Severe Inbreeding Depression Research Articles

Seed priming and abiotic stress tolerance in carrot: Unraveling the mechanisms of improved germination.

Climate change necessitates the development of improved crops capable of withstanding future weather patterns. Carrots (Daucus carota L.), a crucial vegetable crop of global importance, face unique challenges in seed germination and seedling development due to their complex pollination biology and outcrossing reproduction mode with severe inbreeding depression if selfed. This study investigated the effects of salinity and drought stress on carrot seed germination and seedling development, with focus on the roles of seed priming, cellular processes inhibitors, and biochemical responses. Seed priming agents were hypothesized to enhance stress tolerance by modulating specific cellular and biochemical pathways, such as improving osmotic balance, enhancing antioxidant defense mechanisms, and activating stress-responsive genes. We also hypothesized that specific cellular processes and biochemical pathways influence the germination and early seedling growth of carrot seeds under salinity or drought stress. To test that hypothesis, we evaluated the effects of seed priming with various agents (e.g., water, NaCl, PEG, GA3) on germination rates and seedling vigor. Additionally, we investigated the impact of inhibitors (actinomycin D-inhibitor of transcription, cycloheximide-inhibitor of translation, hydroxyurea-inhibitor of DNA synthesis, cytochalasin-inhibitor of actin polymerization) on seed germination under stress conditions. Biochemical responses, including reactive oxygen species (ROS) levels and antioxidant enzyme activities, were analyzed to identify genotype-specific adaptations indicative of stress tolerance. Our results revealed significant variability in germination rates and seedling growth among the studied carrot experimental lines and commercial cultivars under salinity or drought stress Seed priming enhanced germination and seedling vigor by up to 35% under salinity stress and 28% under drought stress, with notable differences observed across the priming agents. The application of inhibitors highlighted the involvement of specific cellular processes in regulation of seed germination under stress. For instance, actinomycin D reduced germination by 40% under salinity stress. Biochemical analyses indicated genotype-specific responses, with variations in ROS levels and antioxidant enzyme activities such as superoxide dismutase and peroxidase. ROS levels increased by 50% under drought stress, whereas antioxidant enzyme activities varied substantially among genotypes. These findings underscored the importance of genotype-specific adaptations in conferring salinity or drought tolerance in carrot seedlings. Future research integrating omics approaches (e.g., transcriptomics, proteomics, metabolomics) will provide deeper insights into the molecular mechanisms that regulate stress tolerance, to aid in the development of more resilient carrot varieties suitable for cultivation under adverse environmental conditions.

Analysis of inbreeding depression in five S1 Cassava families of elite varieties at the seedling nursery and clonal evaluation trial stages.

Background Cassava is an outcrossing, highly heterozygous plant that is reported to suffer from inbreeding depression. However, unraveling recessive traits and exploring additive genes would require a limited level of inbreeding for the genetic improvement of cassava. Method The impact of inbreeding depression (ID) on agronomic and biotic tolerance of cassava was evaluated using the S1 progenies of five African cassava varieties (TMS 30572, TME 419, TMS 98/0505, TMS 01/1371, and TMS 98/0002) at the seedling and clonal evaluation stages. Results At both trial stages, the effects of ID were severe on average performance of fresh root yield and fresh foliage yield; moderate on harvest index, dry matter content, vigor, and tolerance to cassava mosaic disease, cassava bacterial blight, and cassava anthracnose diseases; and less severe on plant height. Further examination of S1 families using molecular markers showed varying levels of heterozygosity at several loci across the genome. In addition, the degree of heterozygosity and ID varied by the S1 family. The TMS 01/1371 family showed the lowest degree of heterozygosity and ID on the average performance of different agronomic attributes, indicating that inbreeding may be strategically explored in this family to increase genetic gain and identify useful recessive traits. Lastly, the observed depression from inbreeding was higher in seedling evaluation than in clonal evaluation trials for fresh root yield, fresh foliage yield, harvest index, and dry matter content. Conclusion S1 individuals showing relatively low heterozygosity based on SNP data were selected as parents to advance genetic gain in cassava. Generally, reduced heterozygosity was prominent in traits with severe ID impacts on average phenotypic performance. Our results highlight the relative importance of exploring non-additive genetic effects and transgressive segregations for favorable allele combinations in cassava improvement.

