Associations of autozygosity with a broad range of human phenotypes

In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44-66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding.

Genome-wide autozygosity is associated with lower general cognitive ability

Inbreeding depression refers to lower fitness among offspring of genetic relatives. This reduced fitness is caused by the inheritance of two identical chromosomal segments (autozygosity) across the genome, which may expose the effects of (partially) recessive deleterious mutations. Even among outbred populations, autozygosity can occur to varying degrees due to cryptic relatedness between parents. Using dense genome-wide single-nucleotide polymorphism (SNP) data, we examined the degree to which autozygosity associated with measured cognitive ability in an unselected sample of 4854 participants of European ancestry. We used runs of homozygosity-multiple homozygous SNPs in a row-to estimate autozygous tracts across the genome. We found that increased levels of autozygosity predicted lower general cognitive ability, and estimate a drop of 0.6 s.d. among the offspring of first cousins (P=0.003-0.02 depending on the model). This effect came predominantly from long and rare autozygous tracts, which theory predicts as more likely to be deleterious than short and common tracts. Association mapping of autozygous tracts did not reveal any specific regions that were predictive beyond chance after correcting for multiple testing genome wide. The observed effect size is consistent with studies of cognitive decline among offspring of known consanguineous relationships. These findings suggest a role for multiple recessive or partially recessive alleles in general cognitive ability, and that alleles decreasing general cognitive ability have been selected against over evolutionary time.

Sibling competition does not magnify inbreeding depression in North American Arabidopsis lyrata

About half of all angiosperms have some form of molecular self-incompatibility to promote outcrossing. If self-incompatibility breaks down, inbreeding depression (δ) is the main barrier to the evolution of self-fertilisation (selfing). If inbreeding depression is lower than 50% (δ < 0.5), the inherent transmission advantage of selfers should theoretically drive the evolution of selfing. However, this does not always happen in practice. For example, despite frequent breakdowns of self-incompatibility in North American Arabidopsis lyrata, selfing has only evolved in few populations. This is surprising given that previous inbreeding-depression estimates were well below the 0.5 threshold. Here, we test whether this could be due to underestimation of true inbreeding depression in competition-free environments. Specifically, we tested whether direct competition between crossed and selfed siblings magnified inbreeding-depression estimates in A. lyrata. We found that this was neither the case for belowground nor for aboveground biomass. For reproductive traits, there was hardly any significant inbreeding depression regardless of competition. Combined with previous findings that drought stress and inducing defence also did not magnify inbreeding depression, our results suggest that the relatively low estimates of inbreeding depression for biomass are indeed realistic estimates of the true inbreeding depression in North American A. lyrata.

Changes in floral biology and inbreeding depression in native and invaded regions of Datura stramonium

Plant populations invading new environments might compromise their fitness contribution to the next generation, because of the lack of native specialist pollinators and/or potential mates. Thus, changes in plant mating system and traits linked to it are expected in populations colonising new environments where selection would favour selfing and floral traits that maximise reproductive output. To test this, we studied native (Mexico) and non-native (Spain) populations of the obligate sexual reproducing annual weed Datura stramonium. Flower size, herkogamy, total number of seeds per plant, number of visits by and type of pollinators, and inbreeding depression were assessed in native and non-native populations. Finally, we measured phenotypic selection on corolla size and herkogamy in each population. Flower size and herkogamy showed wide and similar variation in both ranges. However, the largest average flower size was found in one non-native population whereas the highest average positive herkogamy was detected in one native population. On average, flowers in the native range received more visits by pollinators. Hawkmoths were the main visitors in the native populations while only bees were observed visiting flowers in Spain's populations. Only in the native range was inbreeding depression detected. Selection to reduce herkogamy was found only in one native population. Absence of both inbreeding depression and selection on floral traits suggest a change in mating system of D. stramonium in a new range where generalist pollinators may be promoting high reproductive success. Selection against deleterious alleles might explain the reduction of inbreeding depression, promoting the evolution of selfing.

