DMC1 stabilizes crossovers at high and low temperatures during wheat meiosis

Effective chromosome synapsis and crossover formation during meiosis are essential for fertility, especially in grain crops such as wheat. These processes function most efficiently in wheat at temperatures between 17-23 °C, although the genetic mechanisms for such temperature dependence are unknown. In a previously identified mutant of the hexaploid wheat reference variety 'Chinese Spring' lacking the long arm of chromosome 5D, exposure to low temperatures during meiosis resulted in asynapsis and crossover failure. In a second mutant (ttmei1), containing a 4 Mb deletion in chromosome 5DL, exposure to 13 °C led to similarly high levels of asynapsis and univalence. Moreover, exposure to 30 °C led to a significant, but less extreme effect on crossovers. Previously, we proposed that, of 41 genes deleted in this 4 Mb region, the major meiotic gene TaDMC1-D1 was the most likely candidate for preservation of synapsis and crossovers at low (and possibly high) temperatures. In the current study, using RNA-guided Cas9, we developed a new Chinese Spring CRISPR mutant, containing a 39 bp deletion in the 5D copy of DMC1, representing the first reported CRISPR-Cas9 targeted mutagenesis in Chinese Spring, and the first CRISPR mutant for DMC1 in wheat. In controlled environment experiments, wild-type Chinese Spring, CRISPR dmc1-D1 and backcrossed ttmei1 mutants were exposed to either high or low temperatures during the temperature-sensitive period from premeiotic interphase to early meiosis I. After 6-7 days at 13 °C, crossovers decreased by over 95% in the dmc1-D1 mutants, when compared with wild-type plants grown under the same conditions. After 24 hours at 30 °C, dmc1-D1 mutants exhibited a reduced number of crossovers and increased univalence, although these differences were less marked than at 13 °C. Similar results were obtained for ttmei1 mutants, although their scores were more variable, possibly reflecting higher levels of background mutation. These experiments confirm our previous hypothesis that DMC1-D1 is responsible for preservation of normal crossover formation at low and, to a certain extent, high temperatures. Given that reductions in crossovers have significant effects on grain yield, these results have important implications for wheat breeding, particularly in the face of climate change.

Assessing the Heat Tolerance of Meiosis in Spanish Landraces of Tetraploid Wheat Triticum turgidum

Heat stress alters the number and distribution of meiotic crossovers in wild and cultivated plant species. Hence, global warming may have a negative impact on meiosis, fertility, and crop productions. Assessment of germplasm collections to identify heat-tolerant genotypes is a priority for future crop improvement. Durum wheat, Triticum turgidum, is an important cultivated cereal worldwide and given the genetic diversity of the durum wheat Spanish landraces core collection, we decided to analyse the heat stress effect on chiasma formation in a sample of 16 landraces of T. turgidum ssp. turgidum and T. turgidum ssp. durum, from localities with variable climate conditions. Plants of each landrace were grown at 18–22 °C and at 30 °C during the premeiotic temperature-sensitive stage. The number of chiasmata was not affected by heat stress in three genotypes, but decreased by 0.3–2 chiasmata in ten genotypes and more than two chiasmata in the remaining three ones. Both thermotolerant and temperature-sensitive genotypes were found in the two subspecies, and in some of the agroecological zones studied, which supports that genotypes conferring a heat tolerant meiotic phenotype are not dependent on subspecies or geographical origin. Implications of heat adaptive genotypes in future research and breeding are discussed.

Caught in the Act: Live-Cell Imaging of Plant Meiosis

Live-cell imaging is a powerful method to obtain insights into cellular processes, particularly with respect to their dynamics. This is especially true for meiosis, where chromosomes and other cellular components such as the cytoskeleton follow an elaborate choreography over a relatively short period of time. Making these dynamics visible expands understanding of the regulation of meiosis and its underlying molecular forces. However, the analysis of meiosis by live-cell imaging is challenging; specifically in plants, a temporally resolved understanding of chromosome segregation and recombination events is lacking. Recent advances in live-cell imaging now allow the analysis of meiotic events in plants in real time. These new microscopy methods rely on the generation of reporter lines for meiotic regulators and on the establishment of ex vivo culture and imaging conditions, which stabilize the specimen and keep it alive for several hours or even days. In this review, we combine an overview of the technical aspects of live-cell imaging in plants with a summary of outstanding questions that can now be addressed to promote live-cell imaging in Arabidopsis and other plant species and stimulate ideas on the topics that can be addressed in the context of plant meiotic recombination.

Pericentromeric chromatin reorganisation follows the initiation of recombination and coincides with early events of synapsis in cereals

The reciprocal exchange of genetic information between homologous chromosomes during meiotic recombination is essential to secure balanced chromosome segregation and to promote genetic diversity. The chromosomal position and frequency of reciprocal genetic exchange shapes the efficiency of breeding programmes and influences crop improvement under a changing climate. In large genome cereals, such as wheat and barley, crossovers are consistently restricted to subtelomeric chromosomal regions, thus preventing favourable allele combinations being formed within a considerable proportion of the genome, including interstitial and pericentromeric chromatin. Understanding the key elements driving crossover designation is therefore essential to broaden the regions available for crossovers. Here, we followed early meiotic chromatin dynamism in cereals through the visualisation of a homologous barley chromosome arm pair stably transferred into the wheat genetic background. By capturing the dynamics of a single chromosome arm at the same time as detecting the undergoing events of meiotic recombination and synapsis, we showed that subtelomeric chromatin of homologues synchronously transitions to an open chromatin structure during recombination initiation. By contrast, pericentromeric and interstitial regions preserved their closed chromatin organisation and become unpackaged only later, concomitant with initiation of recombinatorial repair and the initial assembly of the synaptonemal complex. Our results raise the possibility that the closed pericentromeric chromatin structure in cereals may influence the fate decision during recombination initiation, as well as the spatial development of synapsis, and may also explain the suppression of crossover events in the proximity of the centromeres.

