Prediction of rates of inbreeding in selected populations

A method is presented for the prediction of rate of inbreeding for populations with discrete generations. The matrix of Wright's numerator relationships is partitioned into 'contribution' matrices which describe the contribution of the Mendelian sampling of genes of ancestors in a given generation to the relationship between individuals in later generations. These contributions stabilize with time and the value to which they stabilize is shown to be related to the asymptotic rate of inbreeding and therefore also the effective population size, Ne approximately 2N/(mu 2r + sigma 2r), where N is the number of individuals per generation and mu r and sigma 2r are the mean and variance of long-term relationships or long-term contributions. These stabilized values are then predicted using a recursive equation via the concept of selective advantage for populations with hierarchical mating structures undergoing mass selection. Account is taken of the change in genetic parameters as a consequence of selection and also the increasing 'competitiveness' of contemporaries as selection proceeds. Examples are given and predicted rates of inbreeding are compared to those calculated in simulations. For populations of 20 males and 20, 40, 100 or 200 females the rate of inbreeding was found to increase by as much as 75% over the rate of inbreeding in an unselected population depending on mating ratio, selection intensity and heritability of the selected trait. The prediction presented here estimated the rate of inbreeding usually within 5% of that calculated from simulation.     

Effect of selected sugar beet herbicides on germination of various Chenopodium album populations

Seeds of various fat-hen populations (Chenopodium album L.), mostly originating from sugar beet fields, were subjected to treatments with the following herbicides: metamitron, acetochlor, dimethenamid-P and S-metolachlor. Herbicides were applied either incorporated into a sandy Loam soil (2005-2007) and/or on filter paper in Petri dishes (2006-2007). Results between experiments were highly contrasting. Soil applications of metamitron, acetochlor and S-metolachlor were stimulating germination in the 2005 experiments, whereas in the 2006-2007 experiments effects were ranging from slightly stimulating to highly inhibitory.     

Hepatitis E virus infection in selected Brazilian populations

A retrospective study on the prevalence of hepatitis E virus (HEV) infection was conducted in selected populations in Rio de Janeiro, Brazil. A total of 1,115 subjects were tested including 146 patients with acute Non-A Non-B Non-C (NANBNC) viral hepatitis, 65 hemodialysis patients, 93 blood donors, 102 intravenous drug users (IVDUs), 304 pregnant women, 145 individuals living in the rural area and 260 individuals living in the urban area. In order to characterize a favorable epidemiological set for enterically transmitted infection in the studied populations we also evaluated the prevalence of anti-HAV IgG (hepatitis A virus) antibodies. Specific antibodies to HEV (anti-HEV IgG) were detected by a commercial EIA and specific antibodies to HAV (anti-HAV IgG) were detected using a competitive "in house" EIA. We found a high prevalence of anti-HAV IgG in these populations, that could indicate some risk for infections transmitted via the fecal-oral route. The anti-HEV IgG prevalence among the different groups were: 2.1% in patients with acute NANBNC viral hepatitis, 6.2% in hemodialysis patients, 4.3% in blood donors, 11.8% in IVDUs, 1% in pregnant women, and 2.1% in individuals form the rural area. Among individuals living in the urban area we did not find a single positive serum sample. Our results demonstrated the presence of anti-HEV IgG in almost all studied populations; however, further studies are necessary to establish the real situation of HEV epidemiology in Rio de Janeiro, Brazil.     

Methods for predicting rates of inbreeding in selected populations

Summary In selected populations, families superior for the selected trait are likely to contribute more offspring to the next generation than inferior families and, as a consequence, the rate of inbreeding is likely to be higher in selected populations than in randomly mated populations of the same structure. Methods to predict rates of inbreeding in selected populations are discussed. The method of Burrows based on probabilities of coselection is reappraised in conjunction with the transition matrix method of Woolliams. The method of Latter based on variances and covariances of family size is also examined. These methods are one-generation approaches in the sense that they only account for selective advantage over a single generation, from parents to offspring. Two-generation methods are developed that account for selective advantage over two generations, from grandparent to grandoffspring as well as from parent to offspring. Predictions are compared to results from simulation. The best one-generation method was found to underpredict rates of inbreeding by 10–25%, and the two-generation methods were found to underpredict rates of inbreeding by 9–18%.     

