Quantitative variation for apomictic reproduction in the genus Boechera (Brassicaceae)

Widespread application of apomixis in agriculture requires further study of natural apomicts

Apomixis, or asexual reproduction through seeds, is frequent in nature but does not exist in any major crop species, yet the phenomenon has captivated researchers for decades given its potential for clonal seed production and plant breeding. A discussion on whether this field will benefit from the continued study of natural apomicts is warranted given the recent outstanding progress in engineering apomixis. Here, we summarize what is known about its genetic control and the status of applying synthetic apomixis in agriculture. We argue there is still much to be learned from natural apomicts, and learning from them is necessary to improve on current progress and guarantee the effective application of apomixis beyond the few genera it has shown promise in so far. Specifically, we stress the value of studying the repeated evolution of natural apomicts in a phylogenetic and comparative -omics context. Finally, we identify outstanding questions in the field and discuss how technological advancements can be used to help close these knowledge gaps. In particular, genomic resources are lacking for apomicts, and this must be remedied for widespread use of apomixis in agriculture.

Apomixis and the paradox of sex in plants

BACKGROUND

The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species.

SCOPE

This review compares the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity in comparison to asexuality are discussed in the light of developmental, evolutionary, genetic and phylogenetic studies.

CONCLUSIONS

Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms for oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles and prolonged multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is not well understood. In plants in general, the costs of mating are low because of predominant hermaphroditism. Phylogenetic patterns in the archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long-term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.

Differential expression and evolutionary diversification of RNA helicases in Boechera sexual and apomictic reproduction

In higher plants, sexual reproduction is characterized by meiosis of the first cells of the germlines, and double fertilization of the egg and central cell after gametogenesis. In contrast, in apomicts of the genus Boechera, meiosis is omitted or altered and only the central cell requires fertilization, while the embryo forms parthenogenetically from the egg cell. To deepen the understanding of the transcriptional basis underlying these differences, we applied RNA-seq to compare expression in reproductive tissues of different Boechera accessions. This confirmed previous evidence of an enrichment of RNA helicases in plant germlines. Furthermore, few RNA helicases were differentially expressed in female reproductive ovule tissues harboring mature gametophytes from apomictic and sexual accessions. For some of these genes, we further found evidence for a complex recent evolutionary history. This included a homolog of Arabidopsis thaliana FASCIATED STEM4 (FAS4). In contrast to AtFAS4, which is a single-copy gene, FAS4 is represented by three homologs in Boechera, suggesting a potential for subfunctionalization to modulate reproductive development. To gain first insights into functional roles of FAS4, we studied Arabidopsis lines carrying mutant alleles. This identified the crucial importance of AtFAS4 for reproduction, as we observed developmental defects and arrest during male and female gametogenesis.

Sex- versus apomixis-specific polymorphisms in the 5'UTR of APOLLO from Boechera shift gene expression from somatic to reproductive tissues in Arabidopsis

Introduction

Among candidate genes underlying the control components of apomixis, APOLLO is known for its strong linkage to apomeiosis in the genus Boechera. The gene has "apo alleles," which are characterized by a set of linked apomixis-specific polymorphisms, and "sex alleles." All apomictic Boechera genotypes are heterozygous for the apo/sex alleles, whereas all sexual genotypes are homozygous for sex alleles.

Methods

In this study, native and synthetic APOLLO promoters were characterized by detecting the expression level of the β-glucuronidase (GUS) gene in Arabidopsis.

Results

Comparing various flower developmental stages in transgenic lines containing different constructs with 2-kb native transgenic lines revealed that changes to the APOLLO promoter causes shifts in tissue and developmental stage specificity of GUS expression. Importantly, several apomixis-specific polymorphisms in the 5'UTR change the timing and location of GUS activity from somatic to reproductive tissues.

Discussion

These synthetic data simulate a plausible evolutionary process, whereby apomixis-specific gene activity can be achieved.

The phenomenon of autonomous endosperm in sexual and apomictic plants

Endosperm is a key nutritive tissue that supports the developing embryo or seedling, and serves as a major nutritional source for human and livestock feed. In sexually-reproducing flowering plants, it generally develops after fertilization. However, autonomous endosperm (AE) formation (i.e. independent of fertilization) is also possible. Recent findings of AE loci/ genes and aberrant imprinting in native apomicts, together with a successful initiation of parthenogenesis in rice and lettuce, have enhanced our understanding of the mechanisms bridging sexual and apomictic seed formation. However, the mechanisms driving AE development are not well understood. This review presents novel aspects related to AE development in sexual and asexual plants underlying stress conditions as the primary trigger for AE. Both application of hormones to unfertilized ovules and mutations that impair epigenetic regulation lead to AE development in sexual Arabidopsis thaliana, which may point to a common pathway for both phenomena. Apomictic-like AE development under experimental conditions can take place due to auxin-dependent gene expression and/or DNA methylation.

Geographical Parthenogenesis in Alpine and Arctic Plants

The term "Geographical parthenogenesis" describes the phenomenon that asexual organisms usually occupy larger and more northern distribution areas than their sexual relatives, and tend to colonize previously glaciated areas. Several case studies on alpine and arctic plants confirm the geographical pattern, but the causal factors behind the phenomenon are still unclear. Research of the last decade in several plant families has shed light on the question and evaluated some of the classical evolutionary theories. Results confirmed, in general, that the advantages of uniparental reproduction enable apomictic plants to re-colonize faster in larger and more northern distribution areas. Associated factors like polyploidy seem to contribute mainly to the spatial separation of sexual and asexual cytotypes. Ecological studies suggest a better tolerance of apomicts to colder climates and temperate extremes, whereby epigenetic flexibility and phenotypic plasticity play an important role in occupying ecological niches under harsh conditions. Genotypic diversity appears to be of lesser importance for the distributional success of asexual plants. Classical evolutionary theories like a reduced pressure of biotic interactions in colder climates and hence an advantage to asexuals (Red Queen hypothesis) did not gain support from studies on plants. However, it is also still enigmatic why sexual outcrossing remains the predominant mode of reproduction also in alpine floras. Constraints for the origin of apomixis might play a role. Interestingly, some studies suggest an association of sexuality with abiotic stresses. Light stress in high elevations might explain why most alpine plants retain sexual reproduction despite other environmental factors that would favor apomixis. Directions for future research will be given.

Reproduction Modes and Conservation Implications in Three Polyploid Sorbus Stenoendemics in Eastern Slovakia (Central Europe)

The remarkable species diversity of the genus Sorbus is a result of polyploidization and frequent hybridization between interacting species of different cytotypes. Moreover, hybridization is possible between several parental taxa. Gametophytic apomixis, which is common among polyploid Sorbus taxa, indicates the role of clonal reproduction in the evolutionary stabilization of hybridogeneous genotypes. The precise determination of the origin of seeds and their quantitative evaluation may elucidate inter-cytotype interactions, the potential role of mixed-cytotype populations in evolutionary success, and the long-term survival of some hybrid species. We investigated the reproduction modes of selected species of Sorbus in mixed-cytotype populations in eastern Slovakia, Central Europe. We determined the pollen quality, seed production rate, and the ploidy level of mature trees, as well as the origin of the embryo and endosperm in seeds of the stenoendemics S. amici-petri, S. dolomiticola, and S. hornadensis. The tetraploids S. amici-petri and S. hornadensis are characterized by regular and highly stainable pollen grains and reproduce predominantly via pseudogamous apomixis. In contrast, triploid S. dolomiticola usually has oval, heterogenous, and weakly stainable pollen grains, suggesting male meiotic irregularities. Although seeds originate via pseudogamous apomixis in S. dolomiticola as well, the ploidy level of sperm cells participating in the fertilization of central cells is usually determined by co-occurring species of different cytotypes. This suggests that maintaining mating partners is necessary for the long-term survival of a triploid species. We documented rare B_III hybrids and the residual sexuality in tetraploids. The distribution of seeds of meiotic and apomeiotic origins in S. amici-petri shows bimodal characteristics; however, genotypes with predominantly sexual seed types are rare. Reproduction modes documented in polyploid stenoendemics of Sorbus and inferred microevolutionary intercytotype relationships highlight the mixed-cytotype populations as the source of biodiversity in apomictic plant complexes. We suggest that conservation efforts should focus on maintaining the species and cytotypic diversity of Sorbus populations, especially when it comes to the conservation of triploid species.

