Systematic approach of polyploidy as an evolutionary genetic and genomic phenomenon in horticultural crops

Polyploidy is thought to be an evolutionary and systematic mechanism for gene flow and phenotypic advancement in flowering plants. It is a natural phenomenon that promotes diversity by creating new permutations enhancing the prime potentials as compared to progenitors. Two different pathways have been recognized in studying polyploidy in nature; mitotic or somatic chromosome doubling and cytogenetics variation. Secondly, the vital influence of being polyploid is its heritable property (unreduced reproductive cells) formed during first and second-division restitution (FDR & SDR). Different approaches either chemical (Colchicine, Oryzalin, Caffeine, Trifuralin, or phosphoric amides) or gaseous i.e. Nitrous oxide have been deliberated as strong polyploidy causing agents. A wide range of cytogenetic practices like chromosomes study, ploidy, genome analysis, and plant morphology and anatomy have been studied in different plant species. Flow cytometry for ploidy and chromosome analysis through fluorescence and genomic in situ hybridization (FISH & GISH) are the basic methods to evaluate heredity substances sampled from leaves and roots. Many horticultural crops have been developed successfully and released commercially for consumption. Moreover, some deep detailed studies are needed to check the strong relationship between unique morphological features and genetic makeup concerning genes and hormonal expression in a strong approach.

Unambiguous chromosome identification reveals the factors impacting irregular chromosome behaviors in allotriploid AAC Brassica

KEY MESSAGE

The major irregular chromosome pairing and mis-segregation were detected during meiosis through unambiguous chromosome identification and found that allotriploid Brassica can undergo meiosis successfully and produce mostly viable aneuploid gametes. Triploids have played a crucial role in the evolution of species by forming polyploids and facilitating interploidy gene transfer. It is widely accepted that triploids cannot undergo meiosis normally and predominantly produce nonfunctional aneuploid gametes, which restricts their role in species evolution. In this study, we demonstrated that natural and synthetic allotriploid Brassica (AAC), produced by crossing natural and synthetic Brassica napus (AACC) with Brassica rapa (AA), exhibits basically normal chromosome pairing and segregation during meiosis. Homologous A chromosomes paired faithfully and generally segregated equally. Monosomic C chromosomes were largely retained as univalents and randomly entered daughter cells. The primary irregular meiotic behaviors included associations of homoeologs and 45S rDNA loci at diakinesis, as well as homoeologous chromosome replacement and premature sister chromatid separation at anaphase I. Preexisting homoeologous arrangements altered meiotic behaviors in both chromosome irregular pairing and mis-segregation by increasing the formation of A-genomic univalents and A-C bivalents, as well as premature sister chromatid separation and homologous chromosome nondisjunction. Meiotic behaviors depended significantly on the genetic background and heterozygous homoeologous rearrangement. AAC triploids mainly generated aneuploid gametes, most of which were viable. These results demonstrate that allotriploid Brassica containing an intact karyotype can proceed through meiosis successfully, broadening our current understanding of the inheritance and role in species evolution of allotriploid.

Local adaptation, recombination, and the fate of neopolyploids

Polyploidy is widely recognized as an important speciation mechanism because it isolates tetraploids from their diploid progenitors. Polyploidy also provides new genetic material that may facilitate adaptive evolution. However, new mutations are more likely to arise after a neopolyploid has already successfully invaded a population. Thus, the role of adaptive forces in establishing a polyploid remains unclear. One solution to this apparent paradox may lie in the capacity of polyploids to suppress recombination among preexisting locally adapted alleles. The local adaptation mechanism requires that spatially heterogeneous selection acts on multiple loci and that gene flow introduces maladapted alleles to the population where the polyploid forms. The mechanism requires neither strong genetic drift nor any intrinsic benefit of genome doubling and can accommodate any mode of gene action. A unique prediction of the mechanism is that adaptive alleles should predate polyploidization, a pattern consistent with observations from a few well-studied polyploids. The mechanism is also consistent with the coexistence of both diploid and tetraploid cytotypes, fitness heterogeneity among independently derived polyploids, and the prevalence of outcrossing among older polyploids. The local adaptation mechanism also makes novel predictions about circumstances favoring polyploid invasions that can be tested using molecular genetic or comparative approaches.

Reproductive Performance of the Alpine Plant Species Ranunculus kuepferi in a Climatic Elevation Gradient: Apomictic Tetraploids Do Not Show a General Fitness Advantage over Sexual Diploids

Previous studies on the mountain plant Ranunculus kuepferi concluded that apomictic self-compatible tetraploids have experienced a niche shift toward a colder climate during the Holocene, which suggests a fitness advantage over the sexual, self-sterile diploid parents under cold and stressful high-mountain conditions. However, there is still a lack of information on whether reproductive development would be advantageous for tetraploids. Here, we report on microsporogenesis, megagametogenesis, the dynamics of flower and seed development, and the consequences for reproductive success in a common garden experiment along a 1000 m climatic elevation gradient and in natural populations. Flower buds were initiated in the year preceding anthesis and passed winter in a pre-meiotic stage. Flower morphology differed in the known cytotype-specific way in that tetraploid flowers produced about twice as many carpels and fewer petals, stamens, and pollen grains than diploid flowers. Tetraploids developed precociously aposporous embryo sacs and showed a high rate of developmental disturbances. Sexual seed formation prevailed in diploids and pseudogamous apomixis in tetraploids. Along the elevation gradient, stigma pollen load, pollen performance, and seed output decreased. Combinations of reproductive traits, namely, bypass of meiosis irregularities and uniparental reproduction, might have promoted the vast expansion of apomictic R. kuepferi lines across the European Alps.

Ice age-driven range shifts of diploids and expanding autotetraploids of Biscutella laevigata within a conserved niche

Early studies of the textbook mixed-ploidy system Biscutella laevigata highlighted diploids restricted to never-glaciated lowlands and tetraploids at high elevations across the European Alps, promoting the hypothesis that whole-genome duplication (WGD) is advantageous under environmental changes. Here we addressed long-held hypotheses on the role of hybridisation at the origin of the tetraploids, their single vs multiple origins, and whether a shift in climatic niche accompanied WGD. Climatic niche modelling together with spatial genetics and coalescent modelling based on ddRAD-seq genotyping of 17 diploid and 19 tetraploid populations was used to revisit the evolution of this species complex in space and time. Diploids differentiated into four genetic lineages corresponding to allopatric glacial refugia at the onset of the last ice age, whereas tetraploids displaying tetrasomic inheritance formed a uniform group that originated from southern diploids before the last glacial maximum. Derived from diploids occurring at high elevation, autotetraploids likely inherited their adaptation to high elevation rather than having evolved it through or after WGD. They further presented considerable postglacial expansion across the Alps and underwent admixture with diploids. Although the underpinnings of the successful expansion of autotetraploids remain elusive, differentiation in B. laevigata was chiefly driven by the glacial history of the Alps.

