An adventurous journey toward and away from fern apomixis: Insights from genome size and spore abortion patterns

PREMISE

Apomixis in ferns is relatively common and obligatory. Sterile hybrids may restore fertility via apomixis at a cost of long-term genetic stagnation. In this study, we outlined apomixis as a possible temporary phase leading to sexuality and analyzed factors relating to transitioning to and away from apomixis, such as unreduced and reduced spore formation in apomict and apo-sex hybrid ferns.

METHODS

We analyzed the genome size of 15 fern species or hybrids ("taxa") via flow cytometry. The number of reduced and unreduced gametophytes was established as a proxy for viable spore formation of either type. We also calculated the spore abortion ratio (sign of reduced spores) in several taxa, including the apo-sex hybrid Dryopteris × critica and its 16 apomictically formed offspring.

RESULTS

Four of 15 sampled taxa yielded offspring variable in genome size. Specifically, each variable taxon formed one viable reduced plant among 12-451 sampled gametophytes per taxon. Thus, haploid spore formation in the studied apomicts was very rare but possible. Spore abortion analyses indicated gradually decreasing abortion (haploid spore formation) over time. In Dryopteris × critica, abortion decreased from 93.8% to mean 89.5% in one generation.

CONCLUSIONS

Our results support apomixis as a transitionary phase toward sexuality. Newly formed apomicts hybridize with sexual relatives and continue to form haploid spores early on. Thus, they may get the genomic content necessary for regular meiosis and restore sexuality. If the missing relative goes extinct, the lineage gets locked into apomixis as may be the case with the Dryopteris affinis complex.

Distinct geographic parthenogenesis in spite of niche conservatism and a single ploidy level: A case of Rubus ser. Glandulosi (Rosaceae)

Asexual organisms often differ in their geographic distributions from their sexual relatives. This phenomenon, termed geographic parthenogenesis, has long been known, but the underlying factors behind its diverse patterns have been under dispute. Particularly problematic is an association between asexuality and polyploidy in most taxa. Here, we present a new system of geographic parthenogenesis on the tetraploid level, promising new insights into this complex topic. We used flow cytometric seed screen and microsatellite genotyping to characterise the patterns of distribution of sexuals and apomicts and genotypic distributions in Rubus ser. Glandulosi across its range. Ecological modelling and local-scale vegetation and soil analyses were used to test for niche differentiation between the reproductive groups. Apomicts were detected only in North-western Europe, sexuals in the rest of the range in Europe and West Asia, with a sharp borderline stretched across Central Europe. Despite that, we found no significant differences in ecological niches. Genotypic richness distributions suggested independence of the reproductive groups and a secondary contact. We argue that unless a niche differentiation (resulting from polyploidy and/or hybridity) evolves, the main factors behind the patterns of geographic parthenogenesis in plants are phylogeographic history and neutral microevolutionary processes, such as clonal turnover.

Effects of species diversity on trait expression of the clonal herb Taraxacum officinale and its relation to genotype diversity and phenotypic plasticity

Plant species respond to varying plant species diversity and associated changes in their abiotic and biotic environment with changes in their phenotype. However, it is not clear to what degree this phenotypic differentiation is due to genotype diversity within populations or phenotypic plasticity of plant individuals. We studied individuals of 16 populations of the clonal herb Taraxacum officinale grown in plant communities of different species richness in a 17-year-old grassland biodiversity experiment (Jena Experiment). We collected 12 individuals in each population to measure phenotypic traits and identify distinct genotypes using microsatellite DNA markers. Plant species richness did not influence population-level genotype and trait diversity. However, it affected the expression of several phenotypic traits, e.g. leaf and inflorescence number, maximum leaf length and seed mass, which increased with increasing plant species richness. Moreover, population-level trait diversity correlated positively with genotype richness for leaf dry matter content (LDMC) and negatively with inflorescence number. For several traits (i.e. seed mass, germination rate, LDMC, specific leaf area (SLA)), a larger portion of variance was explained by genotype identity, while variance in other traits (i.e. number of inflorescences, leaf nitrogen concentration, leaf number, leaf length) resided within genotypes and thus was mostly due to phenotypic plasticity. Overall, our findings show that plant species richness positively affected the population means of some traits related to whole-plant performance, whose variation was achieved through both phenotypic plasticity and genotype composition of a population.

