The condensin subunits SMC2 and SMC4 interact for correct condensation and segregation of mitotic maize chromosomes

Structural Maintenance of Chromosomes 2 (SMC2) and Structural Maintenance of Chromosomes 4 (SMC4) are the core components of the condensin complexes, which are required for chromosome assembly and faithful segregation during cell division. Because of the crucial functions of both proteins in cell division, much work has been done in various vertebrates, but little information is known about their roles in plants. Here, we identified ZmSMC2 and ZmSMC4 in maize (Zea mays) and confirmed that ZmSMC2 associates with ZmSMC4 via their hinge domains. Immunostaining revealed that both proteins showed dynamic localization during mitosis. ZmSMC2 and ZmSMC4 are essential for proper chromosome segregation and for H3 phosphorylation at Serine 10 (H3S10ph) at pericentromeres during mitotic division. The loss of function of ZmSMC2 and ZmSMC4 enlarges mitotic chromosome volume and impairs sister chromatid separation to the opposite poles. Taken together, these findings confirm and extend the coordinated role of ZmSMC2 and ZmSMC4 in maintenance of normal chromosome architecture and accurate segregation during mitosis.

Predicted genetic gains from introgressing chromosome segments from exotic germplasm into an elite soybean cultivar

KEY MESSAGE

To improve an elite soybean line, introgress longer chromosome segments instead of QTL alleles from exotic germplasm. Broadening the diversity of cultivated soybean [Glycine max (L.) Merrill] through introgression of exotic germplasm has been difficult. Our objectives were to (1) determine if introgressing specific chromosome segments (instead of quantitative trait locus alleles) from exotic soybean germplasm has potential for improving an elite cultivar, and (2) identify strategies to introgress and pyramid exotic chromosome segments into an elite cultivar. We estimated genomewide marker effects for yield and other traits in seven crosses between the elite line IA3023 and seven soybean plant introductions (PIs). We then predicted genetic gains from having ≤ 2 targeted recombinations per linkage group. When introgression was modeled for yield while controlling maturity in the seven PI × IA3023 populations, the predicted yield was 8-25% over the yield of IA3023. Correlated changes in maturity, seed traits, lodging, and plant height were generally small but were in the favorable direction. In contrast, selecting the best recombinant inbred (without targeted recombination) in each of the PI × IA3023 populations led to negative or minimal yield gains over IA3023. In one PI × IA3023 population, introgressing and pyramiding only two linkage groups from recombinant inbreds into IA3023 was predicted to achieve an 8% yield gain over IA3023 without sacrificing the performance for other traits. The probability of inheriting intact chromosomes was high enough to allow introgression and pyramiding of chromosome segments in 5-6 generations. Overall, our study suggested that introgressing specific chromosome segments is an effective way to introduce exotic soybean germplasm into an elite cultivar.

Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

During their lifespan, plants respond to a multitude of stressful factors. Dynamic changes in chromatin and concomitant transcriptional variations control stress response and adaptation, with epigenetic memory mechanisms integrating environmental conditions and appropriate developmental programs over the time. Here we analyzed transcriptome and genome-wide histone modifications of maize plants subjected to a mild and prolonged drought stress just before the flowering transition. Stress was followed by a complete recovery period to evaluate drought memory mechanisms. Three categories of stress-memory genes were identified: i) "transcriptional memory" genes, with stable transcriptional changes persisting after the recovery; ii) "epigenetic memory candidate" genes in which stress-induced chromatin changes persist longer than the stimulus, in absence of transcriptional changes; iii) "delayed memory" genes, not immediately affected by the stress, but perceiving and storing stress signal for a delayed response. This last memory mechanism is described for the first time in drought response. In addition, applied drought stress altered floral patterning, possibly by affecting expression and chromatin of flowering regulatory genes. Altogether, we provided a genome-wide map of the coordination between genes and chromatin marks utilized by plants to adapt to a stressful environment, describing how this serves as a backbone for setting stress memory.

Flower bud proteome reveals modulation of sex-biased proteins potentially associated with sex expression and modification in dioecious Coccinia grandis

BACKGROUND

Dioecy is an important sexual system wherein, male and female flowers are borne on separate unisexual plants. Knowledge of sex-related differences can enhance our understanding in molecular and developmental processes leading to unisexual flower development. Coccinia grandis is a dioecious species belonging to Cucurbitaceae, a family well-known for diverse sexual forms. Male and female plants have 22A + XY and 22A + XX chromosomes, respectively. Previously, we have reported a gynomonoecious form (22A + XX) of C. grandis bearing morphologically hermaphrodite flowers (GyM-H) and female flowers (GyM-F). Also, we have showed that foliar spray of AgNO₃ on female plant induces morphologically hermaphrodite bud development (Ag-H) despite the absence of Y-chromosome.