Variability of Reproduction Pathways in the Central-European Populations of Hawthorns with Emphasis on Triploids

The role of apomeiosis, parthenogenesis, and pseudogamy in the asexual reproduction of some plant groups has not been fully elucidated in relation to species diversification. Quantitative analyses of seed origin may help in gaining better understanding of intercytotypic interactions. Asexual reproduction associated with polyploidy and frequent hybridization plays a crucial role in the evolutionary history of the genus Crataegus in North America. In Europe, the genus represents a taxonomically complex and very difficult species group not often studied using a modern biosystematic approach. We investigated the reproduction pathways in mixed-cytotype populations of selected taxa of Crataegus in eastern Slovakia, Central Europe. The investigated accessions were characterized by seed production data and the ploidy level of mature plants as well as the embryo and endosperm tissues of their seeds determined via flow cytometry. Diploid and polyploid hawthorns reproduce successfully; they also produce high numbers of seeds. An exception is represented by an almost sterile triploid. Diploids reproduce sexually. Polyploids shift to asexual reproduction, but pseudogamy seems to be essential for regular seed development. In rare cases, fertilization of unreduced gametes occurs, which offers opportunity for the establishment of new polyploid cytotypes between diploid sexuals and polyploid asexuals. Opposite to sexual diploids, triploids are obligate, and tetraploids almost obligate apomicts. Apomixis is considered to help stabilize individual weakly differentiated polyploid microspecies. Pseudogamy is a common feature and usually leads to unbalanced maternal to paternal contribution in the endosperm of triploid accessions. Parental contribution to endosperm gene dosage is somehow relaxed in triploids. Our Crataegus plant system resembles reproduction in the diploids and polyploids of North American hawthorns. Our data provide support for the hypothesis that polyploidization, shifts in reproduction modes, and hybridization shape the genus diversity also in Central Europe.

Seed size, endosperm and germination variation in sexual and apomictic Boechera

Asexual reproduction results in offspring that are genetically identical to the mother. Among apomictic plants (reproducing asexually through seeds) many require paternal genetic contribution for proper endosperm development (pseudogamous endosperm). We examined phenotypic diversity in seed traits using a diverse panel of sexual and apomictic accessions from the genus Boechera. While genetic uniformity resulting from asexual reproduction is expected to reduce phenotypic diversity in seeds produced by apomictic individuals, pseudogamous endosperm, variable endosperm ploidy, and the deviations from 2:1 maternal:paternal genome ratio in endosperm can all contribute to increased phenotypic diversity among apomictic offspring. We characterized seed size variation in 64 diploid sexual and apomictic (diploid and triploid) Boechera lineages. In order to find out whether individual seed size was related to endosperm ploidy we performed individual seed measurements (projected area and mass) using the phenoSeeder robot system and flow cytometric seed screen. In order to test whether individual seed size had an effect on resulting fitness we performed a controlled growth experiment and recorded seedling life history traits (germination success, germination timing, and root growth rate). Seeds with triploid embryos were 33% larger than those with diploid embryos, but no average size difference was found between sexual and apomictic groups. We identified a maternal effect whereby chloroplast lineage 2 had 30% larger seeds than lineage 3, despite having broad and mostly overlapping geographic ranges. Apomictic seeds were not more uniform in size than sexual seeds, despite genetic uniformity of the maternal gametophyte in the former. Among specific embryo/endosperm ploidy combinations, seeds with tetraploid (automomous) endosperm were on average smaller, and the proportion of such seeds was highest in apomicts. Larger seeds germinated more quickly than small seeds, and lead to higher rates of root growth in young seedlings. Seed mass is under balancing selection in Boechera, and it is an important predictor of several traits, including germination probability and timing, root growth rates, and developmental abnormalities in apomictic accessions.

Variation of Residual Sexuality Rates along Reproductive Development in Apomictic Tetraploids of Paspalum

Most apomictic plants are facultative, maintaining the ability to reproduce sexually at different frequencies depending on the taxa, ploidy, and reproductive stage. In this context, Paspalum species are good model systems for studies evaluating the varying levels of apomixis expression. We aimed to identify, in apomictic tetraploid Paspalum species, the degree of apomixis and residual sexuality in three stages of reproductive development, and if their expression varies along them in order to predict their realized impact on the genetic diversity of future generations. Three main stages in the reproductive development (i.e., ovule, seed, and progeny) were studied in tetraploids from populations of P. cromyorhizon and P. maculosum. Mature ovules were studied using cytoembryological analysis, seeds by flow cytometry, and progeny tests with molecular markers. The expression of sexuality and apomixis was compared in each stage. We observed a decline in expression of sexual reproduction through the consecutive stages, jointly with an increase of apomixis expression. Both species showed at least one tetraploid plant capable of producing progeny by sexual means. These small rates of sexually originated progeny prove the ability of apomictic plants to produce low levels of genetic variation through rare events of sexuality. This study also demonstrates the importance of analyzing different reproductive stages in order to get a whole picture of the reproductive outcomes in plant evolution.

Evolution of an Apomixis-Specific Allele Class in Supernumerary Chromatin of Apomictic Boechera

Asexual reproduction through seeds in plants (i.e., apomixis) is a heritable trait, and apomixis- linked loci have been identified in multiple species. However, direct identification of genomic elements is typically hindered as apomixis-linked loci and are commonly found in recombination-suppressed and repetitive regions. Heterochromatinized elements, such as B chromosomes and other supernumerary chromosomal DNA fragments have long been known to be associated with asexuality in both plants and animals and are prime candidate regions for the evolution of multiple apomixis factors controlling the individual elements of apomixis. Here, we examined molecular evolution, gene regulation, and chromosomal location of a male apomeiosis factor (UPG2), a long noncoding RNA gene, in sexual and apomictic Boechera with and without male apomeiosis (i.e., balanced and unbalanced apomicts). We revealed the origin of the gene in the apomixis genome on an apomixis-specific, supernumerary heterochromatic Boechera chromosome (Boe1). The UPG2 is active in the tapetum at male meiosis. We found allele classes specific to apomictic and sexual Boechera accessions and a third class that shares the features of both and points to a convergent transition state. Sex alleles are found only in some of the sexual accessions and have higher nucleotide divergence and lower transcriptional activity compared to apo alleles. These data demonstrate selective pressure to maintain the function of UPG2 for unreduced pollen formation in apomicts as the occasional transmission of the allele from unbalanced apomicts into sexual organisms that lead to pseudogenization and functional decay of copies in sexual organisms.

Phylogenetic and Expression Analysis of CENH3 and APOLLO Genes in Sexual and Apomictic Boechera Species

Apomictic plants (reproducing via asexual seeds), unlike sexual individuals, avoid meiosis and egg cell fertilization. Consequently, apomixis is very important for fixing maternal genotypes in the next plant generations. Despite the progress in the study of apomixis, molecular and genetic regulation of the latter remains poorly understood. So far APOLLO gene encoding aspartate glutamate aspartate aspartate histidine exonuclease is one of the very few described genes associated with apomixis in Boechera species. The centromere-specific histone H3 variant encoded by CENH3 gene is essential for cell division. Mutations in CENH3 disrupt chromosome segregation during mitosis and meiosis since the attachment of spindle microtubules to a mutated form of the CENH3 histone fails. This paper presents in silico characteristic of APOLLO and CENH3 genes, which may affect apomixis. Furthermore, we characterize the structure of CENH3 by bioinformatic tools, study expression levels of APOLLO and CENH3 transcripts by Real-Time Polymerase Chain Reaction RT-PCR in gynoecium/siliques of the natural diploid apomictic and sexual Boechera species at the stages of meiosis and before and after fertilization. While CENH3 was a single copy gene in all Boechera species, the APOLLO gene have several polymorphic alleles associated with sexual and apomictic reproduction in the Boechera genera. Expression of the APOLLO apo-allele during meiosis was upregulated in gynoecium of apomict B. divaricarpa downregulating after meiosis until the 4th day after pollination (DAP). On the 5th DAP, expression in apomictic siliques increased again. In sexual B. stricta gynoecium and siliques APOLLO apo-allele did not express. Expression of the APOLLO sex-allele during and after meiosis in gynoecium of sexual plants was several times higher than that in apomictic gynoecium. However, after pollination the sex-allele was downregulated in sexual siliques to the level of apomicts and increased sharply on the 5th DAP, while in apomictic siliques it almost did not express. At the meiotic stage, the expression level of CENH3 in the gynoecium of apomicts was two times lower than that of the sexual Boechera, decreasing in both species after meiosis and keep remaining very low in siliques of both species for several days after artificial pollination until the 4th DAP, when the expression level raised in sexual B. stricta siliques exceeding 5 times the level in apomictic B. divaricarpa siliques. We also discuss polymorphism and phylogeny of the APOLLO and CENH3 genes. The results obtained may indicate to a role of the CENH3 and APOLLO genes in the development of apomixis in species of the genus Boechera.