Exploring the role of 28-homobrassinolide in regulation of temperature induced clastogenic aberrations and sugar metabolism of Brassica juncea L

The present research primarily focuses on Brassica juncea's physiological and cytological responses to low and high temperature stress at 4 °C and 44 °C respectively, along with elucidating the protective role of 28-Homobrassinolide (28-homoBL). Cytological investigations performed in floral buds of Brassica juncea L. under temperature (24, 4, 44 °C) stress conditions depict the presence of some abnormalities associated with cytomixis such as chromosome stickiness or agglutination, pycnotic nature of chromatin, irregularities in spindle formation, disoriented chromatins, and non-synchronous chromatin material condensation in Brassicaceae family that subsisted at diploid level (2n = 36). Spindle abnormalities produce various size pollen grains such as sporads micronuclei at some stages of microsporogenesis, polyads, triads, dyads that irrupted the productiveness of pollen grains. Furthermore, sugars play an imperative role in protecting plants under stress besides being energy sources. Therefore, the present study revealed accumulation of total soluble sugars (TSS), with 28-homoBL treatment which pinpoints protective role of 28-homoBL under temperature stress. Sugar profiling was done by using high-performance liquid chromatography (HPLC) which helped in analyzing different sugars both quantitatively and qualitatively under 28-homoBL and temperature stress conditions. The results indicate that the 28-homoBL treatment substantially enhances plant tolerance to heat stress, as evident by higher mitotic indices, fewer chromosomal abnormalities, and significantly more sugar accumulation. The findings of the study acknowledge the potential of 28-homoBL in inducing temperature stress tolerance in B. juncea along with improving the metabolic stability thereby implying application of 28-homoBL in crop strengthening under variable temperature conditions.

Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow.

Friends without benefits: Extensive cytotype sympatry and polyploid persistence in an African geophyte

PREMISE

Polyploidy is a major factor in plant adaptation and speciation. Multiple mechanisms contribute to autopolyploid frequency within populations, but uncertainties remain regarding mechanisms that facilitate polyploid establishment and persistence. Here we aimed to document and predict cytotype distributions of Oxalis obliquifolia Steud. ex A. Rich. across Gauteng, South Africa, and test for evidence of possible mechanisms, including morphological, phenological, and reproductive traits, that may potentially facilitate polyploid persistence.

METHODS

Over 320 O. obliquifolia plants from 25 sites were cytotyped using flow cytometry, and DNA ploidy was confirmed using meiotic chromosome squashes. Cytotypes were mapped and correlations with abiotic variables assessed using ordinations. To assess morphological and phenological associations with cytotype, we grew multiple cytotypes in a common garden, measured phenotypic traits and compared them using linear models and discriminant analyses. Intercytotype reproductive isolation was assessed using crossing experiments, and AMOVAs based on ITS DNA sequences tested for cytogeographic structure.

RESULTS

Six cytotypes were identified, and most sites had multiple cytotypes. Abiotic variables were not predictive of cytotype distribution. A clear gigas effect was present. Differences in flower size and phenology suggested pollinator interactions could play a role in polyploid persistence. Intercytotype crosses produced seed at low frequency. DNA data suggested diploids and polyploids were largely reproductively isolated in situ, and polyploidization events were not frequent enough to explain high cytotype sympatry.

CONCLUSIONS

Diploids and polyploids are behaving as separate species, despite little observable niche differentiation and non-zero potential intercytotype seed set. Tests on biotic interactions and intercytotype F1 fitness may provide insights into diploid and polyploid coexistence.

A metabolic perspective on polyploid invasion and the emergence of life histories: Insights from a mechanistic model

PREMISE

Whole-genome duplication (WGD, polyploidization) has been identified as a driver of genetic and phenotypic novelty, having pervasive consequences for the evolution of lineages. While polyploids are widespread, especially among plants, the long-term establishment of polyploids is exceedingly rare. Genome doubling commonly results in increased cell sizes and metabolic expenses, which may be sufficient to modulate polyploid establishment in environments where their diploid ancestors thrive.

METHODS

We developed a mechanistic simulation model of photosynthetic individuals to test whether changes in size and metabolic efficiency allow autopolyploids to coexist with, or even invade, ancestral diploid populations. Central to the model is metabolic efficiency, which determines how energy obtained from size-dependent photosynthetic production is allocated to basal metabolism as opposed to somatic and reproductive growth. We expected neopolyploids to establish successfully if they have equal or higher metabolic efficiency as diploids or to adapt their life history to offset metabolic inefficiency.

RESULTS

Polyploid invasion was observed across a wide range of metabolic efficiency differences between polyploids and diploids. Polyploids became established in diploid populations even when they had a lower metabolic efficiency, which was facilitated by recurrent formation. Competition for nutrients is a major driver of population dynamics in this model. Perenniality did not qualitatively affect the relative metabolic efficiency from which tetraploids tended to establish.

CONCLUSIONS

Feedback between size-dependent metabolism and energy allocation generated size and age differences between plants with different ploidies. We demonstrated that even small changes in metabolic efficiency are sufficient for the establishment of polyploids.

Defining autopolyploidy: Cytology, genetics, and taxonomy

Autopolyploidy is taxonomically defined as the presence of more than two copies of each genome within an organism or species, where the genomes present must all originate within the same species. Alternatively, "genetic" or "cytological" autopolyploidy is defined by polysomic inheritance: random pairing and segregation of the four (or more) homologous chromosomes present, with no preferential pairing partners. In this review, we provide an overview of methods used to categorize species as taxonomic and cytological autopolyploids, including both modern and obsolete cytological methods, marker-segregation-based and genomics methods. Subsequently, we also investigated how frequently polysomic inheritance has been reliably documented in autopolyploids. Pure or predominantly polysomic inheritance was documented in 39 of 43 putative autopolyploid species where inheritance data was available (91%) and in seven of eight synthetic autopolyploids, with several cases of more mixed inheritance within species. We found no clear cases of autopolyploids with disomic inheritance, which was likely a function of our search methodology. Interestingly, we found seven species with purely polysomic inheritance and another five species with partial or predominant polysomic inheritance that appear to be taxonomic allopolyploids. Our results suggest that observations of polysomic inheritance can lead to relabeling of taxonomically allopolyploid species as autopolyploid and highlight the need for further cytogenetic and genomic investigation into polyploid origins and inheritance types.

Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy

All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants.

Why are triploid quaking aspen (Populus tremuloides) common?

PREMISE

Quaking aspen is a clonal tree species that has mixed ploidy, often with high relative abundance of both diploids and triploids but no haploids or tetraploids. Triploids typically have low fertility, leaving their occurrence apparently unlikely from an evolutionary perspective, unless they provide a "triploid bridge" to generating higher-fitness tetraploids-which are not observed in this species. This study focused on how triploidy can be maintained in quaking aspen.

METHODS

A computational model was used to simulate gamete production, sexual reproduction, asexual reproduction, parent survival, and offspring survival in a population. All parameters were assumed to be cytotype-dependent and environment-independent. Sampling methods were used to identify parameter combinations consistent with observed cytotype frequencies.

RESULTS

Many processes and parameter values were sufficient to yield a moderate frequency of triploids, and very few were necessary. The most plausible route involved higher triploid survival at the parent or offspring stage and limited unreduced gamete production by either diploid or triploid parents. Triploid fertility was helpful but not necessary.

CONCLUSIONS

The coexistence of diploids and triploids in quaking aspen is statistically likely and promoted by the existence of commonly observed, long-lived triploid clones. However, other mechanisms not captured by the model related to environmental variation could also occur. Further empirical data or more complex but difficult-to-parameterize models are needed to gain further insight.