Pollination Syndrome, Florivory, and Breeding System of Satyrium nepalense var. ciliatum (Orchidaceae) in Central Yunnan, China

Research on Satyrium nepalense var. ciliatum (Lindl.) Hook. f. has primarily focused on populations in Northwestern Yunnan, with limited studies on pollination syndromes and insect behavior. In addition, it is geographically limited in its breeding system studies. Here, pollination syndromes, florivory, and breeding systems of S. nepalense var. ciliatum from Liangwang Mountain (Central Yunnan, China) were investigated through field work, microscope, scanning electron microscope (SEM), and parafin section. It was revealed that the pollination syndrome was possessing out-crossing, such as bright color, a developed rostellum, nectar glands in the spur, and food hairs at the lip base. The color and nectar attracted flower visitors, and florivory was observed. Some flower visitors pollinated their companion species. Ants were identified as floral visitors for the first time in Satyrium, although substantial pollination was not observed. Ants might be potential pollinators. S. nepalense var. ciliatum possessed a mixed breeding system, including selfing, out-crossing, and apomixis, with apomixis being predominant in nature. It is suggested that the pollination syndrome, florivory, and pollination competition would contribute to its mixed breeding systems, particularly leading to the occurrence of apomixis.

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.

Phylogenomics of Southern European Taxa in the Ranunculus auricomus Species Complex: The Apple Doesn't Fall Far from the Tree

The taxonomic status of many Southern European taxa of the Ranunculus auricomus complex remains uncertain despite this region's proximity to the native ranges of the sexual progenitor species of the complex. We investigated whether additional sexual progenitor species are present in the Mediterranean region. Utilizing target enrichment of 736 single-copy nuclear gene regions and flow cytometry, we analyzed phylogenomic relationships, the ploidy level, and the reproductive mode in representatives of 16 populations in Southern Europe, with additional sequence data from herbarium collections. Additionally, phased sequence assemblies from suspected nothotaxa were mapped to previously described sexual progenitor species in order to determine hybrid ancestry. We found the majority of Mediterranean taxa to be tetraploid, with hybrid populations propagating primarily via apomixis. Phylogenomic analysis revealed that except for the progenitor species, the Mediterranean taxa are often polyphyletic. Most apomictic taxa showed evidence of mixed heritage from progenitor species, with certain progenitor genotypes having mapped more to the populations from adjacent geographical regions. Geographical trends were found in phylogenetic distance, roughly following an east-to-west longitudinal demarcation of the complex, with apomicts extending to the southern margins. Additionally, we observed post-hybridization divergence between the western and eastern populations of nothotaxa in Southern Europe. Our results support a classification of apomictic populations as nothotaxa, as previously suggested for Central Europe.

Genetic mapping of the LOSS OF PARTHENOGENESIS locus in Pilosella piloselloides and the evolution of apomixis in the Lactuceae

