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PubMed2004

Development of a highly fecund inbred strain of mice.

A highly fecund inbred mouse line has been established from the Quackenbush Swiss (QS) outbred strain by full-sib inbreeding combined with selection for high number of pups born alive (NBA) and low interlitter interval (ILI). After more than 50 generations of inbreeding and selection, this line, named QSi5, has an NBA of 13.4 and an ILI of 29 days, averaged over the first four parities, and a total productivity of 50.7 NBA. With its exceptional reproductive performance, this line will be very useful in the creation of resources (including advanced intercross lines) for analysis of quantitative trait loci for a wide range of traits, and for the cost-effective creation of congenic lines.

Animals↗

PubMed1993

Evolution of MHC genetic diversity: a tale of incest, pestilence and sexual preference.

Evidence from the house mouse (Mus) suggests that the extreme diversity of genes of the major histocompatibility complex (MHC) results from three different forms of selection involving infectious disease (pestilence), inbreeding (incest) and MHC-based mating (sexual) preferences. MHC-based disassortative mating preferences are presumed to have evolved because they reduce homozygosity throughout the genome, and particularly within loci linked to the MHC. Progeny derived from such disassortative matings would enjoy increased fitness because of both reduced levels of inbreeding depression and increased resistance to infectious disease arising from their increased MHC heterozygosity.

Animals↗

PubMed2005

The effect of genetic drift on the variance/covariance components generated by multilocus additive x additive epistatic systems.

The effect of population bottlenecks on the components of the genetic variance/covariance generated by n neutral independent additive x additive loci has been studied theoretically. In its simplest version, this situation can be modelled by specifying the allele frequencies and homozygous effects at each locus, and an additional factor measuring the strength of the n-th order epistatic interaction. The variance/covariance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium over replicates randomly derived from the base population, after t bottlenecks of size N (derived components). Formulae were obtained giving the derived components (and the between-line variance) as functions of the ancestral ones (alternatively, in terms of allele frequencies and effects) and the corresponding inbreeding coefficient F(t). The n-th order derived component of the genetic variance/covariance is continuously eroded by inbreeding, but the remaining components may increase initially until a critical F(t) value is attained, which is inversely related to the order of the pertinent component, and subsequently decline to zero. These changes can be assigned to the between-line variances/covariances of gene substitution and epistatic effects induced by drift. Numerical examples indicate that: (1) the derived additive variance/covariance component will generally exceed its ancestral value unless epistasis is weak; (2) the derived epistatic variance/covariance components will generally exceed their ancestral values unless allele frequencies are extreme; (3) for systems showing equal ancestral additive and total non-additive variance/covariance components, those including a smaller number of epistatic loci may generate a larger excess in additive variance/covariance after bottlenecks than others involving a larger number of loci, provided that F(t) is low. Our results indicate that it is unlikely that the rate of evolution may be significantly accelerated after population bottlenecks, in spite of occasional increments of the derived additive variance over its ancestral value.

Animals↗

PubMed1997

Life-history variation among lines isolated from a laboratory population of Heligmosomoides polygyrus bakeri.

The extent of variation in several life-history traits within a laboratory population of the parasitic nematode, Heligmosomoides polygyrus bakeri, was studied in 10 relatively inbred parasite lines isolated from a stock population and characterized in BALB/c mice after 4, 8 and 11 generations of isolation. As expected, within-line variation for most traits at generation 11 compared to generation 4 significantly decreased (P < 0.01). At each generation of characterization, variation was observed among lines for parasite establishment, rate of development in the host, rate of early egg production, per capita fecundity, short-term and long-term survival and profiles of egg production, rate of decline in egg production, life-long reproductive effort and in vitro egg hatchability. Measures of all traits, except establishment, were highly repeatable. The rate of development was higher at generation 8 compared to the stock (P < 0.0001), and regression analysis revealed that early egg production of lines increased over 11 generations of isolation (P = 0.003). These results, together with the observed decrease (P < 0.01) in total variation of most of the traits over all lines during the process of isolation, suggested an evolutionary response of the traits, probably to the rapid passage of lines every month. The rate of development subsequently decreased between generations 8 and 11 in all lines (P < 0.0001), suggesting that the random genetic drift procedure used to isolate the lines eventually exerted detrimental inbreeding effects on this trait. The evolutionary responses of life-history traits to rapid passage and inbreeding suggest a genetic basis for variation in these life-history traits.