A simple and rapid method for imaging male meiotic cells in anthers of model and non-model plant species

We describe a simple method to view meiotic cells in whole anthers from a range of plants. The method retains spatial organisation and enables simultaneous analysis of many meiotic cells. Understanding the process of male meiosis in flowering plants, and the role of genes involved in this process, offers potential for plant breeding, such as through increasing the level of genetic variation or the manipulation of ploidy levels in the gametes. A key to the characterisation of meiotic gene function and meiosis in non-model crop plants, is the analysis of cells undergoing meiosis, a task made difficult by the inaccessible nature of these cells. Here, we describe a simple and rapid method to analyse plant male meiosis in intact anthers in a range of plant species. This method allows analysis of numerous cells undergoing meiosis and, as meiotic cells stay within the anther, it retains information of the three-dimensional organisation and the location of organelles in meiotic cells. We show that the technique provides information on male meiosis by looking at the synchrony of meiotic progression between and within locules, and comparing wildtype and mutant plants through the chromosome separation stages in Arabidopsis thaliana. Additionally, we demonstrate that the protocol can be adopted to other plants with different floral morphology using Medicago truncatula as an example with small floral buds and the non-model plant kiwifruit (Actinidia chinensis) with larger buds and anthers.

Distal Bias of Meiotic Crossovers in Hexaploid Bread Wheat Reflects Spatio-Temporal Asymmetry of the Meiotic Program

Meiotic recombination generates genetic variation and provides physical links between homologous chromosomes (crossovers) essential for accurate segregation. In cereals the distribution of crossovers, cytologically evident as chiasmata, is biased toward the distal regions of chromosomes. This creates a bottleneck for plant breeders in the development of varieties with improved agronomic traits, as genes situated in the interstitial and centromere proximal regions of chromosomes rarely recombine. Recent advances in wheat genomics and genome engineering combined with well-developed wheat cytogenetics offer new opportunities to manipulate recombination and unlock genetic variation. As a basis for these investigations we have carried out a detailed analysis of meiotic progression in hexaploid wheat (Triticum aestivum) using immunolocalization of chromosome axis, synaptonemal complex and recombination proteins. 5-Bromo-2'-deoxyuridine (BrdU) labeling was used to determine the chronology of key events in relation to DNA replication. Axis morphogenesis, synapsis and recombination initiation were found to be spatio-temporally coordinated, beginning in the gene-dense distal chromosomal regions and later occurring in the interstitial/proximal regions. Moreover, meiotic progression in the distal regions was coordinated with the conserved chromatin cycles that are a feature of meiosis. This mirroring of the chiasma bias was also evident in the distribution of the gene-associated histone marks, H3K4me3 and H3K27me3; the repeat-associated mark, H3K27me1; and H3K9me3. We believe that this study provides a cytogenetic framework for functional studies and ongoing initiatives to manipulate recombination in the wheat genome.

Distal Bias of Meiotic Crossovers in Hexaploid Bread Wheat Reflects Spatio-Temporal Asymmetry of the Meiotic Program

Meiotic recombination generates genetic variation and provides physical links between homologous chromosomes (crossovers) essential for accurate segregation. In cereals the distribution of crossovers, cytologically evident as chiasmata, is biased toward the distal regions of chromosomes. This creates a bottleneck for plant breeders in the development of varieties with improved agronomic traits, as genes situated in the interstitial and centromere proximal regions of chromosomes rarely recombine. Recent advances in wheat genomics and genome engineering combined with well-developed wheat cytogenetics offer new opportunities to manipulate recombination and unlock genetic variation. As a basis for these investigations we have carried out a detailed analysis of meiotic progression in hexaploid wheat (Triticum aestivum) using immunolocalization of chromosome axis, synaptonemal complex and recombination proteins. 5-Bromo-2'-deoxyuridine (BrdU) labeling was used to determine the chronology of key events in relation to DNA replication. Axis morphogenesis, synapsis and recombination initiation were found to be spatio-temporally coordinated, beginning in the gene-dense distal chromosomal regions and later occurring in the interstitial/proximal regions. Moreover, meiotic progression in the distal regions was coordinated with the conserved chromatin cycles that are a feature of meiosis. This mirroring of the chiasma bias was also evident in the distribution of the gene-associated histone marks, H3K4me3 and H3K27me3; the repeat-associated mark, H3K27me1; and H3K9me3. We believe that this study provides a cytogenetic framework for functional studies and ongoing initiatives to manipulate recombination in the wheat genome.