Environmental and Genetic Factors Affecting Apospory Expressivity in Diploid Paspalum rufum

In angiosperms, gametophytic apomixis (clonal reproduction through seeds) is strongly associated with polyploidy and hybridization. The trait is facultative and its expressivity is highly variable between genotypes. Here, we used an F₁ progeny derived from diploid apomictic (aposporic) genotypes of Paspalum rufum and two F₂ families, derived from F₁ hybrids with different apospory expressivity (%AES), to analyze the influence of the environment and the transgenerational transmission of the trait. In addition, AFLP markers were developed in the F₁ population to identify genomic regions associated with the %AES. Cytoembryological analyses showed that the %AES was significantly influenced by different environments, but remained stable across the years. F₁ and F₂ progenies showed a wide range of %AES variation, but most hybrids were not significantly different from the parental genotypes. Maternal and paternal genetic linkage maps were built covering the ten expected linkage groups (LG). A single-marker analysis detected at least one region of 5.7 cM on LG3 that was significantly associated with apospory expressivity. Our results underline the importance of environmental influence in modulating apospory expressivity and identified a genomic region associated with apospory expressivity at the diploid level.

Application-based guidelines for best practices in plant flow cytometry

Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.

Clone worth? Genetic diversity in obligate apomictic Miconia albicans (Melastomataceae)

Apomixis is the asexual production of seeds by plants and, in theory, would render low genetic diversity and even clonal lineages. However, recent studies have shown otherwise, although is not always clear where the genetic diversity of obligate apomicts comes from. We evaluated the genetic diversity among sister seedlings of M. albicans, an obligate apomictic species in Cerrado, Neotropical Savannas in Central Brazil. A total of 50 seedlings from five individuals were analysed using ISSR primers. We obtained 107 fragments, all with good resolution, consistently observed and replicable. The percentage of polymorphic loci ranged from 28.04% to 33.64% and Shannon's information index (I) averaged 0.173. The expected heterozygosity (He) averaged 0.117, similar to the observed for populations of M. albicans and other selfed species. Only two seedlings showed the same genotype (possible clones), but most differed at least for five loci. Most of variance was among progenies (62%), but we found that 38% was within progenies. Genetic distances separated the progenies in two groups, and analogous analyses between individuals reconstructed the original progenies clustering. The results confirmed a relatively high genetic diversity among sister seedling of this obligatory apomictic plant and clones were rare. This diversity can be generated during development, probably by restitutional meiosis or other recombination processes. These differences may accumulate into lineages and populations well adapted to heterogenous Cerrado environment.

Eragrostis curvula, a Model Species for Diplosporous Apomixis

Eragrostis curvula (Schrad.) Ness is a grass with a particular apomictic embryo sac development called Eragrostis type. Apomixis is a type of asexual reproduction that produces seeds without fertilization in which the resulting progeny is genetically identical to the mother plant and with the potential to fix the hybrid vigour from more than one generation, among other advantages. The absence of meiosis and the occurrence of only two rounds of mitosis instead of three during embryo sac development make this model unique and suitable to be transferred to economically important crops. Throughout this review, we highlight the advances in the knowledge of apomixis in E. curvula using different techniques such as cytoembryology, DNA methylation analyses, small-RNA-seq, RNA-seq, genome assembly, and genotyping by sequencing. The main bulk of evidence points out that apomixis is inherited as a single Mendelian factor, and it is regulated by genetic and epigenetic mechanisms controlled by a complex network. With all this information, we propose a model of the mechanisms involved in diplosporous apomixis in this grass. All the genetic and epigenetic resources generated in E. curvula to study the reproductive mode changed its status from an orphan to a well-characterised species.

Apomixis and genetic background affect distinct traits in Hieracium pilosella L. grown under competition

BACKGROUND

Apomixis, the asexual reproduction through seeds, occurs in over 40 plant families and avoids the hidden cost of sex. Apomictic plants are thought to have an advantage in sparse populations and when colonizing new areas but may have a disadvantage in changing environments because they propagate via fixed genotypes. In this study, we separated the influences of different genetic backgrounds (potentially reflecting local adaptation) from those of the mode of reproduction, i.e., sexual vs. apomictic, on nine fitness-related traits in Hieracium pilosella L. We aimed to test whether apomixis per se may provide a fitness advantage in different competitive environments in a common garden setting.

RESULTS

To separate the effects of genetic background from those of reproductive mode, we generated five families of apomictic and sexual full siblings by crossing two paternal with four maternal parents. Under competition, apomictic plants showed reproductive assurance (probability of seeding, fertility), while offspring of sexual plants with the same genetic background had a higher germination rate. Sexual plants grew better (biomass) than apomictic plants in the presence of grass as a competitor but apomictic plants spread further vegetatively (maximum stolon length) when their competitors were sexual plants of the same species. Furthermore, genetic background as represented by the five full-sibling families influenced maximum stolon length, the number of seeds, and total fitness. Under competition with grass, genetic background influenced fecundity, the number of seeds, and germination rate.

CONCLUSIONS

Our results suggest that both the mode of reproduction as well as the genetic background affect the success of H. pilosella in competitive environments. Total fitness, the most relevant trait for adaptation, was only affected by the genetic background. However, we also show for the first time that apomixis per se has effects on fitness-related traits that are not confounded by-and thus independent of-the genetic background.

Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures

Apomixis, a type of asexual reproduction in angiosperms, results in progenies that are genetically identical to the mother plant. It is a highly desirable trait in agriculture due to its potential to preserve heterosis of F₁ hybrids through subsequent generations. However, no major crops are apomictic. Deciphering mechanisms underlying apomixis becomes one of the alternatives to engineer self-reproducing capability into major crops. Parthenogenesis, a major component of apomixis, commonly described as the ability to initiate embryo formation from the egg cell without fertilization, also can be valuable in plant breeding for doubled haploid production. A deeper understanding of transcriptional differences between parthenogenetic and sexual or non-parthenogenetic eggs can assist with pathway engineering. By conducting laser capture microdissection-based RNA-seq on sexual and parthenogenetic egg cells on the day of anthesis, a de novo transcriptome for the Cenchrus ciliaris egg cells was created, transcriptional profiles that distinguish the parthenogenetic egg from its sexual counterpart were identified, and functional roles for a few transcription factors in promoting natural parthenogenesis were suggested. These transcriptome data expand upon previous gene expression studies and will be a resource for future research on the transcriptome of egg cells in parthenogenetic and sexual genotypes.

Differential Epigenetic Marks Are Associated with Apospory Expressivity in Diploid Hybrids of Paspalum rufum

Apomixis seems to emerge from the deregulation of preexisting genes involved in sexuality by genetic and/or epigenetic mechanisms. The trait is associated with polyploidy, but diploid individuals of Paspalum rufum can form aposporous embryo sacs and develop clonal seeds. Moreover, diploid hybrid families presented a wide apospory expressivity variation. To locate methylation changes associated with apomixis expressivity, we compare relative DNA methylation levels, at CG, CHG, and CHH contexts, between full-sib P. rufum diploid genotypes presenting differential apospory expressivity. The survey was performed using a methylation content-sensitive enzyme ddRAD (MCSeEd) strategy on samples at premeiosis/meiosis and postmeiosis stages. Based on the relative methylation level, principal component analysis and heatmaps, clearly discriminate samples with contrasting apospory expressivity. Differential methylated contigs (DMCs) showed 14% of homology to known transcripts of Paspalum notatum reproductive transcriptome, and almost half of them were also differentially expressed between apomictic and sexual samples. DMCs showed homologies to genes involved in flower growth, development, and apomixis. Moreover, a high proportion of DMCs aligned on genomic regions associated with apomixis in Setaria italica. Several stage-specific differential methylated sequences were identified as associated with apospory expressivity, which could guide future functional gene characterization in relation to apomixis success at diploid and tetraploid levels.