Inbreeding in Chinese fir: Insights into the adaptive growth traits of selfed progeny from mRNA, miRNA, and copy number variation.

The impact of inbreeding on biological processes is well documented in individuals with severe inbreeding depression. However, the biological processes influencing the adaptive growth of normal selfed individuals are unknown. Here, we aimed to investigate how inbreeding affects gene expression for adaptive growth of normal selfed seedlings from a self-fertilizing parent in Chinese fir (Cunninghamia lanceolata). Using RNA-seq data from above- and underground tissues of abnormal and normal selfed seedlings, we analyzed GO biological processes network. We also sequenced small RNAs in the aboveground tissues and measured the copy number variations (CNV) of the hub genes. Phenotypic fitness analysis revealed that the normal seedlings were better adapted than their abnormal counterparts. Upregulated differentially expressed genes (DEGs) were associated with development processes, and downregulated DEGs were mainly enriched in fundamental metabolism and stress response. Results of mRNA-miRNA parallel sequencing revealed that upregulated target genes were predominantly associated with development, highlighting their crucial role in phosphorylation in signal transduction networks. We also discovered a moderate correlation (0.1328 < R2 < 0.6257) between CNV and gene expression levels for three hub genes (TMKL1, GT2, and RHY1A). We uncovered the key biological processes underpinning the growth of normal selfed seedlings and established the relationship between CNV and the expression levels of hub genes in selfed seedlings. Understanding the candidate genes involved in the growth of selfed seedlings will help us comprehend the genetic mechanisms behind inbreeding depression in the evolutionary biology of plants.

Analysis of Elimination Effects of Inbreeding on Genotype Frequency in Larval Stages of Chinese Shrimp.

Marine animals possess genomes of considerable complexity and heterozygosity. Their unique reproductive system, characterized by high fecundity and substantial early mortality rates, increases the risk of inbreeding, potentially leading to severe inbreeding depression during various larval developmental stages. In this study, we established a set of inbred families of Fenneropenaeus chinensis, with an inbreeding coefficient of 0.25, and investigated elimination patterns and the manifestations of inbreeding depression during major larval developmental stages. Reduced-representation genome sequencing was utilized to explore the genotype frequency characteristics across two typical elimination stages. The results revealed notable mortality in hatching and metamorphosis into mysis and post-larvae stages. Inbreeding depression was also evident during these developmental stages, with depression rates of 24.36%, 29.23%, and 45.28%. Segregation analysis of SNPs indicated an important role of gametic selection before hatching, accounting for 45.95% of deviation in the zoea stage. During the zygotic selection phase of larval development, homozygote deficiency and heterozygote excess were the main selection types. Summation of the two types explained 82.31% and 89.91% of zygotic selection in the mysis and post-larvae stage, respectively. The overall distortion ratio decreased from 22.37% to 12.86% in the late developmental stage. A total of 783 loci were identified through selective sweep analysis. We also found the types of distortion at the same locus could change after the post-larvae stage. The predominant shifts included a transition of gametic selection toward normal segregation and other forms of distortion to heterozygous excess. This may be attributed to high-intensity selection on deleterious alleles and genetic hitchhiking effects. Following larval elimination, a greater proportion of heterozygous individuals were preserved. We detected an increase in genetic diversity parameters such as expected heterozygosity, observed heterozygosity, and polymorphic information content in the post-larvae stage. These findings suggest the presence of numerous recessive deleterious alleles and their linkage and suggest a major role of the partial dominance hypothesis. The results provide valuable insights into the mechanisms of inbreeding depression in marine animals and offer guidance for formulating breeding strategies in shrimp populations.

Genomic Underpinnings of Population Persistence in Isle Royale Moose.

Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.

Evolution of mixed mating: Effects of among-parent variation in early-acting inbreeding depression coupled with overproduction of ovules

Theoretical models were developed to propose a new mechanism enhancing mixed mating (reproduction by both outcrossing and selfing) in hermaphroditic plants; mixed mating can be maintained if there exists among-parent variation in early-acting inbreeding depression in embryos and parents can replace dead embryos by overproduction of ovules. In the two main models developed, the number of embryos produced is allowed to evolve, parents may overproduce embryos, and among-parent variation in early-acting inbreeding depression does not exist or exists. I found that mixed mating does not evolve if among-parent variation in early-acting inbreeding depression does not exist, whereas it evolves if it exists. If the degree of early-acting inbreeding depression in embryos is variable among parents, parents with the same selfing strategy suffer different effects of early-acting inbreeding depression. Specifically, overproduction of embryos may be insufficient when inbreeding depression is severe but wasteful when it is weak. Hence, it is advantageous to produce a moderate number of embryos to reduce waste of resources. Mixed mating is then advantageous to avoid great reductions in seed number caused by massive loss of selfed embryos in cases of severe inbreeding depression.

Genomic erosion in a demographically recovered bird species during conservation rescue.

The pink pigeon (Nesoenas mayeri) is an endemic species of Mauritius that has made a remarkable recovery after a severe population bottleneck in the 1970s to early 1990s. Prior to this bottleneck, an ex situ population was established from which captive‐bred individuals were released into free‐living subpopulations to increase population size and genetic variation. This conservation rescue led to rapid population recovery to 400–480 individuals, and the species was twice downlisted on the International Union for the Conservation of Nature (IUCN) Red List. We analyzed the impacts of the bottleneck and genetic rescue on neutral genetic variation during and after population recovery (1993–2008) with restriction site‐associated sequencing, microsatellite analyses, and quantitative genetic analysis of studbook data of 1112 birds from zoos in Europe and the United States. We used computer simulations to study the predicted changes in genetic variation and population viability from the past into the future. Genetic variation declined rapidly, despite the population rebound, and the effective population size was approximately an order of magnitude smaller than census size. The species carried a high genetic load of circa 15 lethal equivalents for longevity. Our computer simulations predicted continued inbreeding will likely result in increased expression of deleterious mutations (i.e., a high realized load) and severe inbreeding depression. Without continued conservation actions, it is likely that the pink pigeon will go extinct in the wild within 100 years. Conservation rescue of the pink pigeon has been instrumental in the recovery of the free‐living population. However, further genetic rescue with captive‐bred birds from zoos is required to recover lost variation, reduce expression of harmful deleterious variation, and prevent extinction. The use of genomics and modeling data can inform IUCN assessments of the viability and extinction risk of species, and it helps in assessments of the conservation dependency of populations.

Chromosome-level genome assembly for takin (Budorcas taxicolor) provides insights into its taxonomic status and genetic diversity.

The takin (Budorcas taxicolor) is one of the largest bovid herbivores in the subfamily Caprinae. The takin is at high risk of extinction, but its taxonomic status and genetic diversity remain unclear. In this study, we constructed the first reference genome of Bu. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is ~2.95Gb with a contig N50 of 68.05Mb, which were anchored onto 25+XY chromosomes. We found that the takin was more closely related to muskox than to other Caprinae species. Compared to the common ancestral karyotype of bovidae (2n=60), we found the takin (2n=52) experienced four chromosome fusions and one large translocation. Furthermore, we resequenced nine golden takins from the main distribution area, the Qinling Mountains, and identified 3.3million single nucleotide polymorphisms. The genetic diversity of takin was very low (θπ=0.00028 and heterozygosity=0.00038), among the lowest detected in domestic and wild mammals. Takin genomes showed a high inbreeding coefficient (FROH=0.217), suggesting severe inbreeding depression. The demographic history showed that the effective population size of takins declined significantly from ~100,000years ago. Our results provide valuable information for protection of takins and insights into their evolution.