Is the evolution of carnivory connected with genome size reduction?

PREMISE

As repeatedly shown, the remarkable variation in the genome size of angiosperms can be shaped by extrinsic selective pressures, including nutrient availability. Carnivory has evolved independently in 10 angiosperm clades, but all carnivorous plants share a common affinity to nutrient-poor habitats. As such, carnivory and genome reduction could be responses to the same environmental pressure. Indeed, the smallest genomes among flowering plants are found in the carnivorous family Lentibulariaceae, where a unique mutation in cytochrome c oxidase (COX) is suspected to promote genome miniaturization. Despite these hypotheses, a phylogenetically informed test of genome size and nutrient availability across carnivorous clades has so far been missing.

METHODS

Using linear mixed models, we compared genome sizes of 127 carnivorous plants from 7 diverse angiosperm clades with 1072 of their noncarnivorous relatives. We also tested whether genome size in Lentibulariaceae reflects the presence of the COX mutation.

RESULTS

The genome sizes of carnivorous plants do not differ significantly from those of their noncarnivorous relatives. Based on available data, no significant association between the COX mutation and genome miniaturization could be confirmed, not even when considering polyploidy.

CONCLUSIONS

Carnivory alone does not seem to significantly affect genome size decrease. Plausibly, it might actually counterbalance the effect of nutrient limitation on genome size evolution. The role of the COX mutation in genome miniaturization needs to be evaluated by analysis of a broader data set because current knowledge of its presence across Lentibulariaceae covers less than 10% of the species diversity in this family.

Dmc1 is a candidate for temperature tolerance during wheat meiosis

KEY MESSAGE

The meiotic recombination gene Dmc1 on wheat chromosome 5D has been identified as a candidate for the maintenance of normal chromosome synapsis and crossover at low and possibly high temperatures. We initially assessed the effects of low temperature on meiotic chromosome synapsis and crossover formation in the hexaploid wheat (Triticum aestivum L.) variety 'Chinese Spring'. At low temperatures, asynapsis and chromosome univalence have been observed before in Chinese Spring lines lacking the long arm of chromosome 5D (5DL), which led to the proposal that 5DL carries a gene (Ltp1) that stabilises wheat chromosome pairing at low temperatures. In the current study, Chinese Spring wild type and 5DL interstitial deletion mutant plants were exposed to low temperature in a controlled environment room during a period from premeiotic interphase to early meiosis I. A 5DL deletion mutant was identified whose meiotic chromosomes exhibit extremely high levels of asynapsis and chromosome univalence at metaphase I after 7 days at 13 °C, suggesting that Ltp1 is deleted in this mutant. Immunolocalisation of the meiotic proteins ASY1 and ZYP1 on ltp1 mutants showed that low temperature results in a failure to complete synapsis at pachytene. KASP genotyping revealed that the ltp1 mutant has a 4-Mb deletion in 5DL. Of 41 genes within this deletion region, the strongest candidate for the stabilisation of chromosome pairing at low temperatures is the meiotic recombination gene Dmc1. The ltp1 mutants were subsequently treated at 30 °C for 24 h during meiosis and exhibited a reduced number of crossovers and increased univalence, though to a lesser extent than at 13 °C. We therefore renamed our ltp1 mutant 'ttmei1' (temperature-tolerant meiosis 1) to reflect this additional loss of high temperature tolerance.

Following the Formation of Synaptonemal Complex Formation in Wheat and Barley by High-Resolution Microscopy

Wheat and barley have large genomes of 15 Gb and 5.1 Gb, respectively, which is much larger than the human genome (3.3 Gb). The release of their respective genomes has been a tremendous advance the understanding of the genome organization and the ability for deeper functional analysis in particular meiosis. Meiosis is the cell division required during sexual reproduction. One major event of meiosis is called recombination, or the formation of crossing over, a tight link between homologous chromosomes, ensuring gene exchange and faithful chromosome segregation. Recombination is a major driver of genetic diversity but in these large genome crops, the vast majority of these events is constrained at the end of their chromosomes. It is estimated that in barley, about 30% of the genes are located within the poor recombining centromeric regions, making important traits, such as resistance to pest and disease for example, difficult to access. Increasing recombination in these crops has the potential to speed up breeding program and requires a good understand of the meiotic mechanism. However, most research on recombination in plant has been carried in Arabidopsis thaliana which despite many of the advantages it brings for plant research, has a small genome and more spread out of recombination compare to barley or wheat. Advance in microscopy and cytological procedures have emerged in the last few years, allowing to follow meiotic events in these crops. This protocol provides the steps required for cytological preparation of barley and wheat pollen mother cells for light microscopy, highlighting some of the differences between the two cereals.

Genome-Wide Transcription During Early Wheat Meiosis Is Independent of Synapsis, Ploidy Level, and the Ph1 Locus

Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologs and homoeologs at the onset of meiosis. In turn, these chromatin changes, can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-seq data derived from six different genotypes: wheat, wheat-rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the Ph1 locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the telomere bouquet is forming and synapsis between homologs is beginning. The six genotypes exhibit different levels of synapsis and chromatin structure at this stage; therefore, recombination and consequently segregation, are also different. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the Ph1 locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. Further studies in wheat and other polyploid species will be required to reveal whether these observations are specific to wheat meiosis.