The spread of infectious asexuality through haploid pollen

The mechanisms of initiation and transmission of apomixis (asexual reproduction through seeds) in natural plant populations are important for understanding the evolution of reproductive variation. Here, we used the phylogenetic diversity of the genus Boechera (Brassicaceae), together with natural diversity in pollen types produced by apomictic lines, to test whether hybridization triggers the transition to asexuality, and whether a 'triploid bridge' is required for the formation of polyploid apomicts. We performed crosses between diploid sexual recipient and diploid apomictic donor lines and tested whether the mating system (interspecific hybridization vs intraspecific outcrossing) or pollen type (haploid vs diploid) influenced the transmission of apomixis from diploid apomictic donors into sexual recipients. We used genetic markers and flow cytometric analyses of embryo and endosperm in seeds to infer the reproductive mode. Within a single generation, initiation of both diploid and polyploid apomixis in sexual Boechera can occur. Diploid apomixis is transmitted through haploid pollen (infectious asexuality) and polyploids can form through multiple pathways. The three functional elements of apomixis occasionally segregate. Variation in pollen ploidy and the segregation of apomixis elements drive reproductive diversity of hybrids and outcrosses and can be utilized for apomixis initiation in crop breeding programs.

Identifying the fitness consequences of sex in complex natural environments

In the natural world, sex prevails, despite its costs. Although much effort has been dedicated to identifying the intrinsic costs of sex (e.g., the cost of males), few studies have identified the ecological fitness consequences of sex. Furthermore, correlated biological traits that differ between sexuals and asexuals may alter these costs, or even render the typical costs of sex irrelevant. We conducted a large-scale, multisite, reciprocal transplant using multiple sexual and asexual genotypes of a native North American wildflower to show that sexual genotypes have reduced lifetime fitness, despite lower herbivory. We separated the effects of sex from those of hybridity, finding that overwinter survival is elevated in asexuals regardless of hybridity, but herbivores target hybrid asexuals more than nonhybrid asexual or sexual genotypes. Survival is lowest in homozygous sexual lineages, implicating inbreeding depression as a cost of sex. Our results show that the consequences of sex are shaped not just by sex itself, but by complex natural environments, correlated traits, and the identity and availability of mates.

Genetic Dissection of Apomixis in Dandelions Identifies a Dominant Parthenogenesis Locus and Highlights the Complexity of Autonomous Endosperm Formation

Apomixis in the common dandelion (Taraxacum officinale) consists of three developmental components: diplospory (apomeiosis), parthenogenesis, and autonomous endosperm development. The genetic basis of diplospory, which is inherited as a single dominant factor, has been previously elucidated. To uncover the genetic basis of the remaining components, a cross between a diploid sexual seed parent and a triploid apomictic pollen donor was made. The resulting 95 triploid progeny plants were genotyped with co-dominant simple-sequence repeat (SSR) markers and phenotyped for apomixis as a whole and for the individual apomixis components using Nomarski Differential Interference Contrast (DIC) microscopy of cleared ovules and seed flow cytometry. From this, a new SSR marker allele was discovered that was closely linked to parthenogenesis and unlinked to diplospory. The segregation of apomixis as a whole does not differ significantly from a three-locus model, with diplospory and parthenogenesis segregating as unlinked dominant loci. Autonomous endosperm is regularly present without parthenogenesis, suggesting that the parthenogenesis locus does not also control endosperm formation. However, the high recovery of autonomous endosperm is inconsistent with this phenotype segregating as the third dominant locus. These results highlight the genetic complexity underlying apomixis in the dandelion and underline the challenge of introducing autonomous apomixis into sexual crops.

Can We Use Gene-Editing to Induce Apomixis in Sexual Plants?

Apomixis, the asexual formation of seeds, is a potentially valuable agricultural trait. Inducing apomixis in sexual crop plants would, for example, allow breeders to fix heterosis in hybrid seeds and rapidly generate doubled haploid crop lines. Molecular models explain the emergence of functional apomixis, i.e., apomeiosis + parthenogenesis + endosperm development, as resulting from a combination of genetic or epigenetic changes that coordinate altered molecular and developmental steps to form clonal seeds. Apomixis-like features and synthetic clonal seeds have been induced with limited success in the sexual plants rice and maize by using gene editing to mutate genes related to meiosis and fertility or via egg-cell specific expression of embryogenesis genes. Inducing functional apomixis and increasing the penetrance of apomictic seed production will be important for commercial deployment of the trait. Optimizing the induction of apomixis with gene editing strategies that use known targets as well as identifying alternative targets will be possible by better understanding natural genetic variation in apomictic species. With the growing availability of genomic data and precise gene editing tools, we are making substantial progress towards engineering apomictic crops.

Chasing the Apomictic Factors in the Ranunculus auricomus Complex: Exploring Gene Expression Patterns in Microdissected Sexual and Apomictic Ovules

Apomixis, the asexual reproduction via seeds, is associated to polyploidy and hybridization. To identify possible signatures of apomixis, and possible candidate genes underlying the shift from sex to apomixis, microarray-based gene expression patterns of live microdissected ovules at four different developmental stages were compared between apomictic and sexual individuals of the Ranunculus auricomus complex. Following predictions from previous work on mechanisms underlying apomixis penetrance and expressivity in the genus, gene expression patterns were classified into three categories based on their relative expression in apomicts compared to their sexual parental ancestors. We found evidence of misregulation and differential gene expression between apomicts and sexuals, with the highest number of differences detected during meiosis progression and emergence of aposporous initial (AI) cells, a key developmental stage in the ovule of apomicts where a decision between divergent reproductive pathways takes place. While most of the differentially expressed genes (DEGs) could not be annotated, gene expression was classified into transgressive, parent of origin and ploidy effects. Genes related to gametogenesis and meiosis demonstrated patterns reflective of transgressive and genome dosage effects, which support the hypothesis of a dominant factor controlling apomixis in Ranunculus and modulated by secondary modifiers. Three genes with probable functions in sporogenesis and gametogenesis development are identified and characterized for future studies.

Sexual modulation in a polyploid grass: a reproductive contest between environmentally inducible sexual and genetically dominant apomictic pathways

In systems alternating between sexual and asexual reproduction, sex increases under unfavorable environmental conditions. In plants producing sexual and asexual (apomictic) seeds, studies on the influence of environmental factors on sex are equivocal. We used Paspalum intermedium to study environmental effects on the expression of sexual and apomictic developments, and on resulting reproductive fitness variables. Flow cytometric and embryological analyses were performed to characterize ploidy and reproductive modes, and effects of local climatic conditions on sexual and apomictic ovule and seed frequencies were determined. Seed set and germination data were collected and used to estimate reproductive fitness. Frequencies of sexual and apomictic ovules and seeds were highly variable within and among populations. Apomictic development exhibited higher competitive ability but lower overall fitness. Frequencies of sexual reproduction in facultative apomictic plants increased at lower temperatures and wider mean diurnal temperature ranges. We identified a two-fold higher fitness advantage of sexuality and a Tug of War between factors intrinsic to apomixis and environmental stressors promoting sexuality which influence the distribution of sex in apomictic populations. This points toward a crucial role of local ecological conditions in promoting a reshuffling of genetic variability that may be shaping the adaptative landscape in apomictic P. intermedium plants.

Epigenetic Patterns and Geographical Parthenogenesis in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae)

Polyploidization and the shift to apomictic reproduction are connected to changes in DNA cytosine-methylation. Cytosine-methylation is further sensitive to environmental conditions. We, therefore, hypothesize that DNA methylation patterns would differentiate within species with geographical parthenogenesis, i.e., when diploid sexual and polyploid apomictic populations exhibit different spatial distributions. On natural populations of the alpine plant Ranunculus kuepferi, we tested differences in methylation patterns across two cytotypes (diploid, tetraploid) and three reproduction modes (sexual, mixed, apomictic), and their correlation to environmental data and geographical distributions. We used methylation-sensitive amplified fragment-length polymorphism (methylation-sensitive AFLPs) and scored three types of epiloci. Methylation patterns differed independently between cytotypes versus modes of reproduction and separated three distinct combined groups (2x sexual + mixed, 4x mixed, and 4x apomictic), with differentiation of 4x apomicts in all epiloci. We found no global spatial autocorrelation, but instead correlations to elevation and temperature gradients in 22 and 36 epiloci, respectively. Results suggest that methylation patterns in R. kuepferi were altered by cold conditions during postglacial recolonization of the Alps, and by the concomitant shift to facultative apomixis, and by polyploidization. Obligate apomictic tetraploids at the highest elevations established a distinct methylation profile. Methylation patterns reflect an ecological gradient rather than the geographical differentiation.