Patterns of genomic variation reveal a single evolutionary origin of the wild allotetraploid Mimulus sookensis

Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger "instantaneous" speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage, but how often this scenario occurs is unclear. Here, we investigate the evolutionary history of the wild allotetraploid Mimulus sookensis, which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin. One M. sookensis subgenome is clearly derived from the selfer Mimulus nasutus, which organellar variation suggests is the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both Mimulus decorus and M. guttatus, two outcrossing diploids with geographic ranges that overlap broadly with M. sookensis. This study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploid's predisposition to self-fertilize.

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

Polyploidy in maize: from evolution to breeding

Polyploidy played an important role in the evolution of the three most important crops: wheat, maize and rice, each of them providing a unique model for studying allopolyploidy, segmental alloploidy or paleopolyploidy. However, its genetic and evolutionary role is still vague. The undelying mechanisms and consequences of polyploidy remain fundamental objectives in the study of eukaryotes. Maize is one of the underutilized crops at the polyploid level. This species has no stable natural polyploids, the existing ones being artificially obtained. From the experimental polyploid series of maize, only the tetraploid forms (4n = 40) are of interest. They are characterized by some valuable morphological, physiological and biochemical features, superior to the diploid forms from which they originated, but also by some drawbacks such as: reduced fertility, slower development, longer vegetation period, low productivity and adaptedness. Due to these barriers to using tetraploids in field production, maize tetraploids primarily found utility in scientific studies regarding genetic variability, inbreeding, heterosis and gene dosage effect. Since the first mention of a triploid maize plant to present, many scientists and schools, devoted their efforts to capitalize on the use of polyploidy in maize. Despite its common disadvantages as a crop, significant progress in developing tetraploid maize with good agronomic performance was achieved leading to registered tetraploid maize varieties. In this review we summarize and discuss the different aspects of polyploidy in maize, such as evolutionary context, methods of induction, morphology, fertility issue, inheritance patterns, gene expression and potential use.

Phylogenomics identifies parents of naturally occurring tetraploid bananas

BACKGROUND

Triploid bananas are almost sterile. However, we succeeded in harvesting seeds from two edible triploid banana individuals (Genotype: ABB) in our conservation repository where various wild diploid bananas were also grown. The resulting rare offspring survived to seedling stages. DNA content analyses reveal that they are tetraploid. Since bananas contain maternally inherited plastids and paternally inherited mitochondria, we sequenced and assembled plastomes and mitogenomes of these seedlings to trace their hybridization history.

RESULTS

The coding sequences of both organellar genomic scaffolds were extracted, aligned, and concatenated for constructing phylogenetic trees. Our results suggest that these tetraploid seedlings be derived from hybridization between edible triploid bananas and wild diploid Musa balbisiana (BB) individuals. We propose that generating female triploid gametes via apomeiosis may allow the triploid maternal bananas to produce viable seeds.

CONCLUSIONS

Our study suggests a practical avenue towards expanding genetic recombination and increasing genetic diversity of banana breeding programs. Further cellular studies are needed to understand the fusion and developmental processes that lead to formation of hybrid embryos in banana reproduction, polyploidization, and evolution.

Genome-wide identification and drought stress-induced expression analysis of the NHX gene family in potato

NHX proteins are transmembrane antiporters belonging to the cation/proton antiporter gene family, with a conserved Na+ (K+)/H+ exchange (PF00999) protein domain. NHXs play a prominent role in plant growth, development, and defense. However, the role of NHX gene family in potato (Solanum tuberosum L.) is yet to be known. In this study, we conducted a genome-wide analysis of the potato NHX gene family. A total of 25 StNHX family members were identified to be unevenly distributed on 10 chromosomes. The proteins ranged in length from 252 to 1,153 amino acids, with molecular masses ranging from 27516.32 to 127860.87 kD, and isoelectric points (pI) ranging from 4.96 to 9.3. Analyses of gene structures and conserved motifs indicated that StNHX genes in the same phylogenetic cluster are conserved. Phylogenetic analysis divided the StNHX genes into three subfamilies (Classes I, II, and III). Synteny analysis indicated that StNHX gene family Class III of NHX and all Arabidopsis thaliana NHXs shared a close evolutionary relationship. Analysis of cis-acting elements in the upstream 1,500 bp promoter region of potato NHX genes showed that these genes could be regulated by light, stress, and hormones such as abscisic acid and gibberellic acid. Protein-protein interaction network analysis indicated that StNHX proteins may participate in the regulation of potato growth and stress response. Besides, To determine a potential role of these genes in tissue development and drought response, we analyzed the RNA-seq data of different DM potato tissues. The results showed that NHX genes exhibited distinct tissue-specific expression patterns. We further examined the expression patterns of StNHX in different tissues (leaves, roots, shoots, tubers, stolons, and flowers) during the flowering stage in 'Jizhangshu NO.8.' potato. The qRT-PCR results further confirmed the importance of StNHX genes in potato plant growth and development. We further analyzed the RNA-seq data (DM potato) under different abiotic stresses (salt, drought, and heat), and found that the expression of StNHX genes was induced under abiotic stress. qRT-PCR analysis of shoots and roots of 'Jizhangshu NO.8.' potato treated for 0, 6, 12, and 24 h with 15% PEG6000 confirmed that the 25 StNHX genes are involved in the response to drought stress in potato. The results of this study may be useful for selecting appropriate candidate genes for the breeding of new drought-tolerant potato varieties. Furthermore, this study lays a foundation for prospective analysis of StNHX gene functions.

Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae)

BACKGROUND AND AIMS

Polyploidy is considered one of the main mechanisms of plant evolution and speciation. In the Mediterranean Basin, polyploidy has contributed to making this region a biodiversity hotspot, along with its geological and climatic history and other ecological and biogeographical factors. The Mediterranean genus Centaurium (Gentianaceae) comprises ~25 species, of which 60 % are polyploids, including tetraploids and hexaploids. To date, the evolutionary history of centauries has been studied using Sanger sequencing phylogenies, which have been insufficient to fully understand the phylogenetic relationships in this lineage. The goal of this study is to gain a better understanding of the evolutionary history of Centaurium by exploring the mechanisms that have driven its diversification, specifically hybridization and polyploidy. We aim to identify the parentage of hybrid species, at the species or clade level, as well as assessing whether morphological traits are associated with particular ploidy levels.

METHODS

We sequenced RADseq markers from 42 samples of 28 Centaurium taxa, and performed phylogenomic analyses using maximum likelihood, summary coalescent SVDquartets and Neighbor-Net approaches. To identify hybrid taxa, we used PhyloNetworks and the fastSTRUCTURE algorithm. To infer the putative parental species of the allopolyploids, we employed genomic analyses (SNIPloid). The association between different traits and particular ploidy levels was explored with non-metric multidimensional scaling.

KEY RESULTS

Our phylogenetic analyses confirmed the long-suspected occurrence of recurrent hybridization. The allopolyploid origin of the tetraploid C. serpentinicola and the hexaploids C. mairei, C. malzacianum and C. centaurioides was also confirmed, unlike that of C. discolor. We inferred additional signatures of hybridization events within the genus and identified morphological traits differentially distributed in different ploidy levels.