RESULTS

To identify sex-related differences, total proteomes from male, female, GyM-H and Ag-H flower buds at early and middle stages of development were analysed by label-free proteomics. Protein search against the cucumber protein sequences (Phytozome) as well as in silico translated C. grandis flower bud transcriptome database, resulted in the identification of 2426 and 3385 proteins (FDR ≤ 1%), respectively. The latter database was chosen for further analysis as it led to the detection of higher number of proteins. Identified proteins were annotated using BLAST2GO pipeline. SWATH-MS-based comparative abundance analysis between Female_Early_vs_Male_Early, Ag_Early_vs_Female_Early, GyM-H_Middle_vs_Male_Middle and Ag_Middle_vs_ Male_Middle led to the identification of 650, 1108, 905 and 805 differentially expressed proteins, respectively, at fold change ≥1.5 and P ≤ 0.05. Ethylene biosynthesis-related candidates as highlighted in protein interaction network were upregulated in female buds compared to male buds. AgNO₃ treatment on female plant induced proteins related to pollen development in Ag-H buds. Additionally, a few proteins governing pollen germination and tube growth were highly enriched in male buds compared to Ag-H and GyM-H buds.

CONCLUSION

Overall, current proteomic analysis provides insights in the identification of key proteins governing dioecy and unisexual flower development in cucurbitaceae, the second largest horticultural family in terms of economic importance. Also, our results suggest that the ethylene-mediated stamen inhibition might be conserved in dioecious C. grandis similar to its monoecious cucurbit relatives. Further, male-biased proteins associated with pollen germination and tube growth identified here can help in understanding pollen fertility.

Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data

BACKGROUND

Our study is the first to provide RNA-Seq data analysis related to transcriptomic responses towards drought across different crops. The aim was to identify and map which genes play a key role in drought response on leaves across different crops. Forty-two RNA-seq samples were analyzed from 9 published studies in 7 plant species (Arabidopsis thaliana, Solanum lycopersicum, Zea mays, Vitis vinifera, Malus X domestica, Solanum tuberosum, Triticum aestivum).

RESULTS

Twenty-seven (16 up-regulated and 11 down-regulated) drought-regulated genes were commonly present in at least 7 of 9 studies, while 351 (147 up-regulated and 204 down-regulated) were commonly drought-regulated in 6 of 9 studies. Across all kind of leaves, the drought repressed gene-ontologies were related to the cell wall and membrane re-structuring such as wax biosynthesis, cell wall organization, fatty acid biosynthesis. On the other hand, drought-up-regulated biological processes were related to responses to osmotic stress, abscisic acid, water deprivation, abscisic-activated signalling pathway, salt stress, hydrogen peroxide treatment. A common metabolic feature linked to drought response in leaves is the repression of terpenoid pathways. There was an induction of AL1 (alfin-like), UGKYAH (trihelix), WRKY20, homeobox genes and members of the SET domain family in 6 of 9 studies. Several genes involved in detoxifying and antioxidant reactions, signalling pathways and cell protection were commonly modulated by drought across the 7 species. The chromosome (Chr) mapping of these key abiotic stress genes highlighted that Chr 4 in Arabidopsis thaliana, Chr 1 in Zea mays, Chr 2 and Chr 5 in Triticum aestivum contained a higher presence of drought-related genes compared to the other remaining chromosomes. In seedling studies, it is worth notice the up-regulation of ERF4 and ESE3 (ethylene), HVA22 (abscisic acid), TIR1 (auxin) and some transcription factors (MYB3, MYB94, MYB1, WRKY53 and WRKY20). In mature leaves, ERF1 and Alfin-like 1 were induced by drought while other transcription factors (YABBY5, ARR2, TRFL2) and genes involved phospholipid biosynthesis were repressed.

CONCLUSIONS

The identified and mapped genes might be potential targets of molecular breeding activities to develop cultivars with enhanced drought resistance and tolerance across different crops.

Meiotic abnormalities affect genetic constitution and pollen viability in dicots from Indian cold deserts

BACKGROUND

Meiotic abnormalities lead to morphological and genetic variations which caused not only to evolution but also intraspecific reproductive barriers. During present study of detailed meiotic course in dicotyledonous plants sampled from Indian cold deserts, various meiotic abnormalities have been detected. For this, the plant materials fixed in Carnoy's fixative and studied detailed meiotic course by standard squash method in 1% acetocarmine.

RESULTS

Meiotic abnormalities have been presently detected in 71 species which include multiple associations in diploids (Achillea millefolium L.), multivalents and univalents in polyploids (4 species), cytomixis (40 species), chromosome stickiness (20 species), nonsynchronous disjunction of bivalents (32 species), interbivalent connections (15 species), synaptic mutants (2 species), syncyte meiocytes (2 species), abnormal spindles (7 species), and fusion of pollen grains (1 species), laggards and chromatin bridges, hypo-, hyperploid PMCs, monads, dyads, triads, tetrads with micronuclei and polyads.

