Evaluation of major genetic loci contributing to inbreeding depression for survival and early growth in a selfed family of Pinus taeda

The magnitude of fitness effects at genetic loci causing inbreeding depression at various life stages has been an important question in plant evolution. We used genetic mapping in a selfed family of loblolly pine (Pinus taeda L.) to gain insights on inbreeding depression for early growth and viability. Two quantitative trait loci (QTLs) were identified that explain much of the phenotypic variation in height growth through age 3 and may account for more than 13% inbreeding depression in this family. One of these QTLs maps to the location of cad-nl, a lignin biosynthesis mutation. Both QTLs show evidence of overdominance, although evidence for true versus pseudo-overdominance is inconclusive. Evidence of directional dominance for height growth was noted throughout the genome, suggesting that additional loci may contribute to inbreeding depression. A chlorophyll-deficiency mutation, spf did not appear to be associated with growth effects, but had significant effects on survival through age 3. Previously identified embryonic viability loci had little or no overall effect on germination, survival, or growth. Our results challenge, at least in part, the prevailing hypothesis that inbreeding depression for growth is due to alleles of small effect. However, our data support predictions that loci affecting inbreeding depression are largely stage specific.     

Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield

To understand the genetic basis of inbreeding depression and heterosis in rice, main-effect and epistatic QTL associated with inbreeding depression and heterosis for grain yield and biomass in five related rice mapping populations were investigated using a complete RFLP linkage map of 182 markers, replicated phenotyping experiments, and the mixed model approach. The mapping populations included 254 F(10) recombinant inbred lines derived from a cross between Lemont (japonica) and Teqing (indica) and two BC and two testcross hybrid populations derived from crosses between the RILs and their parents plus two testers (Zhong 413 and IR64). For both BY and GY, there was significant inbreeding depression detected in the RI population and a high level of heterosis in each of the BC and testcross hybrid populations. The mean performance of the BC or testcross hybrids was largely determined by their heterosis measurements. The hybrid breakdown (part of inbreeding depression) values of individual RILs were negatively associated with the heterosis measurements of their BC or testcross hybrids, indicating the partial genetic overlap of genes causing hybrid breakdown and heterosis in rice. A large number of epistatic QTL pairs and a few main-effect QTL were identified, which were responsible for >65% of the phenotypic variation of BY and GY in each of the populations with the former explaining a much greater portion of the variation. Two conclusions concerning the loci associated with inbreeding depression and heterosis in rice were reached from our results. First, most QTL associated with inbreeding depression and heterosis in rice appeared to be involved in epistasis. Second, most ( approximately 90%) QTL contributing to heterosis appeared to be overdominant. These observations tend to implicate epistasis and overdominance, rather than dominance, as the major genetic basis of heterosis in rice. The implications of our results in rice evolution and improvement are discussed.     

Whole-genome characterization of embryonic stage inbreeding depression in a selfed loblolly pine family

Inbreeding depression is important in the evolution of plant populations and mating systems. Previous studies have suggested that early-acting inbreeding depression in plants is primarily due to lethal alleles and possibly epistatic interactions. Recent advances in molecular markers now make genetic mapping a powerful tool to study the genetic architecture of inbreeding depression. We describe a genome-wide evaluation of embryonic viability loci in a selfed family of loblolly pine (Pinus taeda L.), using data from AFLP markers from an essentially complete genome map. Locus positions and effects were estimated from segregation ratios using a maximum-likelihood interval mapping procedure. We identified 19 loci showing moderately deleterious to lethal embryonic effects. These loci account for >13 lethal equivalents, greater than the average of 8.5 lethal equivalents reported for loblolly pine. Viability alleles show predominantly recessive action, although potential overdominance occurs at 3 loci. We found no evidence for epistasis in the distribution of pairwise marker correlations or in the regression of fitness on the number of markers linked to deleterious alleles. The predominant role of semilethal alleles in embryonic inbreeding depression has implications for the evolution of isolated populations and for genetic conservation and breeding programs in conifers.     

A major QTL affects temperature sensitive adult lethality and inbreeding depression in life span in <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Background  

The 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.     

