Individual Heterozygosity Research Articles

Thematic Layers of Genomic Susceptibility for Conservation Monitoring.

Population genomics has great potential to inform applied conservation management and associated policy. However, the bioinformatic analyses and interpretation of population genomic datasets can be daunting and difficult to convey to nonspecialists, including on-the-ground conservationists that work with many state, federal and international agencies. We think that individual population genomic metrics of interest can be interpolated and ultimately distilled into thematic GIS layers that represent spatiotemporal genomic potential (or conversely, susceptibility) in conservation monitoring. As examples relevant to ongoing conservation efforts, we use introgressive hybridisation and individual heterozygosity to illustrate a conceptual approach for mapping population genomic susceptibility. The general framework of thematic layers could be extended to integrate key genomic metrics (e.g., runs of homozygosity and genomic load) that are relevant to many conservation efforts.

Study of the Genetic Mechanisms of Siberian Stone Pine (Pinus sibirica Du Tour) Adaptation to the Climatic and Pest Outbreak Stresses Using Dendrogenomic Approach.

A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms of adaptation and assess the adaptive genetic potential of Siberian stone pine (Pinus sibirica Du Tour) populations. The data obtained are necessary for predicting the effect of climate change and mitigating its negative consequences. Presented are the results of an association analysis of the variation of 84,853 genetic markers (single nucleotide polymorphisms-SNPs) obtained by double digest restriction-site associated DNA sequencing (ddRADseq) and 110 individual phenotypic traits, including dendrophenotypes based on the dynamics of tree-ring widths (TRWs) of 234 individual trees in six natural populations of Siberian stone pine, which have a history of extreme climatic stresses (e.g., droughts) and outbreaks of defoliators (e.g., pine sawfly [Neodiprion sertifer Geoff.]). The genetic structure of studied populations was relatively weak; samples are poorly differentiated and belong to genetically similar populations. Genotype-dendrophenotype associations were analyzed using three different approaches and corresponding models: General Linear Model (GLM), Bayesian Sparse Linear Mixed Model (BSLMM), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), respectively. Thirty SNPs were detected by at least two different approaches, and two SNPs by all three. In addition, three SNPs associated with mean values of recovery dendrophenotype (Rc) averaged across multiple years of climatic stresses were also found by all three methods. The sequences containing these SNPs were annotated using genome annotation of a very closely related species, whitebark pine (P. albicaulis Engelm.). We found that most of the SNPs with supposedly adaptive variation were located in intergenic regions. Three dendrophenotype-associated SNPs were located within the 10 Kbp regions and one in the intron of the genes encoding proteins that play a crucial role in ensuring the integrity of the plant's genetic information, particularly under environmental stress conditions that can induce DNA damage. In addition, we found a correlation of individual heterozygosity with some dendrophenotypes. Heterosis was observed in most of these statistically significant cases; signs of homeostasis were also detected. Although most of the identified SNPs were not assigned to a particular gene, their high polymorphism and association with adaptive traits likely indicate high adaptive potential that can facilitate adaptation of Siberian stone pine populations to the climatic stresses and climate change.

Demographic and genetic impacts of powdery mildew in a young oak (Quercus robur L.) cohort

Key messageBy monitoring a field experiment over nine years, we investigated the impacts of the two main pathogen species Erysiphe quercicola S. Takam. and U. Braun and Erysiphe alphitoides (Griffon and Maubl.) U. Braun and S. Takam causing powdery mildew on a young cohort of pedunculate oak (Quercus robur L.), both from a demographic and genetic point of view using SNP markers. We show that survival rate is affected by mean disease severity. But while the growth-related tolerance to infection of the oak individual seems to be more determinant than resistance against infection, no equalizing effect of the disease could be detected.ContextStudies on the effects of pathogens on the survival and population dynamics of forest trees are scarce. Yet a better understanding of these interactions could prove strategic in the challenging context of climate change.AimsOur general objective was to characterize the demographic and genetic impact of the two main pathogen species Erysiphe quercicola S. Takam. and U. Braun and Erysiphe alphitoides (Griffon and Maubl.) U. Braun and S. Takam causing powdery mildew in the early stages of a Quercus robur L. population.MethodsAn ad hoc field design with two disease exposures, natural and protected, was surveyed over nine years. This enabled a detailed phenotypic monitoring of 1733 emerging individuals from 15 progenies, and the genotyping of 68% of them.ResultsThe pathogen induced high levels of seedling mortality several years after sowing, associated with reduced growth and capacity to overwinter. Fast-growing families showed the highest survival rate under both natural and protected disease exposure. Contrary to a possible trade-off hypothesis between growth and defense, family height potential was not negatively related to disease resistance across the studied oak mother trees. While supporting a deleterious effect of very low individual heterozygosity on the probability of survival, average genomic diversity was not significantly affected by mortality associated with powdery mildew. Our study also points to a few candidate genes for several fitness-related traits.ConclusionOverall, our results suggest that in oak natural populations, infection levels (related to resistance sensu stricto) may be less determinant than growth-related tolerance to infection for the fate of seedlings. However, an equalizing effect of powdery mildew on relative oak genotype performances cannot be excluded at later stages.