Animals↗

PubMed2003

Factors affecting commercial application of embryo technologies in dairy cattle in Europe--a modelling approach.

Reproductive techniques have a major impact on the structure of breeding programmes, the rate of genetic gain and dissemination of genetic gain in populations. This manuscript reviews the impact of reproductive technologies on the underlying components of genetic gain and inbreeding with special reference to the role of female reproductive technology. Evaluation of alternative breeding schemes should be based on genetic gain while constraining inbreeding. Optimum breeding schemes can be characterised by: decreased importance of sib information; increased accuracy at the expense of intensity; and a factorial mating strategy. If large-scale embryo cloning becomes feasible, this will have a small impact on the rate of genetic gain but will have a large impact on the structure of breeding programmes.

Animals↗

PubMed2003

Genetics and conservation biology.

Conservation genetics encompasses genetic management of small populations, resolution of taxonomic uncertainties and management units, and the use of molecular genetic analyses in forensics and to understanding species' biology. The role of genetic factors in extinctions of wild populations has been controversial, but evidence now shows that they make important contributions to extinction risk. Inbreeding has been shown to cause extinctions of wild populations, computer projections indicate that inbreeding depression has important effects on extinction risk, and most threatened species show signs of genetic deterioration. Inappropriate management is likely to result if genetic factors are ignored in threatened species management.

Animals↗

PubMed2001

Population bottleneck and effective size in Bonamia ostreae-resistant populations of Ostrea edulis as inferred by microsatellite markers.

Genetic variability at five microsatellite loci was analysed in three hatchery-propagated populations of the flat oyster, Ostrea edulis. These populations were part of a selection programme for resistance to the protozoan parasite Bonamia ostreae and were produced by mass spawns, without control of the genealogy. Evidence for population bottlenecks and inbreeding was sought. A reduction in the number of alleles, mainly due to the loss of rare alleles, was observed in all selected populations, relative to the natural population from which they were derived. Heterozygote excesses were observed in two populations, and were attributed to substructuring of the population into a small number of families. Pedigree reconstruction showed that these two populations were produced by at most two spawning events involving a limited number of parents. Most individuals within these populations are half or full-sib, as shown by relatedness coefficients. The occurrence of population bottlenecks was supported by estimates of effective number of breeders derived by three methods: temporal variance in allelic frequencies, heterozygote excess, and a new method based on reduction in the number of alleles. The estimates from the different methods were consistent. The evidence for bottleneck and small effective number of breeders are expected to lead to increasing inbreeding, and have important consequences for the future management of the three O. edulis selected populations.

Animals↗

PubMed1998

Biodemography in Siena, Italy.

Data were obtained on surnames of the parents and places of birth of the parents and grandparents of children in Siena, Italy. Isonymy and total inbreeding coefficient, and their random and non-random components, are 0.005, 0.00125, 0.00019 and 0.00106, respectively. Isonymy and inbreeding figures are similar to those of other medium-sized Italian towns, while higher values have been reported for Italian villages and Italian ethnic minorities. City endogamy, and endogamy of Contrada for grandparents have the same values (44.1 and 44.8%, respectively), but for parents, endogamy of Contrada is lower than city endogamy (15.2 and 33.4%, respectively). The difference between the extent of Contrada endogamy expected at random and observed in the parents' generation does not seem to affect the genetic structure of the present population. However, the bulk of marriage migration (more than 70%) is short range, with people coming from Tuscany. There is no statistical difference in marital migration between males and females.

Ethnicity↗

PubMed2001

Genetics of the guppy as a model for experiment in aquaculture.

The guppy, Poecilia reticulata, is one of the most famous tropical ornamental fish in the world. There are many varieties and breeds which have been bred by aqua lists for many years. The guppy has frequently been used as model organism for experiments in fish genetics because of its short life cycle, ease of breeding and reproductive capacity. The laboratory strains which were created from local (Japanese) strains and varieties were used as an experimental genetic model for aquaculture. These laboratory strains were maintained as closed colonies for five to 20 years in our laboratory. One of the roles of model experiments in fish genetics to perform experiments which take a long time in which are commercially important, such as genetic drift, as the effect of inbreeding during the growth and maintenance of population. In this review, we mainly considered the results obtained in our laboratory relating to genetic drift, and the effects of inbreeding, heterosis and inheritance of quantitative traits.

