Environmental variation influences the magnitude of inbreeding depression in Cucurbita pepo ssp. texana (Cucurbitaceae)

Epigenetic Changes Occurring in Plant Inbreeding

Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.

Review: Plant eco-evolutionary responses to climate change: Emerging directions

Contemporary climate change is exposing plant populations to novel combinations of temperatures, drought stress, [CO₂] and other abiotic and biotic conditions. These changes are rapidly disrupting the evolutionary dynamics of plants. Despite the multifactorial nature of climate change, most studies typically manipulate only one climatic factor. In this opinion piece, we explore how climate change factors interact with each other and with biotic pressures to alter evolutionary processes. We evaluate the ramifications of climate change across life history stages,and examine how mating system variation influences population persistence under rapid environmental change. Furthermore, we discuss how spatial and temporal mismatches between plants and their mutualists and antagonists could affect adaptive responses to climate change. For example, plant-virus interactions vary from highly pathogenic to mildly facilitative, and are partly mediated by temperature, moisture availability and [CO₂]. Will host plants exposed to novel, stressful abiotic conditions be more susceptible to viral pathogens? Finally, we propose novel experimental approaches that could illuminate how plants will cope with unprecedented global change, such as resurrection studies combined with experimental evolution, genomics or epigenetics.

Transgenerational impacts of herbivory and inbreeding on reproductive output in Solanum carolinense

PREMISE

Plant maternal effects on offspring phenotypes are well documented. However, little is known about how herbivory on maternal plants affects offspring fitness. Furthermore, while inbreeding is known to reduce plant reproductive output, previous studies have not explored whether and how such effects may extend across generations. Here, we addressed the transgenerational consequences of herbivory and maternal plant inbreeding on the reproduction of Solanum carolinense offspring.

METHODS

Manduca sexta caterpillars were used to inflict weekly damage on inbred and outbred S. carolinense maternal plants. Cross-pollinations were performed by hand to produce seed from herbivore-damaged outbred plants, herbivore-damaged inbred plants, undamaged outbred plants, and undamaged inbred plants. The resulting seeds were grown in the greenhouse to assess emergence rate and flower production in the absence of herbivores. We also grew offspring in the field to examine reproductive output under natural conditions.

RESULTS

We found transgenerational effects of herbivory and maternal plant inbreeding on seedling emergence and reproductive output. Offspring of herbivore-damaged plants had greater emergence, flowered earlier, and produced more flowers and seeds than offspring of undamaged plants. Offspring of outbred maternal plants also had greater seedling emergence and reproductive output than offspring of inbred maternal plants, even though all offspring were outbred. Moreover, the effects of maternal plant inbreeding were more severe when plant offspring were grown in field conditions.

CONCLUSIONS

This study demonstrates that both herbivory and inbreeding have fitness consequences that extend across generations even in outbred progeny.

Responses of a legume to inbreeding and the intensity of novel and familiar stresses

It is often assumed that the negative effects of inbreeding on fitness (inbreeding depression, ID) are particularly strong under stressful conditions. However, ID may be relatively mild under types of stress that plant populations have experienced for a long time, because environment-specific deleterious alleles may already have been purged. We examined the performance of open- and self-pollinated progeny of the short-lived calcareous grassland plant Anthyllis vulneraria under three intensities of each of five types of stress. Drought, nutrient deficiency, and defoliation were chosen as stresses typical for the habitat of origin, while shade and waterlogging were expected to be novel, unfamiliar stresses for A. vulneraria. The stresses reduced plant biomass by up to 91%, and the responses of the plants were mostly in line with the functional equilibrium hypothesis. There was significant ID in biomass (δ = 0.17), leaf chlorophyll content, and the number of root nodules of the legume, but the magnitude of ID was independent of the stress treatments. In particular, there was no significant interaction between inbreeding and the intensity of any stress type, and ID was not higher under novel than under familiar stresses. In addition, phenotypic plasticity in biomass allocation, leaf functional traits and in root nodulation of the legume to the various stress treatments was not influenced by inbreeding. Our findings do not support the common hypothesis of stronger ID under stressful environments, not even if the stresses are novel to the plants.