CONCLUSIONS

This study highlights the important role that hybridization has played in the evolution of a Mediterranean genus such as Centaurium, leading to a polyploid complex, which facilitated its diversification and may exemplify that of other Mediterranean groups.

Influence of polyploidy on morphology and distribution of the Cypress Spurge (Euphorbia cyparissias, Euphorbiaceae)

Polyploidy can cause differences in phenotypic and physiological traits among different cytotypes of the same species. Polyploids may have larger organs or occupy different ecological niches than their diploid counterparts, therefore they are hypothesized to have larger distributions or prosper in stressful environments, such as higher elevations. The Cypress spurge (Euphorbia cyparissias L.; Euphorbiaceae) is a widespread European heteroploid species including di- (2x), tetra- (4x) and hexaploid (6x) cytotypes. We tested the hypotheses that polyploids are more widespread and more abundant at higher elevations and have larger organs than their diploid ancestors in the case of E. cyparissias. We also analysed whether genome downsizing had occurred after polyploidisation. We conducted a comprehensive geographic sampling of 617 populations of E. cyparissias throughout Europe. We estimated their relative genome size using flow cytometry and inferred ploidy level of each population. We scored 13 morphological traits of vegetative and seed characters and performed statistical analyses. The study indicates that polyploidisation facilitated colonisation of new areas in E. cyparissias, where the tetraploids are most widespread, whereas the diploids are limited to putative Pleistocene refugia, mostly in southern Europe. On the other hand, the three ploidies do not differ in their elevational distribution. Although some quantitative morphological traits exhibited an increasing trend with increasing ploidy, most traits did not differ significantly among the three ploidies, and there was no overall phenotypic differentiation among them. Given that individuals of different ploidies thrive in similar habitats across the same elevations, we suggest that ecological segregation following polyploidisation is a more important trigger for morphological differentiation than polyploidisation itself in autopolyploid plants. The study demonstrates that polyploidisation can be crucial for the colonisation of new areas and for range expansion, but it does not necessarily influence elevational distribution nor confer a different phenotype.

Plant kleptomaniacs: geographical genetic patterns in the amphi-apomictic Rubus ser. Glandulosi (Rosaceae) reveal complex reticulate evolution of Eurasian brambles

BACKGROUND AND AIMS

Rubus ser. Glandulosi provides a unique model of geographical parthenogenesis on a homoploid (2n = 4x) level. We aim to characterize evolutionary and phylogeographical patterns in this taxon and shed light on the geographical differentiation of apomicts and sexuals. Ultimately, we aim to evaluate the importance of phylogeography in the formation of geographical parthenogenesis.

METHODS

Rubus ser. Glandulosi was sampled across its Eurasian range together with other co-occurring Rubus taxa (587 individuals in total). Double-digest restriction site-associated DNA sequencing (ddRADseq) and modelling of suitable climate were used for evolutionary inferences.

KEY RESULTS

Six ancestral species were identified that contributed to the contemporary gene pool of R. ser. Glandulosi. Sexuals were introgressed from Rubus dolichocarpus and Rubus moschus in West Asia and from Rubus ulmifolius agg., Rubus canescens and Rubus incanescens in Europe, whereas apomicts were characterized by alleles of Rubus subsect. Rubus. Gene flow between sexuals and apomicts was also detected, as was occasional hybridization with other taxa.

CONCLUSIONS

We hypothesize that sexuals survived the last glacial period in several large southern refugia, whereas apomicts were mostly restricted to southern France, whence they quickly recolonized Central and Western Europe. The secondary contact of sexuals and apomicts was probably the principal factor that established geographical parthenogenesis in R. ser. Glandulosi. Sexual populations are not impoverished in genetic diversity along their borderline with apomicts, and maladaptive population genetic processes probably did not shape the geographical patterns.

Covering the bases: Population genomic structure of Lemna minor and the cryptic species L. japonica in Switzerland

Duckweeds, including the common duckweed Lemna minor, are increasingly used to test eco-evolutionary theories. Yet, despite its popularity and near-global distribution, the understanding of its population structure (and genetic variation therein) is still limited. It is essential that this is resolved, because of the impact genetic diversity has on experimental responses and scientific understanding. Through whole-genome sequencing, we assessed the genetic diversity and population genomic structure of 23 natural Lemna spp. populations from their natural range in Switzerland. We used two distinct analytical approaches, a reference-free kmer approach and the classical reference-based one. Two genetic clusters were identified across the described species distribution of L. minor, surprisingly corresponding to species-level divisions. The first cluster contained the targeted L. minor individuals and the second contained individuals from a cryptic species: Lemna japonica. Within the L. minor cluster, we identified a well-defined population structure with little intra-population genetic diversity (i.e., within ponds) but high inter-population diversity (i.e., between ponds). In L. japonica, the population structure was significantly weaker and genetic variation between a subset of populations was as low as within populations. This study revealed that L. japonica is more widespread than previously thought. Our findings signify that thorough genotype-to-phenotype analyses are needed in duckweed experimental ecology and evolution.

Interspecific transfer of genetic information through polyploid bridges

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation.

Chromosome stability of synthetic Triticum turgidum-Aegilops umbellulata hybrids

BACKGROUND

Unreduced gamete formation during meiosis plays a critical role in natural polyploidization. However, the unreduced gamete formation mechanisms in Triticum turgidum-Aegilops umbellulata triploid F1 hybrid crosses and the chromsome numbers and compostions in T. turgidum-Ae. umbellulata F2 still not known.

RESULTS

In this study, 11 T.turgidum-Ae. umbellulata triploid F1 hybrid crosses were produced by distant hybridization. All of the triploid F1 hybrids had 21 chromosomes and two basic pathways of meiotic restitution, namely first-division restitution (FDR) and single-division meiosis (SDM). Only FDR was found in six of the 11 crosses, while both FDR and SDM occurred in the remaining five crosses. The chromosome numbers in the 127 selfed F2 seeds from the triploid F1 hybrid plants of 10 crosses (no F2 seeds for STU 16) varied from 35 to 43, and the proportions of euploid and aneuploid F2 plants were 49.61% and 50.39%, respectively. In the aneuploid F2 plants, the frequency of chromosome loss/gain varied among genomes. The chromosome loss of the U genome was the highest (26.77%) among the three genomes, followed by that of the B (22.83%) and A (11.81%) genomes, and the chromosome gain for the A, B, and U genomes was 3.94%, 3.94%, and 1.57%, respectively. Of the 21 chromosomes, 7U (16.54%), 5 A (3.94%), and 1B (9.45%) had the highest loss frequency among the U, A, and B genomes. In addition to chromosome loss, seven chromosomes, namely 1 A, 3 A, 5 A, 6 A, 1B, 1U, and 6U, were gained in the aneuploids.

CONCLUSION

In the aneuploid F2 plants, the frequency of chromosome loss/gain varied among genomes, chromsomes, and crosses. In addition to variations in chromosome numbers, three types of chromosome translocations including 3UL·2AS, 6UL·1AL, and 4US·6AL were identified in the F2 plants. Furthermore, polymorphic fluorescence in situ hybridization karyotypes for all the U chromosomes were also identified in the F2 plants when compared with the Ae. umbellulata parents. These results provide useful information for our understanding the naturally occurred T. turgidum-Ae. umbellulata amphidiploids.