Population genetic structure in a self-compatible hermaphroditic snail is driven by drift independently of its contemporary mating system.

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self-compatible hermaphrodites, the mating system (e.g., self-fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (N e). This can potentially accelerate genetic drift, particularly in small populations where self-fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (N e) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within-population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and N e estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within-population genetic diversity.

Airports for the genetic rescue of a former agricultural pest

The intensification of agricultural practices and urbanisation are widespread causes of biodiversity loss. However, the role of artificial habitats in genetic rescue is an aspect that is not well understood. Implementing genetic rescue measures to improve gene flow and maintain a viable population of keystone species is a crucial prerequisite for promoting diverse and resilient ecosystems. Landscape fragmentation and modern agricultural methods have caused the decline and the isolation of the remnant colonies of the endangered European ground squirrel (Spermophilus citellus) throughout its range. However, the artificial habitat, such as airport fields with regular grass mowing, provides suitable conditions for this grassland specialist. We measured home range size and genetic variation of seven souslik colonies in western Slovakia. Based on the 6904 ddRAD SNPs, we found significantly higher individual heterozygosity in colonies on airports compared to colonies on pastures. This indicates a potential for higher fitness of individuals from airport colonies, which can serve as a source for evidence-based translocations. Such an intervention can preserve the genetic diversity of small and isolated populations in the region. We emphasize that conservation management strategies would be strengthened including a specific focus on human-made grassland habitats.

Comprehensive genetic analysis reveals the genetic structure and diversity of Calanthe hoshii (Orchidaceae), an endemic species of the Ogasawara Islands: Implications for appropriate conservation of a critically endangered species

AbstractThe Ogasawara Islands, isolated from the continent throughout their geological history, harbor abundant endemic species. However, 32% of the native plant species are on the Japanese Red List, signaling their endangered status. Among these endangered species, Calanthe hoshii stands out as highly susceptible to extinction. Two wild and 89 ex situ individuals were alive in 2020, but the last known wild individual died in October 2021, indicating this species may have become extinct in the wild. Despite the conservation efforts under the Act for the Conservation of Endangered Species of Wild Fauna and Flora, the lack of essential information regarding genetic diversity and population structure among the remaining individuals poses a significant obstacle to developing effective conservation measures. In this research, we conducted a genetic analysis of the wild and ex situ individuals, which revealed notably reduced genetic diversity between individuals, with individual heterozygosity levels (1.0 × 10−5) measuring one‐ninth of those observed within a closely related species Calanthe triplicata (1.5 × 10−4). Comprehensive genetic analysis revealed that C. hoshii consisted of three genetic clusters of different sizes: cluster 1 comprised 95% of the total population, while clusters 2 and 3, with few individuals, were only found in the ex situ populations at Koishikawa Botanical Garden. Since extant C. hoshii maintains a remarkably low genetic diversity at both individual and population levels, it is necessary to consider future management strategies, such as artificial breeding among different clades identified in this study, to safeguard the stability and resilience of this species.

SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts.