Estimating selection on the act of inbreeding in a population with strong inbreeding depression

Inbreeding depression is widely regarded as a driving force in the evolution of dispersal, mate choice and sperm selection. However, due to likely costs of inbreeding avoidance, which are poorly understood, it is unclear to what extent selection to avoid inbreeding is expected in nature. Moreover, there are currently very few empirical estimates of the strength of selection against the act of inbreeding (mating with a relative), as opposed to the fitness costs of being inbred. Here, we use data from the individual-based study of red deer on the Scottish island of Rum, a strongly polygynous system which harbours a large inbreeding load, to estimate selection against the act of inbreeding for each sex. We use pedigree and genomic estimates of relatedness between individuals and measure fitness using both lifetime breeding success (number of calves born) and lifetime reproductive success (number of calves surviving to independence), with the latter incorporating inbreeding depression in calf survival. We find for both sexes that the repeatability of the act of inbreeding was low (< 0.1), suggesting little among-individual variation for this trait on which selection can act. Using the genomic measures, there was significant selection against the act of inbreeding in males, but not in females, and there was considerable uncertainty in the estimate in both sexes. We discuss possible explanations for these patterns and their implications for understanding the evolution of inbreeding avoidance in natural populations.

Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte

Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte.

Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. Mating of close relatives increases the probability that an individual inherits two non-functioning mutations at the same gene, resulting in lower fitness of such matings. We do not know the extent to which inbreeding depression is due to mutations with large-effects versus small-effect polygenic variants. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits and we found that this was consistent with higher predicted ‘genetic load’ in maize based solely on the evolutionary conservation of the sequence variants observed in the population. We also mapped genome positions associated with inbreeding depression, identifying more and larger-effect genetic variants in teosinte than maize. These results suggest that during domestication, some of the rare large-effect variants in teosinte were bred out, but many genetic variants of small effects on inbreeding depression increased in frequency maize.

Optimizing genetic diversity in Australian Holsteins and Jerseys: A comparative analysis of whole-genome and regional inbreeding depression effects

Homozygosity, which can arise from several genetic mechanisms including inbreeding, is frequently observed in the offspring of related parents. This inbreeding can lead to a reduced performance, owing to a phenomenon known as inbreeding depression. This study assessed inbreeding depression using whole-genome and regional approaches in first-lactation Australian Holsteins and Jerseys, involving ∼33,000 Holstein and 7,000 Jersey cows born between 2000 and 2017. These cows had phenotypic records (milk production, fertility, and survival), pedigree records, and genomic data available. We analyzed genome-wide inbreeding depression through a mixed animal model examining 4 measures of inbreeding: pedigree data, runs of homozygosity (ROH) of at least 1 Mb, ROH greater than 8 Mb, and ROH exceeding 16 Mb, which indicates more recent inbreeding. Additionally, unique ROH haplotypes, identified using a sliding-window approach, were incorporated as fixed effects in the model to estimate their effect on the traits of interest. Results indicated that a 1% increase in pedigree inbreeding led to reduced performance across all traits, with estimates of inbreeding depression ranging from 0.11% to 0.45% of the phenotypic mean. In Holsteins, genome-wide estimates (FROH) were significant and reasonably aligned with pedigree estimates, whereas more recent inbreeding (FROH >16 Mb) had between 2.6 and 3.3 times greater effect on inbreeding depression across all traits compared with smaller FROH (≥1 Mb). In Jerseys, more recent inbreeding had a 2.2 to 2.3 times greater reduction in the performance of milk and protein yields for a 1% increase in genomic inbreeding. For both fitness traits in Jerseys, the effects of inbreeding on fertility and survival were not significant. The most negative effects of ROH were also noted in specific traits: Jersey and Holstein cows with unfavorable ROH took significantly longer to recalve and showed marked reductions in production traits. Moreover, increased homozygosity in certain genomic regions, such as BTA25 in Jerseys, markedly reduced performance, highlighting the importance of genomic location in assessing the effects of homozygosity. These data inform next-generation mating programs, emphasizing avoiding inbreeding in genomic regions most susceptible to inbreeding depression, to enhance animal performance.