Pilosella piloselloides var. praealta (syn. P. praealta; Hieracium praealtum) is a versatile model used to study gametophytic apomixis. In this system apomixis is controlled by three loci: one that controls the avoidance of meiosis (LOA), one that controls the avoidance of fertilization (LOP) and a third that controls autonomous endosperm formation (AutE). Using a unique polyhaploid mapping approach the LOP locus was mapped to a 654 kb genomic interval syntenic to linkage group 8 of Lactuca sativa. Polyhaploids form through the gametophytic action of a dominant determinant at LOP, so the mapped region represents both a functional and a physical domain for LOP in P. piloselloides. Allele sequence divergence (ASD) analysis of the PARTHENOGENESIS (PAR) gene within the LOP locus revealed that dominant PAR alleles in Pilosella remain highly similar across the genus, whilst the recessive alleles are more divergent. A previous report noted that dominant PAR alleles in both Pilosella and Taraxacum are modified by the presence of a class II transposable element (TE) in the promoter of the gene. This observation was confirmed and further extended to the related genus Hieracium. Sufficient differences were noted in the structure and location of the TE elements to conclude that TE insertional events had occurred independently in the three genera. Measures of allele crossover amongst the polyhaploids revealed that P. piloselloides is an autopolyploid species with tetrasomic inheritance. It was also noted that the dominant determinant of LOP in P. piloselloides could transmit via a diploid gamete (pollen or egg) but not via a haploid gamete. Using this information, a model is presented of how gametophytic apomixis may have evolved in several members of the Lactuceae, a tribe of the Asteraceae.

Demographic and reproductive impacts of hybridization unrelated to hybrid viability in a native plant

PREMISE

Introduced species can influence native congeners through production of hybrids and introgression, but impacts not involving viable hybrids, such as reduced conspecific offspring and increased asexual seed production, are rarely examined. Here we tested for these demographic and reproductive consequences of hybridization between introduced, domesticated apple (Malus domestica) and native crabapple (M. coronaria) in southern Canada.

METHODS

We applied four pollination treatments (open, M. coronaria, M. domestica, open + M. coronaria) to focal M. coronaria trees across multiple years and assessed the number and reproductive origins of resulting seeds (hybrid or conspecific endosperm and, for each, sexual or asexual embryo) using flow cytometry.

RESULTS

In open-pollinated fruit, 27% of seeds had hybrid endosperm; 52% of embryos were asexual. The number of conspecific embryos (sexual or asexual) per fruit did not decline significantly with increasing hybridization, indicating no seed discounting, but hand pollinations using only domestic apple or crabapple pollen reduced the number of conspecific embryos significantly. Hybridization was not associated with a change in percentage asexual embryos, overall, but there was an increase in asexual embryos in tetraploid seeds, the maternal and most common offspring ploidy.

CONCLUSIONS

We conclude that hybridization can influence native Malus in ways beyond the production of viable hybrids, with significant implications for population dynamics and genetic structure.

Increased Zygote-Derived Plantlet Formation through In Vitro Rescue of Immature Embryos of Highly Apomictic Opuntia ficus-indica (Cactaceae)

O. ficus-indica (prickly pear cactus) is an important forage and food source in arid and semiarid ecosystems and is the most important cactus species in cultivation globally. The high degree of apomixis in the species is a hindrance in plant breeding programs where genetic segregation is sought for the selection of superior genotypes. To understand if in ovulo embryo rescue could increase the proportion of zygotic seedlings, we compared the mature seed-derived seedlings with those regenerated from in vitro embryo rescue at 20, 25, 30, 35, and 40 post-anthesis days (PADs) in four Italian cultivars. The seedlings were classified as apomictic or zygotic based on molecular marker analysis using inter-sequence single repeat (ISSR) primers. Multiple embryos were recovered from all the cultured immature ovules, and plantlets were regenerated and acclimatized to the field post hardening, with success rates ranging from 62% ('Senza spine') to 83% ('Gialla'). The level of polyembryony differed among cultivars and recovery dates, with the highest being 'Rossa', producing 4.8 embryos/ovule at 35 PADs, and 'Gialla', the lowest, with 2.7 at 40 PADs. The maximum number of embryos observed within a single ovule was 14 in 'Trunzara bianca'. ISSR analysis revealed that ovule culture at 35 PADs produced the highest percentage of zygotic seedlings in all the cultivars, from 51% ('Rossa') to 98% ('Gialla'), with a high genotype effect as well. Mature seeds produced much fewer seedlings per seed, ranging from 1.2 in 'Trunzara bianca' to 2.0 in 'Rossa' and a lower percentage of zygotic seedlings (from 14% in 'Rossa' to 63% in 'Gialla'). Our research opens a pathway to increase the availability of zygotic seedlings in O. ficus-indica breeding programs through in ovulo embryo culture.

