Formation of Different Polyploids Through Disrupting Meiotic Crossover Frequencies Based on cntd1 Knockout in Zebrafish

Polyploidy, a significant catalyst for speciation and evolutionary processes in both plant and animal kingdoms, has been recognized for a long time. However, the exact molecular mechanism that leads to polyploid formation, especially in vertebrates, is not fully understood. Our study aimed to elucidate this phenomenon using the zebrafish model. We successfully achieved an effective knockout of the cyclin N-terminal domain containing 1 (cntd1) using CRISPR/Cas9 technology. This resulted in impaired formation of meiotic crossovers, leading to cell-cycle arrest during meiotic metaphase and triggering apoptosis of spermatocytes in the testes. Despite these defects, the mutant (cntd1-/-) males were still able to produce a limited amount of sperm with normal ploidy and function. Interestingly, in the mutant females, it was the ploidy not the capacity of egg production that was altered. This resulted in the production of haploid, aneuploid, and unreduced gametes. This alteration enabled us to successfully obtain triploid and tetraploid zebrafish from cntd1-/- and cntd1-/-/- females, respectively. Furthermore, the tetraploid-heterozygous zebrafish produced reduced-diploid gametes and yielded all-triploid or all-tetraploid offspring when crossed with wild-type (WT) or tetraploid zebrafish, respectively. Collectively, our findings provide direct evidence supporting the crucial role of meiotic crossover defects in the process of polyploidization. This is particularly evident in the generation of unreduced eggs in fish and, potentially, other vertebrate species.

Allium cytogenetics: a critical review on the Indian taxa

The genus Allium Linnaeus, 1753 (tribe Allieae) contains about 800 species worldwide of which almost 38 species are reported in India, including the globally important crops (onion, garlic, leek, shallot) and many wild species. A satisfactory chromosomal catalogue of Allium species is missing which has been considered in the review for the species occurring in India. The most prominent base number is x=8, with few records of x=7, 10, 11. The genome size has sufficient clues for divergence, ranging from 7.8 pg/1C to 30.0 pg/1C in diploid and 15.16 pg/1C to 41.78 pg/1C in polyploid species. Although the karyotypes are seemingly dominated by metacentrics, substantial variation in nucleolus organizing regions (NORs) is noteworthy. The chromosomal rearrangement between A.cepa Linnaeus, 1753 and its allied species has paved way to appreciate genomic evolution within Allium. The presence of a unique telomere sequence and its conservation in Allium sets this genus apart from all other Amaryllids and supports monophyletic origin. Any cytogenetic investigation regarding NOR variability, telomere sequence and genome size in the Indian species becomes the most promising field to decipher chromosome evolution against the background of species diversity and evolution, especially in the Indian subcontinent.

Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis

Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity of the genome can be an evolutionary opportunity, facilitating diversification, adaptation and the evolution of functional novelty. On the other hand, when they first arise, polyploids face a number of challenges, one of the biggest being the meiotic pairing, recombination and segregation of the suddenly more than two copies of each chromosome, which can limit their fertility. Both for developing polyploidy as a crop improvement tool (which holds great promise due to the high and lasting multi-stress resilience of polyploids), as well as for our basic understanding of meiosis and plant evolution, we need to know both the specific nature of the challenges polyploids face, as well as how they can be overcome in evolution. In recent years there has been a dramatic uptick in our understanding of the molecular basis of polyploid adaptations to meiotic challenges, and that is the focus of this review.

Evolution of crossover interference enables stable autopolyploidy by ensuring pairwise partner connections in Arabidopsis arenosa