The effects of stress intensity and stress type on inbreeding depression in Silene vulgaris

Inbreeding depression (ID) is generally assumed to increase under stressful conditions, but a number of studies have found the opposite pattern, that is that crossed offspring were more capable of exploiting benign conditions. Alternatively, the phenotypic variation hypothesis predicts that not stress intensity, but enhanced phenotypic variation in an environment leads to increased ID. We subjected inbred and crossed offspring of Silene vulgaris to drought, simulated herbivory, copper contamination, and two levels of nutrient deficiency and shade. In contrast to the predominant expectation, most stress treatments decreased inbreeding depression. With increasing nutrient limitation, ID decreased strongly, whereas under increasing shade ID did not change. These differences may be due to purging in the population of origin where conditions are nutrient-poor and dry, but not shaded. In contrast to the greenhouse experiment, ID was higher in a field site than in a more benign common garden. However, the predictions of the phenotypic variation hypothesis were met in both the greenhouse and the field versus garden experiment. The results suggest that there may be no general relationship between ID and stress intensity, but specific effects of stress type and the novelty and variability of the environment.

A Bayesian method for the joint estimation of outcrossing rate and inbreeding depression

The population outcrossing rate (t) and adult inbreeding coefficient (F) are key parameters in mating system evolution. The magnitude of inbreeding depression as expressed in the field can be estimated given t and F via the method of Ritland (1990). For a given total sample size, the optimal design for the joint estimation of t and F requires sampling large numbers of families (100-400) with fewer offspring (1-4) per family. Unfortunately, the standard inference procedure (MLTR) yields significantly biased estimates for t and F when family sizes are small and maternal genotypes are unknown (a common occurrence when sampling natural populations). Here, we present a Bayesian method implemented in the program BORICE (Bayesian Outcrossing Rate and Inbreeding Coefficient Estimation) that effectively estimates t and F when family sizes are small and maternal genotype information is lacking. BORICE should enable wider use of the Ritland approach for field-based estimates of inbreeding depression. As proof of concept, we estimate t and F in a natural population of Mimulus guttatus. In addition, we describe how individual maternal inbreeding histories inferred by BORICE may prove useful in studies of inbreeding and its consequences.

Inbreeding alters activities of the stress-related enzymes chitinases and β-1,3-glucanases

Pathogenesis-related proteins, chitinases (CHT) and β-1,3-glucanases (GLU), are stress proteins up-regulated as response to extrinsic environmental stress in plants. It is unknown whether these PR proteins are also influenced by inbreeding, which has been suggested to constitute intrinsic genetic stress, and which is also known to affect the ability of plants to cope with environmental stress. We investigated activities of CHT and GLU in response to inbreeding in plants from 13 Ragged Robin (Lychnis flos-cuculi) populations. We also studied whether activities of these enzymes were associated with levels of herbivore damage and pathogen infection in the populations from which the plants originated. We found an increase in pathogenesis-related protein activity in inbred plants from five out of the 13 investigated populations, which suggests that these proteins may play a role in how plants respond to intrinsic genetic stress brought about by inbreeding in some populations depending on the allele frequencies of loci affecting the expression of CHT and the past levels of inbreeding. More importantly, we found that CHT activities were higher in plants from populations with higher levels of herbivore or pathogen damage, but inbreeding reduced CHT activity in these populations disrupting the increased activities of this resistance-related enzyme in populations where high resistance is beneficial. These results provide novel information on the effects of plant inbreeding on plant–enemy interactions on a biochemical level.

Inbreeding-stress interactions: evolutionary and conservation consequences

The effect of environmental stress on the magnitude of inbreeding depression has a long history of intensive study. Inbreeding-stress interactions are of great importance to the viability of populations of conservation concern and have numerous evolutionary ramifications. However, such interactions are controversial. Several meta-analyses over the last decade, combined with omic studies, have provided considerable insight into the generality of inbreeding-stress interactions, its physiological basis, and have provided the foundation for future studies. In this review, we examine the genetic and physiological mechanisms proposed to explain why inbreeding-stress interactions occur. We specifically examine whether the increase in inbreeding depression with increasing stress could be due to a concomitant increase in phenotypic variation, using a larger data set than any previous study. Phenotypic variation does usually increase with stress, and this increase can explain some of the inbreeding-stress interaction, but it cannot explain all of it. Overall, research suggests that inbreeding-stress interactions can occur via multiple independent channels, though the relative contribution of each of the mechanisms is unknown. To better understand the causes and consequences of inbreeding-stress interactions in natural populations, future research should focus on elucidating the genetic architecture of such interactions and quantifying naturally occurring levels of stress in the wild.

