Isozyme polymorphisms maintained by lethal loci in inbred strains of Aedes triseriatus

We analyzed the progeny of brother-sister matings of two inbred strains of the treehole mosquito, Aedes triseriatus, at several isozyme loci to determine which factors were maintaining heterozygosity at these loci after prolonged inbreeding. The triseriatus Kramer (TK) lines were polymorphic for the Odh and Hbd loci after 12 generations of full-sib mating, and the triseriatus Vero Beach (TV) lines were polymorphic for the Odh, Hk-4, Pgm, and Hbd loci after 14 generations of full-sib mating. Genetic analysis of 22 TK F13 matings and nine TV F15 matings showed that heterozygosity was enforced by lethal loci to which all the polymorphic isozyme loci were linked. The lethal loci formed a balanced lethal system. We determined the relative positions and map distances of lethals and enzyme loci.     

Allozyme variation in populations, full-sib families and selfed lines in Betula pendula Roth

Changes in genetic variability in populations (stand origins), full-sib (FS) families and three generations of selfed lines of Betula pendula were observed based on 15 allozyme loci. Growth vigour, measured as stem volume, and its relationship with heterozygosity was studied to determine the effect of inbreeding. Pooled FS families showed a higher percentage of polymorphic loci (P) and allelic numbers per locus (A) than those of natural populations, but no difference in heterozygosity. There was no difference in allozyme variability between fast-and slow-growing family groups, and heterozygosity was not correlated with stem volume among FS families. Allozyme variability was significantly decreased in advancing generations of selfing, and the further the selfing generation, the lower the heterozygosity and the slower the growth. Observed heterozygosity after advancing generations of inbreeding was increasingly higher than expected, indicating overdominance effects or, alternatively, selection against deleterious homozygotes.     

Heterozygosity in inbred strains of the tree-hole mosquitoAedes triseriatus

Inbred stocks of the tree-hole mosquito Aedes triseriatus from four localities were developed using full-sib mating. The progress of inbreeding was followed electrophoretically at eight variable and six less variable enzyme loci. Rates of fixation of several of these loci were substantially lower than expected. Discrepancies between observed and expected fixation values were evident in the early stages of inbreeding and became larger as inbreeding progressed. Odh, Hbd, Pgm, and Hk-4 were usually not fixed. By the F12 and F14 generations of brother-sister mating, most individuals in the two lines were heterozygotes (Odh and Hbd in the TK lines and Odh, Hbd, Pgm, and Hk-4 in the TV lines). The probability of maintaining heterozygosity at several selectively neutral and unlinked loci simultaneously is very low. Odh, Hbd, Pgm, and Hbd loci are linked to lethal recessives on chromosome 2, creating a balanced lethal system which in turn accounts for the heterozygosity in these inbred mosquitoes.     

Testing for linkage disequilibrium in the New Zealand radiata pine breeding population

Linkage analysis is commonly used to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to assess the relationship between the marker-allele frequency classes obtained from parental genotypes at SSR marker loci and the full-sib family performance (average predicted breeding value of two parents) in radiata pine (Pinus radiata D. Don). For alleles (at a marker locus) that showed significant association, the copy number of that allele in the parents was significantly correlated, either positively or negatively, with the full-sib family performance for various economic traits. Regression of parental breeding value on its genotype at marker loci revealed that most of the markers that showed significant association with full-sib family performance were not significantly associated with the parental breeding values. This suggests that over-representation of the female parents in our sample of 200 full-sib families could have biased the process of detecting marker-trait associations. The evidence for the existence of marker-trait LD in the population studied is rather weak and would require further testing. The exact test for genotypic disequilibrium between pairs of linked or unlinked marker loci revealed non-significant LD. Observed genotypic frequencies at several marker loci were significantly different from the expected Hardy-Weinberg equilibrium. The possibilities of utilising marker-trait associations for early selection, among-family selection and selecting parents for the next generation of breeding are also discussed.     