Polyploidy is a major driver of evolutionary change. Autopolyploids, which arise by within-species whole-genome duplication, carry multiple nearly identical copies of each chromosome. This presents an existential challenge to sexual reproduction. Meiotic chromosome segregation requires formation of DNA crossovers (COs) between two homologous chromosomes. How can this outcome be achieved when more than two essentially equivalent partners are available? We addressed this question by comparing diploid, neo-autotetraploid, and established autotetraploid Arabidopsis arenosa using new approaches for analysis of meiotic CO patterns in polyploids. We discover that crossover interference, the classical process responsible for patterning of COs in diploid meiosis, is defective in the neo-autotetraploid but robust in the established autotetraploid. The presented findings suggest that, initially, diploid-like interference fails to act effectively on multivalent pairing and accompanying pre-CO recombination interactions and that stable autopolyploid meiosis can emerge by evolution of a “supercharged” interference process, which can now act effectively on such configurations. Thus, the basic interference mechanism responsible for simplifying CO patterns along chromosomes in diploid meiosis has evolved the capability to also simplify CO patterns among chromosomes in autopolyploids, thereby promoting bivalent formation. We further show that evolution of stable autotetraploidy preadapts meiosis to higher ploidy, which in turn has interesting mechanistic and evolutionary implications.

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In a neo-autotetraploid, aberrant crossover interference confers aberrant meiosis

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In a stable autotetraploid, regular crossover interference confers regular meiosis

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Crossover and synaptic patterns point to evolution of “supercharged” interference

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Accordingly, evolution of stable autotetraploidy preadapts to higher ploidies

Analytical Methodology of Meiosis in Autopolyploid and Allopolyploid Plants

Meiosis is the cellular process responsible for producing gametes with half the genetic content of the parent cells. Integral parts of the process in most diploid organisms include the recognition, pairing, synapsis, and recombination of homologous chromosomes, which are prerequisites for balanced segregation of half-bivalents during meiosis I. In polyploids, the presence of more than two sets of chromosomes adds to the basic meiotic program of their diploid progenitors the possibility of interactions between more than two chromosomes and the formation of multivalents, which has implications on chromosome segregations and fertility. The mode of how chromosomes behave in meiosis in competitive situations has been the aim of many studies in polyploid species, some of which are considered here. But polyploids are also of interest in the study of meiosis because some of them tolerate the loss of chromosome segments or complete chromosomes as well as the addition of chromosomes from related species. Deletions allow to assess the effect of specific chromosome segments on meiotic behavior. Introgression lines are excellent materials to monitor the behavior of a given chromosome in the genetic background of the recipient species. We focus on this approach here as based on studies carried out in bread wheat, which is commonly used as a model species for meiosis studies. In addition to highlighting the relevance of the use of materials derived from polyploids in the study of meiosis, cytogenetics tools such as fluorescence in situ hybridization and the immunolabeling of proteins interacting with DNA are also emphasized.

Karyotype analysis of eight cultivated Allium species

The karyotypes of Allium, a genus that comprises many crops and ornamental plants, are relatively poorly studied. To extend our knowledge on karyotype structure of the genus, the chromosomal organization of rRNA genes and CMA/DAPI bands was studied. Fluorescence in situ hybridization using 5S and 35S rDNA probes and banding methods (silver staining and CMA₃/DAPI staining) were used to analyze the karyotypes of eight cultivated Allium L. species. Analyzed Allium taxa revealed three different basic chromosome numbers (x = 7, 8, 9) and three different ploidy levels (diploid, triploid, and tetraploid). The rDNA sites chromosomal organization is reported the first time for the six species (A. moly, A. oreophilum, A. karataviense, A. nigrum, A. sphaerocephalon, A. porrum). The Allium species that were analyzed showed a high level of interspecies polymorphism in the number and localization of the rDNA sites. The fluorescence in situ hybridization patterns of 35S rDNA sites were more polymorphic than those of the 5S rDNA in the diploid species. Several groups of similar chromosomes could be distinguished among the chromosomes that had rDNA sites in the polyploid species. Each of the groups had three chromosomes (triploid A. sphaerocephalon L.) or four chromosomes (tetraploid A. porrum L.) suggesting their autopolyploid origin. In the genomes of four of the analyzed species, only some of the 35S rDNA sites were transcriptionally active. Fluorochrome banding revealed that the CMA₃⁺ bands were associated with the 35S rDNA sites in all of the species that were analyzed, except A. fistulosum L. in which positive CMA₃⁺ bands were detected in the terminal position of all of the chromosome arms. The rDNA sequences, nucleolar organizer regions (NORs), and CMA/DAPI bands are very good chromosome markers that allowed to distinguished from two to five pairs of homologous chromosomes in analyzed Allium species. The karyotypes of the studied species could be clearly distinguished by the number and position of the rDNA sites, NORs, and CMA/DAPI bands, which revealed high interspecific differentiation among the taxa.