Influence of Pollen Dispersal and Mating Pattern in Domestication of Intermediate Wheatgrass, a Novel Perennial Food Crop.

Intermediate wheatgrass (IWG) is a perennial forage grass that is currently being domesticated as a grain crop. It is a primarily wind-pollinated outcrossing species and expresses severe inbreeding depression when self-pollinated. Characterization of pollen dispersal, mating parameters, and change in genetic diversity due to pollen movement is currently lacking in IWG. In this study, we examined pollen dispersal in an IWG selection nursery by evaluating 846 progeny from 15 mother plants and traced their parentage to 374 fathers. A set of 2,500 genomic loci was used to characterize the population. We assigned paternity to 769 (91%) progeny and the average number of fathers per mother plant was 37, from an average of 56 progeny examined per mother. An extensive number (80%) of pollination events occurred within 10 m of the mother plants. Pollination success was not correlated with trait attributes of the paternal genotypes. Mating system analysis confirmed that IWG is highly outcrossing and inbreeding was virtually absent. Neither genetic diversity nor the genome-estimated trait values of progeny were significantly affected by pollinator distance. The distance of pollinator in an IWG breeding nursery therefore was not found to be a major contributor in maintaining genetic diversity. These findings reveal the pollen dispersal model in IWG for the first time and its effect on genetic diversity, which will be valuable in designing future IWG breeding populations. Information generated and discussed in this study could be applied in understanding gene flow and genetic diversity of other open-pollinated species.

Père David's Deer (Elaphurus davidianus) in China: Population Dynamics and Challenges

The reintroduction of rare and endangered species is one of the most important approaches to conservation and ecosystem restoration, but it has still proven to be an adventurous undertaking and most reintroduction programmes fail, so successful demonstrations are needed. Père David's deer (Elaphurus davidianus, Milu in Chinese) could be considered one of conservation's great success stories, as this species' path on the road to extinction has been reversed by a combination of ex-situ conservation and successful re-introduction in China. The species had been consigned to an imperial hunting ground when the last Chinese herds were exterminated during the fall of the Qing Dynasty (1644–1912). Fortunately, a few of the last remaining individuals were sent to European zoos. From these animals, a herd was bred on the 14th Duke of Bedford's estate, Woburn Abbey, and between 1985 and 1987, and 38 Milu were donated back to China for re-introduction in Beijing Milu Park (BMP), the former imperial hunting ground. An additional 39 deer were released at Dafeng National Nature Reserve (DFNNR), Jiangsu Province in 1986. In both of these safe and protected locations, the Milu thrived allowing for over 700 Milu to be sent to a further 82 sites throughout the species' original Chinese range over the last 36 years. As a result, the Milu population totaled 9136 by 2021, with 2855 individuals now living back in the wild; while another 5681 individuals inhabit the DFNNR, and 186 reside in BMP. Wild Milu, however, still face significant conservation challenges. The population lacks genetic diversity, leading to severe inbreeding depression and carrying multiple risks, such as high miscarriage rates, a reduced lifespan, and susceptibility to disease. Environmental constraints such as pollution and habitat fragmentation further result in small, fragmented wild populations. Moreover, the species currently lacks a national level conservation master plan, the associated coordinated monitoring platforms, and breeding plans for China's captive populations. Finally, there is now a lack of international cooperation in the conservation of this species. We therefore call for both a national-level conservation master plan in China and international cooperation to develop a shared database and germplasm databank covering Milu across all countries with ex-situ populations, as crucial steps for securing the long-term conservation of Milu and preventing it from ever becoming “extinct in the wild” again.

