A genomewide assessment of inbreeding depression: gene number, function, and mode of action

Genomic insights into the conservation of wild and domestic animal diversity: A review

Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.

Genomic partitioning of inbreeding depression in humans

Across species, offspring of related individuals often exhibit significant reduction in fitness-related traits, known as inbreeding depression (ID), yet the genetic and molecular basis for ID remains elusive. Here, we develop a method to quantify enrichment of ID within specific genomic annotations and apply it to human data. We analyzed the phenomes and genomes of ∼350,000 unrelated participants of the UK Biobank and found, on average of over 11 traits, significant enrichment of ID within genomic regions with high recombination rates (>21-fold; p < 10^-5), with conserved function across species (>19-fold; p < 10^-4), and within regulatory elements such as DNase I hypersensitive sites (∼5-fold; p = 8.9 × 10^-7). We also quantified enrichment of ID within trait-associated regions and found suggestive evidence that genomic regions contributing to additive genetic variance in the population are enriched for ID signal. We find strong correlations between functional enrichment of SNP-based heritability and that of ID (r = 0.8, standard error: 0.1). These findings provide empirical evidence that ID is most likely due to many partially recessive deleterious alleles in low linkage disequilibrium regions of the genome. Our study suggests that functional characterization of ID may further elucidate the genetic architectures and biological mechanisms underlying complex traits and diseases.

Allele Specific Expression (ASE) analysis between Bos Taurus and Bos Indicus cows using RNA-Seq data at SNP level and gene level

In the current study, allele specific expression analysis was performed in two subspecies cows (Bos taurus and Bos indicus) at SNP and gene levels. RNA-Seq data of 21,078,477 and 20940063 paired end reads from pooling of whole blood samples (Leukocyte) from 40 US Holstein (Bos Taurus) and 45 Cholistani cows (Bos indicus) obtained from SRA database in NCBI. Quality control and trimming of row RNA-Seq data were processed by FASTQC and Trimmomatic softwares. The transcriptome was assembled by TopHat2 software in two cow's population by aligning and mapping the RNA-Seq reads on bovine reference genome. The SNPs were discovered by Samtools software and ASE analysis was performed by Chi-square test. Results showed that 50183 and 137954 SNPs were discovered on the assembled transcriptome of Holstein and Cholistani cow samples, respectively, and 15308 SNPs were common in both breeds. 10158 SNPs from 50183 (20%) in Holstein and 31523 SNPs from 137954 (23%) in Cholistani cows were identified as ASE-SNPs. Reference allele and alternative allele count in Holstein and Cholistani cows were 3041 and 7155, respectively. Among 131 discovered SNPs in 41 genes with different expression in Holstein and Cholistani cows, 31 ASE-SNPs (5 in Holstein; 26 in Cholistani cows) were discovered.

Variable inbreeding depression may explain associations between the mating system and herbicide resistance in the common morning glory

Inbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages of Ipomoea purpurea artificially evolved to exhibit divergent levels of herbicide resistance. We examined inbreeding depression in a variety of fitness-related traits in both the growth chamber and in the field, and paired this work with an examination of gene expression changes. We found that, while inbreeding depression was present across many of the traits, lineages artificially selected for increased herbicide resistance often showed no evidence of inbreeding depression in the presence of herbicide, and in fact, showed evidence of outbreeding depression in some traits compared to nonselected control lines and lineages selected for increased herbicide susceptibility. Further, at the transcriptome level, the resistant selection lines had differing patterns of gene expression according to breeding type (inbred vs. outcrossed) compared to the control and susceptible selection lines. Our data together indicate that inbreeding depression may be lessened in populations that are adapting to regimes of strong selection.

A clue to invasion success: genetic diversity quickly rebounds after introduction bottlenecks

One of the fundamental questions in invasion biology is to understand the genetic mechanisms behind success or failure during the establishment of a species. However, major limitations to understanding are usually a lack of spatiotemporal population data and information on the populations’ colonisation history. In a large-scale, detailed study on the bush-cricket Metrioptera roeselii 70 groups of founders were introduced in areas outside the species’ distribution range. We examined how (1) the number of founders (2–32 individuals), (2) the time since establishment (7 or 15 years after introduction) and (3) possible gene flow affected establishment success and temporal genetic changes of the introduced populations. We found higher establishment success in introductions with larger propagule sizes but genetic diversity indices were only partly correlated to propagule size. As expected, introduced populations were more similar to their founder population the larger the propagule size was. However, even if apparent at first, most of the differentiation in the small propagule introductions disappeared over time. Surprisingly, genetic variability was regained to a level comparable to the large and outbreeding founder population only 15 generations after severe demographic bottlenecks. We suggest that the establishment of these populations could be a result of several mechanisms acting in synergy. Here, rapid increase in genetic diversity of few introductions could potentially be attributed to limited gene flow from adjacent populations, behavioural adaptations and/or even increased mutation rate. We present unique insights into genetic processes that point towards traits that are important for understanding species’ invasiveness.

Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster

Epistasis may have important consequences for a number of issues in quantitative genetics and evolutionary biology. In particular, synergistic epistasis for deleterious alleles is relevant to the mutation load paradox and the evolution of sex and recombination. Some studies have shown evidence of synergistic epistasis for spontaneous or induced deleterious mutations appearing in mutation-accumulation experiments. However, many newly arising mutations may not actually be segregating in natural populations because of the erasing action of natural selection. A demonstration of synergistic epistasis for naturally segregating alleles can be achieved by means of inbreeding depression studies, as deleterious recessive allelic effects are exposed in inbred lines. Nevertheless, evidence of epistasis from these studies is scarce and controversial. In this paper, we report the results of two independent inbreeding experiments carried out with two different populations of Drosophila melanogaster. The results show a consistent accelerated inbreeding depression for fitness, suggesting synergistic epistasis among deleterious alleles. We also performed computer simulations assuming different possible models of epistasis and mutational parameters for fitness, finding some of them to be compatible with the results observed. Our results suggest that synergistic epistasis for deleterious mutations not only occurs among newly arisen spontaneous or induced mutations, but also among segregating alleles in natural populations.

Genomic measures of inbreeding in the Norwegian-Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits

Background

Since the 1950s, the Norwegian–Swedish Coldblooded trotter (NSCT) has been intensively selected for harness racing performance. As a result, the racing performance of the NSCT has improved remarkably; however, this improved racing performance has also been accompanied by a gradual increase in inbreeding level. Inbreeding in NSCT has historically been monitored by using traditional methods that are based on pedigree analysis, but with recent advancements in genomics, the NSCT industry has shown interest in adopting molecular approaches for the selection and maintenance of this breed. Consequently, the aims of the current study were to estimate genomic-based inbreeding coefficients, i.e. the proportion of runs of homozygosity (ROH), for a sample of NSCT individuals using high-density genotyping array data, and subsequently to compare the resulting rate of genomic-based F (F_ROH) to that of pedigree-based F (F_PED) coefficients within the breed.

Results

A total of 566 raced NSCT were available for analyses. Average F_ROH ranged from 1.78 to 13.95%. Correlations between F_ROH and F_PED were significant (P < 0.001) and ranged from 0.27 to 0.56, with F_PED and F_ROH from 2000 to 2009 increasing by 1.48 and 3.15%, respectively. Comparisons of ROH between individuals yielded 1403 regions that were present in at least 95% of the sampled horses. The average percentage of a single chromosome covered in ROH ranged from 9.84 to 18.82% with chromosome 31 and 18 showing, respectively, the largest and smallest amount of homozygosity.

Conclusions

Genomic inbreeding coefficients were higher than pedigree inbreeding coefficients with both methods showing a gradual increase in inbreeding level in the NSCT breed between 2000 and 2009. Opportunities exist for the NSCT industry to develop programs that provide breeders with easily interpretable feedback on regions of the genome that are suboptimal from the perspective of genetic merit or that are sensitive to inbreeding within the population. The use of molecular data to identify genomic regions that may contribute to inbreeding depression in the NSCT will likely prove to be a valuable tool for the preservation of its genetic diversity in the long term.

Electronic supplementary material

The online version of this article (10.1186/s12711-019-0465-7) contains supplementary material, which is available to authorized users.

Sex-specific effects of inbreeding and early life conditions on the adult oxidative balance

Inbreeding negatively affects various life-history traits, with inbred individuals typically having lower fitness than outbred individuals (= inbreeding depression). Inbreeding depression is often emphasized under environmental stress, but the underlying mechanisms and potential long-lasting consequences of such inbreeding–environment interactions remain poorly understood. Here, we hypothesize that inbreeding–environment interactions that occur early in life have long-term physiological effects, in particular on the adult oxidative balance. We applied a unique experimental design to manipulate early life conditions of inbred and outbred songbirds (Serinus canaria) that allowed us to separate prenatal and postnatal components of early life conditions and their respective importance in inbreeding–environment interactions. We measured a wide variety of markers of oxidative status in adulthood, resulting in a comprehensive account for oxidative balance. Using a Bayesian approach with Markov chain Monte Carlo, we found clear sex-specific effects and we also found only in females small yet significant long-term effects of inbreeding–environment interactions on adult oxidative balance. Postnatal components of early life conditions were most persuasively reflected on adult oxidative balance, with inbred females that experienced disadvantageous postnatal conditions upregulating enzymatic antioxidants in adulthood. Our study provides some evidence that adult oxidative balance can reflect inbreeding–environment interactions early in life, but given the rather small effects that were limited to females, we conclude that oxidative stress might have a limited role as mechanism underlying inbreeding–environment interactions.