Morphogenetic peculiarities of reproductive biology in sugar beet (Beta vulgaris L.) breeding

This review considers the processes of morphogenesis used in the development of propagation methods and the creation of a new starting material for sugar beet. It has been demonstrated that methods of particulation, in vitro microcloning and cell breeding that reflect non-sexual forms of plant reproduction increase the effectiveness of breeding experiments. The review describes the in vitro culture methods maintaing a tendency in plants for vegetative propagation and stimulating increase in genetic variability of properties when mutagens such as ethyl methanesulfonate, alien genetic structures with mf2 and mf3 bacterial genes in Agrobacterium tumefaciens strains, and selective agents (Сd++ ions and abscisic acid) are incorporated into plant cells. It presents the results of using fluorescent microscopy, cytophotometry, biochemical analysis and determining the level of phytohormones and content of nucleic acids in nuclei for forecasting the seed setting ability. It has demonstrated that long self-pollination of plants causes decrease in fertility of pollen grains, resulting in the sterilization of male gametes and the appearance of pistillody flowers. Self-fertile plants isolated from these lines serve as sterility fixers, while the apomixis elements increased the ovule number, additional embryo sacs and embryos. A role of apomixis in contributing to variability in the onto- and phylogenetic development of plants have been substantiated. The review reflects the morphological features of the in vitro development of sexual and somatic cells in embryos during the formation of seedlings based on floral and vegetative embryoidogeny. Use of the SNP and SSR (Unigenes) molecular-genetic markers having a high polymorphism level has appeared effective to characterize the developed breeding material and hybrid components when carrying out crossings. The study of sugar beet starting materials for the presence of TRs mini-satellite loci making it possible to reveal O-type plants-pollinators (sterility fixing agent) and MS-form plants are of interest for breeding as well. The selected material can be widely used in breeding to produce hybrids, allowing for a 2-3- fold reduction of the development period. The review also discusses the prospects for the development and implementation of new methods and original schemes in sugar beet genetics, biotechnology and breeding.

Ovule Transcriptome Analysis Discloses Deregulation of Genes and Pathways in Sexual and Apomictic Limonium Species (Plumbaginaceae)

The genus Limonium Mill. (sea lavenders) includes species with sexual and apomixis reproductive strategies, although the genes involved in these processes are unknown. To explore the mechanisms beyond these reproduction modes, transcriptome profiling of sexual, male sterile, and facultative apomictic species was carried out using ovules from different developmental stages. In total, 15,166 unigenes were found to be differentially expressed with apomictic vs. sexual reproduction, of which 4275 were uniquely annotated using an Arabidopsis thaliana database, with different regulations according to each stage and/or species compared. Gene ontology (GO) enrichment analysis indicated that genes related to tubulin, actin, the ubiquitin degradation process, reactive oxygen species scavenging, hormone signaling such as the ethylene signaling pathway and gibberellic acid-dependent signal, and transcription factors were found among differentially expressed genes (DEGs) between apomictic and sexual plants. We found that 24% of uniquely annotated DEGs were likely to be implicated in flower development, male sterility, pollen formation, pollen-stigma interactions, and pollen tube formation. The present study identifies candidate genes that are highly associated with distinct reproductive modes and sheds light on the molecular mechanisms of apomixis expression in Limonium sp.

A tale of two genomes: What drives mitonuclear discordance in asexual lineages of a freshwater snail?