Animals↗

PubMed1997

Spurious associations in unreplicated selected lines.

Often a single pair of lines that has been selected for high and low expression of a trait is used as an animal model to study new biobehavioral characters thought to be associated with the selected trait. Because of genetic drift at many loci, comparisons of High and Low lines on the new character will frequently produce significant line differences even when there is no association between the selected trait and the new character being studied. In the absence of replicate lines to estimate the degree of genetic drift, effect size can be used to reduce the number of false-positive associations between the original selected trait and the new character. When the heritability of the new character exceeds .40 and the inbreeding coefficient within the selected lines is moderate, High- and Low-line means on the new character will frequently differ by at least one phenotypic SD, but not often differ by more than two SDs, in the absence of any relationship between the selected trait and the new character. If the selected lines are highly inbred, drift effects are greater, resulting in more false-positive associations. Situations posing special difficulty in the absence of replicate lines include the study of characters with low heritability relative to the selected trait and cases in which the lines do not differ greatly on the original selected trait. Studies using selected lines should always report inbreeding coefficients of the generations being studies, relative to the base population from which the lines were derived.

Animals↗

PubMed1975

Genetic mechanisms controlling the domestication of a wild house mouse population (Mus musculus L.).

A controlled reenactment of the domestication process provided information on the relative effects of natural selection, inbreeding, and habitat upon an originally wild house mouse population. Effects were assessed by testing offspring that were bred under either laboratory or simulated natural conditions, systematically inbred or outbred, and postnatally fostered in laboratory or simulated natural habitats. Ten generations of domestication failed to reveal any behavioral differences due to either natural selection or habitat on nine different behavioral tests. Inbreeding strongly reduced intermale aggression, partially reduced resistance to recapture by humans, but failed to affect any of the seven other behaviors.

Agonistic Behavior↗

PubMed1985

Predicting the properties of first cycle inbreds and second cycle hybrids extractable from two, three and four parent crosses.

Standard biometrical genetical models of Mather and Jinks (1982) when made applicable to the means and variances of the 55 early generations produced by crossing four parents and six F1's in all possible combinations provide estimates of genetic parameters that can be used to predict the distributive properties of the first cycle inbreds and second cycle hybrids which could be extracted from any of these generations. Thus we can predict the inbreeding and outbreeding potentials of each generation in the early stages of a breeding programme and formulate the best breeding strategy for harnessing the full genetic potential of the breeding material and choosing the best end product. The 55 generations provide reliable estimates of the predictors and therefore should be used whenever possible. Simpler experiments consisting of the basic generations of the six single crosses, however, are sufficient for obtaining estimates of the predictors of the inbreds and can be used to predict their properties when information about the second cycle hybrids is not required or the remaining generations are not available. Replacement of the F2, backcross, three way cross and double cross generations with their randomly mated progenies is expected to improve the accuracy of predictions in the presence of a linkage disequilibrium. However, the gains made may not be justified against the costs of the additional breeding and the delay in making the predictions. Extensive experimental testing of the theory of these procedures must await the completion of the current field experiments. In the meantime the limited tests conducted on the material extracted from the Nicotiana rustica varieties V1, V2, V5 and V12 have confirmed the familiar conclusions that the V1 X V5 and V2 X V12 differ in their inbreeding and outcrossing potentials.

Alleles↗

PubMed1986

On the choice of mathematical models for the estimation of lethal gene equivalents in man.

A range of mathematical models and error distributions was used to examine the validity of linear regression methods for the calculation of lethal gene equivalents. Because of the restricted span of inbreeding coefficient F values available in human studies and the limited number of data points, equivalent results were obtained with all combinations tested. It was concluded that linear regressions should be employed only for the detection of significant inbreeding effects in man and that their application to the estimation of lethal gene equivalents was not warranted.

Female↗

PubMed2025

Genomic diversity and selection signatures in Asian Zebu Cattle: insights into adaptation and genetic erosion.