The bovine major histocompatibility complex (BoLA): Close linkage of the genes controlling serologically defined antigens and mixed lymphocyte reactivity

Detection of linkage between genetic loci in cattle has been hampered by the lack of large full-sib families. A unique source of full-sib families is now available from embryo transplantation. Lymphocytes from six full-sib families, ranging in size from three to seven siblings, were tested for serologically defined BoLA antigens (BoLA-A). In addition, mixed lymphocyte reactivity (MLR) was tested between all paired combinations of cells within each family to distinguish BoLA-D specificities. Serologically identical siblings within each family were reciprocally nonreactive in MLR, and vice versa; thus, no recombinants were detected between the BoLA-A and the BoLA-D loci. Classical genetic linkage analysis revealed that these loci are significantly closer than 11.9 centimorgans.     

Development and testing of 13 polymorphic microsatellite markers in Larimichthys polyactis (Sciaenidae) using 5' anchored PCR

Larimichthys polyactis is a commercially important marine fish species in southeast Asia. The population crashed due to overfishing in the 1970s, but has since recovered. We developed 13 novel polymorphic microsatellite markers in L. polyactis using 5' anchored PCR. The characteristics of these loci were estimated by analyzing a sample of 30 individuals. A total of 74 alleles were detected, with a mean of 5.7 alleles per locus. There were 2 to 12 alleles, 0.2760 to 0.8247 polymorphism information content, and 0.3214 to 1.000 observed and 0.3097 to 0.8567 expected heterozygosity per locus. The mean observed and expected heterozygosity was 0.6816 and 0.6724, respectively. Three loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni's correction, and no significant linkage disequilibrum between pairs of loci was found. This information will be useful for the analysis of population genetic diversity, and the management of this important fish resource.     

Microsatellite-centromere mapping in the loach, Misgurnus anguillicaudatus

Primer sets for 15 polymorphic microsatellite loci were developed in the loach, Misgurnus anguillicaudatus (Cobitidae) by molecular cloning and sequencing techniques. Mendelian inheritance was confirmed for the 15 loci by examining the genotypic segregation produced with the primer sets in two full-sib families. The loci were mapped in relation to their centromere in four gynogenetic diploid lines, which were induced by inhibition of the second meiotic division after fertilization with genetically inert sperm. Microsatellite-centromere recombination rates ranged between 0.06 and 0.95 under the assumption of complete interference. Thus, these loci are distributed from the centromeres to the telomeres of their respective chromosomes. The success of mitotic gynogenesis, produced by suppression of the first cleavage, was verified by homozygosity at three diagnostic microsatellite loci that exhibited high gene-centromere meiotic recombination rates in the same family. The differences in heterozygosity levels observed with these markers were attributed to differences in the temporal application of heat shock following inert sperm activation.     

Effect of selection against deleterious mutations on the decline in heterozygosity at neutral loci in closely inbreeding populations.

Transition matrices for selfing and full-sib mating were derived to investigate the effect of selection against deleterious mutations on the process of inbreeding at a linked neutral locus. Selection was allowed to act within lines only (selection type I) or equally within and between lines (type II). For selfing lines under selection type I, inbreeding is always retarded, the retardation being determined by the recombination fraction between the neutral and selected loci and the inbreeding depression from the selected locus, irrespective of the selection coefficient (s) and dominance coefficient (h) of the mutant allele. For selfing under selection type II or full-sib mating under both selection types, inbreeding is delayed by weak selection (small s and sh), due to the associative overdominance created at the neutral locus, and accelerated by strong selection, due to the elevated differential contributions between alternative alleles at the neutral locus within individuals and between lines (for selection type II). For multiple fitness loci under selection, stochastic simulations were run for populations with selfing, full-sib mating, and random mating, using empirical estimates of mutation parameters and inbreeding load in Drosophila. The simulations results are in general compatible with empirical observations.     