We use genomic information to tell us stories of evolutionary origins. But what does it mean when different genomes report wildly different accounts of lineage history? This genomic "discordance" can be a consequence of a fascinating suite of natural history and evolutionary phenomena, from the different inheritance mechanisms of nuclear versus cytoplasmic (mitochondrial and plastid) genomes to hybridization and introgression to horizontal transfer. Here, we explore how we can use these distinct genomic stories to provide new insights into the maintenance of sexual reproduction, one of the most important unanswered questions in biology. We focus on the strikingly distinct nuclear versus mitochondrial versions of the story surrounding the origin and maintenance of asexual lineages in Potamopyrgus antipodarum, a New Zealand freshwater snail. While key questions remain unresolved, these data inspire multiple testable hypotheses that can be powerfully applied across a broad range of taxa toward a deeper understanding of the causes and consequences of mitonuclear discordance, the maintenance of sex, and the origin of new asexual lineages.

Genotyping by Sequencing for SNP-Based Linkage Analysis and the Development of KASPar Markers for Male Sterility and Polyembryony in Citrus

Polyembryony and male sterility (MS) are essential characters for citrus breeding. MS, coupled with parthenocarpy, allows for addressing the diversification of diploid seedless mandarin varieties, and nucleocytoplasmic MS is the most prevalent system. Polyembryony limits the use of seed parents in scion breeding programs, and the recovery of monoembryonic hybrids to be used as female parents is a crucial pre-breeding component. The objectives of this work were the identification of SNPs closely linked with the genes implied in these traits for marker-assisted selection. Genotyping by sequencing was used to genotype 61 diploid hybrids from an F1 progeny recovered from crossing 'Kiyomi' and 'Murcott' tangors. A total of 6444 segregating markers were identified and used to establish the two parental genetic maps. They consisted of 1374 and 697 markers encompassing 1416.287 and 1339.735 cM for 'Kiyomi' and 'Murcott', respectively. Phenotyping for MS and polyembryony was performed. The genotype-trait association study identified a genomic region on LG8 which was significantly associated with MS, and a genomic region on LG1 which was significantly associated with polyembryony. Annotation of the identified region for MS revealed 19 candidate genes. One SNP KASPar marker was developed and fully validated for each trait.

Dispersal and establishment traits provide a colonization advantage for a polyploid apomictic plant

PREMISE

Apomictic plants (reproducing asexually through seed) often have larger ranges and occur at higher latitudes than closely related sexuals, a pattern known as geographical parthenogenesis (GP). Explanations for GP include differences in colonizing ability due to reproductive assurance and direct/indirect effects of polyploidy (most apomicts are polyploid) on ecological tolerances. While life history traits associated with dispersal and establishment also contribute to the potential for range expansion, few studies compare these traits in related apomicts and sexuals.

METHODS

We investigated differences in early life history traits between diploid-sexual and polyploid-apomictic Townsendia hookeri (Asteraceae), which displays a classic pattern of GP. Using lab and greenhouse experiments, we measured seed dispersal traits, germination success, and seedling size and survival in sexual and apomictic populations from across the range of the species.

RESULTS

While theory predicts that trade-offs between dispersal and establishment traits should be common, this was largely not the case in T. hookeri. Apomictic seeds had both lower terminal velocity (staying aloft longer when dropped) and higher germination success than sexual seeds. While there were no differences in seedling size between reproductive types, apomicts did, however, have slightly lower seedling survival than sexuals.

CONCLUSIONS

These differences in early life history traits, combined with reproductive assurance conferred by apomixis, suggest that apomicts achieve a greater range through advantages in their ability to both spread and establish.

From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula

INTRODUCTION

In Eragrostis curvula, commonly known as weeping lovegrass, a synthetic diploidization event of the facultative apomictic tetraploid Tanganyika INTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexual reproduction by seeds in which the progeny is genetically identical to the maternal plant.

METHODS

To assess the genomic changes related to ploidy and to the reproductive mode occurring during diploidization, a mapping approach was followed to obtain the first E. curvula pangenome assembly. In this way, gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end reads and mapped against the Victoria genome assembly. The unmapped reads were used for variant calling, while the mapped reads were assembled using Masurca software.