Single nucleotide polymorphism of the growth hormone (GH) encoding gene in inbred and outbred domestic rabbits

Taking into consideration that the growth hormone (GH) gene in rabbits is a candidate for meat production, understanding the genetic diversity and variation in this locus is of particular relevance. The present study comprised 86 rabbits (Oryctolagus cuniculus) divided into 3 groups: New Zealand White (NZW) outbred rabbits; first-generation inbred rabbits (F₁) and second-generation inbred rabbits (F₂). They were analysed by polymerase chain reaction-based restriction fragment length polymorphism method. A 231 bp fragment of the polymorphic site of the GH gene was digested with Bsh1236 restriction enzyme. Single nucleotide polymorphisms for the studied GH locus corresponding to 3 genotypes were detected in the studied rabbit populations: CC, CT and TT. In the synthetic inbred F₁ and F₂ populations, the frequency of the heterozygous genotype CT was 0.696 and 0.609, respectively, while for the homozygous CC genotype the frequency was lower (0.043 and 0.000), and respective values for the homozygous TT genotype were 0.261 and 0.391. This presumed a preponderance of the T allele (0.609 and 0.696) over the C allele (0.391 and 0.304) in these groups. In outbred rabbits, the allele frequencies were 0.613 (allele C) and 0.387 (allele Т); consequently, the frequency of the homozygous CC genotype was higher than that of the homozygous TT genotype (0.300 vs. 0.075). Observed heterozygosity for the GH gene was higher than expected, and the result was therefore a negative inbreeding coefficient (Fis=–0.317 for outbred NZW rabbits; –0.460 for inbred F₁ and –0.438 for inbred F₂), indicating a sufficient number of heterozygous forms in all studied groups of rabbits. The application of narrow inbreeding by breeding full sibs in the synthetic population did not cause a rapid increase in homozygosity.

Genetics of Obesity in Consanguineous Populations: Toward Precision Medicine and the Discovery of Novel Obesity Genes

OBJECTIVE

Consanguinity has been instrumental in the elucidation of many Mendelian genetic diseases. Here, the unique advantage of consanguineous populations was considered in the quest for genes causing obesity.

METHODS

PubMed was searched for articles relevant to consanguinity and obesity published between 1995 and 2016. Some earlier articles of interest were also consulted.

RESULTS

Although obesity is the most heritable disorder, even in outbred populations, only 2% to 5% of severe obesity cases have so far been proven to be caused by single gene mutations. In some highly consanguineous populations, a remarkably higher proportion of obesity cases because of known and novel monogenic variants has been identified (up to 30%).

CONCLUSIONS

Combining the power conferred by consanguinity with current large-capacity sequencing techniques should bring new genetic factors and molecular mechanisms to the fore, unveiling a large part of the yet-elusive neurohumoral circuitry involved in the regulation of energy homeostasis and appetite. Importantly, the undertaking of such initiatives is destined to unfold novel targets for the development of precision medicine relevant to different forms of obesity.

Inbreeding effects on gene-specific DNA methylation among tissues of Chinook salmon

Inbreeding depression is the loss of fitness resulting from the mating of genetically related individuals. Traditionally, the study of inbreeding depression focused on genetic effects, although recent research has identified DNA methylation as also having a role in inbreeding effects. Since inbreeding depression and DNA methylation change with age and environmental stress, DNA methylation is a likely candidate for the regulation of genes associated with inbreeding depression. Here, we use a targeted, multigene approach to assess methylation at 22 growth-, metabolic-, immune- and stress-related genes. We developed PCR-based DNA methylation assays to test the effects of intense inbreeding on intragenic gene-specific methylation in inbred and outbred Chinook salmon. Inbred fish had altered methylation at three genes, CK-1, GTIIBS and hsp70, suggesting that methylation changes associated with inbreeding depression are targeted to specific genes and are not whole-genome effects. While we did not find a significant inbreeding by age interaction, we found that DNA methylation generally increases with age, although methylation decreased with age in five genes, CK-1, IFN-ɣ, HNRNPL, hsc71 and FSHb, potentially due to environmental context and sexual maturation. As expected, we found methylation patterns differed among tissue types, highlighting the need for careful selection of target tissue for methylation studies. This study provides insight into the role of epigenetic effects on ageing, environmental response and tissue function in Chinook salmon and shows that methylation is a targeted and regulated cellular process. We provide the first evidence of epigenetically based inbreeding depression in vertebrates.

