of the odds (LOD) score of 7.7, whereas those on chromosomes 5 and 7 cosegregated with the trait in a sex-specific manner (the QTL close to genetic marker D5 Mit5 reached an LOD score of 7.3 in males, and that close to D7 Mit10 reached an LOD score of 3.2 in females). The male-specific QTL on chromosome 5 appeared to overlap with previously reported QTLs for stroke-associated phenotypes, but an identical gene (or genes) appeared unlikely to control these and the cholesterol traits simultaneously. In the present study, serum cholesterol levels were shown to be highly genetically determined in SHRSP (the heritability estimates are 76% in males and 83% in females), and 3 QTLs with substantial effects were identified. Further work, however, is required to clarify whether the cholesterol trait is related to the etiology of stroke or has been retained by chance through the inbreeding process in SHRSP.

Alleles↗
PubMedDate not supplied

A rapid method for computing the inverse of the gametic covariance matrix between relatives for a marked quantitative trait locus.

The inverse of the gametic covariance matrix between relatives, G(-1), for a marked quantitative trait locus (QTL) is required in best linear unbiased prediction (BLUP) of breeding values if marker data are available on a QTL. A rapid method for computing the inverse of a gametic relationship matrix for a marked QTL without building G itself is presented. The algorithm is particularly useful due to the approach taken in computing inbreeding coefficients by having to compute only few elements of G. Numerical techniques for determining, storing, and computing the required elements of G and the nonzero elements of the inverse are discussed. We show that the subset of G required for computing the inbreeding coefficients and hence the inverse is a tiny proportion of the whole matrix and can be easily stored in computer memory using sparse matrix storage techniques. We also introduce an algorithm to determine the maximum set of nonzero elements that can be found in G(-1) and a strategy to efficiently store and access them. Finally, we demonstrate that the inverse can be efficiently built using the present techniques for very large and inbred populations.

Algorithms↗
PubMedDate not supplied

Pedigree analysis of eight Spanish beef cattle breeds.

The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records. The populations studied were: Alistana and Sayaguesa (minority breeds), Avileña - Negra Ibérica and Morucha ("dehesa" breeds, with a scarce incidence of artificial insemination), and mountain breeds, including Asturiana de los Valles, Asturiana de la Montaña and Pirenaica, with extensive use of AI. The Bruna dels Pirineus breed possesses characteristics which make its classification into one of the former groups difficult. There was a large variation between breeds both in the census and the number of herds. Generation intervals ranged from 3.7 to 5.5 years, tending to be longer as the population size was larger. The effective numbers of herds suggest that a small number of herds behaves as a selection nucleus for the rest of the breed. The complete generation equivalent has also been greatly variable, although in general scarce, with the exception of the Pirenaica breed, with a mean of 3.8. Inbreeding effective population sizes were actually small (21 to 127), especially in the mountain-type breeds. However, the average relatedness computed for these breeds suggests that a slight exchange of animals between herds will lead to a much more favourable evolution of inbreeding. The effective number of founders and ancestors were also variable among breeds, although in general the breeds behaved as if they were founded by a small number of animals (25 to 163).

Animals↗
PubMedDate not supplied

Genetic variability of six French meat sheep breeds in relation to their genetic management.

Some demographic parameters, the genetic structure and the evolution of the genetic variability of six French meat sheep breeds were analysed in relation with their management. Four of these breeds are submitted to more or less intense selection: the Berrichon du Cher (BCH), Blanc du Massif Central (BMC), Charollais (CHA) and Limousin (LIM); the other two breeds are under conservation: the Roussin de La Hague (RLH) and Solognot (SOL). Genealogical data of the recorded animals born from 1970 to 2000 and of their known ancestors were used. The most balanced contributions of the different flocks to the sire-daughter path was found in the SOL. In the BCH, a single flock provided 43% of the sire-AI sire path, whereas the contributions of the flocks were more balanced in the BMC and LIM (the only other breeds where AI is used to a substantial amount). The distribution of the expected genetic contribution of the founder animals was found to be unbalanced, especially in the BCH and LIM. The effective numbers of ancestors (founders or not) for the ewes born from 1996 to 2000 were equal to 35 (BCH), 144 (BMC), 112 (CHA), 69 (LIM), 40 (RLH) and 49 (SOL). Inbreeding was not analysed in the BMC, due to incomplete pedigree information. From 1980 on, the rates of inbreeding, in percentage points per year, were +0.112 (BCH), +0.045 (CHA), +0.036 (LIM), +0.098 (RLH) and +0.062 (SOL). The implications of the observed trends on genetic variability are discussed in relation to the genetic management of each breed. The need for a larger selection basis in the BCH, the efficiency of the rules applied in the SOL to preserve the genetic variability and the need for a more collective organisation in the CHA and RLH are outlined.