Multi-strain infection is a common yet under-investigated phenomenon of many pathogens. Currently, biologists analyzing SNP information sometimes have to discard mixed infection samples as many downstream analyses require monogenomic inputs. Such a protocol impedes our understanding of the underlying genetic diversity, co-infection patterns, and genomic relatedness of pathogens. A scalable tool to learn and resolve the SNP-haplotypes from polygenomic data is an urgent need in molecular epidemiology. We develop a slice sampling Markov Chain Monte Carlo algorithm, named SNP-Slice, to learn not only the SNP-haplotypes of all strains in the populations but also which strains infect which hosts. Our method reconstructs SNP-haplotypes and individual heterozygosities accurately without reference panels and outperforms the state-of-the-art methods at estimating the multiplicity of infections and allele frequencies. Thus, SNP-Slice introduces a novel approach to address polygenomic data and opens a new avenue for resolving complex infection patterns in molecular surveillance. We illustrate the performance of SNP-Slice on empirical malaria and HIV datasets and provide recommendations for using our method on empirical datasets. The implementation of the SNP-Slice algorithm, as well as scripts to analyze SNP-Slice outputs, are available at https://github.com/nianqiaoju/snp-slice.

Multiple paternity, fertilization success, and male quality: Mating system variation in the eelgrass, Zostera marina.

Genetic diversity can modulate a population's response to a changing environment and plays a critical role in its ecological function. While multiple processes act to maintain genetic diversity, sexual reproduction remains the primary driving force. Eelgrass (Zostera marina) is an important habitat-forming species found in temperate coastal ecosystems across the globe. Recent increases in sea surface temperatures have resulted in shifts to a mixed-annual life-history strategy (i.e., displaying characteristics of both annual and perennial meadows) at its southern edge-of-range. Given that mating systems are intimately linked to standing levels of genetic variation, understanding the scope of sexual reproduction can illuminate the processes that shape genetic diversity. To characterize edge-of-range eelgrass mating systems, developing seeds on flowering Z. marina shoots were genotyped from three meadows in Topsail, North Carolina. In all meadows, levels of multiple mating were high, with shoots pollinated by an average of eight sires (range: 3-16). The number of fertilized seeds (i.e., reproductive success) varied significantly across sires (range: 1-25) and was positively correlated with both individual heterozygosity and self-fertilization. Outcrossing rates were high (approx. 70%) and varied across spathes. No clones were detected, and kinship among sampled flowering shoots was low, supporting observed patterns of reproductive output. Given the role that genetic diversity plays in enhancing resistance to and resilience from ecological disturbance, disentangling the links between life history, sexual reproduction, and genetic variation will aid in informing the management and conservation of this key foundation species.

Low-coverage sequencing and Wahlund effect severely bias estimates of inbreeding, heterozygosity and effective population size in North American wolves.

vonHoldt etal. ((2024), Molecular Ecology, 33, e17231) (vH24) used low-coverage (average ~ 7X read depth) restriction site-associated DNA sequence data to estimate individual inbreeding and heterozygosity, and recent effective population size (Ne), in Great Lakes (GL) and Northern Rocky Mountain (RM) wolves. They concluded that RM heterozygosity rapidly declined between 1991 and 2020, and that Ne declined substantially in GL and RM over the last 50 generations. Here, we evaluate the effects of low sequence coverage and sampling strategy on vH24's findings and provide general recommendations for using sequence data to evaluate inbreeding, heterozygosity and Ne. Low-coverage sequencing resulted in downwardly biased estimates of individual inbreeding and heterozygosity, and an erroneous large temporal decline in RM heterozygosity due to declining read depth through time. Additionally, vH24's sampling strategy-which combined individuals from several genetically differentiated populations and across at least eight wolf generations-is expected to have resulted in severe downward bias in estimates of recent Ne for RM. We recommend using high-coverage sequence data ( 15-20X) to estimate inbreeding and heterozygosity. Carefully filtering individuals, loci and genotypes, and using genotype imputation or likelihoods can help to minimise bias when low-coverage sequence data must be used. For estimation of contemporary Ne, the marginal benefits of using more than 103-104 loci are small, so aggressive filtering of loci with low average read depth potentially can retain most individuals without sacrificing much precision. Individuals are relatively more valuable than loci because analyses of contemporary Ne should focus on roughly single-generation samples from local breeding populations.

Outbreeding reduces survival during metamorphosis in a headwater stream salamander.

Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.