RESULTS

The length of the assembly was 28,982,419 bp distributed in 18,032 contigs, and the variable genes annotated in these contigs rendered 3,952 gene models. Functional annotation of the genes showed that the reproductive pathway was differentially enriched. PCR amplification in gDNA and cDNA of Tanganyika INTA and Victoria was conducted to validate the presence/absence variation in five genes related to reproduction and ploidy. The polyploid nature of the Tanganyika INTA genome was also evaluated through the variant calling analysis showing the single nucleotide polymorphism (SNP) coverage and allele frequency distribution with a segmental allotetraploid pairing behavior.

DISCUSSION

The results presented here suggest that the genes were lost in Tanganyika INTA during the diploidization process that was conducted to suppress the apomictic pathway, affecting severely the fertility of Victoria cv.

Apomictic Malus plants exhibit abnormal pollen development

Apomixis is the asexual reproduction through seeds that leads to the production of genetically uniform progeny. It has become an important tool in plant breeding because it facilitates the retention of genotypes with desirable traits and allows seeds to be obtained directly from mother plants. Apomixis is rare in most economically important crops, but it occurs in some Malus species. Here, the apomictic characteristics of Malus were examined using four apomictic and two sexually reproducing Malus plants. Results from transcriptome analysis showed that plant hormone signal transduction was the main factor affecting apomictic reproductive development. Four of the apomictic Malus plants examined were triploid, and pollen was either absent or present in very low densities in the stamen. Variation in the presence of pollen was associated with variation in the apomictic percentage; specifically, pollen was absent in the stamens of tea crabapple plants with the highest apomictic percentage. Furthermore, pollen mother cells failed to progress normally into meiosis and pollen mitosis, a trait mostly observed in apomictic Malus plants. The expression levels of meiosis-related genes were upregulated in apomictic plants. Our findings indicate that our simple method of detecting pollen abortion could be used to identify apple plants that are capable of apomictic reproduction.

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.

Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

BACKGROUND AND AIMS

Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species.

METHODS

Some 362 forage grass accessions from international germplasm collections were studied, and ploidy was determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima.

KEY RESULTS

Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids.

CONCLUSIONS

We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for Urochloa brizantha, U. decumbens and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and assist in measuring and conserving biodiversity in grasslands.

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.

Evolutionary Potential of Parthenogenesis-Bisexual Lineages within Triploid Apomictic Thelytoky in Cacopsylla ledi (Flor, 1861) (Hemiptera, Psylloidea) in Fennoscandia

A widely accepted hypothesis is that parthenogenesis is an evolutionary dead end since it is selectively advantageous in the short term only but results in lowered diversification rates. Triploid apomictic parthenogenesis might represent an exception, as in favorable environments, triploid females are able to produce rare males and diploid females. The aim of the present study was to analyze the modes of reproduction and their evolutionary implications in the parthenogenetic psyllid Cacopsylla ledi (Flor, 1861) from Fennoscandia. The cytogenetic assessment of ploidy levels and the analysis of the COI haplotype revealed two geographically separated bisexual lineages implying genuine bisexual populations. The southern lineage occurring south of latitude 65° N in Finland showed a COI haplotype different from that of parthenogenetic triploids in the same population but identical to the haplotype of specimens in a genuine bisexual population in the Czech Republic. This allows us to suggest that bisexuals in southern Fennoscandia represent the original bisexual C. ledi. By contrast, in the northern bisexual lineage north of latitude 65° N, rare males and diploid females carried the same haplotype as triploids in the same population, having been produced by the triploids. In the Kola Peninsula, a genuine bisexual population of presumably rare male/diploid female origin was discovered. As this population is geographically isolated from populations of the ancestral bisexual C. ledi, it can develop into a new bisexual species through peripatric speciation during evolution. Our findings demonstrate that apomictic triploid parthenogenesis is not necessarily an evolutionary dead end but is able to lead to the emergence of a new bisexual species of parthenogenetic origin.