Recent approaches into the genetic basis of inbreeding depression in plants

Predictions for the evolution of mating systems and genetic load vary, depending on the genetic basis of inbreeding depression (dominance versus overdominance, epistasis and the relative frequencies of genes of large and small effect). A distinction between the dominance and overdominance hypotheses is that deleterious recessive mutations should be purged in inbreeding populations. Comparative studies of populations differing in their level of inbreeding and experimental approaches that allow selection among inbred lines support this prediction. More direct biometric approaches provide strong support for the importance of partly recessive deleterious alleles. Investigators using molecular markers to study quantitative trait loci (QTL) often find support for overdominance, though pseudo-overdominance (deleterious alleles linked in repulsion) may bias this perception. QTL and biometric studies of inbred lines often find evidence for epistasis, which may also contribute to the perception of overdominance, though this may be because of the divergent lines initially crossed in QTL studies. Studies of marker segregation distortion commonly uncover genes of major effect on viability, but these have only minor contributions to inbreeding depression. Although considerable progress has been made in understanding the genetic basis of inbreeding depression, we feel that all three aspects merit more study in natural plant populations.     

Genetic diversity at neutral and adaptive loci determines individual fitness in a long-lived territorial bird

There is compelling evidence about the manifest effects of inbreeding depression on individual fitness and populations' risk of extinction. The majority of studies addressing inbreeding depression on wild populations are generally based on indirect measures of inbreeding using neutral markers. However, the study of functional loci, such as genes of the major histocompatibility complex (MHC), is highly recommended. MHC genes constitute an essential component of the immune system of individuals, which is directly related to individual fitness and survival. In this study, we analyse heterozygosity fitness correlations of neutral and adaptive genetic variation (22 microsatellite loci and two loci of the MHC class II, respectively) with the age of recruitment and breeding success of a decimated and geographically isolated population of a long-lived territorial vulture. Our results indicate a negative correlation between neutral genetic diversity and age of recruitment, suggesting that inbreeding may be delaying reproduction. We also found a positive correlation between functional (MHC) genetic diversity and breeding success, together with a specific positive effect of the most frequent pair of cosegregating MHC alleles in the population. Globally, our findings demonstrate that genetic depauperation in small populations has a negative impact on the individual fitness, thus increasing the populations' extinction risk.     

An association between a floral trait and inbreeding depression

Abstract.— Inbreeding depression is a general phenomenon that is well documented in many plants and animals. Furthermore, it is generally considered to be the driving force behind mating-system evolution. Traditionally, the focus has been on the mean level of inbreeding depression in populations. However, more recently, the variation in inbreeding depression among individuals within populations has been shown to be influential in mating-system evolution. One set of theories predicts that genetic associations will develop between a mating-system locus and loci causing inbreeding depression, whereas another suggests either that no such association will occur or that it will be difficult to detect empirically. Here, we focus on variation in inbreeding depression among individuals and present empirical evidence of a genetic association between genes causing inbreeding depression and a floral trait influencing the mating system (i.e., selfing rate). We found a positive association between inbreeding depression and herkogamy (the degree to which the stigma and anthers are separated) in an annual plant, Gilia achilleifolia . These results are consistent with theory predicting that an individual's history of inbreeding will affect its level of inbreeding depression and highlight the potential importance of genetic associations between selfing-modifier traits and viability in mating-system evolution.     

Marker-based inferences about fecundity genes contributing to inbreeding depression in Mimulus guttatus.

Eight unlinked isozyme loci were used as genetic markers to characterize fecundity genes contributing to inbreeding depression in two selfed progeny arrays of Mimulus guttatus. Five fecundity traits were measured. Six of eight marked chromosomal segments were significantly associated with the expression of these traits. The number of genes detected for five traits in two progeny arrays varied, with an average of 2.8 genes per trait. Individual segments explained 1.44-9.29%, and together accounted for 3.85-11.32%, of phenotypic variation. Of 20 significant associations, 10 could be interpreted as exhibiting partial dominance, 7 overdominance, 3 partial recessivity, and 0 underdominance. Significant pairwise epistasis was rare. The results of this study suggest that inbreeding depression is caused by many deleterious genes of relatively small, partially dominant effects.     