Study of the Genetic Adaptation Mechanisms of Siberian Larch (Larix sibirica Ledeb.) Regarding Climatic Stresses Based on Dendrogenomic Analysis

Dendrogenomics is a new interdisciplinary approach that allows joint analysis of dendrological and genomic data and opens up new ways to study the temporal dynamics of forest treelines, delineate spatial and temporal population structures, decipher individual tree responses to abiotic and biotic stresses, and evaluate the adaptive genetic potential of forest tree populations. These data are needed for the prediction of climate change effects and mitigation of the negative effects. We present here an association analysis of the variation of 27 individual tree traits, including adaptive dendrophenotypes reflecting the individual responses of trees to drought stress, such as the resistance (Rt), recovery (Rc), resilience (Rs), and relative resilience (RRs) indexes measured in 136 Siberian larch trees in 5 populations in the foothills of the Batenevsky Ridge (Kuznetsk Alatau, Republic of Khakassia, Russia), with variation of 9742 SNPs genotyped using ddRADseq in the same trees. The population structure of five closely located Siberian larch populations was relatively weak (FST = 0.018). We found that the level of individual heterozygosity positively correlated with the Rc and RR indices for the five studied drought periods and partly with the Rs indices for three drought periods. It seems that higher individual heterozygosity improves the adaptive capabilities of the tree. We also discovered a significant negative relationship between individual heterozygosity and the Rt index in four out of five periods, which means that growth slows down during droughts more in trees with higher individual heterozygosity and is likely associated with energy and internal resource reallocation toward more efficient water and energy usage and optimization of larch growth during drought years. We found 371 SNPs with potentially adaptive variations significantly associated with the variation of adaptive dendrophenotypes based on all three different methods of association analysis. Among them, 26 SNPs were located in genomic regions carrying functional genes: 21 in intergenic regions and 5 in gene-coding regions. Based on the obtained results, it can be assumed that these populations of Siberian larch have relatively high standing adaptive genetic variation and adaptive potential underlying the adaptations of larch to various climatic conditions.

Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii).

Identifying and analysing isolated populations is critical for conservation. Isolation can make populations vulnerable to local extinction due to increased genetic drift and inbreeding, both of which should leave imprints of decreased genome-wide heterozygosity. While decreases in heterozygosity among populations are frequently investigated, fewer studies have analysed how heterozygosity varies among individuals, including whether heterozygosity varies geographically along lines of discrete population structure or with continuous patterns analogous to isolation by distance. Here we explore geographical patterns of differentiation and individual heterozygosity in the threatened eastern barred bandicoot (Perameles gunnii) in Tasmania, Australia, using genomic data from 85 samples collected between 2008 and 2011. Our analyses identified two isolated demes undergoing significant genetic drift, and several areas of fine-scale differentiation across Tasmania. We observed discrete genetic structures across geographical barriers and continuous patterns of isolation by distance, with little evidence of recent or historical migration. Using a recently developed analytical pipeline for estimating autosomal heterozygosity, we found individual heterozygosities varied within demes by up to a factor of two, and demes with low-heterozygosity individuals also still contained those with high heterozygosity. Spatial interpolation of heterozygosity scores clarified these patterns and identified the isolated Tasman Peninsula as a location where low-heterozygosity individuals were more common than elsewhere. Our results provide novel insights into the relationship between isolation-driven genetic structure and local heterozygosity patterns. These may help improve translocation efforts, by identifying populations in need of assistance, and by providing an individualised metric for identifying source animals for translocation.

Comparative Analysis of Microsatellite and SNP Markers for Genetic Management of Red Deer.

The analysis of population genetic structure and individual multilocus heterozygosity are crucial for wildlife management and conservation. Microsatellite markers have traditionally been used to assess these genetic parameters. However, single-nucleotide polymorphisms (SNPs) are becoming increasingly popular. Our goal here was to determine to what extent SNPs can provide better insights than microsatellites into the overall genetic status and population genetic processes in the species. To this end, we genotyped 210 red deer (Cervus elaphus) in the Spanish wild population with both 11 microsatellites and 31,712 SNPs. We compared parameters related to population genetic structure and individual multilocus heterozygosity obtained with both types of markers. Our results showed correlations between parameters measured using both microsatellites and SNPs, particularly those related to the level of genetic diversity and genetic differentiation. However, we found notably lower precision of microsatellites in measuring the distribution of genetic diversity among individuals. We conclude that microsatellites can be used to monitor the overall genetic status and detect broad patterns in red deer populations. Nevertheless, the greater precision of SNPs in inferring genetic structure and multilocus heterozygosity leads us to encourage scientists and wildlife managers to prioritize their use whenever possible.