Environmental stress increases selection against and dominance of deleterious mutations in inbred families of the Pacific oyster Crassostrea gigas

The deleterious effects of inbreeding are well documented and of major concern in conservation biology. Stressful environments have generally been shown to increase inbreeding depression; however, little is known about the underlying genetic mechanisms of the inbreeding-by-stress interaction and to what extent the fitness of individual deleterious mutations is altered under stress. Using microsatellite marker segregation data and quantitative trait locus (QTL) mapping methods, I performed a genome scan for deleterious mutations affecting viability (viability or vQTL) in two inbred families of the Pacific oyster Crassostrea gigas, reared in a stressful, nutrient-poor diet and a favourable, nutrient-rich diet, which had significant effects on growth and survival. Twice as many vQTL were detected in the stressful diet compared with the favourable diet, resulting primarily from substantially greater mortality of homozygous genotypes. At vQTL, estimates of selection (s) and dominance (h) were greater in the stressful environment (= 0.86 vs. 0.54 and = 0.35 vs. 0.18, in stressful and nonstressful diets, respectively). There was no evidence of interaction between vQTL. Individual vQTL differed across diets in selection only, or in both selection and dominance, and some vQTL were not affected by diet. These results suggest that stress-associated increases in selection against individual deleterious alleles underlie greater inbreeding depression with stress. Furthermore, the finding that inbreeding-by-environment interaction appears, to some extent, to be locus specific, helps to explain previous observations of lineage-specific expression of inbreeding depression and environment-specific purging, which have important implications for conservation and evolutionary biology.

Seasonal stress drives predictable changes in inbreeding depression in field-tested captive populations of Drosophila melanogaster

Recent meta-analyses conducted across a broad range of taxa have demonstrated a strong linear relationship between the change in magnitude of inbreeding depression under stress and stress level, measured as fitness loss in outbred individuals. This suggests that a general underlying response may link stress and inbreeding depression. However, this relationship is based primarily on laboratory data, and it is unknown whether natural environments with multiple stressors and fluctuating stress levels alter how stress affects inbreeding depression. To test whether the same pattern persists in the field, we investigated the effect of seasonal variation on stress level and inbreeding depression in a 3-year field study measuring the productivity of captive populations of inbred and outbred Drosophila melanogaster. We found cold winter temperatures were most stressful and induced the greatest inbreeding depression. Furthermore, these data, collected under natural field conditions, conformed to the same predictive linear relationship seen in Drosophila laboratory studies, with inbreeding depression increasing by 0.17 lethal equivalents for every 10 per cent increase in stress level. Our results suggest that under natural conditions stress level is a primary determinant of the magnitude of inbreeding depression and should be considered when assessing extinction vulnerability in small populations.

Variation in inbreeding depression and plasticity across native and non-native field environments

BACKGROUND AND AIMS

Since the early 1990s, research on genetic variation of phenotypic plasticity has expanded and empirical research has emphasized the role of the environment on the expression of inbreeding depression. An emerging question is how these two evolutionary ecology mechanisms interact in novel environments. Interest in this area has grown with the need to understand the establishment of populations in response to climate change, and to human-assisted transport to novel environments.

METHODS

We compare performance in the field of outcrossed (O) and inbred lines (S1, S2) from 20 maternal families from each of two native populations of Mimulus guttatus. The experiment was planted in California in each population's home site, in the other populations's home site, in a novel site within the native range of M. guttatus, and in a novel site within the non-native range in North America. The experiment included nearly 6500 individuals. Survival, sexual reproduction and above-ground biomass were examined in order to evaluate inbreeding depression, and stem diameter and plant height were examined in order to evaluate phenotypic plasticity.

KEY RESULTS

Across all field sites, approx. 36 % of plants survived to flowering. Inbreeding depression differed among sites and outcrossed offspring generally outperformed selfed offspring. However, in the native-novel site, self-progeny performed better or equally well as outcross progeny. Significant phenotypic plasticity and genetic variation in plasticity was detected in the two architectural traits measured. The absolute value of plasticity showed the most marked difference between home and non-native novel site or non-native-novel site. Evidence was detected for an interaction between inbreeding and plasticity for stem diameter.

CONCLUSIONS

The results demonstrate that during initial population establishment, both inbreeding depression and phenotypic plasticity vary among field sites, and may be an important response to environments outside a species' currently occupied range. However, the interaction between inbreeding and plasticity may be limited and environment-dependent.