MeioCapture: an efficient method for staging and isolation of meiocytes in the prophase I sub-stages of meiosis in wheat

BACKGROUND

Molecular analysis of meiosis has been hindered by difficulties in isolating high purity subpopulations of sporogenous cells representing the succeeding stages of meiosis. Isolation of purified male meiocytes from defined meiotic stages is crucial in discovering meiosis specific genes and associated regulatory networks.

RESULTS

We describe an optimized method termed MeioCapture for simultaneous isolation of uncontaminated male meiocytes from wheat (Triticum spp.), specifically from the pre-meiotic G2 and the five sub-stages of meiotic prophase I. The MeioCapture protocol builds on the traditional anther squash technique and the capillary collection method, and involves extrusion of intact sporogenous archesporial columns (SACs) containing meiocytes. This improved method exploits the natural meiotic synchrony between anthers of the same floret, the correlation between the length of anthers and meiotic stage, and the occurrence of meiocytes in intact SACs largely free of somatic cells. The main advantage of MeioCapture, compared to previous methods, is that it allows simultaneous collection of meiocytes from different sub-stages of prophase I at a very high level of purity, through correlation of stages with anther sizes. A detailed description is provided for all steps, including the collection of tissue, isolation and size sorting of anthers, extrusion of intact SACs, and staging of meiocytes. Precautions for individual steps throughout the procedure are also provided to facilitate efficient isolation of pure meiocytes. The proof-of-concept was successfully established in wheat, and a light microscopic atlas of meiosis, encompassing all stages from pre-meiosis to telophase II, was developed.

CONCLUSION

The MeioCapture method provides an essential technique to study the molecular basis of chromosome pairing and exchange of genetic information in wheat, leading to strategies for manipulating meiotic recombination frequencies. The method also provides a foundation for similar studies in other crop species.

Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms

Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.

Short periods of high temperature during meiosis prevent normal meiotic progression and reduce grain number in hexaploid wheat (Triticum aestivum L.)

Exposure of wheat to high temperatures during male meiosis prevents normal meiotic progression and reduces grain number. We define a temperature-sensitive period and link heat tolerance to chromosome 5D. This study assesses the effects of heat on meiotic progression and grain number in hexaploid wheat (Triticum aestivum L. var. Chinese Spring), defines a heat-sensitive stage and evaluates the role of chromosome 5D in heat tolerance. Plants were exposed to high temperatures (30 or 35 °C) in a controlled environment room for 20-h periods during meiosis and the premeiotic interphase just prior to meiosis. Examination of pollen mother cells (PMCs) from immature anthers immediately before and after heat treatment enabled precise identification of the developmental phases being exposed to heat. A temperature-sensitive period was defined, lasting from premeiotic interphase to late leptotene, during which heat can prevent PMCs from progressing through meiosis. PMCs exposed to 35 °C were less likely to progress than those exposed to 30 °C. Grain number per spike was reduced at 30 °C, and reduced even further at 35 °C. Chinese Spring nullisomic 5D-tetrasomic 5B (N5DT5B) plants, which lack chromosome 5D, were more susceptible to heat during premeiosis-leptotene than Chinese Spring plants with the normal (euploid) chromosome complement. The proportion of plants with PMCs progressing through meiosis after heat treatment was lower for N5DT5B plants than for euploids, but the difference was not significant. However, following exposure to 30 °C, in euploid plants grain number was reduced (though not significantly), whereas in N5DT5B plants the reduction was highly significant. After exposure to 35 °C, the reduction in grain number was highly significant for both genotypes. Implications of these findings for the breeding of thermotolerant wheat are discussed.

Dual effect of the wheat Ph1 locus on chromosome synapsis and crossover

Allopolyploids must possess a mechanism for facilitating synapsis and crossover (CO) between homologues, in preference to homoeologues (related chromosomes), to ensure successful meiosis. In hexaploid wheat, the Ph1 locus has a major effect on the control of these processes. Studying a wheat mutant lacking Ph1 provides an opportunity to explore the underlying mechanisms. Recently, it was proposed that Ph1 stabilises wheat during meiosis, both by promoting homologue synapsis during early meiosis and preventing MLH1 sites on synapsed homoeologues from becoming COs later in meiosis. Here, we explore these two effects and demonstrate firstly that whether or not Ph1 is present, synapsis between homoeologues does not take place during the telomere bouquet stage, with only homologous synapsis taking place during this stage. Furthermore, in wheat lacking Ph1, overall synapsis is delayed with respect to the telomere bouquet, with more synapsis occurring after the bouquet stage, when homoeologous synapsis is also possible. Secondly, we show that in the absence of Ph1, we can increase the number of MLH1 sites progressing to COs by altering environmental growing conditions; we show that higher nutrient levels in the soil or lower temperatures increase the level of both homologue and homoeologue COs. These observations suggest opportunities to improve the exploitation of the Ph1 wheat mutant in breeding programmes.