Long-term growth decline is not reflected in crown condition of European beech after a recent extreme drought

Global warming poses a major threat to forest ecosystems around the world. In Central Europe, vitality losses and tree mortality have already been observed in various regions, especially after extreme drought episodes such as the 2018–2020 drought. European beech (Fagus sylvatica L.), which is the dominating deciduous tree species in large parts of temperate Europe, also suffered from the recent drought. In Germany, for example, losses in crown condition were observed. Within individual stands, however, the crown condition of beech differed strongly from non–/weakly damaged trees (hereafter referred to as vital trees) to severely damaged/dead trees (non-vital trees). Tree characteristics and micro-site conditions were apparently similar. Hence, we checked whether differences in growth behavior exist and (or) developed over time and assessed if observed differences between the non–/vital individuals might be genetically driven. We found that the climate sensitivity as well as the drought resistance of tree growth did not consistently differ between non–/vital trees. In both groups, a growing importance of water availability for tree growth was apparent. Further, long-term growth decline was widespread in both vital and non-vital trees, suggesting severe stress and future risks of tree mortality irrespective of crown condition. Only at one out of nine sites, we found significant differences in individual heterozygosity, signaling potential differences in the adaptation of trees to environmental stress. As a consequence, our study highlights that crown condition after an extreme drought is a poorer indicator of tree vitality than ring width in beech stands in Germany.

Polymorphism of the fibroblast growth factor 2 gene (FGF 2) in Holstein cattle in the conditions of the Republic of Tatarstan

The basic fibroblast growth factor is a signaling protein encoded by the FGF2 gene. The FGF2 gene is expressed by the endometrium of cattle and is an important factor contributing to the preservation of pregnancy in ruminants, regulates the expression of interferon-? (IFNT), which is involved in the production of milk. The aim of the work is to identify the polymorphism of the FGF2 gene (SNP11646 A ? G substitution) in intron 1 in the Tatarstan population of Holstein cows. 270 Holstein dairy cows were genotyped by PCR-RFLP. As a result of identification, three genotypes were identified: AA – 19.6%, AG – 42.6 and GG – 37.8 %, and the observed distribution of alleles A – 0.409 and G – 0.591. The population is in genetic equilibrium balance, but there is a shift an increase towards heterozygosity of individuals.

Genetic diversity and sperm characteristics are not associated in two bluethroat (Luscinia svecica) populations

Individual heterozygosity may influence the expression of fitness‐related traits, via genome‐wide or local genetic effects. Earlier studies have shown negative relationships between heterozygosity and sperm variation, predominantly in captive, highly inbred populations. Little is known about the possible influence of variation in heterozygosity on sperm traits in wild, outbred populations. We studied two populations of the bluethroat, one from the widely distributed northern subspecies Luscinia. s. svecica and the other from the smaller, more patchily distributed subspecies breeding along the French coast of Brittany L. s. namnetum. The two subspecies differed significantly in body size, plumage colour, sperm traits and the degree of genetic diversity. However, there was no evidence that sperm traits (total length and motility) were influenced by the degree of heterozygosity at the individual level. In contrast, we found that male body size was positively related to heterozygosity across both populations, indicating a possible relationship between overall genetic diversity and general vigour or ability to obtain food. We conclude that sperm traits are unrelated to levels of heterozygosity in the studied outbred and weakly genetically depauperate bluethroat populations.

Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data

Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.

Genetic resources of the oldest trees of Pinus sylvestris L. from the last natural forest in Europe

The last fragments of primeval forests in the European lowlands have survived in the Białowieża Forest (BF). A characteristic feature of its forest stands is a complex and multi-age structure. From a genetic perspective, old trees represent a genetic pool that is a product of the selection forces acting over centuries. Therefore, it is extremely important to make a genetic inventory of such old trees and preserve their genetic resources for future generations. The aims of this study were: 1) genotyping the oldest trees of Pinus sylvestris in the Sitki Reserve of the Białowieża Forest in Poland; and 2) characterisation of the genetic structure of this old Scots pine tree stand. In total, 98 old trees aged above 100 years were analysed using eight nuclear microsatellite markers. The first study on the genotyping of the oldest Scots pine trees in the BF, indicated that each of the trees has a unique genotype, so it can be unambiguously identified by a genetic profile. Overall, 85% of trees showed an individual heterozygosity of 0.5 or higher. We demonstrated, that eight polymorphic microsatellite loci of the nuclear genome are sufficient to create an individual genetic profile of each tree. Our results will provide necessary background information for the conservation of native genetic resources of Pinus sylvestris.