CONCLUSIONS

Consequently, variable sized apparently fertile pollen grains and considerable amount of sterile pollen grains are resulted as end products which lead to different genetic constitution (aneuploids and polyploids) and curtailed sexual reproductive success in these species.

Uncovering key small RNAs associated with gametocidal action in wheat

Gametocidal (Gc) chromosomes can kill gametes that lack them by causing chromosomal breakage to ensure their preferential transmission, and they have been exploited in genetic breeding. The present study investigated the possible roles of small RNAs (sRNAs) in Gc action. By sequencing two small RNA libraries from the anthers of Triticum aestivum cv. Chinese Spring (CS) and the Chinese Spring-Gc 3C chromosome monosomic addition line (CS-3C), we identified 239 conserved and 72 putative novel miRNAs, including 135 differentially expressed miRNAs. These miRNAs were predicted to target multiple genes with various molecular functions relevant to the features of Gc action, including sterility and genome instability. The transgenic overexpression of miRNA, which was up-regulated in CS-3C, reduced rice fertility. The CS-3C line exhibited a genome-wide reduction in 24 nt siRNAs compared with that of the CS line, particularly in transposable element (TE) and repetitive DNA sequences. Corresponding to this reduction, the bisulfite sequencing analysis of four retro-TE sequences showed a decrease in CHH methylation, typical of RNA-directed DNA methylation (RdDM). These results demonstrate that both miRNA-directed regulation of gene expression and siRNA-directed DNA methylation of target TE loci could play a role in Gc action.

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice

The non-random spatial packing of chromosomes in the nucleus plays a critical role in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome. We found subtle features including chromatin loops, gene loops, and off-/near-diagonal intensive interaction regions. Gene chromatin loops associated with H3K27me3 could be positively involved in gene expression. In addition to insulated enhancing effects for neighbor gene expression, the identified rice gene loops could bi-directionally (+/-) affect the expression of looped genes themselves. Finally, web-interleaved off-diagonal IHIs/KEEs (Interactive Heterochromatic Islands or KNOT ENGAGED ELEMENTs) could trap transposable elements (TEs) via the enrichment of silencing epigenetic marks. In parallel, the near-diagonal FIREs (Frequently Interacting Regions) could positively affect the expression of involved genes. Our results suggest that the chromatin packing pattern in rice is generally similar to that in Arabidopsis thaliana but with clear differences at specific structural levels. We conclude that genomic composition, epigenetic modification, and transcriptional activity could act in combination to shape global and local chromatin packing in rice. Our results confirm recent observations in rice and A. thaliana but also provide additional insights into the patterns and features of chromatin organization in higher plants.

Is the diversification of Mediterranean Basin plant lineages coupled to karyotypic changes?

The Mediterranean Basin region, home to 25,000 plant species, is included in the worldwide list of hotspots of biodiversity. Despite the indisputably important role of chromosome transitions in plant evolution and diversification, no reference study to date has dealt with the possible relationship between chromosome evolution and lineage diversification in the Mediterranean Basin. Here we study patterns of diversification, patterns of chromosome number transition (either polyploidy or dysploidy) and the relationship between the two for 14 Mediterranean Basin angiosperm lineages using previously published phylogenies. We found a mixed pattern, with half of the lineages displaying a change in chromosome transition rates after the onset of the Mediterranean climate (six increases, one decrease) and the other half (six) experiencing constant rates of chromosome transitions through time. We have also found a heterogeneous pattern regarding diversification rates, with lineages exhibiting moderate (five phylogenies) or low (six) initial diversification rates that either increased (six) or declined (five) through time. Our results reveal no clear link between diversification rates and chromosome number transition rates. By promoting the formation of new habitats and driving the extinction of many species, the Mediterranean onset and the posterior Quaternary climatic oscillations could have been key for the establishment of new chromosomal variants in some plant phylogenies but not in others. While the biodiversity of the Mediterranean Basin may be partly influenced by the chromosomal diversity of its lineages, this study concludes that lineage diversification in the region is largely decoupled from karyotypic evolution.

Visualization of chromosome condensation in plants with large chromosomes

BACKGROUND

Most data concerning chromosome organization have been acquired from studies of a small number of model organisms, the majority of which are mammals. In plants with large genomes, the chromosomes are significantly larger than the animal chromosomes that have been studied to date, and it is possible that chromosome condensation in such plants was modified during evolution. Here, we analyzed chromosome condensation and decondensation processes in order to find structural mechanisms that allowed for an increase in chromosome size.