An AFLP linkage map for Douglas-fir based upon multiple full-sib families

An amplified fragment length polymorphism (AFLP) linkage map for coastal Douglas-fir (Pseudotsuga menziesii) was constructed from eight full-sib families each consisting of 40 progeny. These families were part of the British Columbia Ministry of Forests second-generation progeny test program and represent typical family sizes used in progeny trials. For map construction, ten primer pairs using EcoRI+3 and MseI+4 were employed to identify and assay AFLP loci that segregated in backcross configurations. A new technique was used to obtain a single recombination rate for each pair of marker loci: for each locus pair, a recombination rate and log-odd value were estimated across all segregating families using a joint maximum likelihood function that considered the full dataset of segregating genotypes. The resulting matrix of recombination rates between all pairs of loci was used to construct an integrated linkage map using JoinMap. The final map consisted of 19 linkage groups spanning 938.6 cM at an average distance of 9.3 cM between markers. The simultaneous integration of data from multiple families may provide an effective way to construct a linkage map, using the genetic resources inherent in most tree improvement programs, where progeny tests of small size are conducted. The statistical property of number of families used is briefly discussed. For our data, at least three to four families greatly increased the chance of obtaining an informative locus in at least one family. Families as small as ten are adequate for closely linked loci (<10 cM), while the size used in our study (40) is adequate for loci within 30 cM.     

Absence of association between heterozygosity and biomass production in Salix exigua Nutt

The relations between heterozygosity derived from a total of 12 variable isoenzyme loci and total above-ground leafless biomass production were examined in four full-sib families of Salix exigua, a willow species important in breeding efforts for short-rotation intensive-culture plantations. Relations were investigated by comparing the performance of heterozygotes with that of corresponding homozygotes in locus by locus comparisons, by investigating multiple regression models with individual loci as independent variables, and by employing the adaptive distance model. All these analytical approaches resulted in the manifestation of the absence of any relations between isoenzyme loci and biomass production. Possible reasons that may account for these results are discussed. Received: 8 October 1999 / Accepted: 4 November 1999     

Effect of rate of inbreeding on inbreeding depression in Drosophila melanogaster

Summary This experiment was designed to study the relationship between rate of inbreeding and observed inbreeding depression of larval viability, adult fecundity and cold shock mortality in Drosophila melanogaster. Rates of inbreeding used were full-sib mating and closed lines of N=4 and N=20. Eight generations of mating in the N=20 lines, three generations in the N=4 lines and one generation of full-sib mating were synchronised to simultaneously produce individuals with an expected level of inbreeding coefficient (F) of approximately 0.25. Inbreeding depression for the three traits was significant at F=0.25. N=20 lines showed significantly less inbreeding depression than full-sib mated lines for larval viability at approximately the same level of F. A similar trend was observed for fecundity. No effect of rate of inbreeding depression was found for cold shock mortality, but this trait was measured with less precision than the other two. Natural selection acting on loci influencing larval viability and fecundity during the process of inbreeding could explain these results. Selection is expected to be more effective with slow rates of inbreeding because there are more generations and greater opportunity for selection to act before F=0.25 is reached. Selection intensities seem to have been different in the three traits measured. Selection was most intense for larval viability, less intense for fecundity and, perhaps, negligible at loci influencing cold shock mortality.     

Effect of Mating Structure on Variation in Linkage Disequilibrium

Measurement of linkage disequilibrium involves two sampling processes. First, there is the sampling of gametes in the population to form successive generations, and this generates disequilibrium dependent on the effective population size (N_e) and the mating structure. Second, there is sampling of a finite number (n) of individuals to estimate the population disequilibrium.——Two-locus descent measures are used to describe the mating system and are transformed to disequilibrium moments at the final sampling. Approximate eigenvectors for the transition matrix of descent measures are used to obtain formulae for the variance of the observed disequilibria as a function of N_e, mating structure, n, and linkage or recombination parameter.——The variance of disequilibrium is the same for monoecious populations with or without random selfing and for dioecious populations with random pairing for each progeny. With monogamy, the variance is slightly higher, the proportional difference being greater for unlinked loci.     