Protein coding variation in the J:ARC and J:DO outbred laboratory mouse stocks provides a molecular basis for distinct research applications.

Outbred laboratory mice (Mus musculus) are readily available and have high fecundity, making them a popular choice in biomedical research, especially toxicological and pharmacological applications. Direct high throughput genome sequencing (HTS) of these widely used research animals is an important genetic quality control measure that enhances research reproducibility. HTS data have been used to confirm the common origin of outbred stocks and to molecularly define distinct outbred populations. But these data have also revealed unexpected population structure and homozygosity in some populations; genetic features that emerge when outbred stocks are not properly maintained. We used exome sequencing to discover and interrogate protein-coding variation in a newly established population of Swiss-derived outbred stock (J:ARC) that is closely related to other, commonly used CD-1 outbred populations. We used these data to describe the genetic architecture of the J:ARC population including heterozygosity, minor allele frequency, LD decay, and we defined novel, protein-coding sequence variation. These data reveal the expected genetic architecture for a properly maintained outbred stock and provide a basis for the on-going genetic quality control. We also compared these data to protein-coding variation found in a multiparent outbred stock, the Diversity Outbred (J:DO). We found that the more recently derived, multiparent outbred stock has significantly higher interindividual variability, greater overall genetic variation, higher heterozygosity, and fewer novel variants than the Swiss-derived J:ARC stock. However, among the novel variants found in the J:DO stock, significantly more are predicted to be protein-damaging. The fact that individuals from this population can tolerate a higher load of potentially damaging variants highlights the buffering effects of allelic diversity and the differing selective pressures in these stocks. While both outbred stocks offer significant individual heterozygosity, our data provide a molecular basis for their intended applications, where the J:DO are best suited for studies requiring maximum, population-level genetic diversity and power for mapping, while the J:ARC are best suited as a general-purpose outbred stock with robust fecundity, relatively low allelic diversity, and less potential for extreme phenotypic variability.

NON-SPECIFIC HETEROSIS ON A COMPLEX OF FEATURES OF ADAPTABILITY ON THE EXAMPLE OF MINI-PIGS

The authors studied the genetic diversity of the reproductive nucleus of mini-pigs at the Institute of Cytology and Genetics (IC&G) of the Siberian Branch of the Russian Academy of Sciences (SB RAS). To do this, the authors used the indicators of individual homo- and heterozygosity, calculated based on the «blood fractions» of large and small forms of domestic pigs, initial for the breeding group. The study showed that the average value of individual heterozygosity (conditionally actual) is 0.800±0.004, while homozygosity for the contribution of large and small forms of the domestic pig is 0.020±0.002 and 0.180±0.010, respectively. The indicator «blood fraction» can have two interpretations: 1) the probability of transmission of the ancestral allele in several generations; 2) the proportion of the genome of the ancestor that is present in the descendant. The authors determined their frequencies, which turned out to be 0.424 and 0.576 as if assuming the presence of a hypothetical locus with different alleles in the large and small forms of the domestic pig (respectively Ak and Am). The authors calculated heterozygosity for the breeding nucleus based on these frequencies while respecting the Hardy-Weinberg law. As a result, it turned out that the unbiased value is 0.493±0.067, which is significantly (P<0.001) less than the observed conditional-actual value. Selection is carried out according to a set of signs of general fitness (state of health, reproductive qualities, the viability of offspring, etc.) during the formation of the reproductive core of the breeding group of mini-pigs of the IC&G SB RAS. Therefore, the authors concluded that the increased heterozygosity of the breeding stock is due to the preferential selection of heterozygotes. But since selection is carried out according to a set of signs of general fitness, it can be stated that in the reproductive core of the selection group there is an effect of nonspecific heterosis due to heterozygosity. As a result, selection into the reproductive nucleus of individuals with high values of individual heterozygosity calculated by the proposed method can provide heterosis based on general adaptiveness.