Starvation resistance and tissue-specific gene expression of stress-related genes in a naturally inbred ant population

Starvation is one of the most common and severe stressors in nature. Not only does it lead to death if not alleviated, it also forces the starved individual to allocate resources only to the most essential processes. This creates energetic trade-offs which can lead to many secondary challenges for the individual. These energetic trade-offs could be exacerbated in inbred individuals, which have been suggested to have a less efficient metabolism. Here, we studied the effect of inbreeding on starvation resistance in a natural population of Formica exsecta ants, with a focus on survival and tissue-specific expression of stress, metabolism and immunity-related genes. Starvation led to large tissue-specific changes in gene expression, but inbreeding had little effect on most of the genes studied. Our results illustrate the importance of studying stress responses in different tissues instead of entire organisms.

Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression

Knowledge of which genes and pathways are affected by inbreeding may help understanding the genetic basis of inbreeding depression, the potential for purging (selection against deleterious recessive alleles), and the transition from outcrossing to selfing. Arabidopsis lyrata is a predominantly self-incompatible perennial plant, closely related to the selfing model species A. thaliana. To examine how inbreeding affects gene expression, we compared the transcriptome of experimentally selfed and outcrossed A. lyrata originating from two Scandinavian populations that express similar inbreeding depression for fitness (∂ ≈ 0.80). The number of genes significantly differentially expressed between selfed and outcrossed individuals were 2.5 times higher in the Norwegian population (≈ 500 genes) than in the Swedish population (≈ 200 genes). In both populations, a majority of genes were upregulated on selfing (≈ 80%). Functional annotation analysis of the differentially expressed genes showed that selfed offspring were characterized by 1) upregulation of stress-related genes in both populations and 2) upregulation of photosynthesis-related genes in Sweden but downregulation in Norway. Moreover, we found that reproduction- and pollination-related genes were affected by inbreeding only in Norway. We conclude that inbreeding causes both general and population-specific effects. The observed common effects suggest that inbreeding generally upregulates rather than downregulates gene expression and affects genes associated with stress response and general metabolic activity. Population differences in the number of affected genes and in effects on the expression of photosynthesis-related genes show that the genetic basis of inbreeding depression can differ between populations with very similar levels of inbreeding depression.

Generation-based life table analysis reveals manifold effects of inbreeding on the population fitness in Plutella xylostella

Understanding how inbreeding affects fitness is biologically important for conservation and pest management. Despite being a worldwide pest of many economically important cruciferous crops, the influence of inbreeding on diamondback moth, Plutella xylostella (L.), populations is currently unknown. Using age-stage-specific life tables, we quantified the inbreeding effects on fitness-related traits and demographic parameters of P. xylostella. Egg hatching rate, survival and fecundity of the inbred line significantly declined compared to those of the outbred line over time. The inbred P. xylostella line showed significantly lower intrinsic rate of increase (r), net reproduction rate (R₀), and finite increase rate (λ), and increasing generation time (T). Inbreeding effects vary with developmental stages and the fitness-related traits can be profoundly affected by the duration of inbreeding. Our work provides a foundation for further studies on molecular and genetic bases of the inbreeding depression for P. xylostella.

Complex effects of inbreeding on biparental cooperation

There is mounting evidence that inbreeding can have detrimental effects on the fitness of outbred individuals that interact with or depend on inbred individuals. However, little is currently known about the behavioral mechanisms by which interactions with inbred individuals induce fitness costs in outbred individuals. Here, we study effects of inbreeding on the behavioral dynamics of biparental cooperation in the burying beetle Nicrophorus vespilloides. To this end, we used a two-by-two factorial design, in which an inbred or outbred female was mated to an inbred or an outbred male and tested for effects on cooperation between male and female parents providing care for their joint offspring. We found no evidence that inbred parents provided less care than outbred parents. Nevertheless, partners of inbred parents increased the amount of care they provided, leading to overcompensation. Our study shows that inbreeding can have strong and complex effects on the behavioral dynamics of biparental cooperation and that these effects are mediated mainly through changes in the partner's behavior. We suggest that similar effects of inbreeding on outbred individuals may extend to other social contexts, such as cooperative breeding and mating.

Flies who cannot take the heat: genome-wide gene expression analysis of temperature-sensitive lethality in an inbred line of Drosophila melanogaster

Fitness decreases associated with inbreeding depression often become more pronounced in a stressful environment. The functional genomic causes of these inbreeding-by-environment (I × E) interactions, and of inbreeding depression in general, are poorly known. To further our understanding of I × E interactions, we performed a genome-wide gene expression study of a single inbred line that suffers from temperature-sensitive lethality. We confirmed that increased differential expression between the thermosensitive line and the control line occurs at the restrictive temperature. This demonstrates that I × E interactions in survival are reflected in similar I × E interactions at the gene expression level. To make an impression of the cellular response associated with the lethal effect, we analysed all functional annotation terms that were overrepresented among the differentially expressed genes. Some sets of differentially expressed genes function in the general stress response, and these are more likely to also be differentially expressed in other studies of inbreeding, inbreeding depression, immunity and heat stress. Other sets of differentially expressed genes are shared with studies of gene expression in inbred lines, but not studies of the response to extrinsic stress, and represent a general transcriptomic signature of inbreeding. Finally, some sets of genes have an annotation that is not reported in other studies. These we consider to be candidates for the genes harbouring the mutations responsible for the thermosensitive phenotype, as these mutations are expected to be unique to this line. These genes may also serve as candidate QTL in studies of thermal tolerance and heat resistance.