Anther-stigma separation is associated with inbreeding depression in Datura stramonium,a predominantly self-fertilizing annual

Abstract.— Genetically based variation in outcrossing rate generates lineages within populations that differ in their history of inbreeding. According to some models, mating-system modifiers in such populations will demonstrate both linkage and identity disequilibrium with fitness loci, resulting in lineage-specific inbreeding depression. Other models assert that differences among families in levels of inbreeding depression are mainly attributable to random accumulation of genetic load, unrelated to variation at mating-system loci. We measured female reproductive success of selfed and outcrossed progeny from naturally occurring lineages of Datura stramonium , a predominantly self-fertilizing annual weed that has heritable variation in stigma-anther separation, a trait that influences selfing rates. Progeny from inbred lineages (as identified by high degree of anther-stigma overlap) showed equal levels of seed production, regardless of cross type. Progeny from mixed lineages (as identified by relatively high separation between anthers and stigma) showed moderate levels of inbreeding depression. We found a significant correlation between anther-stigma separation and relative fitness of selfed and outcrossed progeny, suggesting that family-level inbreeding depression may be related to differences among lineages in inbreeding history in this population. Negative inbreeding depression in putatively inbred lineages may be due in part to additive effects or to epistatic interactions among loci.     

Individual Variation in Inbreeding Depression: The Roles of Inbreeding History and Mutation

We use mutation-selection recursion models to evaluate the relative contributions of mutation and inbreeding history to variation among individuals in inbreeding depression and the ability of experiments to detect associations between individual inbreeding depression and mating system genotypes within populations. Poisson mutation to deleterious additive or recessive alleles generally produces far more variation among individuals in inbreeding depression than variation in history of inbreeding, regardless of selfing rate. Moreover, variation in inbreeding depression can be higher in a completely outcrossing or selfing population than in a mixed-mating population. In an initially random mating population, the spread of a dominant selfing modifier with no pleiotropic effects on male outcross success causes a measurable increase in inbreeding depression variation if its selfing rate is large and inbreeding depression is caused by recessive lethals. This increase is observable during a short period as the modifier spreads rapidly to fixation. If the modifier alters selfing rate only slightly, it fails to spread or causes no measurable increase in inbreeding depression variance. These results suggest that genetic associations between mating loci and inbreeding depression loci could be difficult to demonstrate within populations and observable only transiently during rapid evolution to a substantially new selfing rate.     

Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components

The genetic basis underlying inbreeding depression and heterosis for three grain yield components of rice was investigated in five interrelated mapping populations using a complete RFLP linkage map, replicated phenotyping, and the mixed model approach. The populations included 254 F(10) recombinant inbred lines (RILs) derived from a cross between Lemont (japonica) and Teqing (indica), two backcross (BC) and two testcross populations derived from crosses between the RILs and the parents plus two testers (Zhong413 and IR64). For the yield components, the RILs showed significant inbreeding depression and hybrid breakdown, and the BC and testcross populations showed high levels of heterosis. The average performance of the BC or testcross hybrids was largely determined by heterosis. The inbreeding depression values of individual RILs were negatively associated with the heterosis measurements of the BC or testcross hybrids. We identified many epistatic QTL pairs and a few main-effect QTL responsible for >65% of the phenotypic variation of the yield components in each of the populations. Most epistasis occurred between complementary loci, suggesting that grain yield components were associated more with multilocus genotypes than with specific alleles at individual loci. Overdominance was also an important property of most loci associated with heterosis, particularly for panicles per plant and grains per panicle. Two independent groups of genes appeared to affect grain weight: one showing primarily nonadditive gene action explained 62.1% of the heterotic variation of the trait, and the other exhibiting only additive gene action accounted for 28.1% of the total trait variation of the F(1) mean values. We found no evidence suggesting that pseudo-overdominance from the repulsive linkage of completely or partially dominant QTL for yield components resulted in the overdominant QTL for grain yield. Pronounced overdominance resulting from epistasis expressed by multilocus genotypes appeared to explain the long-standing dilemma of how inbreeding depression could arise from overdominant genes.     

Sensitive males: inbreeding depression in an endangered bird

Attempts to conserve threatened species by establishing new populations via reintroduction are controversial. Theory predicts that genetic bottlenecks result in increased mating between relatives and inbreeding depression. However, few studies of wild sourced reintroductions have carefully examined these genetic consequences. Our study assesses inbreeding and inbreeding depression in a free-living reintroduced population of an endangered New Zealand bird, the hihi (Notiomystis cincta). Using molecular sexing and marker-based inbreeding coefficients estimated from 19 autosomal microsatellite loci, we show that (i) inbreeding depresses offspring survival, (ii) male embryos are more inbred on average than female embryos, (iii) the effect of inbreeding depression is male-biased and (iv) this population has a substantial genetic load. Male susceptibility to inbreeding during embryo and nestling development may be due to size dimorphism, resulting in faster growth rates and more stressful development for male embryos and nestlings compared with females. This work highlights the effects of inbreeding at early life-history stages and the repercussions for the long-term population viability of threatened species.     

