Cause Of Inbreeding Depression Research Articles

Effect of inbreeding on pollen tube growth in diploid and tetraploid Chamerion angustifolium: Do polyploids mask mutational load in pollen?

Deleterious recessive mutations are an important determinant of fitness (mutational load) in the sporophytic phase of plants and a major cause of inbreeding depression; however, their role in gametophyte function is less well documented but may account for variation in pollen tube growth and siring ability, especially between diploid and polyploid plants, which can mask the load. We investigated the role of mutational load in pollen performance using the perennial polyploid Chamerion angustifolium by comparing tube growth of pollen, in styles and in growth medium, from inbred (selfed) and outbred diploids to that of inbred and outbred tetraploids. Pollen from tetraploids is expected to mask deleterious mutations more effectively in the outbred condition but reveal them after inbreeding. In contrast, gametophytes from diploids should express the same genetic load in inbred or outbred plants. Pollen tube growth measured in growth medium was highest in outbred tetraploids and generally lower in inbred than outbred plants. The effect of selfing was significant in pollen from tetraploids but not diploids. The differential effect of selfing was also evident in the proportion of pollen reaching the base of styles, but the ploidy × pollination interaction was not significant. Selfing also had a negative effect on sporophyte fitness but was greater in diploids than tetraploids. Pollen performance is influenced by the expression of mutational load, which is masked in polyploids. This effect may partly explain strong siring success of tetraploids in this species.

Examining the cause of high inbreeding depression: analysis of whole-genome sequence data in 28 selfed progeny of Eucalyptus grandis.

The genome-wide heterozygosity at 9590 genes, all heterozygous in a single Eucalyptus grandis parent tree, was examined in a group of 28 S1 offspring. Heterozygosity ranged from 52-79%, averaging 65.5%, much higher than the 50% expected under random segregation, supporting the occurrence of strong (47%) selection against homozygosity. The expected pattern of heterozygosity from theoretical calculations and simulations for recessive detrimentals (pseudo-overdominance) and intrinsic heterozygote advantage was examined and compared with that observed. The observed patterns are consistent with at least several detrimental loci with large effects on both parental chromosomes of the 11 pairs. It is likely that 100 or more genes, many with substantial effects on viability, are contributing to this inbreeding depression. Although our genome-wide analysis of nearly 10000 genes strongly suggested that pseudo-overdominance was responsible for the observed high inbreeding depression, heterozygote advantage could not be excluded. Finding inconvertible evidence of the cause of inbreeding depression still presents a difficult challenge. This study is the first theoretical examination of the genomic effect of inbreeding in a forest tree and provides an approach to analyze these data to determine the extent and cause of inbreeding depression across other plant genomes.

Candidate Transcriptomic Sources of Inbreeding Depression in Drosophila melanogaster

The genomic causes of inbreeding depression are poorly known. Several studies have found widespread transcriptomic alterations in inbred organisms, but it remains unclear which of these alterations are causes of the depression and which are mere responses to the ensuing physiological stress induced by increased homozygosity due to inbreeding. Attempting to differentiate causes from responses, we made a c-DNA microarray analysis of inbreeding depression in Drosophila melanogaster. The rationale of the experiment was that, while depression is a general phenomenon involving reductions in fitness in different inbred lines, its first genetic causes would be different for each inbred line, as they are expected to be caused by the fixation of rare deleterious genes. We took four sets of inbred sublines, each set descending from a different founding pair obtained from a large outbred stock, and compared the expression of the three most depressed sublines and the three least depressed sublines from each set. Many changes in expression were common to all sets, but fourteen genes, grouped in four expression clusters, showed strong set-specific changes, and were therefore possible candidates to be sources of the inbreeding depression observed.

Epigenetics as a new avenue for the role of inbreeding depression in evolutionary ecology

Epigenetics as a new avenue for the role of inbreeding depression in evolutionary ecology

Genome sequence and analysis of the tuber crop potato

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

Something Old and Something New: Wedding Recombinant Inbred Lines with Traditional Line Cross Analysis Increases Power to Describe Gene Interactions