RESULTS

We found that anaphase and telophase chromosomes of plants with large chromosomes (average 2C DNA content exceeded 0.8 pg per chromosome) contained chromatin-free cavities in their axial regions in contrast to well-characterized animal chromosomes, which have high chromatin density in the axial regions. Similar to animal chromosomes, two intermediates of chromatin folding were visible inside condensing (during prophase) and decondensing (during telophase) chromosomes of Nigella damascena: approximately 150 nm chromonemata and approximately 300 nm fibers. The spatial folding of the latter fibers occurs in a fundamentally different way than in animal chromosomes, which leads to the formation of chromosomes with axial chromatin-free cavities.

CONCLUSION

Different compaction topology, but not the number of compaction levels, allowed for the evolution of increased chromosome size in plants.

Rye (Secale cereale) supernumerary (B) chromosomes associated with heat tolerance during early stages of male sporogenesis

BACKGROUND AND AIMS

Rye supernumerary (B) chromosomes have an accumulation mechanism involving the B subtelomeric domain highly enriched in D1100- and E3900-related sequences. In this work, the effects of heat stress during the early stages of male meiosis in 0B and +B plants were studied.

METHODS

In-depth cytological analyses of chromatin structure and behaviour were performed on staged rye meiocytes utilizing DAPI, fluorescence in situ hybridization and 5-methylcytosine immune labelling. Quantitative real-time PCR was used to measure heat effects on the expression of the Hsp101 gene as well as the 3·9- and 2·7-kb E3900 forms in various tissues and meiotic stages.

KEY RESULTS AND CONCLUSIONS

Quantitative real-time PCR established that heat induced equal up-regulation of the Hsp101 gene in 0B and 2B plants, with a marked peak in anthers with meiocytes staged at pachytene. Heat also resulted in significant up-regulation of E3900-related transcripts, especially at pachytene and for the truncated 2·7-kb form of E3900. Cytological heat-induced anomalies in prophase I, measured as the frequency of anomalous meiocytes, were significantly greater in 0B plants. Whereas telomeric sequences were widely distributed in a manner close to normal in the majority of 2B pachytene cells, most 0B meiocytes displayed abnormally clustered telomeres after chromosome pairing had occurred. Relevantly, bioinformatic analysis revealed a significantly high-density heat responsive cis regulatory sequence on E3900, clearly supporting stress-induced response of transcription for the truncated variant. Taken together, these results are the first indication that rye B chromosomes have implications on heat tolerance and may protect meiocytes against heat stress-induced damage.

Analysis of transposable elements and organellar DNA in male and female genomes of a species with a huge Y chromosome reveals distinct Y centromeres

Few angiosperms have distinct Y chromosomes. Among those that do are Silene latifolia (Caryophyllaceae), Rumex acetosa (Polygonaceae) and Coccinia grandis (Cucurbitaceae), the latter having a male/female difference of 10% of the total genome (female individuals have a 0.85 pg genome, male individuals 0.94 pg), due to a Y chromosome that arose about 3 million years ago. We compared the sequence composition of male and female C. grandis plants and determined the chromosomal distribution of repetitive and organellar DNA with probes developed from 21 types of repetitive DNA, including 16 mobile elements. The size of the Y chromosome is largely due to the accumulation of certain repeats, such as members of the Ty1/copia and Ty3/gypsy superfamilies, an unclassified element and a satellite, but also plastome- and chondriome-derived sequences. An abundant tandem repeat with a unit size of 144 bp stains the centromeres of the X chromosome and the autosomes, but is absent from the Y centromere. Immunostaining with pericentromere-specific markers for anti-histone H3Ser10ph and H2AThr120ph revealed a Y-specific extension of these histone marks. That the Y centromere has a different make-up from all the remaining centromeres raises questions about its spindle attachment, and suggests that centromeric or pericentromeric chromatin might be involved in the suppression of recombination.

The arrangement of Brachypodium distachyon chromosomes in interphase nuclei

The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biological processes, such as DNA replication, transcription, and repair. However, detailed data about the CT arrangement in monocotyledonous plants are scarce. In this study, chromosome painting was used to analyse the distribution and associations of individual chromosomes in the 3-D preserved nuclei of Brachypodium distachyon root cells in order to determine the factors that may have an impact on the homologous CT arrangement. It was shown that the frequency of CT association is linked to the steric constraints imposed by the limited space within the nucleus and may depend on chromosome size and morphology as well as on the nuclear shape. Furthermore, in order to assess whether the distribution of interphase chromosomes is random or is subject to certain patterns, a comparison between the experimental data and the results of a computer simulation (ChroTeMo), which was based on a fully probabilistic distribution of the CTs, was performed. This comparison revealed that homologous chromosome arm CTs associate more often than if they were randomly arranged inside the interphase nucleus.