Indigenous cattle breeds in Asia are highly adapted to their local environments providing essential commodities such as meat, milk and draught power while also playing a key role in traditional ceremonies, and sports. Despite ongoing efforts to characterize and conserve these breeds, the increasing trend of indiscriminate crossbreeding of Zebu cattle with high-yielding taurine breeds, threatens their genetic diversity. This study investigates the population structure, inbreeding levels, effective population size, gene flow and identification of selection footprints of Asian Zebu (Bos indicus) cattle. Using an Axiom 60 K SNP chip, we analyzed genotypes from 1303 cattle across 36 populations in nine countries, including seven taurine outgroups and 29 Zebu populations from Bangladesh, Cambodia, India, Myanmar, Pakistan, and Sri Lanka. Zebu populations demonstrated moderate genetic diversity, with heterozygosity levels averaging 0.356, inbreeding coefficients ranging from 0.026 to 0.074 and genetic differentiation (FST) varied between 0.01 and 0.11. Breed clusters aligned closely with their geographic locations except for Achai (Pakistan) and Baru Harak (Sri Lanka) breeds that appeared in both Zebu and taurine clusters indicating evidence of taurine admixture. Genomic analyses identified regions under selection using extended haplotype homozygosity (EHH) and fixation index (FST) methods. Candidate genes associated with key biological functions related to environmental responsiveness, including heat tolerance (HSP90AA1), immunity (RIPK3), metabolism and fertility (REC8, CLIC4, TSSK4), were identified, reflecting adaptive traits critical for Zebu survival and utility across diverse environments. These findings provide valuable insights for conservation and management strategies aimed at preserving the unique genetic diversity of Asian Bos indicus breeds.

Animals↗

PubMed2026

Low-pass whole-genome sequencing reveals genomic diversity and ecotype-specific adaptation in indigenous Tigrayan chickens.

Indigenous chickens play a critical role in food security and climate resilience in smallholder systems, yet their genomic diversity and adaptive potential remain insufficiently characterised. This study employed low-pass whole-genome sequencing (LP-WGS; 0.2-1.99×) to investigate genomic diversity, population structure, inbreeding and candidate environment-associated genomic variation in 33 chickens from highland, midland, and lowland agroecologies in the Tigray region of northern Ethiopia. After imputation and stringent filtering, 23.4 million high-confidence SNPs were retained, including ~ 17% novel variants, indicating substantial uncharacterised genetic diversity in these populations. SNP density (13.8 ± 8.6 SNPs/kb) was comparable to values reported from high-coverage Ethiopian chicken datasets, demonstrating the suitability of LP-WGS for population genomics in resource-limited settings. Marked differences in genomic diversity were observed among ecotypes: midland chickens showed the highest nucleotide diversity (π = 0.00267), followed by lowland (π = 0.00233), whereas highland chickens showed the lowest diversity (π = 0.00203) and elevated genomic inbreeding (FROH and FHOM ≈ 0.18). Population structure analyses revealed clear genetic separation among ecotypes. PCA (13.91% variation explained) distinguished lowland chickens along PC1 and separated highland from midland along PC2, while ADMIXTURE and FST patterns supported three major ancestral genomic backgrounds. Functional annotation of private missense variants uncovered distinct adaptive signatures reflecting the contrasting agroecological conditions. Highland chickens showed enrichment of candidate genes potentially involved in physiological processes relevant to high-altitude environments, including cold response, angiogenesis, cardiovascular regulation and metabolic homeostasis (eg., PARP1, ACOX2, ITGB3, EDNRB, SOX8, and SOX10). Midland chickens exhibited candidate signals of selection in genes with known roles in innate antiviral immunity, bacterial defence and inflammatory regulation (eg., BAK1, CLSTN1, CYSLTR1, CYSLTR2, CXCR7, GIPR, DSCAM, GDAP1, TLR3, TLR4, TLR7, IFIH1, ADORA1, EPHB1, and TMPRSS2). Lowland chickens displayed candidate variants associated with heat-stress response, DNA damage repair, oxidative balance and cardiovascular support under extreme temperatures (e.g., MLH1, BDKRB1, GPR19, FLT1, CCL18, TGM2, and RAMP3). Overall, the results indicate substantial genomic differentiation among ecotypes and suggest candidate environment-associated genetic divergence across Tigray's diverse agroecological zones. These populations may represent important reservoirs of adaptive genetic variation for climate-resilient poultry breeding, warranting further functional validation and conservation-oriented management.