In this paper we present a novel approach to quantifying genetic architecture that combines recombinant inbred lines (RIL) with line cross analysis (LCA). LCA is a method of quantifying directional genetic effects (i.e. summed effects of all loci) that differentiate two parental lines. Directional genetic effects are thought to be critical components of genetic architecture for the long term response to selection and as a cause of inbreeding depression. LCA typically begins with two inbred parental lines that are crossed to produce several generations such as F1, F2, and backcrosses to each parent. When a RIL population (founded from the same P1 and P2 as was used to found the line cross population) is added to the LCA, the sampling variance of several nonadditive genetic effect estimates is greatly reduced. Specifically, estimates of directional dominance, additive x additive, and dominance x dominance epistatic effects are reduced by 92%, 94%, and 56% respectively. The RIL population can be simultaneously used for QTL identification, thus uncovering the effects of specific loci or genomic regions as elements of genetic architecture. LCA and QTL mapping with RIL provide two qualitatively different measures of genetic architecture with the potential to overcome weaknesses of each approach alone. This approach provides cross-validation of the estimates of additive and additive x additive effects, much smaller confidence intervals on dominance, additive x additive and dominance x dominance estimates, qualitatively different measures of genetic architecture, and the potential when used together to balance the weaknesses of LCA or RIL QTL analyses when used alone.

The Functional Genomics of Inbreeding Depression: A New Approach to an Old Problem

The fitness consequences of inbreeding have attracted the attention of biologists since the time its harmful effects were first recognized by Charles Darwin. Although inbreeding depression has been a central theme in biological research for over a century, little is known about its underlying molecular basis. With the generation of vast amounts of DNA sequence information and the advent of microarrays we are now able to describe biological processes from a total genomic perspective. This article reviews the ways in which microarrays have advanced our understanding of the molecular basis of inbreeding depression, including our first look at the number of genes associated with inbreeding depression, which genes or functional classes of genes are responsible for the decrease in fitness associated with inbreeding, the underlying cause of inbreeding depression—overdominance or partially recessive deleterious alleles—and environmental influences on gene-expression patterns.

A major QTL affects temperature sensitive adult lethality and inbreeding depression in life span in Drosophila melanogaster

BackgroundThe study of inbreeding depression has major relevance for many disciplines, including conservation genetics and evolutionary biology. Still, the molecular genetic basis of this phenomenon remains poorly characterised, as knowledge on the mechanistic causes of inbreeding depression and the molecular properties of genes that give rise to or modulate its deleterious effects is lacking. These questions warrant the detailed study of genetic loci giving rise to inbreeding depression. However, the complex and polygenic nature of general inbreeding depression makes this a daunting task. Study of inbreeding effects in specific traits, such as age-specific mortality and life span, provide a good starting point, as a limited set of genes is expected to be involved.ResultsHere we report on a QTL mapping study on inbreeding related and temperature sensitive lethality in male Drosophila melanogaster. The inbreeding effect was expressed at moderately high temperature, and manifested itself as severe premature mortality in males, but not in females. We used a North Carolina crossing design 3 to estimate average dominance ratio and heritability. We found the genetic basis of the lethal effect to be relatively simple, being due mainly to a single recessive QTL on the left arm of chromosome 2. This locus colocalised with a QTL that conditioned variation in female life span, acting as an overdominant locus for this trait. Male life span was additionally affected by variation at the X-chromosome.ConclusionThis demonstrates that analysis of large conditional lethal effects is a viable strategy for delineating genes which are sensitive to inbreeding depression.

Inbreeding, inbreeding depression and extinction

Inbreeding is unavoidable in small, isolated populations and can cause substantial fitness reductions compared to outbred populations. This loss of fitness has been predicted to elevate extinction risk giving it substantial conservation significance. Inbreeding may result in reduced fitness for two reasons: an increased expression of deleterious recessive alleles (partial dominance hypothesis) or the loss of favourable heterozygote combinations (overdominance hypothesis). Because both these sources of inbreeding depression are dependent upon dominance variance, inbreeding depression is predicted to be greater in life history traits than in morphological traits. In this study we used replicate inbred and control lines of Drosophila simulans to address three questions:1) is inbreeding depression greater in life history than morphological traits? 2) which of the two hypotheses is the major underlying cause of inbreeding depression? 3) does inbreeding elevate population extinction risk? We found that inbreeding depression was significantly greater in life history traits compared to morphological traits, but were unable to find unequivocal support for either the overdominance or partial dominance hypotheses as the genetic basis of inbreeding depression. As predicted, inbred lines had a significantly greater extinction risk.