Inbreeding interferes with the heat-shock response

Inbreeding is typically detrimental to individual fitness, with negative effects being often exaggerated in stressful environments. However, the causal mechanisms underlying inbreeding depression in general and the often increased susceptibility to stress in particular are not well understood. We here test whether inbreeding interferes with the heat-shock response, comprising an important component of the stress response which may therefore underscore sensitivity to stress. To this end we subjected the tropical butterfly Bicyclus anynana to a full-factorial design with three temperatures and three levels of inbreeding, and measured the expression of heat-shock protein (HSP) 70 via qPCR. HSP70 expression increased after exposure to heat as compared with cold or control conditions. Most strikingly, inbreeding strongly interfered with the heat-shock response, with inbred individuals showing a very weak upregulation of HSP70 only. Our results thus indicate that, in our study organism, interference with the heat-shock response may be one mechanism underlying reduced fitness of inbred individuals, especially when exposed to stressful conditions. However, these indications need to be corroborated using a broader range of different temperatures, genes and taxa.

Inbreeding depression in livestock species: review and meta-analysis

Inbreeding, by virtue of its consequence on traits of interest, is a topic of major interest for geneticists and animal breeders. Based on meta-analysis conducted on 57 studies and seven livestock species considering a wide variety of selected traits, it was estimated that inbreeding depression corresponds to on average a decrease of 0.137 percent of the mean of a trait per 1 percent of inbreeding. The decrease was larger for production traits (reduction of 0.351%) than for other trait categories. For populations raised as purebreds, inbreeding depression may impact the economic income of breeders. There is a need for studies assessing the existence of an inbreeding purge phenomenon as well as the impact of inbreeding on adaptation capacities of livestock species. Promises brought by the development of dense genotyping as well as functional genomics will increase the capacities to improve our understanding and management of the phenomenon.

Inbreeding effects on standard metabolic rate investigated at cold, benign and hot temperatures in Drosophila melanogaster

Inbreeding increases homozygosity, which is known to affect the mean and variance of fitness components such as growth, fecundity and mortality rate. Across inbred lines inbreeding depression is typically observed and the variance between lines is increased in inbred compared to outbred lines. It has been suggested that damage incurred from increased homozygosity entails energetic cost associated with cellular repair. However, little is known about the effects of inbreeding on standard metabolic rate. Using stop-flow respirometry we performed repeated measurements of metabolic rate in replicated lines of inbred and outbred Drosophila melanogaster at stressful low, benign and stressful high temperatures. The lowest measurements of metabolic rate in our study are always associated with the low activity period of the diurnal cycle and these measurements therefore serve as good estimates of standard metabolic rate. Due to the potentially added costs of genetic stress in inbred lines we hypothesized that inbred individuals have increased metabolic rate compared to outbred controls and that this is more pronounced at stressful temperatures due to synergistic inbreeding by environment interactions. Contrary to our hypothesis we found no significant difference in metabolic rate between inbred and outbred lines and no interaction between inbreeding and temperature. Inbreeding however effected the variance; the variance in metabolic rate was higher between the inbred lines compared to the outbred control lines with some inbred lines having very high or low standard metabolic rate. Thus genetic drift and not inbreeding per se seem to explain variation in metabolic rate in populations of different size.

Interactions between insect herbivores and plant mating systems

Self-pollination is common in plants, and limited seed and pollen dispersal can create localized inbreeding even within outcrossing plants. Consequently, insects regularly encounter inbred plants in nature. Because inbreeding results in elevated homozygosity, greater expression of recessive alleles, and subsequent phenotypic changes in inbred plants, inbreeding may alter plant-insect interactions. Recent research has found that plant inbreeding alters resistance and tolerance to herbivores, alters the attraction and susceptibility of plants to insects that vector plant pathogens, and alters visitation rates of insect pollinators. These results suggest that interactions with insects can increase or decrease inbreeding depression (the loss of fitness due to self-fertilization) and subsequently alter the evolution of selfing within plant populations. Future work needs to focus on the mechanisms underlying genetic variation in the effects of inbreeding on plant-insect interactions and the consequences of altered plant-insect interactions on the evolution of plant defense and plant mating systems.