Phenotypic variation seems not to be associated with the genetic profile in Zygopetalum (Orchidaceae): a case study of a high-elevation rocky complex

BACKGROUND

Hybridization associated with polyploidy studies is rare in the tropics. The genus Zygopetalum (Orchidaceae) was investigated here as a case study of Neotropical plants. In the rocky highlands of the Ibitipoca State Park (ISP), southeast Brazil, individuals with intermediate colors and forms between the species Z. maculatum and Z. triste were commonly identified.

METHODS AND RESULTS

Chromosomal analysis and DNA quantity showed a uniform population. Regardless of the aspects related to the color and shape of floral structures, all individuals showed 2n = 96 chromosomes and an average of 14.05 pg of DNA. Irregularities in meiosis associated with chromosome number and C value suggest the occurrence of polyploidy. The genetic distance estimated using ISSR molecular markers revealed the existence of genetic variability not related to morphological clusters. Morphometric measurements of the flower pieces revealed that Z. maculatum shows higher variation than Z. triste although lacking a defined circumscription.

CONCLUSION

The observed variation can be explained by the polyploid and phenotypic plasticity resulting from the interaction of the genotypes with the heterogeneous environments observed in this habitat.

Whole-genome duplication in the Multicellularity Long Term Evolution Experiment

Whole-genome duplication (WGD) is widespread across eukaryotes and can promote adaptive evolution1-4. However, given the instability of newly-formed polyploid genomes5-7, understanding how WGDs arise in a population, persist, and underpin adaptations remains a challenge. Using our ongoing Multicellularity Long Term Evolution Experiment (MuLTEE)8, we show that diploid snowflake yeast (Saccharomyces cerevisiae) under selection for larger multicellular size rapidly undergo spontaneous WGD. From its origin within the first 50 days of the experiment, tetraploids persist for the next 950 days (nearly 5,000 generations, the current leading edge of our experiment) in ten replicate populations, despite being genomically unstable. Using synthetic reconstruction, biophysical modeling, and counter-selection experiments, we found that tetraploidy evolved because it confers immediate fitness benefits in this environment, by producing larger, longer cells that yield larger clusters. The same selective benefit also maintained tetraploidy over long evolutionary timescales, inhibiting the reversion to diploidy that is typically seen in laboratory evolution experiments. Once established, tetraploidy facilitated novel genetic routes for adaptation, playing a key role in the evolution of macroscopic multicellular size via the origin of evolutionarily conserved aneuploidy. These results provide unique empirical insights into the evolutionary dynamics and impacts of WGD, showing how it can initially arise due to its immediate adaptive benefits, be maintained by selection, and fuel long-term innovations by creating additional dimensions of heritable genetic variation.

The genetic consequences of range expansion and its influence on diploidization in polyploids

Despite newly formed polyploids being subjected to myriad fitness consequences, the relative prevalence of polyploidy both contemporarily and in ancestral branches of the tree of life suggests alternative advantages that outweigh these consequences. One proposed advantage is that polyploids may more easily colonize novel habitats such as deglaciated areas. However, previous research conducted in diploids suggests that range expansion comes with a fitness cost as deleterious mutations may fix rapidly on the expansion front. Here, we interrogate the potential consequences of expansion in polyploids by conducting spatially explicit forward-in-time simulations to investigate how ploidy and inheritance patterns impact the relative ability of polyploids to expand their range. We show that under realistic dominance models, autopolyploids suffer greater fitness reductions than diploids as a result of range expansion due to the fixation of increased mutational load that is masked in the range core. Alternatively, the disomic inheritance of allopolyploids provides a shield to this fixation resulting in minimal fitness consequences. In light of this advantage provided by disomy, we investigate how range expansion may influence cytogenetic diploidization through the reversion to disomy in autotetraploids. We show that under a wide range of parameters investigated for two models of diploidization, disomy frequently evolves more rapidly on the expansion front than in the range core, and that this dynamic inheritance model has additional effects on fitness. Together our results point to a complex interaction between dominance, ploidy, inheritance, and recombination on fitness as a population spreads across a geographic range.

Epigenetic histone H3 phosphorylation marks discriminate between univalent- and bivalent-forming chromosomes during canina asymmetrical meiosis

BACKGROUND AND AIMS

Dogroses (Rosa sect. Caninae) are mostly pentaploid, bearing 2n = 5x = 35 chromosomes in somatic cells. They evolved a unique form of asymmetrical meiosis characterized by two types of chromosomes: (1) chromosomes forming bivalents and distributed in the normal sexual way; and (2) chromosomes occurring as univalents and transferred by a female gamete only. In the mature pollen of pentaploid species, seven bivalent-derived chromosomes are transmitted to offspring, and 21 unpaired univalent chromosomes are eliminated during microsporogenesis. To discriminate between bivalent- and univalent-forming chromosomes, we studied histone H3 phosphorylation patterns regulating meiotic chromosome condensation and segregation.

METHODS

We analysed histone modification patterns during male canina meiosis in two representative dogrose species, 5x Rosa canina and 5x Rosa rubiginosa, by immunohistochemical and molecular cytogenetics approaches. Immunostaining of meiotic cells included α-tubulin, histone H3 phosphorylation (H3S10p, H3S28p and H3T3p) and methylation (H3K4me3 and H3K27me3) marks. In addition, fluorescent in situ hybridization was carried out with an 18S rDNA probe.

KEY RESULTS

In the first meiotic division, univalent chromosomes underwent equational division into chromatids, while homologues in bivalents were segregated as regular dyads. In diakinesis, bivalent chromosomes displayed strong H3 phosphorylation signals in proximal regions, spreading to the rest of the chromosome. In contrast, in univalents, the H3 phosphorylation signals were weaker, occurring mostly outside proximal regions largely overlapping with the H3K4me3 signals. Reduced phosphorylation was associated with relative under-condensation of the univalent chromosomes, particularly at early diakinesis.

CONCLUSIONS

We hypothesize that the absence of pairing and/or recombination in univalent chromosomes negatively affects the histone H3 phosphorylation of their chromatin and perhaps the loading of meiotic-specific cohesins. This apparently destabilizes cohesion of sister chromatids, leading to their premature split in the first meiotic division.

The global distribution of angiosperm genome size is shaped by climate

Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.

Exploring the patterns of evolution: Core thoughts and focus on the saltational model

The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.

The emerging importance of cross-ploidy hybridisation and introgression

Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest in natural hybridisation fuelled by developments in genomics has led to an improved understanding of the genetic factors that promote or prevent species cross-mating. Despite this body of work overturning many widely held assumptions about the genetic barriers to hybridisation, it is still widely thought that ploidy differences between species will be an absolute barrier to hybridisation and introgression. Here, we revisit this assumption, reviewing findings from surveys of polyploidy and hybridisation in the wild. In a case study in the British flora, 203 hybrids representing 35% of hybrids with suitable data have formed via cross-ploidy matings, while a wider literature search revealed 59 studies (56 in plants and 3 in animals) in which cross-ploidy hybridisation has been confirmed with genetic data. These results show cross-ploidy hybridisation is readily overlooked, and potentially common in some groups. General findings from these studies include strong directionality of hybridisation, with introgression usually towards the higher ploidy parent, and cross-ploidy hybridisation being more likely to involve allopolyploids than autopolyploids. Evidence for adaptive introgression across a ploidy barrier and cases of cross-ploidy hybrid speciation shows the potential for important evolutionary outcomes.

Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato

KEY MESSAGE

Multiple QTLs control unreduced pollen production in potato. Two major-effect QTLs co-locate with mutant alleles of genes with homology to AtJAS, a known regulator of meiotic spindle orientation. In diploid potato the production of unreduced gametes with a diploid (2n) rather than a haploid (n) number of chromosomes has been widely reported. Besides their evolutionary important role in sexual polyploidisation, unreduced gametes also have a practical value for potato breeding as a bridge between diploid and tetraploid germplasm. Although early articles argued for a monogenic recessive inheritance, the genetic basis of unreduced pollen production in potato has remained elusive. Here, three diploid full-sib populations were genotyped with an amplicon sequencing approach and phenotyped for unreduced pollen production across two growing seasons. We identified two minor-effect and three major-effect QTLs regulating this trait. The two QTLs with the largest effect displayed a recessive inheritance and an additive interaction. Both QTLs co-localised with genes encoding for putative AtJAS homologs, a key regulator of meiosis II spindle orientation in Arabidopsis thaliana. The function of these candidate genes is consistent with the cytological phenotype of mis-oriented metaphase II plates observed in the parental clones. The alleles associated with elevated levels of unreduced pollen showed deleterious mutation events: an exonic transposon insert causing a premature stop, and an amino acid change within a highly conserved domain. Taken together, our findings shed light on the natural variation underlying unreduced pollen production in potato and will facilitate interploidy breeding by enabling marker-assisted selection for this trait.

Physiology, gene expression, and epiphenotype of two Dianthus broteri polyploid cytotypes under temperature stress

Increasing evidence supports a major role for abiotic stress response in the success of plant polyploids, which usually thrive in harsh environments. However, understanding the ecophysiology of polyploids is challenging due to interactions between genome doubling and natural selection. Here, we investigated physiological responses, gene expression, and the epiphenotype of two related Dianthus broteri cytotypes-with different genome duplications (4× and 12×) and evolutionary trajectories-to short extreme temperature events (42/28 °C and 9/5 °C). The 12× cytotype showed higher expression of stress-responsive genes (SWEET1, PP2C16, AI5L3, and ATHB7) and enhanced gas exchange compared with 4×. Under heat stress, both ploidies had greatly impaired physiological performance and altered gene expression, with reduced cytosine methylation. However, the 12× cytotype exhibited remarkable physiological tolerance (maintaining gas exchange and water status via greater photochemical integrity and probably enhanced water storage) while down-regulating PP2C16 expression. Conversely, 4× D. broteri was susceptible to thermal stress despite prioritizing water conservation, showing signs of non-stomatal photosynthetic limitations and irreversible photochemical damage. This cytotype also presented gene-specific expression patterns under heat, up-regulating ATHB7. These findings provide insights into divergent stress response strategies and physiological resistance resulting from polyploidy, highlighting its widespread influence on plant function.

Polyploidization: A Biological Force That Enhances Stress Resistance

Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.

Karyotype Variability in Wild Narcissus poeticus L. Populations from Different Environmental Conditions in the Dinaric Alps

Narcissus poeticus L. (Amaryllidaceae), a facultative serpentinophyte, is a highly variable species and particularly important ancestor of cultivated daffodils, but is rarely studied in field populations. This study, based on natural populations in the Balkans, focused on karyotype variability, genome size, ploidy and the presence of B chromosomes. Thirteen native populations from different environmental and soil conditions were collected and analyzed using flow cytometry to estimate nuclear genome size, fluorescence in situ hybridization (FISH) for physical mapping of rDNA, fluorochrome labeling (chromomycin and Hoechst) for heterochromatin organization and silver nitrate staining of nucleoli for determining rRNA gene activity. The organization of rDNA and natural triploids is reported here for the first time. The presence of individuals with B chromosomes (in 9/13 populations) and chromosomal rearrangements was also detected. The observed B chromosome showed three different morphotypes. The most frequent submetacentric type showed four different patterns, mainly with active ribosomal genes. The results obtained show that N. poeticus has a dynamic genome with variable genome size due to the presence of polyploidy, B chromosomes and chromosomal rearrangements. It is hypothesized that the observed changes reflect the response of the genome to different environmental conditions, where individuals with B chromosomes appear to have certain adaptive advantages.

Gamete sex and elevation affect genetically based variation for unreduced gamete production in a mixed-ploidy plant

PREMISE

Unreduced gametes are the primary mechanism of neopolyploid formation. Their production in diploid populations is arguably maladaptive, but the magnitude and patterns of genetically based variation maintained in natural populations are poorly understood.

METHODS

We examined variation in male and female unreduced gamete production among plants from different elevations in fireweed, Chamerion angustifolium, grown in a common environment. Using seeds from three high-elevation and three low-elevation diploid populations in one study, and a single diploid population in another, we estimated realized rates of unreduced male (sperm) and female (egg) gamete production by reciprocally pollinating diploid and tetraploid plants and estimating the incidence of tetraploid seeds using flow cytometry.

RESULTS

Unreduced gamete frequencies per plant were similar in the two studies (0.12% vs. 0.08%). High-elevation populations had a greater percentage of fruit with seeds from unreduced gametes, but a lower percentage of seeds per fruit than low-elevation populations. Female unreduced gamete frequencies differed among elevations, but male frequencies did not, and the gamete sexes were not correlated at the plant level.

CONCLUSIONS

We conclude that genetically based variation for unreduced gametes is maintained within and among natural populations, despite their fitness disadvantages, suggesting that local selection may be ineffective at purging them under some conditions.

Downregulation of the expression of subgenomic chromosome A7 genes promotes plant height in resynthesized allopolyploid Brassica napus

KEY MESSAGE

Homoeolog expression bias and the gene dosage effect induce downregulation of genes on chromosome A7, causing a significant increase in the plant height of resynthesized allopolyploid Brassica napus. Gene expression levels in allopolyploid plants are not equivalent to the simple average of the expression levels in the parents and are associated with several non-additive expression phenomena, including homoeolog expression bias. However, hardly any information is available on the effect of homoeolog expression bias on traits. Here, we studied the effects of gene expression-related characteristics on agronomic traits using six isogenic resynthesized Brassica napus lines across the first ten generations. We found a group of genes located on chromosome A7 whose expression levels were significantly negatively correlated with plant height. They were expressed at significantly lower levels than their homoeologous genes, owing to allopolyploidy rather than inheritance from parents. Homoeolog expression bias resulted in resynthesized allopolyploids with a plant height similar to their female Brassica oleracea parent, but significantly higher than that of the male Brassica rapa parent. Notably, aneuploid lines carrying monosomic and trisomic chromosome A7 had the highest and lowest plant heights, respectively, due to changes in the expression bias of homoeologous genes because of alterations in the gene dosage. These findings suggest that the downregulation of the expression of homoeologous genes on a single chromosome can result in the partial improvement of traits to a significant extent in the nascent allopolyploid B. napus.

