Increased heterozygosity and allele variants are seen in Texel compared to Suffolk sheep

In this study, the Suffolk and Texel sheep breeds were compared for microsatellite marker heterozygosity throughout seven chromosomal regions in the sheep genome. A total of 623 Texel animals and 489 Suffolk animals in five and three half-sib families, respectively, were genotyped for microsatellite markers across the seven different chromosomes. Using the observed allele frequencies, the expected levels of heterozygosity were calculated for each family. The expected levels of heterozygosity did not significantly differ between the breeds across all regions studied. However, levels of expected heterozygosity were 32% higher in Texel animals on chromosome 4 due to a region of increased heterozygosity between BMS648 and BM3212. The number of allelic variants significantly differed between the breeds, solely due to a region of increased number of alleles on chromosome 20. This region of higher numbers of allele variants in the Texel breed extended from the MHC to c. 15cM distal to the MHC region incorporating markers OMHC1, CSRD226, TGLA387 and BM1818, which had 3.30, 7.02, 3.09 and 6.75 more alleles in Texel than in Suffolk animals, respectively. No difference was observed in the variance of allele frequency between the two breeds. It is proposed that previous selective sweeps may have reduced numbers of alleles and levels of heterozygosity in the Suffolk breed.</p

Voter models with heterozygosity selection

This paper studies variations of the usual voter model that favor types that are locally less common. Such models are dual to certain systems of branching annihilating random walks that are parity preserving. For both the voter models and their dual branching annihilating systems we determine all homogeneous invariant laws, and we study convergence to these laws started from other initial laws.Comment: Published in at http://dx.doi.org/10.1214/07-AAP444 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Origin of 2N gametes in C. reticulata cv fortune mandarin

Citrus are most important fruit crop worldwide. Seed1essness is a key characteristic for the fresh fruit market and the development of triploid hybrids is one strategy developed by several groups over the world. Indeed, triploid hybrids are generally sterile and produce seedless fruits and do not pollinate other varieties. Triploid citlllS hybrids can be obtained by several strategies, including hybridization betwe6n diploid parents. Mechanism of 2n gamete formation and its implication on parental heterozygosity restitution is a main parameter determining the genetic and phenotypic structure of the triploid population. In the case of Citrus it has been shown that the 2n gametes are of maternaI origin. It has been proposed that the origin of 2n gametes is from the second division restitution (SDR) in Clementines and from the first division restitution (FDR) in sweet oranges. No data is available for other genotypes and particularly 'Fortune', a mandarin hybrid producing very high rate of triploids in 2x x 2x crosses and massively used to create triploid progenies. The aim of this work was to analyse the mechanism of 2n gamete formation in 'Fortune' mandarin genotype. One hundred and five triploid hybrids from the crosses between 'Fortune' as female diploid parent and 'Murcott' or 'Mandarino ComÛIl' as male diploid parents were genotyped for twenty- four codominant molecular SSRs (Simple Sequence Repeat) markers using a capillary genetic fragment analyzer. Estimation of ailelic doses from relative peaks area ailowed inferring the female and male gamete structures and thus the heterozygosity restitution in the 2n gametes.; this demonstrated that ail triploid arise from 2n megaspores. The unimodal distribution of heterozygosity restitution in the 2n megaspores among the analyzed genotypes suggests that an these 2n gametes arise from a same mechanism. Restitution of maternaI heterozygosity for the used rnarkers makes suppose that underlying mechanism in the 2n gamete formation is SDR. Indeed there are six markers with less than 50% of maternaI heterozygosity restitution, which is incompatible with FDR hypothesis. SDR hypothesis is coherent with the results published in case of the clementine, which is one of the parents of the 'Fortune' variety. Under this hypothesis, the relatively high global heterozygosity restitution level (60,95%) should indicate that a majority of the analyzed markers are far frorn the centromeres. This genetic struc turation will soon be confronted with phenotypic variability and compared with structuration obtained with other triploid creation strategies such as 2x x 4x hybridization. (Texte intégral

The limits of mean-field heterozygosity estimates under spatial extension in simulated plant populations

Computational models of evolutionary processes are increasingly required to incorporate multiple and diverse sources of data. A popular feature to include in population genetics models is spatial extension, which reflects more accurately natural populations than does a mean field approach. However, such models necessarily violate the mean field assumptions of classical population genetics, as do natural populations in the real world. Recently, it has been questioned whether classical approaches are truly applicable to the real world. Individual based models (IBM) are a powerful and versatile approach to achieve integration in models. In this study an IBM was used to examine how populations of plants deviate from classical expectations under spatial extension. Populations of plants that used three different mating strategies were placed in a range of arena sizes giving crowded to sparse occupation densities. Using a measure of population density, the pollen communication distance (Pcd), the deviation exhibited by outbreeding populations differed from classical mean field expectations by less than 5% when Pcd was less than 1, and over this threshold value the deviation significantly increased. Populations with an intermediate mating strategy did not have such a threshold and deviated directly with increasing isolation between individuals. Populations with a selfing strategy were influenced more by the mating strategy than by increased isolation. In all cases pollen dispersal was more influential than seed dispersal. The IBM model showed that mean field calculations can be reasonably applied to natural outbreeding plant populations that occur at a density in which individuals are less than the average pollen dispersal distance from their neighbors

Homozygosity and risk of childhood death due to invasive bacterial disease.