The wheat Phs-A1 pre-harvest sprouting resistance locus delays the rate of seed dormancy loss and maps 0.3 cM distal to the PM19 genes in UK germplasm

The precocious germination of cereal grains before harvest, also known as pre-harvest sprouting, is an important source of yield and quality loss in cereal production. Pre-harvest sprouting is a complex grain defect and is becoming an increasing challenge due to changing climate patterns. Resistance to sprouting is multi-genic, although a significant proportion of the sprouting variation in modern wheat cultivars is controlled by a few major quantitative trait loci, including Phs-A1 in chromosome arm 4AL. Despite its importance, little is known about the physiological basis and the gene(s) underlying this important locus. In this study, we characterized Phs-A1 and show that it confers resistance to sprouting damage by affecting the rate of dormancy loss during dry seed after-ripening. We show Phs-A1 to be effective even when seeds develop at low temperature (13 °C). Comparative analysis of syntenic Phs-A1 intervals in wheat and Brachypodium uncovered ten orthologous genes, including the Plasma Membrane 19 genes (PM19-A1 and PM19-A2) previously proposed as the main candidates for this locus. However, high-resolution fine-mapping in two bi-parental UK mapping populations delimited Phs-A1 to an interval 0.3 cM distal to the PM19 genes. This study suggests the possibility that more than one causal gene underlies this major pre-harvest sprouting locus. The information and resources reported in this study will help test this hypothesis across a wider set of germplasm and will be of importance for breeding more sprouting resilient wheat varieties.

CHR729 Is a CHD3 Protein That Controls Seedling Development in Rice

CHD3 is one of the chromatin-remodeling factors that contribute to controlling the expression of genes associated with plant development. Loss-of-function mutants display morphological and growth defects. However, the molecular mechanisms underlying CHD3 regulation of plant development remain unclear. In this study, a rice CHD3 protein, CHR729, was identified. The corresponding mutant line (t483) exhibited late seed germination, low germination rate, dwarfism, low tiller number, root growth inhibition, adaxial albino leaves, and short and narrow leaves. CHR729 encoded a nuclear protein and was expressed in almost all organs. RNA-sequencing analysis showed that several plant hormone-related genes were up- or down-regulated in t483 compared to wild type. In particular, expression of the gibberellin synthetase gibberellin 20 oxidase 4 gene was elevated in the mutant. Endogenous gibberellin assays demonstrated that the content of bioactive GA₃ was reduced in t483 compared to wild type. Moreover, the seedling dwarfism, late seed germination, and short root length phenotypes of t483 were partially rescued by treatment with exogenous GA₃. These results suggest that the rice CHD3 protein CHR729 plays an important role in many aspects of seedling development and controls this development via the gibberellin pathway.

Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus

Breeding new varieties with low seed glucosinolate (GS) concentrations has long been a prime target in Brassica napus. In this study, a novel association mapping methodology termed 'associative transcriptomics' (AT) was applied to a panel of 101 B. napus lines to define genetic regions and also candidate genes controlling total seed GS contents. Over 100,000 informative single-nucleotide polymorphisms (SNPs) and gene expression markers (GEMs) were developed for AT analysis, which led to the identification of 10 SNP and 7 GEM association peaks. Within these peaks, 26 genes were inferred to be involved in GS biosynthesis. A weighted gene co-expression network analysis provided additional 40 candidate genes. The transcript abundance in leaves of two candidate genes, BnaA.GTR2a located on chromosome A2 and BnaC.HAG3b on C9, was correlated with seed GS content, explaining 18.8 and 16.8% of phenotypic variation, respectively. Resequencing of genomic regions revealed six new SNPs in BnaA.GTR2a and four insertions or deletions in BnaC.HAG3b. These deletion polymorphisms were then successfully converted into polymerase chain reaction-based diagnostic markers that can, due to high linkage disequilibrium observed in these regions of the genome, be used for marker-assisted breeding for low seed GS lines.

Quantitative high resolution mapping of HvMLH3 foci in barley pachytene nuclei reveals a strong distal bias and weak interference

In barley (Hordeum vulgare L.), chiasmata (the physical sites of genetic crossovers) are skewed towards the distal ends of chromosomes, effectively consigning a large proportion of genes to recombination coldspots. This has the effect of limiting potential genetic variability, and of reducing the efficiency of map-based cloning and breeding approaches for this crop. Shifting the sites of recombination to more proximal chromosome regions by forward and reverse genetic means may be profitable in terms of realizing the genetic potential of the species, but is predicated upon a better understanding of the mechanisms governing the sites of these events, and upon the ability to recognize real changes in recombination patterns. The barley MutL Homologue (HvMLH3), a marker for class I interfering crossovers, has been isolated and a specific antibody has been raised. Immunolocalization of HvMLH3 along with the synaptonemal complex transverse filament protein ZYP1, used in conjunction with fluorescence in situ hybridization (FISH) tagging of specific barley chromosomes, has enabled access to the physical recombination landscape of the barley cultivars Morex and Bowman. Consistent distal localization of HvMLH3 foci throughout the genome, and similar patterns of HvMLH3 foci within bivalents 2H and 3H have been observed. A difference in total numbers of HvMLH3 foci between these two cultivars has been quantified, which is interpreted as representing genotypic variation in class I crossover frequency. Discrepancies between the frequencies of HvMLH3 foci and crossover frequencies derived from linkage analysis point to the existence of at least two crossover pathways in barley. It is also shown that interference of HvMLH3 foci is relatively weak compared with other plant species.