The long-term effects of a life-prolonging heat treatment on the Drosophila melanogaster transcriptome suggest that heat shock proteins extend lifespan

Heat-induced hormesis, i.e. the beneficial effect of mild heat-induced stress, increases the average lifespan of many organisms. This effect, which depends on the heat shock factor, decreases the log mortality rate weeks after the stress has ceased. To identify candidate genes that mediate this lifespan-prolonging effect late in life, we treated flies with mild heat stress (34 °C for 2 h) 3 times early in life and compared the transcriptomic response in these flies versus non-heat-treated controls 10-51 days after the last heat treatment. We found significant transcriptomic changes in the heat-treated flies. Several hsp70 probe sets were up-regulated 1.7-2-fold in the mildly stressed flies weeks after the last heat treatment (P<0.01). This result was unexpected as the major Drosophila heat shock protein, Hsp70, is reported to return to normal levels of expression shortly after heat stress. We conclude that the heat shock response, and Hsp70 in particular, may be central to the heat-induced increase in the average lifespan in flies that are exposed to mild heat stress early in life.

Selection on overdominant genes maintains heterozygosity along multiple chromosomes in a clonal lineage of honey bee

Correlations between fitness and genome-wide heterozygosity (heterozygosity-fitness correlations, HFCs) have been reported across a wide range of taxa. The genetic basis of these correlations is controversial: do they arise from genome-wide inbreeding ("general effects") or the "local effects" of overdominant loci acting in linkage disequilibrium with neutral loci? In an asexual thelytokous lineage of the Cape honey bee (Apis mellifera capensis), the effects of inbreeding have been homogenized across the population, making this an ideal system in which to detect overdominant loci, and to make inferences about the importance of overdominance on HFCs in general. Here we investigate the pattern of zygosity along two chromosomes in 42 workers from the clonal Cape honey bee population. On chromosome III (which contains the sex-locus, a gene that is homozygous-lethal) and chromosome IV we show that the pattern of zygosity is characterized by loss of heterozygosity in short regions followed by the telomeric restoration of heterozygosity. We infer that at least four selectively overdominant genes maintain heterozygosity on chromosome III and three on chromosome IV via local effects acting on neutral markers in linkage disequilibrium. We conclude that heterozygote advantage and local effects may be more common and evolutionarily significant than is generally appreciated.

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.

Proteomic characterization of inbreeding-related cold sensitivity in Drosophila melanogaster

Inbreeding depression is a widespread phenomenon of central importance to agriculture, medicine, conservation biology and evolutionary biology. Although the population genetic principles of inbreeding depression are well understood, we know little about its functional genomic causes. To provide insight into the molecular interplay between intrinsic stress responses, inbreeding depression and temperature tolerance, we performed a proteomic characterization of a well-defined conditional inbreeding effect in a single line of Drosophila melanogaster, which suffers from extreme cold sensitivity and lethality. We identified 48 differentially expressed proteins in a conditional lethal line as compared to two control lines. These proteins were enriched for proteins involved in hexose metabolism, in particular pyruvate metabolism, and many were found to be associated with lipid particles. These processes can be linked to known cold tolerance mechanisms, such as the production of cryoprotectants, membrane remodeling and the build-up of energy reserves. We checked mRNA-expression of seven genes with large differential protein expression. Although protein expression poorly correlated with gene expression, we found a single gene (CG18067) that, after cold shock, was upregulated in the conditional lethal line both at the mRNA and protein level. Expression of CG18067 also increased in control flies after cold shock, and has previously been linked to cold exposure and chill coma recovery time. Many differentially expressed proteins in our study appear to be involved in cold tolerance in non-inbred individuals. This suggest the conditional inbreeding effect to be caused by misregulation of physiological cold tolerance mechanisms.

Research progress in allele-specific expression and its regulatory mechanisms

Although the majority of genes are expressed equally from both alleles, some genes are differentially expressed. Organisms possess characteristics to preferentially express a particular allele under regulatory factors, which is termed allele-specific expression (ASE). It is one of the important genetic factors that lead to phenotypic variation and can be used to identify the variance of gene regulation factors. ASE indicates mechanisms such as DNA methylation, histone modifications, and non-coding RNAs function. Here, we review a broad survey of progress in ASE studies, and what this simple yet very effective approach can offer in functional genomics, and possible implications toward our better understanding of the underlying mechanisms of complex traits.