Reliability of pedigree-based and genomic evaluations in selected populations

Background

Reliability is an important parameter in breeding. It measures the precision of estimated breeding values (EBV) and, thus, potential response to selection on those EBV. The precision of EBV is commonly measured by relating the prediction error variance (PEV) of EBV to the base population additive genetic variance (base PEV reliability), while the potential for response to selection is commonly measured by the squared correlation between the EBV and breeding values (BV) on selection candidates (reliability of selection). While these two measures are equivalent for unselected populations, they are not equivalent for selected populations. The aim of this study was to quantify the effect of selection on these two measures of reliability and to show how this affects comparison of breeding programs using pedigree-based or genomic evaluations.

Methods

Two scenarios with random and best linear unbiased prediction (BLUP) selection were simulated, where the EBV of selection candidates were estimated using only pedigree, pedigree and phenotype, genome-wide marker genotypes and phenotype, or only genome-wide marker genotypes. The base PEV reliabilities of these EBV were compared to the corresponding reliabilities of selection. Realized genetic selection intensity was evaluated to quantify the potential of selection on the different types of EBV and, thus, to validate differences in reliabilities. Finally, the contribution of different underlying processes to changes in additive genetic variance and reliabilities was quantified.

Results

The simulations showed that, for selected populations, the base PEV reliability substantially overestimates the reliability of selection of EBV that are mainly based on old information from the parental generation, as is the case with pedigree-based prediction. Selection on such EBV gave very low realized genetic selection intensities, confirming the overestimation and importance of genotyping both male and female selection candidates. The two measures of reliability matched when the reductions in additive genetic variance due to the Bulmer effect, selection, and inbreeding were taken into account.

Conclusions

For populations under selection, EBV based on genome-wide information are more valuable than suggested by the comparison of the base PEV reliabilities between the different types of EBV. This implies that genome-wide marker information is undervalued for selected populations and that genotyping un-phenotyped female selection candidates should be reconsidered.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0145-1) contains supplementary material, which is available to authorized users.     

Control of phenotypic variability in selected populations of Drosophila melanogaster

Summary In order to collect information on the mechanism determining the observed increase of wing length phenotypic variability in selected Drosophila lines, reciprocal crosses were made between +/vg and vg/vg flies within each selected population.The results obtained suggest that in our lines the increased phenotypic variability may be produced by maternally inherited agents whose activity seems to be changed according to which of the two alleles, vg or vg ⁺, is present at the vestigial locus.     

The role of selected immunoregulatory cell populations in autoimmune demyelination

Much experimental and clinical evidence has been accumulated indicating the complexity of regulatory processes associated with autoimmune demyelination. Even slight disbalance of immunoregulatory circuits may result in the loss of proper control of self antigen specific immune reaction. Here, we discuss the immunoregulatory potential of several immune (dendritic cells and regulatory T cells), as well as non-immune cell populations (mesenchymal stem cells and astrocytes) with regard to their possible role in autoimmune demyelination.     