Animals↗

PubMed2005

Unfolding of population structure in Baltic sheep breeds using microsatellite analysis.

Studies of domestic animals are performed on breeds, but a breed does not necessarily equate to a genetically defined population. The division of sheep from three native and four modern Baltic sheep breeds was studied using 21 microsatellite loci and applying a Bayesian clustering method. A traditional breed-wise approach was compared to that relying on the pattern of molecular diversity. In this study, a breed was found to be inconsistent with a distinct genetic population for three reasons: (i) a lack of differentiation between modern Baltic breeds, since the majority of the studied sheep formed a single population; (ii) the presence of individuals of foreign ancestry within the breed; and (iii) an undefined local Saaremaa sheep was referred to as a breed, but was shown to consist of separate populations. In the breed-wise approach, only the clearly distinct Ruhnu sheep demonstrated low within-breed variation, although the newly identified Saaremaa populations also have low variability. Providing adequate management recommendations for the Saaremaa sheep is not possible without further studies, but the potential harmful effects of inbreeding in the Ruhnu sheep could be reduced through the use of two genetically related Saaremaa populations. In other breeds, excessive crossing appears to be a larger concern than inbreeding. Assigning individuals into populations based on the pattern of genetic diversity offers potentially unbiased means of elucidating the genetic population structure of species. Combining these genetic populations with phenotypic and aetiological data will enable formulation of the most informed recommendations for gene resource management.

Animals↗

PubMed2005

Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees.

The theoretical impacts of anthropogenic habitat degradation on genetic resources have been well articulated. Here we use a simulation approach to assess the magnitude of expected genetic change, and review 31 studies of 23 neotropical tree species to assess whether empirical case studies conform to theory. Major differences in the sensitivity of measures to detect the genetic health of degraded populations were obvious. Most studies employing genetic diversity (nine out of 13) found no significant consequences, yet most that assessed progeny inbreeding (six out of eight), reproductive output (seven out of 10) and fitness (all six) highlighted significant impacts. These observations are in line with theory, where inbreeding is observed immediately following impact, but genetic diversity is lost slowly over subsequent generations, which for trees may take decades. Studies also highlight the ecological, not just genetic, consequences of habitat degradation that can cause reduced seed set and progeny fitness. Unexpectedly, two studies examining pollen flow using paternity analysis highlight an extensive network of gene flow at smaller spatial scales (less than 10 km). Gene flow can thus mitigate against loss of genetic diversity and assist in long-term population viability, even in degraded landscapes. Unfortunately, the surveyed studies were too few and heterogeneous to examine concepts of population size thresholds and genetic resilience in relation to life history. Future suggested research priorities include undertaking integrated studies on a range of species in the same landscapes; better documentation of the extent and duration of impact; and most importantly, combining neutral marker, pollination dynamics, ecological consequences, and progeny fitness assessment within single studies.

Computer Simulation↗

PubMed2006

Self-fertilization in mosses: a comparison of heterozygote deficiency between species with combined versus separate sexes.

Self-fertilization is a key difference of adaptive significance between species with combined versus separate sexes. In haploid-dominant species such as mosses and ferns, species with either combined or separate sexes (monoicous and dioicous, respectively) have the potential to self-fertilize (intergametophytic selfing), but being monoicous allows an additional mode of selfing (intragametophytic selfing). We used allozyme electrophoresis to estimate deviations from expected levels of heterozygosity under Hardy-Weinberg equilibrium to infer selfing rates in 10 moss species from 36 New Zealand populations. We found that while there were deficiencies of heterozygotes compared to expectation in both monoicous and dioicous mosses, monoicous species had significantly higher levels of heterozygote deficiency than dioicous species (F(IS)=0.89+/-0.12 and 0.41+/-0.11, respectively). Estimated selfing rates suggest that selfing occurs frequently in monoicous populations, and rarely in dioicous populations. However, in two dioicous species (Polytrichadelphus magellanicus and Breutelia pendula), we found significant indications of mixed mating or biparental inbreeding in a handful of populations. These data provide the first analysis of heterozygote deficiency and selfing among haploid-dominant species with breeding system variation, and we discuss our results with respect to the consequences of inbreeding depression and the evolution of breeding systems.

Bryophyta↗