Replication factor C1 (RFC1) is required for double-strand break repair during meiotic homologous recombination in Arabidopsis

Replication factor C1 (RFC1), which is conserved in eukaryotes, is involved in DNA replication and checkpoint control. However, a RFC1 product participating in DNA repair at meiosis has not been reported in Arabidopsis. Here, we report functional characterization of AtRFC1 through analysis of the rfc1-2 mutant. The rfc1-2 mutant displayed normal vegetative growth but showed silique sterility because the male gametophyte was arrested at the uninucleus microspore stage and the female at the functional megaspore stage. Expression of AtRFC1 was concentrated in the reproductive organ primordia, meiocytes and developing gametes. Chromosome spreads showed that pairing and synapsis were normal, and the chromosomes were broken when desynapsis began at late prophase I, and chromosome fragments remained in the subsequent stages. For this reason, homologous chromosomes and sister chromatids segregated unequally, leading to pollen sterility. Immunolocalization revealed that the AtRFC1 protein localized to the chromosomes during zygotene and pachytene in wild-type but were absent in the spo11-1 mutant. The chromosome fragmentation of rfc1-2 was suppressed by spo11-1, indicating that AtRFC1 acted downstream of AtSPO11-1. The similar chromosome behavior of rad51 rfc1-2 and rad51 suggests that AtRFC1 may act with AtRAD51 in the same pathway. In summary, AtRFC1 is required for DNA double-strand break repair during meiotic homologous recombination of Arabidopsis.

Nondisjunction in favor of a chromosome: the mechanism of rye B chromosome drive during pollen mitosis

B chromosomes (Bs) are supernumerary components of the genome and do not confer any advantages on the organisms that harbor them. The maintenance of Bs in natural populations is possible by their transmission at higher than Mendelian frequencies. Although drive is the key for understanding B chromosomes, the mechanism is largely unknown. We provide direct insights into the cellular mechanism of B chromosome drive in the male gametophyte of rye (Secale cereale). We found that nondisjunction of Bs is accompanied by centromere activity and is likely caused by extended cohesion of the B sister chromatids. The B centromere originated from an A centromere, which accumulated B-specific repeats and rearrangements. Because of unequal spindle formation at the first pollen mitosis, nondisjoined B chromatids preferentially become located toward the generative pole. The failure to resolve pericentromeric cohesion is under the control of the B-specific nondisjunction control region. Hence, a combination of nondisjunction and unequal spindle formation at first pollen mitosis results in the accumulation of Bs in the generative nucleus and therefore ensures their transmission at a higher than expected rate to the next generation.

Polycomb repressive complex 2 controls the embryo-to-seedling phase transition

Polycomb repressive complex 2 (PRC2) is a key regulator of epigenetic states catalyzing histone H3 lysine 27 trimethylation (H3K27me3), a repressive chromatin mark. PRC2 composition is conserved from humans to plants, but the function of PRC2 during the early stage of plant life is unclear beyond the fact that it is required for the development of endosperm, a nutritive tissue that supports embryo growth. Circumventing the requirement of PRC2 in endosperm allowed us to generate viable homozygous null mutants for FERTILIZATION INDEPENDENT ENDOSPERM (FIE), which is the single Arabidopsis homolog of Extra Sex Combs, an indispensable component of Drosophila and mammalian PRC2. Here we show that H3K27me3 deposition is abolished genome-wide in fie mutants demonstrating the essential function of PRC2 in placing this mark in plants as in animals. In contrast to animals, we find that PRC2 function is not required for initial body plan formation in Arabidopsis. Rather, our results show that fie mutant seeds exhibit enhanced dormancy and germination defects, indicating a deficiency in terminating the embryonic phase. After germination, fie mutant seedlings switch to generative development that is not sustained, giving rise to neoplastic, callus-like structures. Further genome-wide studies showed that only a fraction of PRC2 targets are transcriptionally activated in fie seedlings and that this activation is accompanied in only a few cases with deposition of H3K4me3, a mark associated with gene activity and considered to act antagonistically to H3K27me3. Up-regulated PRC2 target genes were found to act at different hierarchical levels from transcriptional master regulators to a wide range of downstream targets. Collectively, our findings demonstrate that PRC2-mediated regulation represents a robust system controlling developmental phase transitions, not only from vegetative phase to flowering but also especially from embryonic phase to the seedling stage.