Inbreeding and competitive ability in the common shrew (Sorex araneus)

Common shrews (Sorex araneus) maintain a foraging territory for most of their immature life. Possessing a high-quality territory is vital for overwinter survival in the harsh boreal climate, and hence, competitive ability in territorial disputes is expected to be an important component of individual fitness. To test possible association between individual inbreeding and fitness, we used neutral arena trials to assess the competitive performance of young common shrews. The experiment involved pairs of individuals originating from small island populations, where breeding must often occur between related individuals, and from large outbred mainland populations. The percentage of neutral arena tests that an individual won was highly significantly explained by internal relatedness, a surrogate measure of individual inbreeding, measured using ten microsatellite markers. Body size, sex, learning, and population type (mainland vs island) made no significant contributions. Even a low level of individual inbreeding may lead to significant adverse consequences in multiple territorial contests, which may represent a significant cause of inbreeding depression in many wild vertebrate populations.

Inbreeding depression in fecundity and inbred line extinction in the bulb mite, Rhizoglyphus robini.

This study investigated the magnitude of inbreeding depression in fecundity, and whether the depression is purged during six generations of sib mating in the bulb mite, Rhizoglyphus robini. The progeny resulting from a single generation of brother-sister mating suffered significant inbreeding depression in fecundity. During the following six generations of continuous sib-mating, 58% lines were lost, 45% because of sterility and 13% because of preadult mortality. The lines were then outcrossed, and their inbreeding depression compared with that of the base population. The inbreeding depression for the outcrossed population was 0.15, and for the base population 0.19, but the difference was not significant. The lack of significant purging of inbreeding depression indicates that it was caused either by detrimental genes of small effect, or by the breaking down of overdominant relations between alleles. However, the large proportion of extinct lines points to the former mechanism as a predominant cause of inbreeding depression. Theory predicts that the probability of line extinction with inbreeding increases with its load of mutations. If phenotypic variation in fecundity was partly because of differences in numbers of mutations carried by individuals, the fecundity of the line founder could be expected to correlate with the probability that the line derived from it will survive long-term inbreeding. Indeed, fecundity of founder females was significantly associated with line survival, which suggests that line extinction rate may be used as a method to study individual mutational loads, for example, in studies of sexual selection.

Landscape structure, habitat fragmentation, and the ecology of insects

Landscape structure, habitat fragmentation, and the ecology of insects

Strategies to manage inbreeding accumulation in swine breeding company nucleus herds: Some case studies

Modern swine breeding is undergoing a series of changes that affect the underlying strategies for genetic improvement. Increased competition among fewer breeding companies requires rapid genetic improvement to maintain competitive advantage. The result is intense selection pressure within swine industry nucleus populations. Selection pressure is enhanced through the use of artificial insemination, embryo transfer, and, potentially, marker-assisted selection. This increased selection pressure raises concerns due to the more rapid accumulation of inbreeding within these populations. The current strategies used to control the accumulation of inbreeding are somewhat simplistic. The methods often include arbitrary restrictions on the percentage of sows mated to a single sire, the number of sires retained from a full and half-sib family, the avoidance of matings between closely related individuals, and elimination of families presumed to be segregating for alleles with deleterious effects on fitness. As demonstrated by classic genetic theory, when the previously listed methods to minimize inbreeding are used, inbreeding is delayed, but it is inevitably accumulated within nucleus herds. The rate of accumulation typically is between 0.3 and 0.6% per annum. Composite lines addressing specific market needs, particularly for terminal sires, may offer short-term solutions for nucleus level inbreeding. Most parent and terminal products are produced from line crosses wherein inbreeding is eliminated in the resulting progeny. Understanding the causes of inbreeding depression continues to be important in order to improve the performance of purelines in multiplication, leading to more efficient transfer of genetic improvement.

THE ROLE OF GENES OF LARGE EFFECT ON INBREEDING DEPRESSION IN MIMULUS GUTTATUS.