Gene Function Rather than Reproductive Mode Drives the Evolution of RNA Helicases in Sexual and Apomictic Boechera

In higher plants, sexual and asexual reproductions through seeds (apomixis) have evolved as alternative strategies. Evolutionary advantages leading to coexistence of both reproductive modes are currently not well understood. It is expected that accumulation of deleterious mutations leads to a rapid elimination of apomictic lineages from populations. In this line, apomixis originated repeatedly, likely from deregulation of the sexual pathway, leading to alterations in the development of reproductive lineages (germlines) in apomicts as compared with sexual plants. This potentially involves mutations in genes controlling reproduction.

Increasing evidence suggests that RNA helicases are crucial regulators of germline development. To gain insights into the evolution of 58 members of this diverse gene family in sexual and apomictic plants, we applied target enrichment combined with next-generation sequencing to identify allelic variants from 24 accessions of the genus Boechera, comprising sexual, facultative, and obligate apomicts. Interestingly, allelic variants from apomicts did not show consistently increased mutation frequency. Either sequences were highly conserved in any accession, or allelic variants preferentially harbored mutations in evolutionary less conserved C- and N-terminal domains, or presented high mutation load independent of the reproductive mode. Only for a few genes allelic variants harboring deleterious mutations were only identified in apomicts. To test if high sequence conservation correlates with roles in fundamental cellular or developmental processes, we analyzed Arabidopsis thaliana mutant lines in VASA-LIKE (VASL), and identified pleiotropic defects during ovule and reproductive development. This indicates that also in apomicts mechanisms of selection are in place based on gene function.

Apomixis Technology: Separating the Wheat from the Chaff

Projections indicate that current plant breeding approaches will be unable to incorporate the global crop yields needed to deliver global food security. Apomixis is a disruptive innovation by which a plant produces clonal seeds capturing heterosis and gene combinations of elite phenotypes. Introducing apomixis into hybrid cultivars is a game-changing development in the current plant breeding paradigm that will accelerate the generation of high-yield cultivars. However, apomixis is a developmentally complex and genetically multifaceted trait. The central problem behind current constraints to apomixis breeding is that the genomic configuration and molecular mechanism that initiate apomixis and guide the formation of a clonal seed are still unknown. Today, not a single explanation about the origin of apomixis offer full empirical coverage, and synthesizing apomixis by manipulating individual genes has failed or produced little success. Overall evidence suggests apomixis arise from a still unknown single event molecular mechanism with multigenic effects. Disentangling the genomic basis and complex genetics behind the emergence of apomixis in plants will require the use of novel experimental approaches benefiting from Next Generation Sequencing technologies and targeting not only reproductive genes, but also the epigenetic and genomic configurations associated with reproductive phenotypes in homoploid sexual and apomictic carriers. A comprehensive picture of most regulatory changes guiding apomixis emergence will be central for successfully installing apomixis into the target species by exploiting genetic modification techniques.

Ploidy-Dependent Effects of Light Stress on the Mode of Reproduction in the Ranunculus auricomus Complex (Ranunculaceae)

Polyploidy in angiosperms is an influential factor to trigger apomixis, the reproduction of asexual seeds. Apomixis is usually facultative, which means that both sexual and apomictic seeds can be formed by the same plant. Environmental abiotic stress, e.g. light stress, can change the frequency of apomixis. Previous work suggested effects of stress treatments on meiosis and megasporogenesis. We hypothesized that polyploidy would alter the stress response and hence reproductive phenotypes of different cytotypes. The main aims of this research were to explore with prolonged photoperiods, whether polyploidy alters proportions of sexual ovule and sexual seed formation under light stress conditions. We used three facultative apomictic, pseudogamous cytotypes of the Ranunculus auricomus complex (diploid, tetraploid, and hexaploid). Stress treatments were applied by extended light periods (16.5 h) and control (10 h) in climate growth chambers. Proportions of apomeiotic vs. meiotic development in the ovule were evaluated with clearing methods, and mode of seed formation was examined by single seed flow cytometric seed screening (ssFCSS). We further studied pollen stainability to understand effects of pollen quality on seed formation. Results revealed that under extended photoperiod, all cytotypes produced significantly more sexual ovules than in the control, with strongest effects on diploids. The stress treatment affected neither the frequency of seed set nor the proportion of sexual seeds nor pollen quality. Successful seed formation appears to be dependent on balanced maternal: paternal genome contributions. Diploid cytotypes had mostly sexual seed formation, while polyploid cytotypes formed predominantly apomictic seeds. Pollen quality was in hexaploids better than in diploids and tetraploids. These findings confirm our hypothesis that megasporogenesis is triggered by light stress treatments. Comparisons of cytotypes support the hypothesis that ovule development in polyploid plants is less sensitive to prolonged photoperiods and responds to a lesser extent with sexual ovule formation. Polyploids may better buffer environmental stress, which releases the potential for aposporous ovule development from somatic cells, and may facilitate the establishment of apomictic seed formation.

Differential activity of F-box genes and E3 ligases distinguishes sexual versus apomictic germline specification in Boechera

Germline specification is the first step during sexual and apomictic plant reproduction, and takes place in the nucellus of the ovule, a specialized domain of the reproductive flower tissues. In each case, a sporophytic cell is determined to form the sexual megaspore mother cell (MMC) or an apomictic initial cell (AIC). These differ in their developmental fates: while the MMC undergoes meiosis, the AIC modifies or omits meiosis to form the female gametophyte. Despite great interest in these distinct developmental processes, little is known about their gene regulatory basis. To elucidate the gene regulatory networks underlying germline specification, we conducted tissue-specific transcriptional profiling using laser-assisted microdissection and RNA sequencing to compare the transcriptomes of nucellar tissues between different sexual and apomictic Boechera accessions representing four species and two ploidy levels. This allowed us to distinguish between expression differences caused by genetic background or reproductive mode. Statistical data analysis revealed 45 genes that were significantly differentially expressed, and which potentially play a role for determination of the reproductive mode. Based on annotations, these included F-box genes and E3 ligases that most likely relate to genes previously described as regulators important for germline development. Our findings provide novel insights into the transcriptional basis of sexual and apomictic reproduction.

A little bit of sex prevents mutation accumulation even in apomictic polyploid plants

Background

In the absence of sex and recombination, genomes are expected to accumulate deleterious mutations via an irreversible process known as Muller’s ratchet, especially in the case of polyploidy. In contrast, no genome-wide mutation accumulation was detected in a transcriptome of facultative apomictic, hexaploid plants of the Ranunculus auricomus complex. We hypothesize that mutations cannot accumulate in flowering plants with facultative sexuality because sexual and asexual development concurrently occurs within the same generation. We assume a strong effect of purging selection on reduced gametophytes in the sexual developmental pathway because previously masked recessive deleterious mutations would be exposed to selection.

Results

We test this hypothesis by modeling mutation elimination using apomictic hexaploid plants of the R. auricomus complex. To estimate mean recombination rates, the mean number of recombinants per generation was calculated by genotyping three F1 progeny arrays with six microsatellite markers and character incompatibility analyses. We estimated the strength of purging selection in gametophytes by calculating abortion rates of sexual versus apomictic development at the female gametophyte, seed and offspring stage. Accordingly, we applied three selection coefficients by considering effects of purging selection against mutations on (1) male and female gametophytes in the sexual pathway (additive, s = 1.000), (2) female gametophytes only (s = 0.520), and (3) on adult plants only (sporophytes, s = 0.212). We implemented recombination rates into a mathematical model considering the three different selection coefficients, and a genomic mutation rate calculated from genome size of our plants and plant-specific mutation rates. We revealed a mean of 6.05% recombinants per generation. This recombination rate eliminates mutations after 138, 204 or 246 generations, depending on the respective selection coefficients (s = 1.000, 0.520, and 0.212).

Conclusions

Our results confirm that the empirically observed frequencies of facultative recombination suffice to prevent accumulation of deleterious mutations via Muller’s ratchet even in a polyploid genome. The efficiency of selection is in flowering plants strongly increased by acting on the haplontic (reduced) gametophyte stage.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1495-z) contains supplementary material, which is available to authorized users.