Genome-wide identification, interaction of the MADS-box proteins in Zanthoxylum armatum and functional characterization of ZaMADS80 in floral development

As a typical dioecious species, Zanthoxylum armatum establishes apomictic reproduction, hence only female trees are cultivated. However, male and hermaphrodite flowers have recently appeared in female plants, resulting in a dramatic yield reduction. To date, the genetic basis underlying sex determination and apomixis in Z. armatum has been largely unknown. Here, we observed abortion of the stamen or carpel prior to primordium initiation, thus corroborating the potential regulation of MADS-box in sex determination. In Z. armatum, a total of 105 MADS-box genes were identified, harboring 86 MIKC-type MADSs with lack of FLC orthologues. Transcriptome analysis revealed candidate MADSs involved in floral organ identity, including ten male-biased MADSs, represented by ZaMADS92/81/75(AP3/PI-like), and twenty-six female-specified, represented by ZaMADS80/49 (STK/AGL11-like) and ZaMADS42 (AG-like). Overexpressing ZaMADS92 resulted in earlier flowering, while ZaMADS80 overexpression triggered precocious fruit set and parthenocarpy as well as dramatic modifications in floral organs. To characterize their regulatory mechanisms, a comprehensive protein-protein interaction network of the represented MADSs was constructed based on yeast two-hybrid and bimolecular fluorescence complementation assays. Compared with model plants, the protein interaction patterns in Z. armatum exhibited both conservation and divergence. ZaMADS70 (SEP3-like) interacted with ZaMADS42 and ZaMADS48 (AP3-like) but not ZaMADS40 (AP1-like), facilitating the loss of petals in Z. armatum. The ZaMADS92/ZaMADS40 heterodimer could be responsible for accelerating flowering in ZaMADS92-OX lines. Moreover, the interactions between ZaMADS80 and ZaMADS67(AGL32-like) might contribute to apomixis. This work provides new insight into the molecular mechanisms of MADS-boxes in sex organ identity in Z. armatum.

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.

Diverged subpopulations in tropical Urochloa (Brachiaria) forage species indicate a role for facultative apomixis and varying ploidy in their population structure and evolution

BACKGROUND

Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. Here we aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction.

METHODS

We explored the genetic diversity of 111 accessions from the five Urochloa species used to develop commercial cultivars. These accessions were conserved from wild materials collected at their centre of origin in Africa, and they tentatively represent the complete Urochloa gene pool used in breeding programmes. We used RNA-sequencing to generate 1.1 million single nucleotide polymorphism loci. We employed genetic admixture, principal component and phylogenetic analyses to define subpopulations.

RESULTS

We observed three highly differentiated subpopulations in U. brizantha, which were unrelated to ploidy: one intermixed with U. decumbens, and two diverged from the former and the other species in the complex. We also observed two subpopulations in U. humidicola, unrelated to ploidy; one subpopulation had fewer accessions but included the only characterized sexual accession in the species. Our results also supported a division of U. decumbens between diploids and polyploids, and no subpopulations within U. ruziziensis and U. maxima.

CONCLUSIONS

Polyploid U. decumbens are more closely related to polyploid U. brizantha than to diploid U. decumbens, which supports the divergence of both polyploid groups from a common tetraploid ancestor and provides evidence for the hybridization barrier of ploidy. The three differentiated subpopulations of apomictic polyploid U. brizantha accessions constitute diverged ecotypes, which can probably be utilized in hybrid breeding. Subpopulations were not observed in non-apomictic U. ruziziensis. Sexual Urochloa polyploids were not found (U. brizantha, U. decumbens) or were limited to small subpopulations (U. humidicola). The subpopulation structure observed in the Urochloa sexual-apomictic multiploidy complexes supports geographical parthenogenesis, where the polyploid genotypes exploit the evolutionary advantage of apomixis, i.e. uniparental reproduction and clonality, to occupy extensive geographical areas.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.