A new theory for the evolution of polyandry as a means of inbreeding avoidance

We propose a novel theory for the evolution of polyandry driven by genetic benefits to females whose offspring interbreed. In species with an ecology characterized by frequent colonization of new habitat patches, consanguineous matings may be common during the early stages of colonization, but genetic diversity may grow as new colonizers arrive. We show that with levels of inbreeding depression similar to those found in predominantly inbreeding populations, a polyandrous female can benefit her descendants since matings among her brood are mainly between half siblings rather than full siblings. We examine the invasion by a polyandrous phenotype using explicit genetic models in which costs of inbreeding are themselves subject to selection. In common with other models of inbreeding, we find that underlying high levels of inbreeding tend to purge deleterious recessive alleles, and hence these are unlikely to maintain sufficient inbreeding depression to favour polyandry. However, if costs of inbreeding are due to overdominance, biologically realistic levels of inbreeding depression result in genetic benefits large enough to favour polyandry provided it is not too costly. The potential significance of polyandry as a mechanism to reduce inbreeding in grandchildren will depend upon the genetic basis of inbreeding depression in natural, inbreeding populations.     

Inbreeding depression due to overdominance in partially self-fertilizing plant populations

The effect of the rate of partial self-fertilization and viability selection on the magnitude of inbreeding depression was investigated for the overdominance genetic model. The influence of these factors was determined for populations with equilibrium genotypic frequencies. Inbreeding depression was measured as the normalized disadvantage in mean viability of selfed progeny as compared to outcrossed progeny. When caused by symmetric homozygous disadvantage at a single locus it is shown always to be less than one-third. Moreover, for fixed rates of self-fertilization, its maximum value is found at intermediate levels of homozygous disadvantage. As the rate of self-fertilization increases, inbreeding depression increases and the homozygote viability that results in maximum depression tends toward one-half the heterozygote viability. Symmetric selection against homozygotes at multiple loci can lead to substantially higher values than selection at a single-locus. As the number of independent loci involved increases, inbreeding depression can reach high levels even though the selfing rate is low. Viability distributions for progenies produced from both random mating and self-fertilization were derived for the case of symmetric selection at independently assorting multiple loci. Distributions of viabilities in progenies resulting from mixtures of selfing and outcrossing were shown to be bimodal when inbreeding depression is high.     

BREEDING SYSTEM IN LIMNANTHES ALBA: SEVERAL ALTERNATIVE MEASURES

Seven populations of Limnanthes alba were described for their rates of outbreeding, amount of genetic variability, and response to enforced selfing in terms of inbreeding depression. Outcrossing rates, estimated by using two genetic marker loci, varied between 43 and 97%. Heterozygosity level was found to be in the range of 12 and 27 percent, whereas percent polymorphic loci varied twofold (between 29 and 57%) among populations. Inbreeding depression was found to be significant in four of seven populations for number of flowers per plant, plant height, and seed set per flower. There was no association between observed patterns of inbreeding response and predictions from the genetic variation parameters, so that variations in outbreeding rates and consequences need a detailed quantitative verification. In populations showing no inbreeding depression, autofertility seemed to increase with inbreeding (presumably accompanied by natural selection) and to be under genetic control. This is relevant to the hypothesis on the origin of inbreeders under conditions lacking pollinators, e.g., colonization of marginal areas.     

Interval Mapping of Viability Loci Causing Heterosis in Arabidopsis

The genetic basis of heterosis has implications for many problems in genetics and evolution. Heterosis and inbreeding depression affect human genetic diseases, maintenance of genetic variation, evolution of breeding systems, agricultural productivity, and conservation biology. Despite decades of theoretical and empirical studies, the genetic basis of heterosis has remained unclear. I mapped viability loci contributing to heterosis in Arabidopsis. An overdominant factor with large effects on viability mapped to a short interval on chromosome I. Homozygotes had 50% lower viability than heterozygotes in this chromosomal region. Statistical analysis of viability data in this cross indicates that observed viability heterosis is better explained by functional overdominance than by pseudo-overdominance. Overdominance sometimes may be an important cause of hybrid vigor, especially in habitually inbreeding species. Finally, I developed a maximum likelihood interval mapping procedure that can be used to examine chromosomal regions showing segregation distortion or viability selection.     