Meiotic Crossing Over in Maize Knob Heterochromatin

There is ample evidence that crossing over is suppressed in heterochromatin associated with centromeres and nucleolus organizers (NORs). This characteristic has been attributed to all heterochromatin, but the generalization may not be justified. To investigate the relationship of crossing over to heterochromatin that is not associated with centromeres or NORs, we used a combination of fluorescence in situ hybridization of the maize 180-bp knob repeat to show the locations of knob heterochromatin and fluorescent immunolocalization of MLH1 protein and AFD1 protein to show the locations of MLH1 foci on maize synaptonemal complexes (SCs, pachytene chromosomes). MLH1 foci correspond to the location of recombination nodules (RNs) that mark sites of crossing over. We found that MLH1 foci occur at similar frequencies per unit length of SC in interstitial knobs and in the 1 µm segments of SC in euchromatin immediately to either side of interstitial knobs. These results indicate not only that crossing over occurs within knob heterochromatin, but also that crossing over is not suppressed in the context of SC length in maize knobs. However, because there is more DNA per unit length of SC in knobs compared to euchromatin, crossing over is suppressed (but not eliminated) in knobs in the context of DNA length compared to adjacent euchromatin.

Meiosis in autopolyploid and allopolyploid Arabidopsis

All newly formed polyploids face a challenge in meiotic chromosome segregation due to the presence of an additional set of chromosomes. Nevertheless, naturally occurring auto and allopolyploids are common and generally show high fertility, showing that evolution can find solutions. Exactly how meiosis is adapted in these cases, however, remains a mystery. The rise of Arabidopsis as a model genus for polyploid and meiosis research has seen several new studies begin to shed light on this long standing question.

The challenge of evolving stable polyploidy: could an increase in "crossover interference distance" play a central role?

Whole genome duplication is a prominent feature of many highly evolved organisms, especially plants. When duplications occur within species, they yield genomes comprising multiple identical or very similar copies of each chromosome (“autopolyploids”). Such genomes face special challenges during meiosis, the specialized cellular program that underlies gamete formation for sexual reproduction. Comparisons between newly formed (neo)-autotetraploids and fully evolved autotetraploids suggest that these challenges are solved by specific restrictions on the positions of crossover recombination events and, thus, the positions of chiasmata, which govern the segregation of homologs at the first meiotic division. We propose that a critical feature in the evolution of these more effective chiasma patterns is an increase in the effective distance of meiotic crossover interference, which plays a central role in crossover positioning. We discuss the findings in several organisms, including the recent identification of relevant genes in Arabidopsis arenosa, that support this hypothesis.

Meiosis evolves: adaptation to external and internal environments

306 I. 306 II. 307 III. 312 IV. 317 V. 318 319 References 319 SUMMARY: Meiosis is essential for the fertility of most eukaryotes and its structures and progression are conserved across kingdoms. Yet many of its core proteins show evidence of rapid or adaptive evolution. What drives the evolution of meiosis proteins? How can constrained meiotic processes be modified in response to challenges without compromising their essential functions? In surveying the literature, we found evidence of two especially potent challenges to meiotic chromosome segregation that probably necessitate adaptive evolutionary responses: whole-genome duplication and abiotic environment, especially temperature. Evolutionary solutions to both kinds of challenge are likely to involve modification of homologous recombination and synapsis, probably via adjustments of core structural components important in meiosis I. Synthesizing these findings with broader patterns of meiosis gene evolution suggests that the structural components of meiosis coevolve as adaptive modules that may change in primary sequence and function while maintaining three-dimensional structures and protein interactions. The often sharp divergence of these genes among species probably reflects periodic modification of entire multiprotein complexes driven by genomic or environmental changes. We suggest that the pressures that cause meiosis to evolve to maintain fertility may cause pleiotropic alterations of global crossover rates. We highlight several important areas for future research.