Sibship reconstruction demonstrates the extremely low effective population size of striped bass Morone saxatilis in the Santee–Cooper system, South Carolina, USA

For organisms with great fecundity and high mortality in early life stages, such as shellfish or fishes, the need to match reproductive activity with environmental conditions conducive to spawning, fertilization, larval development and recruitment may result in extreme variance in reproductive success among individuals. The main objective of this study was to investigate evidence of large variance in the reproductive success of the striped bass Morone saxatilis in the Santee–Cooper system, South Carolina, USA. Seven microsatellite loci were analysed in 603 recruits representing three yearly cohorts from 1992 to 1994, and a group analysis was performed to identify full-sib families. Large variance in reproductive success was detected, with a few large, full-sib families contributing disproportionately to each of the cohorts. The severity of sweepstakes reproductive success varied among cohorts depending on environmentally imposed mortality. Estimations of the effective number of breeders in these long-lived fish ranged from 24 in 1992 to 44 in 1994. Furthermore, the estimated genetic effective population size ( N _e = 93) is approximately four orders of magnitude lower than estimates of adult census size ( N  =   362 000). Furthermore, the presence of large full-sib families indicates that striped bass engage in pair mating in the wild. Heterogeneity in genetic composition was also observed among cohorts, suggesting that genetically different adults contribute to different cohorts and that chance rather than fitness variation determines reproductive success.     

Further Evidence for Selective Differences between Isoalleles in Drosophila

A number of separate strains of Drosophila pseudoobscura were inbred for 38 generations of brother-sister mating with forced heterozygosity for two alleles of either the octanol dehydrogenase or esterase-5 locus. Crosses were set up within each of these inbred lines such that simple mendelian ratios were expected, and eggs from these crosses were placed on media with additions of simple chemicals likely to interact with alleles of the two loci—octanol and ethanol for the ODH locus and tributyrin and triacetin for the E-5 locus. Similar crosses were set up involving parental flies with normally heterozygous genetic background as a control.—Significant deviations from mendelian expectation were observed in inbred E-5 flies grown on tributyrin, inbred ODH males grown on octanol, and inbred ODH females grown on ethanol. There was also a strong effect of octanol medium on males of one of the inbred E-5 lines, and a weak effect of tributyrin medium on ODH inbred females.—The probability that these results reflect interactions between these loci and the environment is assessed in the light of differences between the present results and those obtained at earlier stages of inbreeding.     

Two-locus,fourth-order gene frequency moments: Implications for the variance of squared linkage disequilibrium and the variance of homozygosity

Identity coefficients are used to construct a sufficient set of equations to determine the fourth-order moments of gene frequencies for two linked loci. This allows the variance of the expected squared linkage disequilibrium to be found. It is shown that the coefficient of variation is generally greater than one and if the mutation rate is small, the standard deviation is more than four times the size of the mean. This demonstrates that squared linkage disequilibrium is a highly variable quantity. The variance of homozygosity for a gene which consists of two sites can also be obtained. Recombination between these sites increases the variance of homozygosity, suggesting that intragenic recombination significantly changes all the expected moments of gene frequencies if 4Nμ > 1.0 and r > μ (where N is the population size, μ is the mutation rate of the gene to neutral alleles, and r is the recombination rate between two sites within the gene).     

Developmental Stability of DROSOPHILA MELANOGASTER under Artificial and Natural Selection in Constant and Fluctuating Environments

Populations of Drosophila melanogaster in constant 25° and fluctuating 20/29° environments showed increases in developmental stability, indicated by decreases in bilateral asymmetry of sterno-pleural chaeta number. In both environments, rates of decrease in asymmetry were greater under natural selection (control lines) than under artificial stabilizing selection. Overall mean asymmetry was greater in the fluctuating environment.—There was no evidence that decreased asymmetry was due to heterozygosity, and the decline in asymmetry was not explained by the decline in chaeta number in the lines under only natural selection. However, the decline was consistent with changes in total phenotypic variance and environmental variance.—The divergence between lines after 39 generations of selection was seen in differences in asymmetry and also in the genotype-environment interaction expressed in cross-culturing experiments.     