SNP-based parentage analyses over two successive generations demonstrates the feasibility of efficient production of inbred lines in the Pacific oyster (Crassostrea gigas) by self-fertilization of simultaneous hermaphrodites despite severe inbreeding depression

The Pacific oyster, Crassostrea gigas, is a species in which true male and true female well as hermaphrodite individuals have been reported. Among the latter, most are sequential, with one or more sex changes throughout their live, while a few (<2%) are simultaneous hermaphrodites (SH) which may self-fertilize. Sex determinism and its functional bases remain unclear is this species. In this study, one SH oyster was found among a mature broodstock and used to produce a progeny by self-fertilization. Several thousand offspring were obtained for this family (SF1) but only 73 SF1 oysters survived following an episode of mass mortality at the spat stage. Six of them were conditioned for reproduction and three were found to be SH, and one produced a limited but viable progeny by self-fertilization (SF2). Oysters were sampled and genotyped with 226 SNP markers, confirming that the SF1 and the SF2 oysters were produced by self-fertilization over two successive generations. To our knowledge, it is the second study reporting the feasibility of production on an inbred line of Pacific oysters by self-fertilization using a simultaneous hermaphrodite as primary genitor, and the first study to generate two successive generations of selfing. Observed mean inbreeding coefficient of SF2 oysters produced by selfing for two generations was 0.61, ranging from 0.46 to 0.80. This coefficient was lower than the expected theoretical value (0.8125), suggesting that the most homozygous offspring died at early stages due to inbreeding depression. Our study demonstrates that inbred lines of Pacific oysters can be produced by self-fertilization but may exhibit higher heterozygosity than theoretically expected due to better survival of the most heterozygous offspring.

In Vitro Gynogenesis in Leek (Allium ampeloprasum L.).

Leek (A. ampeloprasum L.) is an economically important vegetable crop from Alliaceae family. It is a non-bulb forming biennial species grown for its pseudostem and leaves. Leek is a tetraploid with one of the largest genomes known among cultivated plant species. It has enormous economic importance all around the world for many purposes such as vegetable, medicinal herb, and food seasoning. Production and consumption of leek is in rise all around the world and breeders are trying to develop new F1 hybrid varieties with desired agronomical traits. Although self-compatible, leek shows high tendency toward outcrossing and display severe inbreeding depression when selfed with its own pollen. Therefore, inbred development through classical breeding techniques is very difficult in this crop. Traditional leek genotypes are highly heterozygous, open pollinated varieties. There is a high demand for F1 hybrid varieties with resistance to biotic and abiotic stresses and high-quality plants. Our group is trying to incorporate gynogenesis-based doubled haploid technology to leek improvement programs. Over the years, many experiments were carried out to determine the gynogenic potential of donor leek genotypes of different genetic backgrounds in different induction media. Here, we report a protocol allowing production of green gynogenic leek plants via single step culture of unopened flower buds. Ploidy levels of gynogenic regenerants are determined by flow cytometry analysis. A majority of the gynogenic leek regenerants produced survived well in vivo.

Creation of a highly homozygous diploid potato using the S locus inhibitor (Sli) gene

Potato is a heterozygous autotetraploid crop propagated as tubers. Diploid potatoes, which are mostly self-incompatible due to gametophytic self-incompatibility, are often used to reduce genetic complexity. The discovery of the S locus inhibitor (Sli) gene has created a way to develop diploid inbred lines and perform F1 hybrid breeding in potato. However, residual heterozygosity found in advanced-generation selfed progenies has posed the question of whether a minimum level of heterozygosity is necessary to maintain self-fertility. We continued selfing and finally identified a highly homozygous diploid potato among tenth-generation selfed progeny, which was homozygous at all 18,579 genome-wide single nucleotide polymorphism (SNP) markers surveyed. The S10 plants suffered severe inbreeding depression in terms of fertility and vigor, showing a small number of mature flowers and extremely slow growth. Although asexual techniques such as anther culture followed by chromosome doubling can result in completely homozygous diploid potatoes, all previously derived plants were male sterile. In contrast, continuous selfing using Sli swept out all lethal alleles and selected for self-fertility, which generated a highly homozygous diploid potato retaining male and female fertility and tuberization ability under long days.