Rapid multipoint linkage analysis of recessive traits in nuclear families, including homozygosity mapping.

Homozygosity mapping is a powerful strategy for mapping rare recessive traits in children of consanguineous marriages. Practical applications of this strategy are currently limited by the inability of conventional linkage analysis software to compute, in reasonable time, multipoint LOD scores for pedigrees with inbreeding loops. We have developed a new algorithm for rapid multipoint likelihood calculations in small pedigrees, including those with inbreeding loops. The running time of the algorithm grows, at most, linearly with the number of loci considered simultaneously. The running time is not sensitive to the presence of inbreeding loops, missing genotype information, and highly polymorphic loci. We have incorporated this algorithm into a software package, MAPMAKER/HOMOZ, that allows very rapid multipoint mapping of disease genes in nuclear families, including homozygosity mapping. Multipoint analysis with dozens of markers can be carried out in minutes on a personal workstation.     

Environment-dependent inbreeding depression: its ecological and evolutionary significance

Inbreeding depression is a major evolutionary and ecological force that influences population dynamics and the evolution of inbreeding-avoidance traits such as mating systems and dispersal. There is now compelling evidence that inbreeding depression is environment-dependent. Here, we discuss ecological and evolutionary consequences of environment-dependent inbreeding depression. The environmental dependence of inbreeding depression may be caused by environment-dependent phenotypic expression, environment-dependent dominance, and environment-dependent natural selection. The existence of environment-dependent inbreeding depression challenges classical models of inbreeding as caused by unconditionally deleterious alleles, and suggests that balancing selection may shape inbreeding depression in natural populations; loci associated with inbreeding depression in some environments may even contribute to adaptation to others. Environment-dependent inbreeding depression also has important, often neglected, ecological and evolutionary consequences: it can influence the demography of marginal or colonizing populations and alter adaptive optima of mating systems, dispersal, and their associated traits. Incorporating the environmental dependence of inbreeding depression into theoretical models and empirical studies is necessary for understanding the genetic and ecological basis of inbreeding depression and its consequences in natural populations.     

QTL mapping of inbreeding-related cold sensitivity and conditional lethality in Drosophila melanogaster

Inbreeding depression is a central theme within genetics, and is of specific interest for researchers within evolutionary and conservation genetics and animal and plant breeding. Inbreeding effects are thought to be caused by the joint expression of conditional and unconditional deleterious alleles. Whenever the expression of deleterious alleles is conditional, this can result in extreme environmental sensitivity in certain inbred lineages. Analysis of conditional lethal effects can reveal some of the loci that are sensitive to inbreeding. We performed a QTL (quantitative trait locus) mapping study of inbreeding-related and conditionally expressed lethality in Drosophila melanogaster. The lethal effect was triggered by exposure to a cold shock. We used a North Carolina crossing Design 3 to establish the mapping population, as well as to estimate the average dominance ratio and heritability. We found two QTL on the major autosomes carrying recessive lethals that caused male mortality, one of which also affected female mortality. More detailed study of these loci will provide information on the mechanistic basis and environmental sensitivity of inbreeding depression.     

Consequences of life history for inbreeding depression and mating system evolution in plants

Many plants are perennial, but most studies of inbreeding depression and mating system evolution focus on annuals. This paper extends a population genetic model of inbreeding depression due to recessive deleterious mutations to perennials. The model incorporates life history and mating system variation, and multiplicative selection across many genetic loci. In the absence of substantial mitotic mutation, perennials have higher mean fitness and lower, or even negative, inbreeding depression than annuals with the same mating system. As in annuals, self fertilization exposes deleterious recessive mutations to selection, increasing mean fitness and decreasing inbreeding depression. Including mitotic mutation decreases mean fitness while increasing inbreeding depression. Perenniality introduces a kind of selective sieve, such that strongly recessive mutations contribute disproportionately to mean fitness and inbreeding depression. In the presence of high mitotic mutation, this selective sieve may provide a mechanistic basis for high inbreeding depression observed in some long lived perennials. Without substantial mitotic mutation, it is difficult to reconcile genetically based models of inbreeding depression with the empirical generalization that perennials outcross while related annuals self fertilize.