Origins of Allium ampeloprasum horticultural groups and a molecular phylogeny of the section Allium (Allium: Alliaceae)

The subgenus Allium section Allium includes economically important species, such as garlic and leek, as well as other polyploid minor crops. Phylogenetic studies within this section, with a focus on horticultural groups within A. ampeloprasum, were performed on 31 accessions of 17 species using the nuclear ribosomal DNA internal transcribed spacer (ITS) region and the chloroplast trnL-F and trnD-T regions. The results confirmed the monophyly of section Allium. Four main clades were identified on all ITS analyses but the relationships among those and the remaining species studied within section Allium remained unresolved. Trees based on cpDNA recovered two major clades and a topology only partly congruent with that of the ITS tree. Intra-individual polymorphism of the ITS region proved useful in tracking putative parent species of polyploid taxa. The allopolyploid origin of great headed garlic (GHG), A. iranicum and A. polyanthum was confirmed. No signs of hybridization in leek or kurrat were detected but possible introgression events were identified in pearl onion and bulbous leek. Although GHG is often used as a garlic substitute, molecular analysis revealed only a distant relationship with garlic. We also clarified the previous incorrect classification of cultivated forms within A. ampeloprasum, by showing that leek, kurrat, pearl onion, and bulbous leek should be considered separately from GHG.

Recombination nodules in plants

The molecular events of recombination are thought to be catalyzed by proteins present in recombination nodules (RNs). Therefore, studying RN structure and function should give insights into the processes by which meiotic recombination is regulated in eukaryotes. Two types of RNs have been identified so far, early (ENs) and late (LNs). ENs appear at leptotene and persist into early pachytene while LNs appear in pachytene and remain into early diplotene. ENs and LNs can be distinguished not only on their time of appearance, but also by such characteristics as shape and size, relative numbers, and association with unsynapsed and/or synapsed chromosomal segments. The function(s) of ENs is not clear, but they may have a role in searching for DNA homology, synapsis, gene conversion and/or crossing over. LNs are well correlated with crossing over. Here, the patterns of ENs and LNs during prophase I in plants are reviewed.

Variable patterns of chromosome synapsis at pachytene in Hordeum vulgare x H. bulbosum hybrids and their parents

Synaptonemal complexes (SC) have been analysed in barley (Hordeum vulgare), H. bulbosum and two F, hybrids between them. These hybrids show different recombination frequencies and at pachytene show significant differences in the total length of SC formed and in the extent of synapsis. Higher recombination frequency in the hybrids was correlated with a greater total SC length. Differences in SC length were also observed between the parental species with H. bulbosum having a greater SC length than H. vulgare. However, species and hybrid can have similar SC lengths but clearly different recombination frequencies and, therefore, the relationship between SC length and recombination is not clear-cut.

Crossing over as assessed by late recombination nodules is related to the pattern of synapsis and the distribution of early recombination nodules in maize

Recombination nodules (RNs) are multicomponent proteinaceous ellipsoids found in association with the synaptonemal complex (SC) during prophase I of meiosis. Numerous early RNs (ENs) are observed during zygotene, and they may be involved in homologous synapsis and early events in recombination. Fewer late RNs (LNs) are observed during pachytene, and they occur at crossover sites. Here we describe the pattern of synapsis and the distribution of ENs and LNs in maize. Synapsis starts almost exclusively at chromosome ends, although later in zygotene there are many interstitial sites of synaptic initiation. ENs do not show interference, except possibly at distances < or = 0.2 micron. The frequency of ENs is higher on distal compared to medial SC segments, and the highest concentration of ENs occurs at synaptic forks. The number of ENs on an SC segment does not change during zygotene. These observations are interpreted to indicate that ENs are assembled at synaptic forks. Like ENs, LNs are more concentrated distally on bivalents but, unlike ENs, LNs show interference. A model is presented that relates the pattern of synapsis and ENs to the pattern of late nodules and crossing over.