The Effect of Inbreeding on Competitive Male-Mating Ability in DROSOPHILA MELANOGASTER

The effect of full-sib inbreeding on competitive male-mating ability (CI♂) in Drosophila melanogaster was investigated in two experiments. In the first, five inbred lines (with reserves) were assessed up to 18 generations. Linear inbreeding depression, of 5.9% per 10% increase in homozygosity, was observed. In a second experiment, 21 inbred lines were tested after three generations of full-sib mating (without reserves), and the decline with inbreeding was more severe, the male competitive index (CI♂) decreasing by 10.7% per 10% increase in F. The difference between these results is attributed to natural selection acting on variation within the inbred lines in extent of homozygosity, which can arise because of the peculiarly strong influence of linkage in Drosophila. Furthermore, differentiation between the lines may have reflected this variation rather than the various effects of different alleles fixed.—These results imply that the genetic variation in male-mating ability is largely due to dominance (no epistasis was detected) and are consonant with the proposition that intermale sexual selection is a very important component of fitness in D. melanogaster . There was no evidence of a positive correlation between male body size and competitive mating ability.     

Gene segregation in induced tetraploid rainbow trout: genetic evidence of preferential pairing of homologous chromosomes

Gene segregation at six protein loci was analysed in progeny from tetraploid males and females obtained by suppression of first mitosis. The triploid full-sib families from five tetraploid males and the diploid gynogenetic lines from four tetraploid females were examined. The proportions of heterozygous gametes (0.83 on the average) were significantly higher than expected from tetrasomic inheritance (0.667) at all the loci studied. This was explained by preferential pairing of homologous chromosomes. The proportions of heterozygous gametes were significantly different between loci, but the variations were not correlated with the gene--centromere distances. Our results showed that, at least for one locus, the homozygous gametes mainly resulted from pairing of homologous chromosomes rather than from pairing of homologous chromosomes, quadrivalent formation, and chromatin exchanges between homologous chromosomes.     

The importance and type of non-additive genetic effects for growth in Eucalyptus globulus

The paper investigates the importance of additive and non-additive genetic variances for growth in Eucalyptus globulus (Tasmanian Blue Gum), based on a large collection of diameter growth data covering 40 sites and more than 4,200 genotypes, most of them cloned, and spanning three generations of breeding. The variance estimates were based on a model accounting for additive, full-sib family and clone within full-sib family terms. The results indicated a small amount of additive genetic variance for diameter ( [^(h)]² = 0.10 ) \left( {{{\widehat{h}}^2} = 0.10} \right) and although non-additive genetic variance was also small, it accounted for a significant proportion of the total genetic variance present, corresponding to 80% of the additive variance. The interpretation of these non-additive effects is difficult. The results suggest, however, a possible role of epistasis. The evidence for this came from a strong observed bias in additive variance when clone effects were removed from the model and a larger than expected variance due to full-sib families relative to the variance due to clones within family. The relatively large proportion of genetic variance for growth that seems to be due to non-additive genetic effects has obvious implications in the breeding and deployment options in eucalypts, and these are briefly discussed.     

Testing mate choice and overdominance at MH in natural families of Atlantic salmon Salmo salar

This study aimed to test mate choice and selection during early life stages on major histocompatibility (MH) genotype in natural families of Atlantic salmon Salmo salar spawners and juveniles, using nine microsatellites to reconstruct families, one microsatellite linked to an MH class I gene and one minisatellite linked to an MH class II gene. MH‐based mate choice was only detected for the class I locus on the first year, with lower expected heterozygosity in the offspring of actually mated pairs than predicted under random mating. The genotype frequencies of MH‐linked loci observed in the juveniles were compared with frequencies expected from Mendelian inheritance of parental alleles to detect selection during early life stages. No selection was detected on the locus linked to class I gene. For the locus linked to class II gene, observed heterozygosity was higher than expected in the first year and lower in the second year, suggesting overdominance and underdominance, respectively. Within family, juveniles' body size was linked to heterozygosity at the same locus, with longer heterozygotes in the first year and longer homozygotes in the second year. Selection therefore seems to differ from one locus to the other and from year to year.