Observation of Extensive Chromosome Axis Remodeling during the "Diffuse-Phase" of Meiosis in Large Genome Cereals

The production of balanced fertile haploid gametes requires the faithful separation of paired (synapsed) chromosomes toward the end of meiotic prophase I (desynapsis). This involves the timely dissolution of the synaptonemal complex during the pachytene-diplotene transition, a stage traditionally referred to as the "diffuse stage." In species with large genomes such as, barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) we know most about the early stages of meiotic prophase I. There, synapsis initiates at the telomeric ends of chromosomes and progresses toward the centromeric regions through the ordered assembly of the synaptonemal complex (SC). Synapsis is impacted by recombination (crossing over, CO) which locally modifies the extent of chromatin compaction and extension. CO is uneven along the chromosomes, occurring mainly toward the telomeric regions resulting in a highly skewed distribution of recombination events. However, we know very little about the process of desynapsis which occurs during the "diffuse stage," where the synapsed and recombined chromosomes faithfully desynapse and separate into daughter cells. Here, using 3D-SIM super-resolution immuno-cytology combined with the use of antibodies directed against two crucial SC proteins, ASY1 and ZYP1, we followed the whole of meiosis I (i.e., both synapsis and desynapsis) in both barley and wheat. We showed that synapsis forms a characteristic tri-partite SC structure in zygotene (more clearly seen in barley). Toward the end of meiosis I, as the SC starts to disassemble, we show that extensive chromosome axis remodeling results in the formation of characteristic "tinsel-like" structures in both wheat and barley. By using a mutant (des10) that is severely compromised in polymerization of ZYP1during synapsis, we show that tinsel structure formation during SC dissolution is not dependant on full synapsis and may relate instead to changes in expansion stress. Our observations highlight a potentially new role for ASYNAPSIS1 (ASY1) in desynapsis, in addition to chromosome synapsis and cohesion.

Nutrient reserves may allow for genome size increase: evidence from comparison of geophytes and their sister non-geophytic relatives

BACKGROUND AND AIMS

The genome size of an organism is determined by its capacity to tolerate genome expansion, given the species' life strategy and the limits of a particular environment, and the ability for retrotransposon suppression and/or removal. In some giant-genomed bulb geophytes, this tolerance is explained by their ability to pre-divide cells in the dormant stages or by the selective advantage of larger cells in the rapid growth of their fleshy body. In this study, a test shows that the tendency for genome size expansion is a more universal feature of geophytes, and is a subject in need of more general consideration.

METHODS

Differences in monoploid genome sizes were compared using standardized phylogenetically independent contrasts in 47 sister pairs of geophytic and non-geophytic taxa sampled across all the angiosperms. The genome sizes of 96 species were adopted from the literature and 53 species were newly measured using flow cytometry with propidium iodide staining.

KEY RESULTS

The geophytes showed increased genome sizes compared with their non-geophytic relatives, regardless of the storage organ type and regardless of whether or not vernal geophytes, polyploids or annuals were included in the analyses.

CONCLUSIONS

The universal tendency of geophytes to possess a higher genome size suggests the presence of a universal mechanism allowing for genome expansion. It is assumed that this is primarily due to the nutrient and energetic independence of geophytes perhaps allowing continuous synthesis of DNA, which is known to proceed in the extreme cases of vernal geophytes even in dormant stages. This independence may also be assumed as a reason for allowing large genomes in some parasitic plants, as well as the nutrient limitation of small genomes of carnivorous plants.

Evidence of premeiotic control of chromosome pairing inTriticum aestivum

A genotype of wheat deficient for a pair of chromosomes stabilizing chiasma frequency against extremes of temperature was investigated to determine the position and duration of temperature sensitivity with respect to first metaphase of meiosis. Temperature changes over a critical range, followed by sequential sampling and measurement of chiasma frequency, showed a relatively short temperature-sensitive stage, the position and duration of which were dependent on the final temperature used. Comparison with meiotic timings made independently showed that the temperature-sensitive stage occurred in the premeiotic interphase. Euploid wheat was shown to have a stage in chiasma formation sensitive to high-temperature treatments at a similar time.

Comparison with the work of others showed that the sensitive stage lay between the last premeiotic mitosis and the start of DNA synthesis. This modification of chromosome pairing at a much earlier stage than has been previously demonstrated is further evidence that the processes of chromosome pairing and crossing-over are probably more complex than formerly envisaged.

Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat

Background

Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact.

Results

We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChip^® aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350 transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation, recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to known sequences in NCBI and TIGR databases.

Conclusion

This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat.

Directed motion of telomeres in the formation of the meiotic bouquet revealed by time course and simulation analysis

Chromosome movement is critical for homologous chromosome pairing during meiosis. A prominent and nearly universal meiotic chromosome reorganization is the formation of the bouquet, characterized by the close clustering of chromosome ends at the nuclear envelope. We have used a novel method of in vitro culture of rye anthers combined with fluorescent in situ hybridization (FISH) detection of telomeres to quantitatively study bouquet formation. The three-dimensional distribution of telomeres over time was used to obtain a quantitative profile of bouquet formation intermediates. The bouquet formed through a gradual, continuous tightening of telomeres over approximately 6 h. To determine whether the motion of chromosomes was random or directed, we developed a computer simulation of bouquet formation to compare with our observations. We varied the diffusion rate of telomeres and the amount of directional bias in telomere movement. In our models, the bouquet was formed in a manner comparable to what we observed in cultured meiocytes only when the movement of telomeres was actively directed toward the bouquet site, whereas a wide range of diffusion rates were permitted. Directed motion, as opposed to random diffusion, was required to reproduce our observations, implying that an active process moves chromosomes to cause telomere clustering.