Synthetic cultivar parent number impacts on genetic drift and disease resistance in alfalfa

AbstractAlfalfa (Medicago sativa L.) varieties are generally bred as synthetics. The number of selected parents to create a variety is important during breeding, as alfalfa suffers from severe inbreeding depression. In this study, we tested if there was more genetic drift in synthetic populations with fewer parents (i.e., narrow‐based synthetics) as measured by two parameters: a loss of allelic richness and changes in disease resistance. Out of five base germplasms, parents were selected based on plant field vigor to create derived narrow‐based (six‐parent) and broad‐based (56‐ to 86‐parent) synthetics in order to test the new synthetics compared with their base populations for resistance to four diseases: anthracnose, Phytophthora root rot (PRR), Aphanomyces root rot (ARR), and Fusarium wilt (FW). Using simple sequence repeat (SSR) DNA markers, we also calculated allele frequency changes and allele richness for the original populations and the selected parents of the derived synthetics. Based on the DNA markers, we saw strong evidence of greater genetic drift in the narrow‐based selections compared with the broad‐based selections. The narrow selections had greater allele frequency changes and had fewer (11.5–33.9% fewer) alleles compared with the broad selections and original populations. There was only moderate evidence of genetic drift affecting disease resistance. Within some populations, parent number had an effect on anthracnose and FW resistance, but not PRR or ARR resistance. We suspect that because disease resistance is a complex, often multigenic trait in alfalfa, disease resistance is less influenced by genetic drift, particularly compared with neutral DNA markers.

Lack of strong selection pressures maintains wide variation in floral traits in a food-deceptive orchid.

Angiosperms vary remarkably in traits such as colour, size and shape of flowers, yet such variation generally tends to be low within species. In deceptive orchids, however, large variation in floral traits has been described, not only between but also within populations. Nonetheless, the factors driving variation in floral traits in deceptive orchids remain largely unclear. To identify determinants of variation in floral traits, we investigated patterns of fruit set and selection gradients in the food-deceptive orchid Orchis purpurea, which typically presents large within-population variation in the colour and size of the flowers. Using long-term data, fruit set was quantified in two populations over 16 consecutive years (2004-2019). Artificial hand pollination was performed to test the hypothesis that fruit set was pollinator-limited and that selfing led to decreased seed set and viability. Annual variation (2016-2019) in selection gradients was calculated for three colour traits (brightness, contrast and the number of spots on the labellum), flower size (spur length, labellum length and width) and plant size (number of flowers, plant height). Fruit set was, on average, low (~12 %) and severely pollinator-limited. Opportunities for selection varied strongly across years, but we found only weak evidence for selection on floral traits. In contrast, there was strong and consistent positive selection on floral display. Selfing led to reduced production of viable seeds and hence severe inbreeding depression (δ = 0.38). Overall, these results demonstrate that the large variation in flower colour and size that is regularly observed in natural O. purpurea populations is maintained by the consistent lack of strong selection pressures on these traits through time.

Assembly and characterisation of a unique onion diversity set identifies resistance to Fusarium basal rot and improved seedling vigour

Key messageA unique, global onion diversity set was assembled, genotyped and phenotyped for beneficial traits. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers.Conserving biodiversity is critical for safeguarding future crop production. Onion (Allium cepa L.) is a globally important crop with a very large (16 Gb per 1C) genome which has not been sequenced. While onions are self-fertile, they suffer from severe inbreeding depression and as such are highly heterozygous as a result of out-crossing. Bulb formation is driven by daylength, and accessions are adapted to the local photoperiod. Onion seed is often directly sown in the field, and hence seedling establishment is a critical trait for production. Furthermore, onion yield losses regularly occur worldwide due to Fusarium basal rot caused by Fusarium oxysporum f. sp. cepae. A globally relevant onion diversity set, consisting of 10 half-sib families for each of 95 accessions, was assembled and genotyping carried out using 892 SNP markers. A moderate level of heterozygosity (30–35%) was observed, reflecting the outbreeding nature of the crop. Using inferred phylogenies, population structure and principal component analyses, most accessions grouped according to local daylength. A high level of intra-accession diversity was observed, but this was less than inter-accession diversity. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers, confirming the utility of the diversity set for discovering beneficial traits. The onion diversity set and associated trait data therefore provide a valuable resource for future germplasm selection and onion breeding.