The steps from sexual reproduction to apomixis

In this paper, an interaction model of apomixis-related genes was constructed to analyze the emergence of apomictic types. It is speculated that apomixis technology will be first implemented in gramineous plants. Apomixis (asexual seed formation) is a phenomenon in which a plant bypasses the most fundamental aspects of sexual reproduction-meiosis and fertilization-to form a viable seed. Plants can form seeds without fertilization, and the seed genotype is consistent with the female parent. The development of apomictic technology would be revolutionary for agriculture and for food production as it would reduce costs and breeding times and also avoid many complications typical of sexual reproduction (e.g. incompatibility barriers) and of vegetative propagation (e.g. viral transfer). The application of apomictic reproductive technology has the potential to revolutionize crop breeding. This article reviews recent advances in apomixis in cytology and molecular biology. The general idea of identifying apomixis was proposed and the process of the emergence of non-fusion types was discussed. To better understand the apomixis mechanism, an apomixis regulatory model was established. At the same time, the realization of apomixis technology is proposed, which provides reference for the research and application of apomixis.

Apospory and Diplospory in Diploid Boechera (Brassicaceae) May Facilitate Speciation by Recombination-Driven Apomixis-to-Sex Reversals

Apomixis (asexual seed formation) in angiosperms occurs either sporophytically, through adventitious embryony, or gametophytically, where an unreduced female gametophyte (embryo sac) forms and produces an unreduced egg that develops into an embryo parthenogenetically. Multiple types of gametophytic apomixis occur, and these are differentiated based on where and when the unreduced gametophyte forms, a process referred to as apomeiosis. Apomeiotic gametophytes form directly from ameiotic megasporocytes, as in Antennaria-type diplospory, from unreduced spores derived from 1st division meiotic restitutions, as in Taraxacum-type diplospory, or from cells of the ovule wall, as in Hieracium-type apospory. Multiple types of apomeiosis occasionally occur in the same plant, which suggests that the different types occur in response to temporal and/or spatial shifts in termination of sexual processes and onset timing of apomeiosis processes. To better understand the origins and evolutionary implications of apomixis in Boechera (Brassicaceae), we determined apomeiosis type for 64 accessions representing 44 taxonomic units. Plants expressing apospory and diplospory were equally common, and these generally produced reduced and unreduced pollen, respectively. Apospory and diplospory occurred simultaneously in individual plants of seven taxa. In Boechera, apomixis perpetuates otherwise sterile or semisterile interspecific hybrids (allodiploids) through multiple generations. Accordingly, ample time, in these multigenerational clones, is available for rare meioses to produce haploid, intergenomically recombined male and female gametes. The fusion of such gametes could then produce segmentally autoploidized progeny. If sex re-emerges among such progeny, then new and genomically unique sexual species could evolve. Herein, we present evidence that such apomixis-facilitated speciation is occurring in Boechera, and we hypothesize that it might also be occurring in facultatively apomictic allodiploids of other angiospermous taxa.

Heterochronic reproductive developmental processes between diploid and tetraploid cytotypes of Paspalum rufum

BACKGROUND AND AIMS

Apomixis is an asexual reproductive mode via seeds that generate maternal clonal progenies. Although apomixis in grasses is mainly expressed at the polyploid level, some natural diploid genotypes of Paspalum rufum produce aposporous embryo sacs in relatively high proportions and are even able to complete apomixis under specific conditions. However, despite the potential for apomixis, sexuality prevails in diploids, and apomixis expression is repressed for an as yet undetermind reason. Apomixis is thought to derive from a deregulation of one or a few components of the sexual pathway that could be triggered by polyploidy and/or hybridization. The objectives of this work were to characterize and compare the reproductive development and the timing of apospory initial (AI) emergence between diploid genotypes with potential for apomixis and facultative apomictic tetraploid cytotypes of P. rufum.

METHODS

Reproductive characterization was performed by cytoembryological observations of cleared ovaries and anthers during all reproductive development steps and by quantitative evaluation of the ovule growth parameters.

KEY RESULTS

Cytoembryological observations showed that in diploids, both female and male reproductive development is equally synchronized, but in tetraploids, megasporogenesis and early megagametogenesis are delayed with respect to microsporogenesis and early microgametogenesis. This delay was also seen when ovary growth was taken as a reference parameter. The analysis of the onset of AIs revealed that they emerge during different developmental periods depending on the ploidy level. In diploids, the AIs appeared along with the tetrad (or triad) of female meiocytes, but in tetraploids they appeared earlier, at the time of the megaspore mother cell. In both cytotypes, AIs can be seen even during megagametogenesis.

CONCLUSIONS

Overall observations reveal that female sexual reproductive development is delayed in tetraploids as compared with diploid genotypes, mainly at meiosis. In tetraploids, AIs appear at earlier sexual developmental stages than in diploids, and they accumulate up to the end of megasporogenesis. The longer extension of megasporogenesis in tetraploids could favour AI emergence and also apomixis success.

The Rise of Apomixis in Natural Plant Populations

Apomixis, the asexual reproduction via seed, has many potential applications for plant breeding by maintaining desirable genotypes over generations. Since most major crops do not express natural apomixis, it is useful to understand the origin and maintenance of apomixis in natural plant systems. Here, we review the state of knowledge on origin, establishment and maintenance of natural apomixis. Many studies suggest that hybridization, either on diploid or polyploid cytotypes, is a major trigger for the formation of unreduced female gametophytes, which represents the first step toward apomixis, and must be combined to parthenogenesis, the development of an unfertilized egg cell. Nevertheless, fertilization of endosperm is still needed for most apomictic plants. Coupling of these three steps appears to be a major constraint for shifts to natural apomixis. Adventitious embryony is another developmental pathway toward apomixis. Establishment of a newly arisen apomictic lineage is often fostered by side-effects of polyploidy. Polyploidy creates an immediate reproductive barrier against the diploid parental and progenitor populations; it can cause a breakdown of genetic self-incompatibility (SI) systems which is needed to establish self-fertility of pseudogamous apomictic lineages; and finally, polyploidy could indirectly help to establish an apomictic cytotype in a novel ecological niche by increasing adaptive potentials of the plants. This step may be followed by a phase of diversification and range expansion, mostly described as geographical parthenogenesis. The utilization of apomixis in crops must consider the potential risks of pollen transfer and introgression into sexual crop fields, which might be overcome by using pollen-sterile or cleistogamous variants. Another risk is the escape into natural vegetation and potential invasiveness of apomictic plants which needs careful management and consideration of ecological conditions.

Partitioning Apomixis Components to Understand and Utilize Gametophytic Apomixis

Apomixis is a method of reproduction to generate clonal seeds and offers tremendous potential to fix heterozygosity and hybrid vigor. The process of apomictic seed development is complex and comprises three distinct components, viz., apomeiosis (leading to formation of unreduced egg cell), parthenogenesis (development of embryo without fertilization) and functional endosperm development. Recently, in many crops, these three components are reported to be uncoupled leading to their partitioning. This review provides insight into the recent status of our understanding surrounding partitioning apomixis components in gametophytic apomictic plants and research avenues that it offers to help understand the biology of apomixis. Possible consequences leading to diversity in seed developmental pathways, resources to understand apomixis, inheritance and identification of candidate gene(s) for partitioned components, as well as contribution towards creation of variability are all discussed. The potential of Panicum maximum, an aposporous crop, is also discussed as a model crop to study partitioning principle and effects. Modifications in cytogenetic status, as well as endosperm imprinting effects arising due to partitioning effects, opens up new opportunities to understand and utilize apomixis components, especially towards synthesizing apomixis in crops.

Can obligate apomixis and more stable reproductive assurance explain the distributional successes of asexual triploids in Hieracium alpinum (Asteraceae)?

Although reproductive assurance has been suggested to be one of the most important factors shaping the differential distributional patterns between sexuals and asexuals (geographic parthenogenesis), it has only rarely been studied in natural populations of vascular plants with autonomous apomixis. Moreover, there are almost no data concerning the putative relationship between the level of apomictic versus sexual plant reproduction on one hand, and reproductive assurance on the other. We assessed the level of sexual versus apomictic reproduction in diploid and triploid plants of Hieracium alpinum across its distributional range using flow cytometric analyses of seeds, and compared the level of potential and realized seed set, i.e. reproductive assurance, between the two cytotypes under field and greenhouse conditions. Flow cytometric screening of embryos and endosperms of more than 4,100 seeds showed that diploids produced solely diploid progeny sexually, while triploids produced triploid progeny by obligate apomixis. Potential fruit set was much the same in diploids and triploids from the field and the greenhouse experiment. While in the pollination-limited environment in the greenhouse apomictic triploids had considerably higher realized fruit set than sexual diploids, there was no significant difference between cytotypes under natural conditions. In addition, sexuals varied to a significantly larger extent in realized fruit set than asexuals under both natural and greenhouse conditions. Our results indicate that triploid plants reproduce by obligate apomixis, assuring more stable and predictable fruit reproduction when compared to sexual diploids. This advantage could provide apomictic triploids with a superior colonisation ability, mirrored in a strong geographic parthenogenesis pattern observed in this species.