Meiotic cytology and chromosome behaviour in wild-type Arabidopsis thaliana

This article reviews the historical development of cytology and cytogenetics in Arabidopsis, and summarizes recent developments in molecular cytogenetics, with special emphasis on meiotic studies. Despite the small genome and small chromosomes of Arabidopsis, considerable progress has been made in developing appropriate cytogenetical techniques for chromosome analysis. Fluorescence in situ hybridization (FISH) applied to extended meiotic pachytene chromosomes has resulted in a standardized karyotype (idiogram) for the species that has also been aligned with the genetical map. A better understanding of floral and meiotic development has been achieved by combining cytological studies, based on both sectioning and spreading techniques, with morphometric data and developmental landmarks. The meiotic interphase, preceding prophase I, has been investigated by marking the nuclei undergoing DNA replication with BrdU. This allowed the subclasses of meiotic interphase to be distinguished and also provided a means to time the duration of meiosis and its constituent phases. The FISH technique has been used to analyse in detail the meiotic organization of telomeres and centromeric regions. The results indicate that centromere regions do not play an active role in chromosome pairing and synapsis; however, telomeres pair homologously in advance of general chromosome synapsis. The FISH technique is currently being applied to analysing the pairing and synapsis of interstitial chromosome regions through interphase and prophase I. FISH probes also allow the five bivalents of Arabidopsis to be identified at metaphase I and this has permitted an analysis of chiasma frequencies in individual bivalents, both in wild-type Arabidopsis and in two meiotic mutants.

What controls the length of noncoding DNA?

Several recent studies of genome evolution indicate that the rate of DNA loss exceeds that of DNA gain, leading to an underlying mutational pressure towards collapsing the length of noncoding DNA. That such a collapse is not observed suggests opposing mechanisms favoring longer noncoding regions. The presence of transposable elements alone also does not explain observed features of noncoding DNA. At present, a multidisciplinary approach--using population genetics techniques, large-scale genomic analyses, and in silico evolution--is beginning to provide new and valuable insights into the forces that shape the length of noncoding DNA and, ultimately, genome size. Recombination, in a broad sense, might be the missing key parameter for understanding the observed variation in length of noncoding DNA in eukaryotes.

Patterns of genome size evolution in tetraodontiform fishes

We used flow cytometry to measure genome size in 15 species from seven families and subfamilies of tetraodontiform fishes. Previous studies have found that smooth pufferfishes (Tetraodontidae) have the smallest genome of any vertebrate measured to date (0.7-1.0 picograms diploid). We found that spiny pufferfishes (Diodontidae, sister group to the smooth puffers) possess a genome that is about two times larger (1.6-1.8 pg). Mola mola, a member of the sister group to Diodontidae and Tetraodontidae, also has a relatively large genome (1.7 pg). Parsimony analysis of this pattern indicates that the plesiomorphic condition for Molidae (Diodontidae, Tetraodontidae) is a genome size of 1.6-1.8 pg, and that tiny genome size is a derived character unique to smooth puffers. However, an alternative explanation is that the ancestor of Tetraodontidae acquired a heritable tendency toward decreasing genome size, such as a new or modified deletion mechanism, and genome size in all of the tetraodontid lineages has been decreasing in parallel since the split from Diodontidae. Small genome size (1.1-1.3 pg) also appears to have evolved independently in some members of Balistoidea (triggerfishes and filefishes) within Tetraodontiformes.

Evolution of genome size: new approaches to an old problem

Eukaryotic genomes come in a wide variety of sizes. Haploid DNA contents (C values) range > 80,000-fold without an apparent correlation with either the complexity of the organism or the number of genes. This puzzling observation, the C-value paradox, has remained a mystery for almost half a century, despite much progress in the elucidation of the structure and function of genomes. Here I argue that new approaches focussing on the genetic mechanisms that generate genome-size differences could shed much light on the evolution of genome size.

Copepod development rates in relation to genome size and 18S rDNA copy number

It is known that body sizes and temperature-independent developmental durations within two genera of calanoid Copepoda (Crustacea) are positively related to nuclear DNA contents of their somatic nuclei. Evidently because of the constraint of similar cell numbers among the species, (nucleotypic) effects of nucleus size on cell size and on cell-level processes are expressed at the whole-organism level. Here, we show that developmental durations of eight species of five genera are also negatively related to their greatly differing numbers of 18S rRNA genes per unit DNA. We propose that levels of rDNA iteration among copepods have been controlled by natural selection to regulate ribosome concentrations, therefore protein production and development rates, independently of the large variations in genome sizes, which are in turn adapted to regulating cell and therefore body sizes.