Dietary boron intakes of selected populations in the United States

Knowledge of daily boron (B) intakes will assist researchers in establishing B requirements and elucidating the metabolic role of B in humans. B concentrations in commonly consumed foods were utilized to approximate the B intake of selected US populations. Triplicate food samples were digested at low temperatures with 16M HNO₃ and 30% H₂O₂, and analyzed by inductively coupled plasma spectroscopy (ICP). Milk and dairy products, juices, and beverages were the largest contributors to dietary B. Total B content of average daily diets ranged from 548 μg for toddlers (2 yr old) to 883 μg for mature males (60–65 yr old), excluding tap water contributions. Toddlers consumed 3.7 times more B than mature males when adjusted for body weight (body wt) and consumed the diet with the highest boron density (1.8 μg/kJ or 0.43 μg/kcal). Adolescent females consumed a diet with the lowest B density (1.12 μg/kJ or 0.26 μg/kcal). Food B concentrations applied to diet records (1020 μg/d) and ICP analysis of the corresponding food composites (1170 μg/d) were comparable (p < 0.05). Current estimations of B in US diets are consistent with reports in the literature stating that normal adult daily B intakes are approx 1 mg. Presented at the symposium “Second International Symposium on the Health Effects of Boron and Its Compounds” held in Irvine, CA, on October 23, 1997. This symposium was presented by the University of California, Irvine. The publication of the symposium was supported by U.S. Borax Inc. Guest editors for this symposium were B. Dwight Culver (University of California, Irvine, CA) and James R. Coughlin (Coughlin and Associates, Newport Coast, CA). US Department of Agriculture, Agricultural Research Service, Northern Plains Area is an equal opportunity/affirmative action employer, and all agency services are available without discrimination.     

Mdg-1 mobile element polymorphism in selected Drosophila melanogaster populations

The changes in mdg-1 mobile element polymorphism that followed artificial selection for either high or low egg-to-adult viability in a Drosophila melanogaster population were investigated. The two selected subpopulations were thus characterized for fecundity, wing length, and number and location of the mdg-1 mobile element by in situ hybridization of the biotinylated-DNA on salivary gland chromosomes. The selected populations that differed greatly in egg-to-adult viability showed the same mean fecundity and identical values for intra and inter components of variances, intraclass correlation coefficient, and fluctuating asymmetry estimated on the wing length measurement. This indicates a non-correlated effect between deleterious mutations affecting viability and other fitness components. However, the two selected populations differed in their pattern of mdg-1 location, although the mean number of insertions per genome was not different from that of the initial population hence, the number of insertions of the mdg-1 mobile element was independent of the effective population size. These results suggest that the mdg-1 copy number was regulated, and that during the selection process, drift and inbreeding made up new insertion patterns of the mdg-1 element in the selected populations. The results are discussed in the light of some recent theoretical models of the population dynamics of transposable elements.     

Protein polymorphism in quail populations selected for large body size

The polymorphism of five enzyme loci (amylase, alkaline phosphatase, albumin, for 4-week body weight was compared to that of the unselected control line (C). Three loci in the C line and two in the P line demonstrated polymorphism. Plasma amylase was separated into six bands and zymograms were classified on the basis of these bands into nine phenotypes. Three of the nine types were of relatively high activity and six were of relatively low activity. All nine types were found in the C line, whereas, all birds of the P line had only the most active type. Two alkaline phosphatase alleles (Akp-2B and Akp-2C) were segregating in the C line. Gene frequencies of alkaline phosphatase for the Akp-2B allele were 0.92 in the C line and 1.00 in the P line. Two albumin alleles (AlbQ1 and AlbQ2) were segregating in both populations. Gene frequencies for the AlbQ1 allele were 0.74 in the C line and 0.81 in the P line. Two red cell esterase-D alleles (Es-DF and Es-DS) were segregating in both populations. The gene frequency for the Es-DS allele (0.61) was higher than that of the Es-DF allele in the C line. In the P line the frequency of the Es-DF allele was higher than that of the Es-DS allele. Heterozygosities of the C and P lines were estimated as 0.2258 and 0.1560 respectively. The relative inbreeding coefficient of the P line, calculated from heterozygosities was 0.31.     