Maternal dominance contributes to subgenome differentiation in allopolyploid fishes

Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.

Time-resolved, integrated analysis of clonally evolving genomes

Clonal genome evolution is a key feature of asexually reproducing species and human cancer development. While many studies have described the landscapes of clonal genome evolution in cancer, few determine the underlying evolutionary parameters from molecular data, and even fewer integrate theory with data. We derived theoretical results linking mutation rate, time, expansion dynamics, and biological/clinical parameters. Subsequently, we inferred time-resolved estimates of evolutionary parameters from mutation accumulation, mutational signatures and selection. We then applied this framework to predict the time of speciation of the marbled crayfish, an enigmatic, globally invasive parthenogenetic freshwater crayfish. The results predict that speciation occurred between 1986 and 1990, which is consistent with biological records. We also used our framework to analyze whole-genome sequencing datasets from primary and relapsed glioblastoma, an aggressive brain tumor. The results identified evolutionary subgroups and showed that tumor cell survival could be inferred from genomic data that was generated during the resection of the primary tumor. In conclusion, our framework allowed a time-resolved, integrated analysis of key parameters in clonally evolving genomes, and provided novel insights into the evolutionary age of marbled crayfish and the progression of glioblastoma.

Drivers of diversification in Linum (Linaceae) by means of chromosome evolution: correlations with biogeography, breeding system and habit

BACKGROUND AND AIMS

Chromosome evolution leads to hybrid dysfunction and recombination patterns and has thus been proposed as a major driver of diversification in all branches of the tree of life, including flowering plants. In this study we used the genus Linum (flax species) to evaluate the effects of chromosomal evolution on diversification rates and on traits that are important for sexual reproduction. Linum is a useful study group because it has considerable reproductive polymorphism (heterostyly) and chromosomal variation (n = 6-36) and a complex pattern of biogeographical distribution.

METHODS

We tested several traditional hypotheses of chromosomal evolution. We analysed changes in chromosome number across the phylogenetic tree (ChromEvol model) in combination with diversification rates (ChromoSSE model), biogeographical distribution, heterostyly and habit (ChromePlus model).

KEY RESULTS

Chromosome number evolved across the Linum phylogeny from an estimated ancestral chromosome number of n = 9. While there were few apparent incidences of cladogenesis through chromosome evolution, we inferred up to five chromosomal speciation events. Chromosome evolution was not related to heterostyly but did show significant relationships with habit and geographical range. Polyploidy was negatively correlated with perennial habit, as expected from the relative commonness of perennial woodiness and absence of perennial clonality in the genus. The colonization of new areas was linked to genome rearrangements (polyploidy and dysploidy), which could be associated with speciation events during the colonization process.

CONCLUSIONS

Chromosome evolution is a key trait in some clades of the Linum phylogeny. Chromosome evolution directly impacts speciation and indirectly influences biogeographical processes and important plant traits.

PloiDB: the plant ploidy database

See also the Commentary on this article by Spoelhof et al., 240: 909–911.

Does the evolution of micromorphology accompany chromosomal changes on dysploid and polyploid levels in the Barnardia japonica complex (Hyacinthaceae)?

BACKGROUND

Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation.

RESULTS

The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels.

CONCLUSIONS

This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.

Incidence and evolutionary relevance of autotriploid cytotypes in a relict member of the genus Daphne (Thymelaeaceae)

Odd ploidy-level cytotypes in sexually reproducing species are considered a dead end due to absent or reduced fertility. If sterility is only partial, however, their contribution to the population gene pool can be augmented by longevity and clonal growth. To test this, we investigated the cytotype origin and spatial pattern, and pollen viability in three relict shrub species of the genus Daphne (Thymelaeaceae Juss.) in central Europe. Daphne cneorum subsp. cneorum is a widespread European species that has a broad ecological amplitude, whereas D. cneorum subsp. arbusculoides and D. arbuscula are narrow endemics of the western Pannonian Plain and the Western Carpathians, respectively. Our study confirmed that all three taxa are diploid. However, of more than a thousand analysed individuals of D. cneorum subsp. cneorum, five in four different populations were triploid. Our data indicate that these triploids most likely originate from recurrent autopolyploidization events caused by the fusion of reduced and unreduced gametes. High pollen viability was observed in all three taxa and in both diploid and triploid cytotypes, ranging from 65 to 100 %. Our study highlights the significant role of odd ploidy-level cytotypes in interploidy gene flow, calling for more research into their reproduction, genetic variability, and overall fitness. Interestingly, while the endemic D. arbuscula differs from D. cneorum based on genetic and genome size data, D. cneorum subsp. arbusculoides was indistinguishable from D. cneorum subsp. cneorum. However, our study reveals that the subspecies differ in the number of flowers per inflorescence. This is the first comprehensive cytogeographic study of this intriguing genus at a regional scale, and in spite of its karyological stability, it contributes to our understanding of genomic evolution in plant species with a wide ecological amplitude.

Genome shock in a synthetic allotetraploid wheat invokes subgenome-partitioned gene regulation, meiotic instability, and karyotype variation

It is becoming increasingly evident that interspecific hybridization at the homoploid level or coupled with whole-genome duplication (i.e. allopolyploidization) has played a major role in biological evolution. However, the direct impacts of hybridization and allopolyploidization on genome structure and function, phenotype, and fitness remains to be fully understood. Synthetic hybrids and allopolyploids are trackable experimental systems that can be used to address this issue. In this study, we resynthesized a pair of reciprocal F1 hybrids and corresponding reciprocal allotetraploids using the two diploid progenitor species of bread wheat (Triticum aestivum, BBAADD), namely T. urartu (AA) and Aegilops tauschii (DD). By comparing phenotypes related to growth, development, and fitness, and by analysing genome expression in both hybrids and allotetraploids in relation to the parents, we found that the types and trends of karyotype variation in the immediately formed allotetraploids were correlated with both instability of meiosis and chromosome- and subgenome-biased expression. We determined clear advantages of allotetraploids over diploid F1 hybrids in several morphological traits including fitness that mirrored the tissue- and developmental stage-dependent subgenome-partitioning of the allotetraploids. The allotetraploids were meiotically unstable primarily due to homoeologous pairing that varied dramatically among the chromosomes. Nonetheless, the manifestation of organismal karyotype variation and the occurrence of meiotic irregularity were not concordant, suggesting a role of functional constraints probably imposed by subgenome- and chromosome-biased gene expression. Our results provide new insights into the direct impacts and consequences of hybridization and allopolyploidization that are relevant to evolution and likely to be informative for future crop improvement approaches using synthetic polyploids.