Animals↗
PubMed2004

Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana.

BACKGROUND: Rates of recombination can vary among genomic regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order. In highly self-fertilizing species such as Arabidopsis thaliana, however, heterozygosity is expected to be strongly reduced and recombination will be much less effective, so that its influence on genome organization should be greatly reduced. RESULTS: Here we investigated theoretically the joint effects of recombination and self-fertilization on base composition, and tested the predictions with genomic data from the complete A. thaliana genome. We show that, in this species, both codon-usage bias and GC content do not correlate with the local rates of crossing over, in agreement with our theoretical results. CONCLUSIONS: We conclude that levels of inbreeding modulate the effect of recombination on base composition, and possibly other genomic features (for example, transposable element dynamics). We argue that inbreeding should be considered when interpreting patterns of molecular evolution.

Arabidopsis↗
PubMed1991

Segregation of genes from donor strain during the production of recombinant congenic strains.

Recombinant congenic strains (RCS) constitute a set of inbred strains which are designed to dissect the genetic control of multigenic traits, such as tumour susceptibility or disease resistance. Each RCS contains a small fraction of the genome of a common donor strain, while the majority of genes stem from a common background strain. We tested at two stages of the inbreeding process in 20 RCS, derived from BALB/cHeA and STS/A, to see whether alleles from the STS/A donor strain are distributed over the RCS in a ratio as would theoretically be expected. Four marker genes (Pep-3; Pgm-1; Gpi-1 and Es-3) located at 4 different chromosomes were selected and the allelic distribution was tested after 3-4 and after 12 generations of inbreeding. The data obtained do not significantly deviate from the expected pattern, thus supporting the validity of the concept of RCS.

Alleles↗
PubMed1993

Development of the KVL segregating inbred strain of the Syrian hamster (Mesocricetus auratus).

A new colony of a single segregating inbred strain of the Syrian hamster (Mesocricetus auratus), designated KVL, has recently been developed at the Royal Veterinary and Agricultural University, Copenhagen, Denmark. The segregation occurs with respect to coat colour (pied gray/pied brown) as a result of inbreeding with forced heterozygosity. After 20 generations average litter size was 6.7 at birth and 5.57 at weaning. Mean generation interval was 89.4 days. An initially significant decrease in productivity (inbreeding depression) levelled out with further generations and has now stabilized. The colony is being maintained.

Animals↗
PubMed2005

Surnames in the Azores: analysis of the isonymy structure.

Geographic isolation is a significant factor to consider when characterizing human populations. The knowledge of the genetic structure of isolated populations has been of great importance to disease-locus positioning and gene identification. To investigate the genetic structure of the Azorean population, we conducted a survey based on the frequencies of surnames listed in the 2001 telephone book. We calculated the following parameters: isonymy (I), the random component of inbreeding (F(ST)), genetic diversity according to Fisher (alpha), Karlin-McGregor's migration rate (v), and Nei's distance. For the 1,271 subscribers and 163 different surnames, Graciosa island presented the lowest value of abundance of surnames (alpha = 15.75), suggesting great genetic isolation compared to the other eight islands. Migration, calculated on the basis of the diversity of surnames within islands, ranged from 0.2747 (Corvo island) to 0.0026 (São Miguel island), indicating that people migrated preferentially toward the economically more developed islands. The value of the random component of inbreeding obtained for the whole population (F(ST) = 0.0039) indicates little genetic differentiation (Wright's F(ST) < 0.05). Moreover, isonymy similarity revealed using the UPGMA method shows three subclusters corresponding to the geographic distribution of the islands.

Azores↗