A model for chromosome structure during the mitotic and meiotic cell cycles

The chromosome scaffold model in which loops of chromatin are attached to a central, coiled chromosome core (scaffold) is the current paradigm for chromosome structure. Here we present a modified version of the chromosome scaffold model to describe chromosome structure and behavior through the mitotic and meiotic cell cycles. We suggest that a salient feature of chromosome structure is established during DNA replication when sister loops of DNA extend in opposite directions from replication sites on nuclear matrix strands. This orientation is maintained into prophase when the nuclear matrix strand is converted into two closely associated sister chromatid cores with sister DNA loops extending in opposite directions. We propose that chromatid cores are contractile and show, using a physical model, that contraction of cores during late prophase can result in coiled chromatids. Coiling accounts for the majority of chromosome shortening that is needed to separate sister chromatids within the confines of a cell. In early prophase I of meiosis, the orientation of sister DNA loops in opposite directions from axial elements assures that DNA loops interact preferentially with homologous DNA loops rather than with sister DNA loops. In this context, we propose a bar code model for homologous presynaptic chromosome alignment that involves weak paranemic interactions of homologous DNA loops. Opposite orientation of sister loops also suppresses crossing over between sister chromatids in favor of crossing over between homologous non-sister chromatids. After crossing over is completed in pachytene and the synaptonemal complex breaks down in early diplotene (= diffuse stage), new contractile cores are laid down along each chromatid. These chromatid cores are comparable to the chromatid cores in mitotic prophase chromosomes. As an aside, we propose that leptotene through early diplotene represent the 'missing' G2 period of the premeiotic interphase. The new chromosome cores, along with sister chromatid cohesion, stabilize chiasmata. Contraction of cores in late diplotene causes chromosomes to coil in a configuration that encourages subsequent syntelic orientation of sister kinetochores and amphitelic orientation of homologous kinetochore pairs on the spindle at metaphase I.

Meiotic chromosomes: integrating structure and function

Meiotic chromosomes have been studied for many years, in part because of the fundamental life processes they represent, but also because meiosis involves the formation of homolog pairs, a feature which greatly facilitates the study of chromosome behavior. The complex events involved in homolog juxtaposition necessitate prolongation of prophase, thus permitting resolution of events that are temporally compressed in the mitotic cycle. Furthermore, once homologs are paired, the chromosomes are connected by a specific structure: the synaptonemal complex. Finally, interaction of homologs includes recombination at the DNA level, which is intimately linked to structural features of the chromosomes. In consequence, recombination-related events report on diverse aspects of chromosome morphogenesis, notably relationships between sisters, development of axial structure, and variations in chromatin status. The current article reviews recent information on these topics in an historical context. This juxtaposition has suggested new relationships between structure and function. Additional issues were addressed in a previous chapter (551).

Organization of the yeast Zip1 protein within the central region of the synaptonemal complex

The yeast Zip1 protein is a component of the central region of the synaptonemal complex (SC). Zip1 is predicted to form an alpha-helical coiled coil, flanked by globular domains at the NH(2) and COOH termini. Immunogold labeling with domain-specific anti-Zip1 antibodies demonstrates that the NH(2)-terminal domain of Zip1 is located in the middle of the central region of the SC, whereas the COOH-terminal domain is embedded in the lateral elements of the complex. Previous studies have shown that overproduction of Zip1 results in the assembly of two types of aggregates, polycomplexes and networks, that are unassociated with chromatin. Our epitope mapping data indicate that the organization of Zip1 within polycomplexes is similar to that of the SC, whereas the organization of Zip1 within networks is fundamentally different. Zip1 protein purified from bacteria assembles into dimers in vitro, and electron microscopic analysis demonstrates that the two monomers within a dimer are arranged in parallel and in register. Together, these results suggest that two Zip1 dimers, lying head-to-head, span the width of the SC.