Severe inbreeding depression is routinely observed in outcrossing species. If inbreeding load is due largely to deleterious alleles of large effect, such as recessive lethals or steriles, then most of it is expected to be purged during brief periods of inbreeding. In contrast, if inbreeding depression is due to the cumulative effects of many deleterious alleles of small effect, then it will be maintained in the face of periodic inbreeding. Whether or not inbreeding depression can be purged with inbreeding in the short term has important implications for the evolution of mating systems and the probability that a small population will go extinct. In this paper I evaluate the extent to which the tremendous inbreeding load in a primarily outcrossing population of the wildflower, Mimulus guttatus, is due to alleles of large effect. To do this, I first constructed a large outbred "ancestral" population by randomly mating plants collected as seeds from a natural population. From this population I formed 1200 lines that were maintained by self-fertilization and single seedling descent: after five generations of selling, 335 lines had survived the inbreeding process. Selection during the line formation is expected to have largely purged alleles of large effect from the collection of highly inbred lines. Because alleles with minor effects on fitness should have been effectively neutral, the inbreeding depression due to this class of genes should have been unchanged. The inbred lines were intercrossed to form a large, outcrossed "purged" population. Finally, I estimated the fitness of outbred and selfed progeny from the ancestral and purged populations to determine the contribution of major deleterious alleles on inbreeding depression. I found that although the average fitness of the outcrossed progeny nearly doubled following purging, the limited decline in inbreeding depression and limited increase in inbred fitness indicates that alleles of large effect are not the principle cause of inbreeding depression in this population. In aggregate, the data suggest that lethals and steriles make a minority contribution to inbreeding depression and that the increased outbred fitness is due primarily to adaptation to greenhouse conditions.

The genetic basis of inbreeding depression.

Data on the effects of inbreeding on fitness components are reviewed in the light of population genetic models of the possible genetic causes of inbreeding depression. Deleterious mutations probably play a major role in causing inbreeding depression. Putting together the different kinds of quantitative genetic data, it is difficult to account for the very large effects of inbreeding on fitness in Drosophila and outcrossing plants without a significant contribution from variability maintained by selection. Overdominant effects of alleles on fitness components seem not to be important in most cases. Recessive or partially recessive deleterious effects of alleles, some maintained by mutation pressure and some by balancing selection, thus seem to be the most important source of inbreeding depression. Possible experimental approaches to resolving outstanding questions are discussed.

EFFECTS OF DIFFERENT LEVELS OF INBREEDING ON PROGENY FITNESS IN PLANTAGO CORONOPUS.

Inbreeding depression (δ) is a major selective force favoring outcrossing in flowering plants. Many phenotypic and genetic models of the evolution of selfing conclude that complete outcrossing should evolve whenever inbreeding depression is greater than one-half, otherwise selfing should evolve. Recent theoretical work, however, has challenged this view and emphasized (1) the importance of variation in inbreeding depression among individuals within a population; and (2) the nature of gene action between deleterious mutations at different loci (epistasis) as important determinants for the evolution of plant mating systems. The focus of this study was to examine the maintenance of inbreeding depression and the relationship between inbreeding level and inbreeding depression at both the population and the individual level in one population of the partially self-fertilizing plant Plantago coronopus (L.). Maternal plants, randomly selected from an area of about 50 m2 in a natural population, were used to establish lines with expected inbreeding coefficients (f) of 0, 0.25, 0.50, 0.75, and 0.875. Inbreeding depression was estimated both in the greenhouse and at the site of origin of the maternal plants by comparing growth, survival, flowering, and seed production of the progeny with different inbreeding coefficients. No significant inbreeding depression for these fitness traits was detected in the greenhouse after 16 weeks. This was in strong contrast to the field, where the traits all displayed significant inbreeding depression and declined with increased inbreeding. The results were consistent with the view that mutation to mildly deleterious alleles is the primary cause of inbreeding depression. At the family level, significantly different maternal line responses (maternal parent × inbreeding level interaction) provide a mechanism for the invasion of a selfing variant into the population through any maternal line exhibiting purging of its genetic load. At the population level, evidence for synergistic epistasis was detected for the probability of flowering, but not for total seed production. At the family level, however, a significant interaction between inbreeding level and maternal families for both traits was observed, indicating that epistasis could play a role in the expression of inbreeding depression among maternal lines.

THE RELATIONSHIP BETWEEN INBREEDING DEPRESSION AND PRIOR INBREEDING AMONG POPULATIONS OF FOUR MIMULUS TAXA.