Polly Wants a Genome: The Lack of Genetic Testing for Pet Parrot Species

Parrots are considered the third most popular pet species, after dogs and cats, in the United States of America. Popular birds include budgerigars, lovebirds and cockatiels and are known for their plumage and vocal learning abilities. Plumage colour variation remains the main driving force behind breeder selection. Despite the birds' popularity, only two molecular genetic tests-bird sexing and pathogen screening-are commercially available to breeders. For a limited number of species, parentage verification tests are available, but are mainly used in conservation and not for breeding purposes. No plumage colour genotyping test is available for any of the species. Due to the fact that there isn't any commercial plumage genotype screening or parentage verification tests available, breeders mate close relatives to ensure recessive colour alleles are passed to the next generation. This, in turn, leads to inbreeding depression and decreased fertility, lower hatchability and smaller clutch sizes, all important traits in commercial breeding systems. This review highlights the research carried out in the field of pet parrot genomics and points out the areas where future research can make a vital contribution to understanding how parrot breeding can be improved to breed healthy, genetically diverse birds.

Preservation and Reproduction of Microminipigs by Cloning Technology

BACKGROUND/AIM

Microminipigs have been maintained in small populations of closed colonies, involving risks of inbreeding depression and genetic drift. In order to avoid these risks, we assessed the applicability of cloning technology.

MATERIALS AND METHODS

Male and female clones were produced from a stock of cryopreserved somatic cells, obtaining offspring by means of natural mating. Phenotypic and genotypic characteristics of original microminipigs, clones and their offspring were analyzed and recorded.

RESULTS AND CONCLUSION

Clones presented characteristics similar to those of the cell-stock data. Although the body weight of clones tended to be heavier than that of the cell-stock data, body weights of their offspring were similar to those of previous reports. Thus, cloned microminipigs have the potential to be a valuable genetic resource for reproduction and breeding. Our proposed methodology might be useful to provide a large number of animals with adequate quality from a limited population with sufficient genetic diversity.

Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer

Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.

Constraining models of dominance for nonsynonymous mutations in the human genome

Dominance is a fundamental parameter in genetics, determining the dynamics of natural selection on deleterious and beneficial mutations, the patterns of genetic variation in natural populations, and the severity of inbreeding depression in a population. Despite this importance, dominance parameters remain poorly known, particularly in humans or other non-model organisms. A key reason for this lack of information about dominance is that it is extremely challenging to disentangle the selection coefficient (s) of a mutation from its dominance coefficient (h). Here, we explore dominance and selection parameters in humans by fitting models to the site frequency spectrum (SFS) for nonsynonymous mutations. When assuming a single dominance coefficient for all nonsynonymous mutations, we find that numerous h values can fit the data, so long as h is greater than ~0.15. Moreover, we also observe that theoretically-predicted models with a negative relationship between h and s can also fit the data well, including models with h = 0.05 for strongly deleterious mutations. Finally, we use our estimated dominance and selection parameters to inform simulations revisiting the question of whether the out-of-Africa bottleneck has led to differences in genetic load between African and non-African human populations. These simulations suggest that the relative burden of genetic load in non-African populations depends on the dominance model assumed, with slight increases for more weakly recessive models and slight decreases shown for more strongly recessive models. Moreover, these results also demonstrate that models of partially recessive nonsynonymous mutations can explain the observed severity of inbreeding depression in humans, bridging the gap between molecular population genetics and direct measures of fitness in humans. Our work represents a comprehensive assessment of dominance and deleterious variation in humans, with implications for parameterizing models of deleterious variation in humans and other mammalian species.

Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs

Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120.

Strongly deleterious mutations influence reproductive output and longevity in an endangered population

Inbreeding depression has been documented in various fitness traits in a wide range of species and taxa, however, the mutational basis is not yet well understood. We investigate how putatively deleterious variation influences fitness and is shaped by individual ancestry by re-sequencing complete genomes of 37 individuals in a natural arctic fox (Vulpes lagopus) population subjected to both inbreeding depression and genetic rescue. We find that individuals with high proportion of homozygous loss of function genotypes (LoFs), which are predicted to exert a strong effect on fitness, generally have lower lifetime reproductive success and live shorter lives compared with individuals with lower proportion of LoFs. We also find that juvenile survival is negatively associated with the proportion of homozygous missense genotypes and positively associated with genome wide heterozygosity. Our results demonstrate that homozygosity of strongly and moderately deleterious mutations can be an important cause of trait specific inbreeding depression in wild populations, and mark an important step towards making more informed decisions using applied conservation genetics.