The dynamic relationship between polyandry and selfish genetic elements

Selfish genetic elements (SGEs) are ubiquitous in eukaryotes and bacteria, and make up a large part of the genome. They frequently target sperm to increase their transmission success, but these manipulations are often associated with reduced male fertility. Low fertility of SGE-carrying males is suggested to promote polyandry as a female strategy to bias paternity against male carriers. Support for this hypothesis is found in several taxa, where SGE-carrying males have reduced sperm competitive ability. In contrast, when SGEs give rise to reproductive incompatibilities between SGE-carrying males and females, polyandry is not necessarily favoured, irrespective of the detrimental impact on male fertility. This is due to the frequency-dependent nature of these incompatibilities, because they will decrease in the population as the frequency of SGEs increases. However, reduced fertility of SGE-carrying males can prevent the successful population invasion of SGEs. In addition, SGEs can directly influence male and female mating behaviour, mating rates and reproductive traits (e.g. female reproductive tract length and male sperm). This reveals a potent and dynamic interaction between SGEs and polyandry highlighting the potential to generate sexual selection and conflict, but also indicates that polyandry can promote harmony within the genome by undermining the spread of SGEs.

A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits

BACKGROUND

Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on complex traits. We examine the effects of multi-trait selection on the genome of a population of US registered Angus beef cattle born over a 50-year period representing approximately 10 generations of selection. We present results from the application of a quantitative genetic model, called Birth Date Selection Mapping, to identify signatures of recent ongoing selection.

RESULTS

We show that US Angus cattle have been systematically selected to alter their mean additive genetic merit for most of the 16 production traits routinely recorded by breeders. Using Birth Date Selection Mapping, we estimate the time-dependency of allele frequency for 44,817 SNP loci using genomic best linear unbiased prediction, generalized least squares, and BayesCπ analyses. Finally, we reconstruct the primary phenotypes that have historically been exposed to selection from a genome-wide analysis of the 16 production traits and gene ontology enrichment analysis.

CONCLUSIONS

We demonstrate that Birth Date Selection Mapping utilizing mixed models corrects for time-dependent pedigree sampling effects that lead to spurious SNP associations and reveals genomic signatures of ongoing selection on complex traits. Because multiple traits have historically been selected in concert and most quantitative trait loci have small effects, selection has incrementally altered allele frequencies throughout the genome. Two quantitative trait loci of large effect were not the most strongly selected of the loci due to their antagonistic pleiotropic effects on strongly selected phenotypes. Birth Date Selection Mapping may readily be extended to temporally-stratified human or model organism populations.

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.

Gene-expression changes caused by inbreeding protect against inbreeding depression in Drosophila

We present a transcriptomic analysis aimed at investigating whether the changes in gene expression that occur under inbreeding generally reduce or enhance inbreeding depression. Discerning between these two alternatives can be addressed only when both changes in expression due to inbreeding and to inbreeding depression are estimated simultaneously. We used Affymetrix 2.0 arrays to study the changes in gene expression associated with both inbreeding and inbreeding depression for fitness in four sets of inbred sublines of Drosophila melanogaster. We found that for most genes showing changes in expression associated with inbreeding, the least depressed sublines were those showing the largest departures in expression from that of the outbred control. This suggests a pattern consistent with a protective role of expression changes against inbreeding effects, and would reveal a new dimension of the transcriptomics of inbreeding. The variation in depression observed could then be due not only to the genetic damages primarily originating that depression, but also possibly to differences in the ability to carry out the appropriate adjustments in gene expression to cope with the inbreeding. We also found that these expression changes with a putative protective role against inbreeding effects show a clear specificity on RNA synthesis and splicing and energy derivation functions.

Genomic toolboxes for conservation biologists

Conservation genetics is expanding its research horizon with a genomic approach, by incorporating the modern techniques of next-generation sequencing (NGS). Application of NGS overcomes many limitations of conservation genetics. First, NGS allows for genome-wide screening of markers, which may lead to a more representative estimation of genetic variation within and between populations. Second, NGS allows for distinction between neutral and non-neutral markers. By screening populations on thousands of single nucleotide polymorphism markers, signals of selection can be found for some markers. Variation in these markers will give insight into functional rather than neutral genetic variation. Third, NGS facilitates the study of gene expression. Conservation genomics will increase our insight in how the environment and genes interact to affect phenotype and fitness. In addition, the NGS approach opens a way to study processes such as inbreeding depression and local adaptation mechanistically. Conservation genetics programs are directed to a fundamental understanding of the processes involved in conservation genetics and should preferably be started in species for which large databases on ecology, demography and genetics are available. Here, we describe and illustrate the connection between the application of NGS technologies and the research questions in conservation. The perspectives of conservation genomics programs are also discussed.