When recessive mutations are the primary cause of inbreeding depression, a negative relationship between the levels of prior inbreeding and inbreeding depression is expected. We tested this prediction using 15 populations chosen a priori to represent a wide range of prior inbreeding among four closely related taxa of the Mimulus guttatus species complex. Artificially selfed and outcrossed progeny were grown under controlled growth-chamber conditions, and inbreeding depression was estimated for each population as one minus the ratio of the fitness of selfed to outcrossed progeny. Estimates of inbreeding depression varied from 0% to 68% among populations. Inbreeding coefficients, estimated from electrophoretic assay of field-collected progenies, ranged from 0.02 to 0.76. All five fitness traits displayed a negative association between inbreeding depression and the inbreeding coefficient, but only height showed a statistically significant correlation. Inbreeding depression was also not correlated with the level of genetic variability. In addition, populations with similar levels of prior inbreeding showed significant differences of inbreeding depression, whereas populations with different levels of prior inbreeding showed similar inbreeding depression. Within populations, inbreeding depression did not differ between progeny selfed one versus two generations. Our results are weakly consistent with the recessive mutation model of inbreeding depression, but suggest that additional factors, including genotype-by-environment interaction and complex modes of inheritance, may influence the expression of inbreeding depression.

Gibberellins and Heterosis in Maize: Quantitative Relationships

To investigate the possible relationship between gibberellins (GA) and heterosis, a diailel from four elite maize, Zea mays L., inbreds (A632, B73, CH807 [from Mo17], and CO109) was studied under controlled environment conditions. Heterosis for plant growth was substantial at 25/15 °C (day/night), as hybrid seedlings emerged more rapidly, were taller, had heavier shoots, and larger leaf areas than the parental inbreds. Gibberellic acid (GA3) at 0.1, 0.5, or 1.0 mg per plant was pipetted into the leaf whorls of 14‐d‐old seedlings. The exogenous GA3 promoted ligule and total height in all genotypes, but the inbreds were maximally influenced. Consequently, potence ratios, representing the overall degree of dominance, were reduced from an average of 7.7 to 1.7 following GA3 application, indicating decreased heterosis. In an experiment at 15 °C, imbibition of seeds in GA3 accelerated germination and seedling growth, particularly shoot elongation of the parental inbreds. Endogenous concentrations of GA1 and GA19 were determined by gas‐chromatography‐selected ion monitoring using [2H]GAs as quantitive internal standards. Highly significant regressions of height, leaf area, relative growth rate, and height increment versus the log of GA concentration were observed. These results are consistent with the theory that GA are one factor involved in the regulation of heterosis of shoot growth in maize, a theory that suggests that a partial deficiency in endogenous GA in maize inbreds limits their growth, and is a contributing cause of inbreeding depression.

On the evolution of genetic incompatibility systems. IV. Modification of response to an existing antigen polymorphism under partial selfing

A 2-locus model of the evolution of self-incompatibility in a population practicing partial selling is presented. An allele is introduced at a modifier locus which influences the strength of the rejection reaction expressed by the style in response to antigens recognized in pollen. Two causes of inbreeding depression are investigated. First, offspring viability depends solely on the source (self or non-self) of the fertilizing pollen. Second, offspring viability declines with the expression of recessive deleterious alleles, segregating at a third (disease) locus, which exhibit an imperfect association with antigen alleles. Evolutionary changes occurring at the disease locus are not considered in this study. The condition under which a modifier allele that intensifies the incompatibility reaction increases when rare depends upon the number of antigens, the frequency of recessive deleterious alleles at the disease locus, and the level of association between the antigen locus and the disease locus. It is the improvement of viability among offspring derived by outcrossing, rather than the prevention of self-fertilization, that may represent the primary evolutionary function of genetic incompatibility systems.

Gibberellins: A Phytohormonal Basis for Heterosis in Maize

Four commercially important maize parental inbreds and their 12 F(1) hybrids were studied to investigate the role of the phytohormone gibberellin (GA) in the regulation of heterosis (hybrid vigor). All hybrids grew faster than any inbred. In contrast, all inbreds showed a greater promotion of shoot growth after the exogenous application of GA(3). Concentrations of endogenous GA(1), the biological effector for shoot growth in maize, and GA(19), a precursor of GA(1), were measured in apical meristematic shoot cylinders for three of the inbreds and their hybrids by gas chromatography-mass spectrometry with selected ion monitoring; deuterated GAs were used as quantitative internal standards. In 34 of 36 comparisons, hybrids contained higher concentrations of endogenous GAs than their parental inbreds. Preferential growth acceleration of the inbreds by exogenous GA(3) indicates that a deficiency of endogenous GA limits the growth of the inbreds and is thus a cause of inbreeding depression. Conversely, the increased endogenous concentration of GA in the hybrids could provide a phytohormonal basis for heterosis for shoot growth.