Autotetraploid Origin of Chinese Cherry Revealed by Chromosomal Karyotype and In Situ Hybridization of Seedling Progenies

Polyploidy is considered a driving force in plant evolution and diversification. Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], an economically important fruit crop native to China, has evolved at the tetraploid level, with a few pentaploid and hexaploid populations. However, its auto- or allo-polyploid origin remains unclear. To address this issue, we analyzed the ploidy levels and rDNA chromosomal distribution in self- and open-pollinated seedling progenies of tetraploid and hexaploid Chinese cherry. Genomic in situ hybridization (GISH) analysis was conducted to reveal the genomic relationships between Chinese cherry and diploid relatives from the genus Cerasus. Both self- and open-pollinated progenies of tetraploid Chinese cherry exhibited tetraploids, pentaploids, and hexaploids, with tetraploids being the most predominant. In the seedling progenies of hexaploid Chinese cherry, the majority of hexaploids and a few pentaploids were observed. A small number of aneuploids were also observed in the seedling progenies. Chromosome 1, characterized by distinct length characteristics, could be considered the representative chromosome of Chinese cherry. The basic Chinese cherry genome carried two 5S rDNA signals with similar intensity, and polyploids had the expected multiples of this copy number. The 5S rDNA sites were located at the per-centromeric regions of the short arm on chromosomes 4 and 5. Three 45S rDNA sites were detected on chr. 3, 4 and 7 in the haploid complement of Chinese cherry. Tetraploids exhibited 12 signals, while pentaploids and hexaploids showed fewer numbers than expected multiples. Based on the GISH signals, Chinese cherry demonstrated relatively close relationships with C. campanulata and C. conradinae, while being distantly related to another fruiting cherry, C. avium. In combination with the above results, our findings suggested that Chinese cherry likely originated from autotetraploidy.

Genome composition in Brassica interspecific hybrids affects chromosome inheritance and viability of progeny

Interspecific hybridization is widespread in nature and can result in the formation of new hybrid species as well as the transfer of traits between species. However, the fate of newly formed hybrid lineages is relatively understudied. We undertook pairwise crossing between multiple genotypes of three Brassica allotetraploid species Brassica juncea (2n = AABB), Brassica carinata (2n = BBCC), and Brassica napus (2n = AACC) to generate AABC, BBAC, and CCAB interspecific hybrids and investigated chromosome inheritance and fertility in these hybrids and their self-pollinated progeny. Surprisingly, despite the presence of a complete diploid genome in all hybrids, hybrid fertility was very low. AABC and BBAC first generation (F1) hybrids both averaged ~16% pollen viability compared to 3.5% in CCAB hybrids: most CCAB hybrid flowers were male-sterile. AABC and CCAB F1 hybrid plants averaged 5.5 and 0.5 seeds per plant, respectively, and BBAC F1 hybrids ~56 seeds/plant. In the second generation (S1), all confirmed self-pollinated progeny resulting from CCAB hybrids were sterile, producing no self-pollinated seeds. Three AABC S1 hybrids putatively resulting from unreduced gametes produced 3, 14, and 182 seeds each, while other AABC S1 hybrids averaged 1.5 seeds/plant (0-8). BBAC S1 hybrids averaged 44 seeds/plant (range 0-403). We also observed strong bias towards retention rather than loss of the haploid genomes, suggesting that the subgenomes in the Brassica allotetraploids are already highly interdependent, such that loss of one subgenome is detrimental to fertility and viability. Our results suggest that relationships between subgenomes determine hybridization outcomes in these species.

Genomic insights into biased allele loss and increased gene numbers after genome duplication in autotetraploid Cyclocarya paliurus

BACKGROUND

Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid-autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual.

RESULTS

Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture.

CONCLUSIONS

Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus.

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.

Global biodiversity data suggest allopolyploid plants do not occupy larger ranges or harsher conditions compared with their progenitors

Understanding the factors determining species' geographical and environmental range is a central question in evolution and ecology, and key for developing conservation and management practices. Shortly after the discovery of polyploidy, just over 100 years ago, it was suggested that polyploids generally have greater range sizes and occur in more extreme conditions than their diploid congeners. This suggestion is now widely accepted in the literature and is attributed to polyploids having an increased capacity for genetic diversity that increases their potential for adaptation and invasiveness. However, the data supporting this idea are mixed. Here, we compare the niche of allopolyploid plants to their progenitor species to determine whether allopolyploidization is associated with increased geographic range or extreme environmental tolerance. Our analysis includes 123 allopolyploid species that exist as only one known ploidy level, with at least one known progenitor species, and at least 50 records in the Global Biodiversity Information Facility (GBIF) database. We used GBIF occurrence data and range modeling tools to quantify the geographic and environmental distribution of these allopolyploids relative to their progenitors. We find no indication that allopolyploid plants occupy more extreme conditions or larger geographic ranges than their progenitors. Data evaluated here generally indicate no significant difference in range between allopolyploids and progenitors, and where significant differences do occur, the progenitors are more likely to exist in extreme conditions. We concluded that the evidence from these data indicate allopolyploidization does not result in larger or more extreme ranges. Thus, allopolyploidization does not have a consistent effect on species distribution, and we conclude it is more likely the content of an allopolyploid's genome rather than polyploidy per se that determines the potential for invasiveness.

The novel expression of clonality following whole-genome multiplication compensates for reduced fertility in natural autopolyploids

Exploring the fitness consequences of whole-genome multiplication (WGM) is essential for understanding the establishment of autopolyploids in diploid parental populations, but suitable model systems are rare. We examined the impact of WGM on reproductive traits in three major cytotypes (2x, 3x, 4x) of Pilosella rhodopea, a species with recurrent formation of neo-autopolyploids in mixed-ploidy populations. We found that diploids had normal female sporogenesis and gametogenesis, high fertility, and produced predominantly euploid seed progeny. By contrast, autopolyploids had highly disturbed developmental programs that resulted in significantly lower seed set and a high frequency of aneuploid progeny. All cytotypes, but particularly triploids, produced gametes of varying ploidy, including unreduced ones, that participated in frequent intercytotype mating. Noteworthy, the reduced investment in sexual reproduction in autopolyploids was compensated by increased production of axillary rosettes and the novel expression of two clonal traits: adventitious rosettes on roots (root-sprouting), and aposporous initial cells in ovules which, however, do not result in functional apomixis. The combination of increased vegetative clonal growth in autopolyploids and frequent intercytotype mating are key mechanisms involved in the formation and maintenance of the largest diploid-autopolyploid primary contact zone ever recorded in angiosperms.

Origin, genetic structure and evolutionary potential of the natural hybrid Ranunculus circinatus × R. fluitans

Understanding the genetic variability of hybrids provides information on their current and future evolutionary role. In this paper, we focus on the interspecific hybrid Ranunculus circinatus × R. fluitans that forms spontaneously within the group Ranuculus L. sect. Batrachium DC. (Ranunculaceae Juss.). Genome-wide DNA fingerprinting using amplified fragment length polymorphisms (AFLP) was employed to determine the genetic variation among 36 riverine populations of the hybrid and their parental species. The results demonstrate a strong genetic structure of R. circinatus × R. fluitans within Poland (Central Europe), which is attributed to independent hybridization events, sterility of hybrid individuals, vegetative propagation, and isolation through geographical distance within populations. The hybrid R. circinatus × R. fluitans is a sterile triploid, but, as we have shown in this study, it may participate in subsequent hybridization events, resulting in a ploidy change that can lead to spontaneous fertility recovery. The ability to produce unreduced female gametes of the hybrid R. circinatus × R. fluitans and the parental species R. fluitans is an important evolutionary mechanism in Ranunculus sect. Batrachium that could give rise to new taxa.