Reproductive pathways in Hieracium s.s. (Asteraceae): strict sexuality in diploids and apomixis in polyploids

Background and Aims

Apomixis or asexual seed reproduction is a key evolutionary mechanism in certain angiosperms providing them with reproductive assurance and isolation. Nevertheless, the frequency of apomixis is largely unknown, especially in groups with autonomous apomixis such as the diploid-polyploid genus Hieracium.

Methods

Using flow cytometric analyses, we determined the ploidy level and reproductive pathways (sexual vs. apomictic) for 7616 seeds originating from 946 plants belonging to >50 taxa sampled at 130 sites across Europe.

Key Results

Diploid seeds produced by diploids were formed exclusively by the sexual pathway after double fertilization of reduced embryo sacs. An absolute majority of tri- and tetraploid seeds (99.6 %) produced by tri- and tetrapolyploid taxa were formed by autonomous apomixis. Only 20 polyploid seeds (0.4 %) were formed sexually. These seeds, which originated on seven polyploid accessions of four taxa, were formed after fertilization of either unreduced embryo sacs through a so-called triploid bridge or reduced embryo sacs, and frequently resulted in progeny with an increased ploidy. In addition, the formation of seedlings with increased ploidy (4x and 6x) was found in two triploid plants. This is the first firm evidence on functional facultative apomixis in polyploid members of Hieracium sensu stricto (s.s.).

Conclusions

The mode of reproduction in Hieracium s.s. is tightly associated with ploidy. While diploids produce seeds exclusively sexually, polyploids produce seeds by obligate or almost obligate apomixis. Strict apomixis can increase the reproductive assurance and this in turn can increase the colonization ability of apomicts. Nevertheless, our data clearly show that certain polyploid plants are still able to reproduce sexually and contribute to the formation of new cytotypes and genotypes. The finding of functional facultative apomicts is essential for future studies focused on evolution, inheritance and ecological significance of apomixis in this genus.

Establishing the cell biology of apomictic reproduction in diploid Boechera stricta (Brassicaceae)

Background and aims

In the Brassicaceae family, apomictic development is characteristic of the genus Boechera. Hybridization, polyploidy and environmental adaptation that arose during the evolution of Boechera may serve as (epi)genetic regulators of apomictic initiation in this genus. Here we focus on Boechera stricta, a predominantly diploid species that reproduces sexually. However, apomictic development in this species has been reported in several studies, indicating non-obligate sexuality.

Methods

A progressive investigation of flower development was conducted using three accessions to assess the reproductive system of B. stricta. We employed molecular and cyto-embryological identification using histochemistry, transmission electron microscopy and Nomarski and epifluorescence microscopy.

Key Results

Data from internal transcribed spacer (ITS) and chloroplast haplotype sequencing, in addition to microsatellite variation, confirmed the B. stricta genotype for all lines. Embryological data indicated irregularities in sexual reproduction manifested by heterochronic ovule development, longevity of meiocyte and dyad stages, diverse callose accumulation during meiocyte-to-gametophyte development, and the formation of triads and tetrads in several patterns. The arabinogalactan-related sugar epitope recognized by JIM13 immunolocalized to one or more megaspores. Furthermore, pollen sterility and a high frequency of seed abortion appeared to accompany reproduction of the accession ES512, along with the initiation of parthenogenesis. Data from flow cytometric screening revealed both sexual and apomictic seed formation.

Conclusion

These results imply that B. stricta is a species with an underlying ability to initiate apomixis, at least with respect to the lines examined here. The existence of apomixis in an otherwise diploid sexual B. stricta may provide the genomic building blocks for establishing highly penetrant apomictic diploids and hybrid relatives. Our findings demonstrate that apomixis per se is a variable trait upon which natural selection could act.

Establishment of Apomixis in Diploid F2 Hybrids and Inheritance of Apospory From F1 to F2 Hybrids of the Ranunculus auricomus Complex

Hybridization and polyploidization play important roles in plant evolution but it is still not fully clarified how these evolutionary forces contribute to the establishment of apomicts. Apomixis, the asexual reproduction via seed formation, comprises several essential alterations in development compared to the sexual pathway. Furthermore, most natural apomicts were found to be polyploids and/or hybrids. The Ranunculus auricomus complex comprises diploid sexual and polyploid apomictic species and represents an excellent model system to gain knowledge on origin and evolution of apomixis in natural plant populations. In this study, the second generation of synthetically produced homoploid (2x) and heteroploid (3x) hybrids derived from sexual R. auricomus species was analyzed for aposporous initial cell formation by DIC microscopy. Complete manifestation of apomixis was determined by measuring single mature seeds by flow cytometric seed screen. Microscopic analysis of the female gametophyte formation indicated spontaneous occurrence of aposporous initial cells and several developmental irregularities. The frequency of apospory was found to depend on dosage effects since a significant increase in apospory was observed, when both F1 parents, rather than just one, were aposporous. Other than in the F1 generation, diploid Ranunculus F2 hybrids formed BIII seeds and fully apomictic seeds. The results indicate that hybridization rather than polyploidization seems to be the functional activator of apomictic reproduction in the synthetic Ranunculus hybrids. In turn, at least two hybrid generations are required to establish apomictic seed formation.

Flow cytometric seed screen data are consistent with models of chromosome inheritance in asymmetrically compensating allopolyploids

Angiosperms have evolved a mechanism of double fertilization, which results in the production of a separate embryo (new individual) and endosperm (nutritive tissue). The flow cytometric seed screen (FCSS) was developed to infer plant reproduction modes based on endosperm-to-embryo DNA content ratio (P_ind ). A ratio of 1.5 indicates sexual reproduction, whereas higher values of ≥2.0 are consistent with apomixis. Although FCSS has been successfully applied to the study of sexual and asexual plants, the limits of FCSS and particularly its potential for determination of reproduction modes in hemisexual plants have not been explored. Here, we evaluated the application of FCSS to the study of reproduction modes in two asymmetrically compensating allopolyploids (ACAs), Onosma arenaria and Rosa canina. These two species are characterized by the presence of asexually inherited univalent-forming and sexually inherited bivalent-forming chromosome sets. They both use asymmetric meiosis, which eliminates univalent-forming chromosome sets from the male gamete and retains them in the female gamete. Different chromosomal behavior in male and female meiosis in these plants is reflected in different theoretically derived P_ind values, which deviate from a sexual 1.5 value. Here, we determined P_ind FCSS-based values in seeds of ACAs, and compared the results to sexual species. As expected, we determined that the mean P_ind is 1.51, 1.52, and 1.52 in the sexual plants, that is, Capsella bursa-pastoris, Crataegus monogyna, and O. pseudoarenaria, respectively. In the ACAs, different mean P_ind values were determined for O. arenaria (1.61) and R. canina (1.82). These values are consistent with the theoretical P_ind values determined based on models of chromosome inheritance. This study highlights the precision of flow cytometry in determining DNA content and it's utility in screening reproduction modes. Additionally, it advocates for more in-depth investigations into rapid screening of accessions where the P_ind ratio has deviated from the 1.5 value typical of sexual species, which may indicate meiotic irregularities.

Admixture, evolution, and variation in reproductive isolation in the Boechera puberula clade

BACKGROUND

Hybridization is very common in plants, and the incorporation of new alleles into existing lineages (i.e. admixture) can blur species boundaries. However, admixture also has the potential to increase standing genetic variation. With new sequencing methods, we can now study admixture and reproductive isolation at a much finer scale than in the past. The genus Boechera is an extraordinary example of admixture, with over 400 hybrid derivates of varying ploidy levels. Yet, few studies have assessed admixture in this genus on a genomic scale.

RESULTS

In this study, we used Genotyping-by-Sequencing (GBS) to clarify the evolution of the Boechera puberula clade, whose six members are scattered across the western United States. We further assessed patterns of admixture and reproductive isolation within the group, including two additional species (B. stricta and B. retrofracta) that are widespread across North America. Based on 14,815 common genetic variants, we found evidence for some cases of hybridization. We find evidence of both recent and more ancient admixture, and that levels of admixture vary across species.