Genome size as a mutation-selection-drift process

A novel method for estimating neutral rates and patterns of DNA evolution in Drosophila takes advantage of the propensity of non-LTR retrotransposable elements to create nonfunctional, transpositionally inactive copies as a product of transposition. For many LINE elements, most copies present in a genome at any one time are nonfunctional "dead-on-arrival" (DOA) copies. Because these are off-shoots of active, transpositionally competent "master" lineages, in a gene tree of a LINE element from multiple samples from related species, the DOA lineages are expected to map to the terminal branches and the active lineages to the internal branches, the primary exceptions being when the sample includes DOA copies that are allelic or orthologous. Analysis of nucleotide substitutions and other changes along the terminal branches therefore allows estimation of the fixation process in the DOA copies, which are unconstrained with respect to protein coding; and under selective neutrality, the fixation process estimates the underlying mutational pattern. We have studied the retroelement Helena in Drosophila. An unexpectedly high rate of DNA loss was observed, yielding a half-life of unconstrained DNA sequences approximately 60-fold faster in Drosophila than in mammals. The high rate of DNA loss suggests a straightforward explanation of the seeming paradox that Drosophila has many fewer pseudogenes than found in mammalian species. Differential rates of deletion in different taxa might also contribute to the celebrated C-value paradox of why some closely related organisms can have very different DNA contents. New data presented here rule out the possibility that the transposition process itself is highly mutagenic, hence the observed linear relation between number of deletions and number of nucleotide substitutions is most easily explained by the hypothesis that both types of changes accumulate in unconstrained sequences over time.

Nuclear DNA amounts in angiosperms

Collected lists of nuclear DNA amounts estimated for a total of almost 1000 angiosperm species were published by Bennett & Smith (Phil. Trans. R. Soc. Lond.B 274, 227—274 (1976)), and by Bennettet al. (Proc. R. Soc. Lond. B 216, 179-199 (1982a)). Subsequently, work on nuclear genome size in flowering plant taxa, and interest in its consequences, has increased. Thus, estimates for 588 angiosperm species not previously listed were published, or communicated to us, between 1982 and mid-1986. As these additional estimates came from more than 50 sources which were either widely scattered in the scientific literature or unpublished personal communications, they are not readily accessible. This, and the many personal enquiries for the information received, shows that a further publication, compiling the new data is needed. This paper, therefore, contains a further supplementary list of absolute DNA amounts. This new compilation includes DNACvalues for 629 angiosperm species not listed in either of the above-mentioned papers, with additional estimates for 119 species already listed by them. These data are assembled primarily for reference purposes. Analysis of citations of the two previously published lists and of personal requests for additional information both show that the major users of genome size information are cell and molecular biologists. Consequently, the species are listed as before in alphabetical order, rather than by any taxonomic scheme, as this was felt to be more helpful to these users

The duration of meiosis

A survey of work on meiotic duration in diploid plants shows that the duration is positively correlated with the DNA content per nucleus and with the mitotic cycle time. However, meiotic duration is not solely determined by the DNA content per nucleus but is also affected by chromosomal organization, DNA structure and the developmental pattern of the organism. Thus, in three polyploid plant species meiosis is much shorter and in three animal species it is much longer than would be expected in diploid plant species having corresponding DNA contents. Differences in meiotic duration in plant species are usually the result of proportional differences in all the stages of meiosis. Factors affecting the initiation, control and duration of meiosis are discussed. The consequences of changes in nuclear DNA content on developmental processes and the life cycle in plants are considered. It is suggested that DNA influences development in two ways, first directly through its informational content, and second indirectly by the physical mechanical effects of its mass independent of its informational content.

The time and duration of female meiosis in wheat, rye and barley

Few recent investigations have been made of female meiosis in cereals, and almost nothing is known about the duration of female meiosis in higher plants. Consequently, the time and duration of female meiosis in Triticum aestivum , Hordeum vulgare and Secale cereale have been studied. The appearance of the embryo sac mother cell (e. m. c.) and of the meiotic nuclei during female meiosis in Hordeum vulgare is described and illustrated. In the species studied, each floret contains only one ovary with a single e. m. c., and meiosis is almost synchronous in the pollen mother cells from all three anthers. Conse­quently, it is possible to make precise comparisons between the stages of male and female development within individual florets. Data from these comparisons, together with know­ledge previously determined of the duration of male meiosis in these species, allowed the estimation of the time and duration of female meiosis fairly accurately for T. aestivum and H. vulgare and approximately for S. cereale . The results showed that for H. vulgar and T. aestivum grown at 20°C, the duration of female meiosis was very similar to the duration of male meiosis. Furthermore, on average male and female meiosis occurred almost synchronously. In S. cereale however, male meiosis preceeded female meiosis by about 15 h. Growing T. aestivum under environmental stress induced asynchrony between male and female development at meiosis. Synchrony was not re-established after a long period under normal conditions. Nuclear DNA content and ploidy level are known to be important factors determining or affecting the duration of male meiosis. These factors appear to play an important role in controlling the duration of female meiosis also.