Inbreeding depression in Solanum carolinense (Solanaceae) under field conditions and implications for mating system evolution

The clonal weed Solanum carolinense exhibits plasticity in the strength of its self-incompatibility (SI) system and suffers low levels of inbreeding depression (δ) in the greenhouse. We planted one inbred and one outbred plant from each of eight maternal plants in a ring (replicated twice) and monitored clonal growth, herbivory, and reproduction over two years. Per ramet δ was estimated to be 0.63 in year one and 0.79 in year two, and outbred plants produced 2.5 times more ramets than inbred plants in the spring of year two. Inbred plants also suffered more herbivore damage than outbred plants in both fields, suggesting that inbreeding compromises herbivore resistance. Total per genet δ was 0.85 over the two years, indicating that S. carolinense is unlikely to become completely self-compatible, and suggesting that plasticity in the SI system is part of a stable mixed-mating system permitting self-fertilization when cross pollen limits seed production.

Among-individual variation in pollen limitation and inbreeding depression in a mixed-mating shrub

BACKGROUND AND AIMS

Variation in inbreeding depression (δ) among individual plants is considered to play a central role in mating system evolution and population genetics. Moreover, such variation could be linked to individual susceptibility to pollen limitation (PL) because those individuals strongly affected by δ for seed production will require more outcross pollen for setting a given number of fruits or seeds. However, no study has tested explicitly for associations between PL and δ at the individual plant level. This study assesses the extent of among-individual variation in PL and δ, the consistency of δ across life stages, and the relationships between individual PL and δ in the mixed-mating shrub Myrtus communis.

METHODS

Controlled hand-pollinations were performed in a natural M. communis population. Marked flowers were monitored until fruit production and a greenhouse experiment was conducted with the seeds produced.

KEY RESULTS

Compared with selfing, outcross-pollination enhanced seed number per fruit, germination rate and seedling growth, but did not enhance fruit-set. Only seed number per fruit was pollen limited and, thus, cumulative pollen limitation depended more on pollen quality (outcross pollen) than on quantity. The effects of δ varied considerably across life stages and individual plants. Cumulative δ was high across individuals (mean δ = 0·65), although there were no positive correlations between δ values at different life stages. Interestingly, maternal plants showing stronger δ for seed production were more pollen limited, but they were also less affected by δ for seedling growth because of a seed size/number trade-off.

CONCLUSIONS

Results show a general inconsistency in δ across life stages and individuals, suggesting that different deleterious loci are acting at different stages. The association between δ and PL at the individual level corroborates the idea that pollen limitation may be 'genotype-dependent' regardless of other factors.

Evidence for inbreeding depression and post-pollination selection against inbreeding in the dioecious plant Silene latifolia

In many species, inbred individuals have reduced fitness. In plants with limited pollen and seed dispersal, post-pollination selection may reduce biparental inbreeding, but knowledge on the prevalence and importance of pollen competition or post-pollination selection after non-self pollination is scarce. We tested whether post-pollination selection favours less related pollen donors and reduces inbreeding in the dioecious plant Silene latifolia. We crossed 20 plants with pollen from a sibling and an unrelated male, and with a mix of both. We found significant inbreeding depression on vegetative growth, age at first flowering and total fitness (22% in males and 14% in females). In mixed pollinations, the unrelated male sired on average 57% of the offspring. The greater the paternity share of the unrelated sire, the larger the difference in relatedness of the two males to the female. The effect of genetic similarity on paternity is consistent with predictions for post-pollination selection, although paternity, at least in some crosses, may be affected by additional factors. Our data show that in plant systems with inbreeding depression, such as S. latifolia, pollen or embryo selection after multiple-donor pollination may indeed reduce inbreeding.

Inbreeding depression in an autotetraploid herb: a three cohort field study

Autotetraploids are predicted to have reduced inbreeding depression relative to diploids. However, recent theory and information on genomic changes following autopolyploidy suggest that inbreeding depression may be closer to diploids. In three consecutive years, self and outcross pollinations were conducted on autotetraploid Campanulastrum americanum, seeds were planted into native sites, and biennial offspring were followed through seed production. Inbred individuals had lower germination rates, reduced survival, were smaller, and flowered later, producing fewer fruits with fewer seeds. Inbred offspring had 6% of the cumulative fitness of outcross offspring. Although performance varied substantially among cohorts, inbreeding depression for cumulative fitness was relatively constant, with delta ranging only from 0.92 to 0.95. C. americanum, like many outcrossing species, expressed very high amounts of inbreeding depression. This supports the hypothesis that inbreeding depression of some autotetraploids may be similar to that of diploids. Furthermore, few studies have measured temporal variation in inbreeding depression. Constant inbreeding depression given a sixfold range in cohort performance suggests that inbreeding depression may be relatively robust to environmental variation experienced by natural populations.