Full-diallel-based analysis of genetic parameters for growth traits in Japanese larch (Larix kaempferi)

Genetic parameters were estimated for tree height (H), diameter at breast height (DBH), and volume from a progeny trial conducted in Japanese larch (Larix kaempferi) in Liaoning, China. A 12 × 12 full-diallel mating design with selfing was adopted, and data were collected in 2005 and 2014 at 20 and 29 years after planting. Based on an analysis of 55 of 144 potential crosses, general combining ability (GCA) and specific combining ability (SCA) were statistically significant for these traits. Variance was larger in SCA than in GCA in 2005, and the ratio of SCA to GCA was lower in 2014. Estimates of narrow-sense heritability were low to moderate, ranging from 0.10 for DBH to 0.14 for H, in 2005 and decreased in all traits except H as the trees aged. The reciprocal effect was not significant. Selfed progeny did not show severe inbreeding depression for survival or growth. The results of this study will facilitate the development of breeding and deployment strategies to increase the efficiency of genetic improvement in Japanese larch.

Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction.

The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annotated reference genomes. To characterize the genome-wide effects of intense inbreeding and isolation, we performed whole-genome sequencing and morphological analysis of an iconic inbred population, the gray wolves (Canis lupus) of Isle Royale. Through population genetic simulations and comparison with wolf genomes from a variety of demographic histories, we find evidence that severe inbreeding depression in this population is due to increased homozygosity of strongly deleterious recessive mutations. Our results have particular relevance in light of the recent translocation of wolves from the mainland to Isle Royale, as well as broader implications for management of genetic variation in the fragmented landscape of the modern world.

The genetic basis of inbreeding depression in potato.

Inbreeding depression confers reduced fitness among the offspring of genetic relatives. As a clonally propagated crop, potato (Solanum tuberosum L.) suffers from severe inbreeding depression; however, the genetic basis of inbreeding depression in potato is largely unknown. To gain insight into inbreeding depression in potato, we evaluated the mutation burden in 151 diploid potatoes and obtained 344,831 predicted deleterious substitutions. The deleterious mutations in potato are enriched in the pericentromeric regions and are line specific. Using three F2 populations, we identified 15 genomic regions with severe segregation distortions due to selection at the gametic and zygotic stages. Most of the deleterious recessive alleles affecting survival and growth vigor were located in regions with high recombination rates. One of these deleterious alleles is derived from a rare mutation that disrupts a gene required for embryo development. This study provides the basis for genome design of potato inbred lines.

Optimal sex allocation under pollen limitation

Most flowering plants are simultaneous hermaphrodites. Within species and even within local populations, sex allocation is usually highly plastic. Here, we link pollen sufficiency to the size of pollen-exchanging groups (i.e., pollen neighborhoods) and to pollen transfer efficiency, using an individual-based game-theoretic framework to determine the stable distribution of sex allocation that does not require the unrealistic assumption of infinitely large, panmictic populations. In the absence of selfing, we obtain the novel result that pollen limitation destabilizes hermaphroditism and favors separate sexes, whereas hermaphroditism remains stable without pollen limitation. With mixed mating, hermaphroditism is stable except when the fitness value of selfed offspring is less than half that of outcrossed offspring (i.e., strong inbreeding depression). In that case, the size of pollen neighborhoods, pollen transfer efficiencies, and the relative fitness of selfed offspring determine whether separate sexes or hermaphroditism is the stable outcome. The model thus predicts that separate sexes can derive from either of two ancestral states: obligate outcrossing under pollen limitation, or mixed mating (competing self-fertilization) under severe inbreeding depression. It also predicts conditions under which variance in sex-allocation among hermaphrodites within pollen exchanging groups along a gradient of pollen limitation can range from high (dioecy) to near zero (equal proportions of male and female investment).