Synapsis in a natural autotetraploid

To test assumptions of the autotetraploid chromosome pairing model regarding events during synapsis, whole-mount spreads of synaptonemal complexes (SCs) of Machaeranthera pinnatifida (=Haplopappus spinulosus) (Asteraceae) (2n = 4x = 16) were analyzed by electron microscopy. On the assumption of one synaptic initiation per chromosome arm, each pachytene quadrivalent is expected to have one partner switch (PS), and the frequency of pachytene quadrivalents for each chromosome is predicted to be 2/3 (or 0.67). However, to the contrary, we observed a range of one to four PSs per pachytene quadrivalent with an overall mean of 1.56. This suggests that the number of synaptic initiations is greater than one per chromosome arm (or >two per chromosome), and the predicted frequency of pachytene quadrivalents should be >8/9 (based on a minimum of three initiations per chromosome). However, in close agreement with the model, the observed pachytene quadrivalent frequency from SCs in this study was 0.69. To explain the apparent discrepancy between the observed frequency of PSs and the observed frequency of quadrivalents, the possibility of nonindependent synaptic initiations and presynaptic alignment are discussed in the context of their potential influence on quadrivalent frequency. Recombination nodules (RNs), which were scored in about half the SC spreads, occurred at a frequency (9.6 per nucleus) comparable with the chiasma frequency at diakinesis (9.3 per nucleus). The frequency of RNs as well as their distribution is consistent with the hypothesis that RNs occur at sites of crossing over and chiasma formation.Key words: autopolyploid, Machaeranthera pinnatifida, meiosis, recombination nodules, synaptonemal complex.

Differences in the synaptic pattern in two autotetraploid cultivars of rye with different quadrivalent frequencies at metaphase I

Synaptic behaviour of the two tetraploids rye cultivars Gigantón (G) and Tetrapico (T) displaying significant differences in their quadrivalent frequencies at metaphase I was analyzed by electron microscopy in surface-spread prophase I nuclei. A different behaviour was observed between the two cultivars; the synaptonemal complex (SC) quadrivalents frequency being significantly higher in G than in T at prophase I. Moreover, the G SC quadrivalents had more synaptic partner exchanges (SPEs) and their location was more distal than the T SC quadrivalents. However, inverse findings were found at metaphase I, the quadrivalent frequency was higher in T than in G. The role that different factors, mainly the number and location of the SPEs and the frequency and distribution of chiasmata, could play in the evolution from prophase I to metaphase I in both cultivars is discussed.Key words: autotetraploid rye, synaptonemal complex, spreading.

MEIOTIC CHROMOSOME ORGANIZATION AND SEGREGATION IN PLANTS

During meiosis, homologous chromosomes are brought together to be recombined and segregated into separate haploid gametes. This requires two cell divisions, an elaborate prophase with five substages, and specialized mechanisms that regulate the association of sister chromatids. This review focuses on plant chromosomes and chromosome-associated structures, such as recombination nodules and kinetochores, that ensure accurate meiotic chromosome segregation.

Chromosome pairing and chiasma formation in autopolyploids of different Lathyrus species

Chromosome pairing and chiasma formation were studied in natural and induced tetraploids (2n = 28) of Lathyrus odoratus (induced), Lathyrus pratensis (natural and induced), Lathyrus sativus (induced), and Lathyrus venosus (natural), as well as in triploids of L. pratensis and diploids of L. odoratus, L. pratensis, and L. sativus. All natural tetraploids appeared to be autotetraploids and their meiotic metaphase I behaviour was very similar to that of the induced autotetraploids, with average numbers of pairing partner switches exceeding 4 or even 5. Multivalent frequencies were high, but the numbers of chiasmata were not much higher than necessary to maintain the configurations. Interstitial chiasmata were common, but not predominant. Fertility was reduced, but sufficient for predominantly vegetatively reproducing species. The triploids of L. pratensis had an even higher multivalent frequency than the tetraploids, but still produced some viable progeny at or close to the tetraploid level, suggesting that in mixed populations of diploids and tetraploids, triploids can contribute to gene flow between the ploidy levels. There was no significant correlation between chiasma frequency and ring bivalent frequency in the diploids and multivalent frequency in the corresponding tetraploids. In the tetraploids, chiasma frequency and multivalent frequency were negatively correlated.Key words: Lathyrus, natural, induced, autotetraploid, triploid, meiosis.