BACKGROUND: Genetic heterozygosity is increasingly being shown to be a key predictor of fitness in natural populations, both through inbreeding depression, inbred individuals having low heterozygosity, and also through chance linkage between a marker and a gene under balancing selection. One important component of fitness that is often highlighted is resistance to parasites and other pathogens. However, the significance of equivalent loci in human populations remains unclear. Consequently, we performed a case-control study of fatal invasive bacterial disease in Kenyan children using a genome-wide screen with microsatellite markers. METHODS: 148 cases, comprising children aged <13 years who died of invasive bacterial disease, (variously, bacteraemia, bacterial meningitis or neonatal sepsis) and 137 age-matched, healthy children were sampled in a prospective study conducted at Kilifi District Hospital, Kenya. Samples were genotyped for 134 microsatellite markers using the ABI LD20 marker set and analysed for an association between homozygosity and mortality. RESULTS: At five markers homozygosity was strongly associated with mortality (odds ratio range 4.7 - 12.2) with evidence of interactions between some markers. Mortality was associated with different non-overlapping marker groups in Gram positive and Gram negative bacterial disease. Homozygosity at susceptibility markers was common (prevalence 19-49%) and, with the large effect sizes, this suggests that bacterial disease mortality may be strongly genetically determined. CONCLUSION: Balanced polymorphisms appear to be more widespread in humans than previously appreciated and play a critical role in modulating susceptibility to infectious disease. The effect sizes we report, coupled with the stochasticity of exposure to pathogens suggests that infection and mortality are far from random due to a strong genetic basis

Recombining your way out of trouble: the genetic architecture of hybrid fitness under environmental stress

Hybridization between species is a fundamental evolutionary force that can both promote and delay adaptation. There is a deficit in our understanding of the genetic basis of hybrid fitness, especially in non-domesticated organisms. We also know little about how hybrid fitness changes as a function of environmental stress. Here, we made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species, exposed populations to ten toxins, and sequenced the most resilient hybrids on low coverage using ddRADseq. We expected to find strong negative epistasis and heterozygote advantage in the hybrid genomes. We investigated three aspects of hybridness: 1) hybridity, 2) interspecific heterozygosity, and 3) epistasis (positive or negative associations between non-homologous chromosomes). Linear mixed effect models revealed strong genotype-by-environment interactions with many chromosomes and chromosomal interactions showing species-biased content depending on the environment. Against our predictions, we found extensive selection against heterozygosity such that homozygous allelic combinations from the same species were strongly overrepresented in an otherwise hybrid genomic background. We also observed multiple cases of positive epistasis between chromosomes from opposite species, confirmed by epistasis- and selection-free simulations, which is surprising given the large divergence of the parental species (~15% genome-wide). Together, these results suggest that stress-resilient hybrid genomes can be assembled from the best features of both parents, without paying high costs of negative epistasis across large evolutionary distances. Our findings illustrate the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of hybrid populations

A preliminary study of genetic factors that influence susceptibility to bovine tuberculosis in the British cattle herd

Associations between specific host genes and susceptibility to Mycobacterial infections such as tuberculosis have been reported in several species. Bovine tuberculosis (bTB) impacts greatly the UK cattle industry, yet genetic predispositions have yet to be identified. We therefore used a candidate gene approach to study 384 cattle of which 160 had reacted positively to an antigenic skin test (‘reactors’). Our approach was unusual in that it used microsatellite markers, embraced high breed diversity and focused particularly on detecting genes showing heterozygote advantage, a mode of action often overlooked in SNP-based studies. A panel of neutral markers was used to control for population substructure and using a general linear model-based approach we were also able to control for age. We found that substructure was surprisingly weak and identified two genomic regions that were strongly associated with reactor status, identified by markers INRA111 and BMS2753. In general the strength of association detected tended to vary depending on whether age was included in the model. At INRA111 a single genotype appears strongly protective with an overall odds ratio of 2.2, the effect being consistent across nine diverse breeds. Our results suggest that breeding strategies could be devised that would appreciably increase genetic resistance of cattle to bTB (strictly, reduce the frequency of incidence of reactors) with implications for the current debate concerning badger-culling

Continuous and Discontinuous Phase Transitions in the evolution of a polygenic trait under stabilizing selective pressure

The presence of phenomena analogous to phase transition in Statistical Mechanics, has been suggested in the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. By using numerical simulations of a model system, we analyze the evolution of a population of $N$ diploid hermaphrodites in random mating regime. The population evolves under the effect of drift, selective pressure in form of viability on an additive polygenic trait, and mutation. The analysis allows to determine a phase diagram in the plane of mutation rate and strength of selection. The involved pattern of phase transitions is characterized by a line of critical points for weak selective pressure (smaller than a threshold), whereas discontinuous phase transitions, characterized by metastable hysteresis, are observed for strong selective pressure. A finite size scaling analysis suggests the analogy between our system and the mean field Ising model for selective pressure approaching the threshold from weaker values. In this framework, the mutation rate, which allows the system to explore the accessible microscopic states, is the parameter controlling the transition from large heterozygosity (disordered phase) to small heterozygosity (ordered one).Comment: 8 pages, 7 figures, 1 tabl