Protein polymorphism in quail populations selected for large body size

The polymorphism of five enzyme loci (amylase, alkaline phosphatase, albumin, for 4-week body weight was compared to that of the unselected control line (C). for 4 week body weight was compared to that of the unselected control line (C). Three loci in the C line and two in the P line demonstrated polymorphism. Plasma amylase was separated into six bands and zymograms were classified on the basis of these bands into nine phenotypes. Three of the nine types were of relatively high activity and six were of relatively low activity. All nine types were found in the C line, whereas, all birds of the P line had only the most active type. Two alkaline phosphatase alleles (Akp-2^B and Akp-2^C) were segregating in the C line. Gene frequencies of alkaline phosphatase for the Akp-2^B allele were 0.92 in the C line and 1.00 in the P line. Two albumin alleles (Alb^Q1 and Alb^Q2) were segregating in both populations. Gene frequencies for the Alb^Q1 allele were 0.74 in the C line and 0.81 in the P line. Two red cell esterase-D alleles (Es-D^F and Es-D^s) were segregating in both populations. The gene frequency for the Es-D^s allele (0.61) was higher than that of the Es-D^F allele in the C line. In the P line the frequency of the Es-D^F allele was higher than that of the Es-D^s allele. Heterozygosities of the C and P lines were estimated as 0.2258 and 0.1560 respectively. The relative inbreeding coefficient of the P line, calculated from heterozygosities was 0.31.     

Temporal changes in allele frequencies in two reciprocally selected maize populations

The effects of breeding on allele frequency changes at 82 restriction fragment length polymorphism (RFLP) loci were examined in two maize (Zea mays L.) populations undergoing reciprocal recurrent selection, Iowa Stiff Stalk Synthetic and Iowa Corn Borer Synthetic #1. After 12 cycles of selection, approximately 30% of the alleles were extinct and 10% near fixation in each population. A test of selective neutrality identified several loci in each population whose allele frequency changes cannot be explained by genetic drift; interpopulation mean expected heterozygosity increased for that subset of 28 loci but not for the remaining 54 loci. Mean expected heterozygosity within the two subpopulations decreased 39%, while the between-population component of genetic variation increased from 0.5% to 33.4% of the total. Effective population size is a key parameter for discerning allele frequency changes due to genetic drift versus those resulting from selection and genetic hitchhiking. Empirical estimates of effective population size for each population were within the range predicted by the breeding method. Received: 10 June 1998 / Accepted: 29 April 1999     

褪黑素对睡眠的调节

褪黑素独特的昼夜分泌节律有固定的相位关系。多年来的研究表明,在日行性运行,生理性的褪黑素浓度升高是睡眠的促发因子。外源性慢性给予褪黑素以调节睡眠节律为主;而急性给药,又 可观察到直接的催眠效果。褪黑素影响睡眠的机制是多方面的,它可通过对各种神经内分泌系统、神经递质及其受体、视交叉上核、体温以及神经免疫免疫的作用来参与睡眠的调节。     

Prevalence of antibodies interactive with HTLV-I antigens in selected Solomon Islands populations

Serum samples obtained in 1986 from healthy individuals in three distinct Solomon Islands populations were screened for antibodies to human lymphotropic virus type I (HTLV-I). One of the populations tested lives on the remote Polynesian outlier atoll, Ontong Java. The other two groups, the Baegu and the Lau, are Melanesians living on Malaita, the most populous of the larger Solomon Islands. Eighty-eight of a total of 601 (14.6%) sera tested were repeatably reactive in an enzyme-linked immunosorbent assay (ELISA) that uses as antigen a lysate of HTLV-I viral particles. The prevalence of antibodies interactive with HTLV-I viral particles. The prevalence of antibodies interactive with HTLV-I antigens varied among the three groups, ranging from 8.5% (16/188) in the Baegu, through 13% (7/54) in the Lau, to 18.1% (65/359) among the Ontong Java population. The specificity of the screening ELISA was confirmed by protein immunoblot. No serum samples were obtained from children under 9 years of age. Although 121 of the 601 sera came from children between the ages of 9 and 19, none of these were reactive in the HTLV-I ELISA. Starting in the third decade, the prevalence of HTLV-I seropositivity increased with age, from 8.8% (10/113) between the ages of 20 and 29 to a peak of 25.9% (15/58) and 25% (15/60) in the sixth and seventh decade, respectively. This age-specific prevalence pattern is strikingly similar to that which is seen in populations where HTLV-I infection is endemic.