CONCLUSIONS

We present evidence for a monophyletic origin of the B. puberula group, and a split of B. puberula into two subspecies. Further, when inferring reproductive isolation on the basis of presence and absence of admixture, we found that the accumulation of reproductive isolation between species does not seem to occur linearly with time since divergence in this system. We discuss our results in the context of sexuality and asexuality in Boechera.

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species.

Hybrid asexuality as a primary postzygotic barrier between nascent species: On the interconnection between asexuality, hybridization and speciation

Although sexual reproduction is ubiquitous throughout nature, the molecular machinery behind it has been repeatedly disrupted during evolution, leading to the emergence of asexual lineages in all eukaryotic phyla. Despite intensive research, little is known about what causes the switch from sexual reproduction to asexuality. Interspecific hybridization is one of the candidate explanations, but the reasons for the apparent association between hybridization and asexuality remain unclear. In this study, we combined cross-breeding experiments with population genetic and phylogenomic approaches to reveal the history of speciation and asexuality evolution in European spined loaches (Cobitis). Contemporary species readily hybridize in hybrid zones, but produce infertile males and fertile but clonally reproducing females that cannot mediate introgressions. However, our analysis of exome data indicates that intensive gene flow between species has occurred in the past. Crossings among species with various genetic distances showed that, while distantly related species produced asexual females and sterile males, closely related species produce sexually reproducing hybrids of both sexes. Our results suggest that hybridization leads to sexual hybrids at the initial stages of speciation, but as the species diverge further, the gradual accumulation of reproductive incompatibilities between species could distort their gametogenesis towards asexuality. Interestingly, comparative analysis of published data revealed that hybrid asexuality generally evolves at lower genetic divergences than hybrid sterility or inviability. Given that hybrid asexuality effectively restricts gene flow, it may establish a primary reproductive barrier earlier during diversification than other "classical" forms of postzygotic incompatibilities. Hybrid asexuality may thus indirectly contribute to the speciation process.

Pathways to polyploidy: indications of a female triploid bridge in the alpine species Ranunculus kuepferi (Ranunculaceae)

Polyploidy is one of the most important evolutionary processes in plants. In natural populations, polyploids usually emerge from unreduced gametes which either fuse with reduced ones, resulting in triploid offspring (triploid bridge), or with other unreduced gametes, resulting in tetraploid embryos. The frequencies of these two pathways, and male versus female gamete contributions, however, are largely unexplored. Ranunculus kuepferi occurs with diploid, triploid and autotetraploid cytotypes in the Alps, whereby diploids are mostly sexual, while tetraploids are facultative apomicts. To test for the occurrence of polyploidization events by triploid bridge, we investigated 551 plants of natural populations via flow cytometric seed screening. We assessed ploidy shifts in the embryo to reconstruct female versus male gamete contributions to polyploid embryo and/or endosperm formation. Seed formation via unreduced egg cells (BIII hybrids) occurred in all three cytotypes, while only in one case both gametes were unreduced. Polyploids further formed seeds with reduced, unfertilized egg cells (polyhaploids and aneuploids). Pollen was highly variable in diameter, but only pollen >27 μm was viable, whereby diploids produced higher proportions of well-developed pollen. Pollen size was not informative for the formation of unreduced pollen. These results suggest that a female triploid bridge via unreduced egg cells is the major pathway toward polyploidization in R. kuepferi, maybe as a consequence of constraints of endosperm development. Triploids resulting from unreduced male gametes were not observed, which explains the lack of obligate sexual tetraploid individuals and populations. Unreduced egg cell formation in diploids represents the first step toward apomixis.

Apomixis frequency under stress conditions in weeping lovegrass (Eragrostis curvula)

To overcome environmental stress, plants develop physiological responses that are triggered by genetic or epigenetic changes, some of which involve DNA methylation. It has been proposed that apomixis, the formation of asexual seeds without meiosis, occurs through the temporal or spatial deregulation of the sexual process mediated by genetic and epigenetic factors influenced by the environment. Here, we explored whether there was a link between the occurrence of apomixis and various factors that generate stress, including drought stress, in vitro culture, and intraspecific hybridization. For this purpose, we monitored the embryo sacs of different weeping lovegrass (Eragrostis curvula [Schrad.] Nees) genotypes after the plants were subjected to these stress conditions. Progeny tests based on molecular markers and genome methylation status were analyzed following the stress treatment. When grown in the greenhouse, the cultivar Tanganyika INTA generated less than 2% of its progeny by sexual reproduction. Plants of this cultivar subjected to different stresses showed an increase of sexual embryo sacs, demonstrating an increased expression of sexuality compared to control plants. Plants of the cv. Tanganyika USDA did not demonstrate the ability to generate sexual embryo sacs under any conditions and is therefore classified as a fully apomictic cultivar. We found that this change in the prevalence of sexuality was correlated with genetic and epigenetic changes analyzed by MSAP and AFLPs profiles. Our results demonstrate that different stress conditions can alter the expression of sexual reproduction in facultative tetraploid apomictic cultivars and when the stress stops the reproductive mode shift back to the apomixis original level. These data together with previous observations allow us to generate a hypothetical model of the regulation of apomixis in weeping lovegrass in which the genetic/s region/s that condition apomixis, is/are affected by ploidy, and is/are subjected to epigenetic control.

Structure and expression of dna methyltransferase genes from apomictic and sexual Boechera species

In this study, we determined the structure of DNA methyltransferase (DNMT) genes in apomict and sexual Boechera species and investigated the expression levels during seed development. Protein and DNA sequences of diploid sexual Boechera stricta DNMT genes obtained from Phytozome 10.3 were used to identify the homologues in apomicts, Boechera holboellii and Boechera divaricarpa. Geneious R8 software was used to map the short-paired reads library of B. holboellii whole genome or B. divaricarpa transcriptome reads to the reference gene sequences. We determined three DNMT genes; for Boechera spp. METHYLTRANSFERASE1 (MET1), CHROMOMETHYLASE 3 (CMT3) and DOMAINS REARRANGED METHYLTRANSFERASE 1/2 (DRM2). We examined the structure of these genes with bioinformatic tools and compared with other DNMT genes in plants. We also examined the levels of expression in silique tissues after fertilization by semi-quantitative PCR. The structure of DNMT proteins in apomict and sexual Boechera species share common features. However, the expression levels of DNMT genes were different in apomict and sexual Boechera species. We found that DRM2 was upregulated in apomictic Boechera species after fertilization. Phylogenetic trees showed that three genes are conserved among green algae, monocotyledons and dicotyledons. Our results indicated a deregulation of DNA methylation machinery during seed development in apomicts.

Pathways to polyploidy: indications of a female triploid bridge in the alpine species Ranunculus kuepferi (Ranunculaceae)

Polyploidy is one of the most important evolutionary processes in plants. In natural populations, polyploids usually emerge from unreduced gametes which either fuse with reduced ones, resulting in triploid offspring (triploid bridge), or with other unreduced gametes, resulting in tetraploid embryos. The frequencies of these two pathways, and male versus female gamete contributions, however, are largely unexplored. Ranunculus kuepferi occurs with diploid, triploid and autotetraploid cytotypes in the Alps, whereby diploids are mostly sexual, while tetraploids are facultative apomicts. To test for the occurrence of polyploidization events by triploid bridge, we investigated 551 plants of natural populations via flow cytometric seed screening. We assessed ploidy shifts in the embryo to reconstruct female versus male gamete contributions to polyploid embryo and/or endosperm formation. Seed formation via unreduced egg cells (B_III hybrids) occurred in all three cytotypes, while only in one case both gametes were unreduced. Polyploids further formed seeds with reduced, unfertilized egg cells (polyhaploids and aneuploids). Pollen was highly variable in diameter, but only pollen >27 μm was viable, whereby diploids produced higher proportions of well-developed pollen. Pollen size was not informative for the formation of unreduced pollen. These results suggest that a female triploid bridge via unreduced egg cells is the major pathway toward polyploidization in R. kuepferi, maybe as a consequence of constraints of endosperm development. Triploids resulting from unreduced male gametes were not observed, which explains the lack of obligate sexual tetraploid individuals and populations. Unreduced egg cell formation in diploids represents the first step toward apomixis.