The effects of polyploidy on meiotic duration and pollen development in cereal anthers

The anther is useful for the study of development because it provides comparisons between mitotic and meiotic divisions; between nuclear behaviour during the sporophyte and gametophyte stages; and between cell cycles and divisions involving cells with different nuclear DNA contents. The duration of the period from the immediately premeiotic mitosis until the start of leptotene at 20 °C was estimated to be about 48 h in hexaploid Chinese Spring wheat ( Triticum aestivum ), and about 42 h in diploid Petkus Spring rye ( Secale cereale ). Comparisons of the durations of meiosis and of pollen maturation in wheat, in rye and in Triticale genotypes showed that in all three the durations of these stages of development decreased as ploidy level increased. Within each ploidy level, genotypes with higher nuclear DNA content had longer meiotic durations. Differences in both meiotic duration and pollen maturation resulted from proportional differences in the duration of all component stages. These results obtained from comparisons of a closely related group of species in the Gramineae are similar to the results obtained previously (Bennett 1971) from comparisons of plant species taken from widely different families. Data in animals showing positive linear relationship between meiotic duration and the duration of spermatogenesis are collected. Possible causes of the faster rates of development during meiosis and pollen maturation in polyploid cereal species, and of the constant proportions between the durations of all their constituent stages, are discussed.

Nucleolar patterns in antheridial filaments of mono- and dioecious Chara spp. (Characeae) with different DNA C-values

Using NOR-silver-staining technique, nucleolar arrangements have been studied in antheridial filaments among 5 taxa of Chara with different genome sizes: monoecious Chara vulgaris L., C. fragilis Desv., C. contraria Kütz, and dioecious: Chara aspera Willd., and Chara tomentosa L. It is argued that due to a chain-series of regulatory processes establishing correlations between nucleolar cycles and consecutive cell growth cycles, the diminution of nucleoli observed throughout the development of antheridial filaments is a common and widespread feature of spermatogenesis shared by all the studied species. It is probably a controlling mechanism acting over the morphogenetic reduction of cell dimensions and cessation of mitotic divisions.

A model for effective pairing and recombination at meiosis based on early replicating sites (R-bands) along chromosomes

A model for meiotic pairing is proposed in which early replicating sites (R-band equivalent) along chromosomes are envisaged as sites for synaptic initiation. Only within such sites will "effective" pairing for recombination be established. Pairing in later replicating (G- and C-band equivalent) regions will be "ineffective" and will not provide for the stringent requirements of the crossover process. Exchange events might be predetermined at S-phase, and possibly at junctions between early and later replicating sequences, these being seen as vulnerable sites for breakage. Temporal shifts in replication from early to late S, are postulated to produce localized pairing disruption and lowering of crossover values as regions of chromatin shift from being effectively to ineffectively paired.

Nucleotide sequences of highly repeated DNAs; compilation and comments

The nucleotide sequence data from highly repeated DNAs of inverte-brates and mammals are summarized and briefly discussed. Very similar conclusions can be drawn from the two data bases. Sequence complexities can vary from 2 bp to at least 359 bp in invertebrates and from 3 bp to at least 2350 bp in mammals. The larger sequences may or may not exhibit a substructure. Significant sequence variation occurs for any given repeated array within a species, but the sources of this heterogeneity have not been systematically partitioned. The types of alterations in a basic repeating unit can involve base changes as well as deletions or additions which can vary from 1 bp to at least 98 bp in length. These changes indicate that sequenceper seis unlikely to be under significant biological constraints and may sensibly be examined by analogy to Kimura's neutral theory for allelic variation. It is not possible with the present evidence to discriminate between the roles ofneutralandselectivemechanisms in the evolution of highly repeated DNA.

Tandemly repeated arrays are constantly subjected to cycles of amplification and deletion by mechanisms for which the available data stem largely from ribosomal genes. It is a matter of conjecture whether the solutions to the mechanistic puzzles involved in amplification or rapid redeployment of satellite sequences throughout a genome will necessarily give any insight into biological functions.

The lack of significant somatic effects when the satellite DNA content of a genome is significantly perturbed indicates that the hunt for specific functions at thecellularlevel is unlikely to prove profitable.

The presence or in some cases theamountof satellite DNA on a chromosome, however, can have significant effects in the germ line. There the data show that localized condensed chromatin, rich in satellite DNA, can have the effect of rendering adjacent euchromatic regionsrec−, or of altering levels of recombination on different chromosomes. No data stemming from natural populations however are yet available to tell us if these effects are of adaptive or evolutionary significance.

Rye chromosome translocations in hexaploid wheat: a re-evaluation of the loss of heterochromatin from rye chromosomes

Using in situ hybridization techniques, we have been able to identify the translocated chromosomes resulting from whole arm interchanges between homoeologous chromosomes of wheat and rye. This was possible because radioactive probes are available which recognize specific sites of highly repeated sequence DNA in either rye or wheat chromosomes. The translocated chromosomes analysed in detail were found in plants from a breeding programme designed to substitute chromosome 2R of rye into commercial wheat cultivars. The distribution of rye highly repeated DNA sequences showed modified chromosomes in which (a) most of the telomeric heterochromatin of the short arm and (b) all of the telomeric heterochromatin of the long arm, had disappeared. Subsequent analyses of these chromosomes assaying for wheat highly repeated DNA sequences showed that in type (a), the entire short arm of 2R had been replaced by the short arm of wheat chromosome 2B and in (b), the long arm of 2R had been replaced by the long arm of 2B. The use of these probes has also allowed us to show that rye heterochromatin has little effect on the pairing of the translocated wheat arm to its wheat homologue during meiosis. We have also characterized the chromosomes resulting from a 1B-1R translocation event.From these results, we suggest that the observed loss of telomeric heterochromatin from rye chromosomes in wheat is commonly due to wheat-rye chromosome translocations.