The consequences of mating over a range of parental genetic similarity in a selfing allopolyploid plant species

In diploids, F(1) offspring performance is expected to increase with increasing genetic dissimilarity between the parents until an optimum is reached because outbreeding mitigates inbreeding depression and maximizes heterosis. However, many flowering plant species are derived through allopolyploidization, i.e. interspecific hybridization with genome doubling. This mode of plant speciation can be expected to considerably alter the consequences of inbreeding and outbreeding. We investigated the F1 fitness consequences of mating over a range of (genetic) distances in the allohexaploid plant species Geum urbanum. Offspring was raised under controlled conditions (632 plants). The performance of outcrossed progeny was not significantly better than that of their selfed half-siblings and did not increase with parental genetic dissimilarity (0-0.83). Our findings support low, if any, inbreeding depression and heterosis. We attribute this to the peculiar state of quasi-permanent heterozygosity in allopolyploids and frequent selfing.

Analysis of the effects of inbreeding on lifespan and starvation resistance in Drosophila melanogaster

Because of their decreased overall fitness and genetic variability inbred individuals are expected to show reduced survival and lifespan under most environmental conditions as compared with outbred individuals. Whereas evidence for the deleterious effects of inbreeding on lifespan has been previously provided, only a few studies have investigated effects of inbreeding on survival under starved conditions. In the present study we compared the abilities of inbred and outbred adult Drosophila melanogaster to survive under starved and fed conditions. We found that inbreeding reduced lifespan but had no effect on starvation resistance. The results indicate highly trait specific consequences of inbreeding. Possible mechanisms behind the observed results are discussed.

Candidate genes detected in transcriptome studies are strongly dependent on genetic background

Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds.

Modifier locus of the skeletal muscle involvement in Emery-Dreifuss muscular dystrophy

Autosomal dominant Emery-Dreifuss muscular dystrophy is caused by mutations in LMNA gene encoding lamins A and C. The disease is characterized by early onset joint contractures during childhood associated with humero-peroneal muscular wasting and weakness, and by the development of a cardiac disease in adulthood. Important intra-familial variability characterized by a wide range of age at onset of myopathic symptoms (AOMS) has been recurrently reported, suggesting the contribution of a modifier gene. Our objective was to identify a modifier locus of AOMS in relation with the LMNA mutation. To map the modifier locus, we genotyped 291 microsatellite markers in 59 individuals of a large French family, where 19 patients carrying the same LMNA mutation, exhibited wide range of AOMS. We performed Bayesian Markov Chain Monte Carlo-based joint segregation and linkage methods implemented in the Loki software, and detected a strong linkage signal on chromosome 2 between markers D2S143 and D2S2244 (211 cM) with a Bayes factor of 28.7 (empirical p value = 0.0032). The linked region harbours two main candidate genes, DES and MYL1 encoding desmin and light chain of myosin. Importantly, the impact of the genotype on the phenotype for this locus showed an overdominant effect with AOMS 2 years earlier for the homozygotes of the rare allele and 37 years earlier for the heterozygotes than the homozygotes for the common allele. These results provide important highlights for the natural history and for the physiopathology of Emery-Dreifuss muscular dystrophy.

When it comes to inbreeding: slower is better

The extent to which genetic diversity is lost from inbred populations is important for conservation biology, evolutionary ecology, and plant and animal breeding. This importance stems from the fact that the amount of genetic diversity a population has is expected to correlate with evolutionary potential. A population's ability to avert extinction during rapidly changing environmental conditions, or the magnitude of response to selection on a trait, depend on the ability of the genome to maintain potentially adaptive genetic variation in the face of random genetic drift. Although a few previous studies have demonstrated that the rate of inbreeding affects the amount of genetic diversity maintained, the elegant work of Demontis et al., in this issue, clearly demonstrates that slow inbreeding maintains more genetic diversity than fast inbreeding and that the primary mechanism could be balancing selection. In their study, populations that took 19 generations, rather than one generation, to reach the same level of inbreeding maintained 10% higher levels of allelic richness and 25% higher levels of heterozygosity. The use of specifically chosen molecular markers not expected to be neutral makes this study especially noteworthy, as the study provides evidence concerning the mechanisms underlying the maintenance of genetic diversity in the face of inbreeding.

A hierarchical Bayesian model for a novel sparse partial diallel crossing design

Partial diallel crossing designs are in common use among evolutionary geneticists, as well as among plant and animal breeders. When the goal is to make statements about populations represented by a given set of lines, it is desirable to maximize the number of lines sampled given a set number of crosses among them. We propose an augmented round-robin design that accomplishes this. We develop a hierarchical Bayesian model to estimate quantitative genetic parameters from our scheme. For example, we show how to partition genetic effects into specific and general combining abilities, and the method provides estimates of heritability, dominance, and genetic correlations in the face of complex and unbalanced designs. We test our approach with simulated and real data. We show that although the models slightly overestimate genetic variances, main effects are assessed accurately and precisely. We also illustrate how our approach allows the construction of posterior distributions of combinations of parameters by calculating narrow-sense heritability and a genetic correlation between activities of two enzymes.