Variation in the intensity of inbreeding depression among successive life-cycle stages and generations in gynodioecious Silene vulgaris (Caryophyllaceae)

Inbreeding depression is one of the hypotheses explaining the maintenance of females within gynodioecious plant populations. However, the measurement of fitness components in selfed and outcrossed progeny depends on life-cycle stage and the history of inbreeding. Comparative data indicate that strong inbreeding depression is more likely to occur at later life-cycle stages. We used hermaphrodite individuals of Silene vulgaris originating from three populations located in different valleys in the Swiss Alps to investigate the effect of two generations of self- and cross-fertilization on fitness components among successive stages of the life cycle in a glasshouse experiment. We detected significant inbreeding depression for most life-cycle stages including: the number of viable and aborted seeds per fruit, probability of germination, above ground biomass, probability of flowering, number of flowers per plant, flower size and pollen viability. Overall, the intensity of inbreeding depression increased among successive stages of the life cycle and cumulative inbreeding depression was significantly stronger in the first generation (delta approximately 0.5) compared with the second generation (delta approximately 0.35). We found no evidence for synergistic epistasis in our experiment. Our finding of more intense inbreeding depression during later stages of the life cycle may help to explain the maintenance of females in gynodioecious populations of S. vulgaris because purging of genetic load is less likely to occur.

Inbreeding depression and mixed mating in Leptosiphon jepsonii: a comparison of three populations

BACKGROUND AND AIMS

Inbreeding depression is thought to play a central role in the evolution and maintenance of cross-fertilization. Theory indicates that inbreeding depression can be purged with self-fertilization, resulting in positive feedback for the selection of selfing. Variation among populations of Leptosiphon jepsonii in the timing and rate of self-fertilization provides an opportunity to study the evolution of inbreeding depression and mating systems. In addition, the hypothesis that differences in inbreeding depression for male and female fitness can stabilize mixed mating in L. jepsonii is tested.

METHODS

In a growth room experiment, inbreeding depression was measured in three populations with mean outcrossing rates ranging from 0.06 to 0.69. The performance of selfed and outcrossed progeny is compared at five life history stages. To distinguish between self-incompatibility and early inbreeding depression, aborted seeds and unfertilized ovules were counted in selfed and outcrossed fruits. In one population, pollen and ovule production was quantified to estimate inbreeding depression for male and female fitness.

KEY RESULTS

Both prezygotic barriers and inbreeding depression limited self seed set in the most outcrossing population. Cumulative inbreeding depression ranged from 0.297 to 0.501, with the lowest value found in the most selfing population. Significant inbreeding depression for early life stages was found only in the more outcrossing populations. Inbreeding depression was not significant for pollen or ovule production.

CONCLUSIONS

The results provide modest support for the hypothesized relationship between inbreeding depression and mating systems. The absence of early inbreeding depression in the more selfing populations is consistent with theory on purging. Differences in male and female expression of inbreeding depression do not appear to stabilize mixed mating in L. jepsonii. The current estimates of inbreeding depression for L. jepsonii differ from those of previous studies, underscoring the effects of environmental variation on its expression.

Modes and rates of selfing and associated inbreeding depression in the self-incompatible plant Senecio squalidus (Asteraceae): a successful colonizing species in the British Isles

The strength of the self-incompatibility (SI) response in Senecio squalidus was measured across its British range. Geographic variation in SI was investigated and the extent and inheritance of pseudo-self-compatibility (PSC) and inbreeding depression were determined. Mean self-fruit-set per capitulum was calculated for individuals and sample populations. The heritability of PSC and the magnitude of inbreeding depression were assessed by comparing selfing rates and fitness trait values between SI and PSC parent-progeny lines. SI was found to be strongly expressed in S. squalidus throughout its British range, with only 3.1% of the individuals sampled showing PSC. This PSC had relatively low heritability with stronger expression of SI in selfed progeny relative to PSC parents. Inbreeding depression was shown to be great in S. squalidus, with mean life history stage values ranging from 0.18 to 0.25. The strength of SI in S. squalidus appears not to have weakened in response to its rapid colonization of Britain. The avoidance of inbreeding depression is likely to be the primary factor maintaining strong SI in this successful colonizing species.