Meiotically asynapsis-induced aneuploidy in autopolyploid Arabidopsis thaliana

The patterns of homologue segregation are the basis for euploidy or aneuploidy formation in diploids and allo-/auto-polyploids. Homologue segregation in diploids resembles that in allopolyploids during meiosis; however, meiotic chromosome behavior in autopolyploids is complicated by multiplication of homologous chromosome components. Obviously, loss of single chromosomes (or segmented chromosomes) frequently leads to abortion of reproductive gametes in diploids and allopolyploids. In contrast, the consequence of chromosome loss in autopolyploids is effortlessly compensated for by the presence of multiplied chromosome complements. Here, we use the meiotically asynaptic gene asy1, in combination with polyploidization, to elucidate aneuploidy formation in autotetraploid Arabidopsis. The results indicate that, due to homologous asynapsis in meiotic prophase I, retarded chromosome losses could induce aneuploidy during gametogenesis in autotetraploid asy1. The severe loss of individual chromosomes probably reaches the haploid genome among selfed or backcrossed progeny, leading to stochastic chromosome loss in Arabidopsis. Reciprocal crosses of autotetraploid asy1 with wild-type prove a pathway of duoparental transmission of aneuploidy (hypoploidy and hyperploidy). Viable hypoploids over-transmit via male gametes; conversely, viable hyperploids transmit mainly in female gametogenesis. This result suggests a more stringent maternal restriction of ploidy transmission in autopolyploid Arabidopsis.

[The transcriptome analysis of barley (Hordeum vulgare L.) using the Affymetrix Barley1 GeneChip]

An alternative to complete genome sequencing is development and analysis of ESTs-fragments of transcribed coding DNA sequences. The EST collections also enhanced the development of cDNA microarray technologies, which make possible assessing the transcription levels of several thousand genes in a studied tissue of an organism in the same experiment. This paper provides an overview of the results of experiments with a barley microarray, Affymetrix Barley1 GeneChip. The variation in transcription levels of over 22000 genes in germinating barley grain of 150 barley double haploid lines produced by crossing cultivars Steptoe and Morex. Variation in gene expression of each gene is a quantitative trait, which can be mapped in population of double haploids as the genetic loci determining its variation (expressed QTL or eQTL). A regulatory locus (eQTL) can colocalize with the corresponding gene on genetic map (cis-eQTL) or be distant from it, frequently on another chromosome (trans-eQTL). Thus, it is possible to detect and analyze cis- and trans-regulatory loci for genes on a genome-wide scale. The design of the Affymetrix oligonucleotide arrays makes it possible not only to concurrently test the transcription level of several thousand genes, but also to simultaneously detect the polymorphic regions in cDNA sequences, thereby finding a considerable fraction of all nucleotide substitutions between the compared genotypes. Two types of data (the expression levels of several thousand genes and the presence of polymorphic sites in their sequences) can be obtained concurrently when processing the results of the same experiment. The details of both procedures are illustrated with explanatory examples.

SMC proteins and their multiple functions in higher plants

In plants as in other eukaryotes, SMC (Structural Maintenance of Chromosome) protein complexes and proteins interacting with them are essential for sister chromatid cohesion, chromosome condensation, DNA repair and recombination. The presence of paralogous genes for various components of the different SMC complexes allowed diversification of their biological functions during evolution of higher plants. Here I summarize the multiple functions of plant SMC complexes and some of the particularities these proteins show in comparison to those of other organisms.

[Functional and mutational variations of heterochromatic region in the maize nucleolus organizer (NO) (variation of the NO heterochromatic region)]

The following facts are considered in connection with the problem of population polymorphism at heterochromatic regions of maize chromosomes: (a) variation (1-3 microm) of the heterochromatic region of nucleolus organizer (NO knob) in pollen mother cell at the pachytene stage; (b) presumably function-dependent variation of the degree of its compaction (from a compact state in the majority of plants to a puff-like state); (c) the presence of rearrangements in the NO knob region (duplications and deletion); and (d) homozygous (in all cases) state of the NO knob. Deletion is combined with alterations in the structure of chromosomal NO and the overall karyotype. It is assumed that inbreeding and MGEs influence the mutability of the NO locus and activation of the gene set controlling cytokinesis, chemical reduplication, and, possibly, rDNA amplification. The mutation was classified as a systemic mutation. The mechanisms of NO knob homozygotization in meiosis (mitosis) and the mechanisms of maintenance of the polymorphism at functionally inactive chromosome knob regions in maize populations are compared.

Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize

Barbara McClintock reported that the Ac/Ds transposable element system can generate major chromosomal rearrangements (MCRs), but the underlying mechanism has not been determined. Here, we identified a series of chromosome rearrangements derived from maize lines containing pairs of closely linked Ac transposable element termini. Molecular and cytogenetic analyses showed that the MCRs in these lines comprised 17 reciprocal translocations and two large inversions. The breakpoints of all 19 MCRs are delineated by Ac termini and characteristic 8-base-pair target site duplications, indicating that the MCRs were generated by precise transposition reactions involving the Ac termini of two closely linked elements. This alternative transposition mechanism may have contributed to chromosome evolution and may also occur during V(D)J recombination resulting in oncogenic translocations.

Locus interactions underlie seed yield in soybeans resistant to Heterodera glycines

In soybean (Glycine max L. Merr.) combining resistance to cyst nematode (SCN; Heterodera glycines I.) with high seed yield remains problematic. Molecular markers linked to quantitative trait loci (QTL) have not provided a solution. Sets of markers describing a collection of favorable alleles (linkats) may assist plant breeders seeking to combine both traits. The objective of this analysis was to identify linkats in genomic regions underlying seed yield and root SCN resistance QTL. Used were groups of cultivars selected from a single recombinant inbred (RIL) population derived from 'Essex' by 'Forrest' (ExF). The yield was measured at four locations. SCN resistance was determined in greenhouse assays. The mean seed yield was used to define 3 groups (each n = 30), high, medium and low. SCN resistance formed 2 groups (SCN resistant (n = 21) and SCN susceptible (n = 69)). Microsatellite markers (213) alleles were compared with seed yield and root SCN (Hetrodera glycines) resistance using mean analysis. The number, size and position of potential linkats were determined. Loci, genomic regions and linkats associated with seed yield were identified on linkage group (LG) K and with root resistance to SCN e on LG E, G, and D1b+W. A method to identify co-localized genomic regions is presented.

Epigenomic consequences of immortalized plant cell suspension culture

Plant cells grown in culture exhibit genetic and epigenetic instability. Using a combination of chromatin immunoprecipitation and DNA methylation profiling on tiling microarrays, we have mapped the location and abundance of histone and DNA modifications in a continuously proliferating, dedifferentiated cell suspension culture of Arabidopsis. We have found that euchromatin becomes hypermethylated in culture and that a small percentage of the hypermethylated genes become associated with heterochromatic marks. In contrast, the heterochromatin undergoes dramatic and very precise DNA hypomethylation with transcriptional activation of specific transposable elements (TEs) in culture. High throughput sequencing of small interfering RNA (siRNA) revealed that TEs activated in culture have increased levels of 21-nucleotide (nt) siRNA, sometimes at the expense of the 24-nt siRNA class. In contrast, TEs that remain silent, which match the predominant 24-nt siRNA class, do not change significantly in their siRNA profiles. These results implicate RNA interference and chromatin modification in epigenetic restructuring of the genome following the activation of TEs in immortalized cell culture.

ASY1 mediates AtDMC1-dependent interhomolog recombination during meiosis in Arabidopsis

ASY1 is an Arabidopsis protein required for synapsis and crossover formation during meiosis. The chronology of meiotic recombination has been investigated in wild type and an asy1 mutant. We observe a delay between the appearance of chromatin-associated AtSPO11-1 foci and DNA double-strand break (DSB) formation, which occurs contemporaneously with chromosome axis formation and transition of ASY1 from chromatin-associated foci to a linear axis-associated signal. DSBs are formed independently of ASY1 in an AtSPO11-1-dependent manner. They are partially restored in Atspo11-1-3 using cisplatin, but their control appears abnormal. Axis morphogenesis is independent of ASY1, but axis structure may be compromised in asy1. Localization of the strand exchange proteins AtRAD51 and AtDMC1 to the chromatin occurs asynchronously shortly after DSB formation, with AtDMC1 localizing in advance of AtRAD51. In wild-type nuclei, both recombinases form numerous foci that persist for approximately 12 h before gradually decreasing in number. In asy1, initial localization of AtDMC1 is normal, but declines abruptly such that interhomolog recombination is severely compromised. Limited ASY1-independent, DMC1-dependent interhomolog recombination remains, but appears restricted to subtelomeric sequences where the homologs are fortuitously in proximity. Thus, ASY1 plays a key role in coordinating the activity of the RecA homologs to create a bias in favor of interhomolog recombination.

Cytological events in explants of Arabidopsis thaliana during early callogenesis

Leaf explants of diploid (2n = 2x = 10) and autotetraploid (2n = 4x = 20) plants of Arabidopsis thaliana ecotype Columbia were cytologically and cytogenetically analysed to determine the time and the mechanisms of the process of polyploidization. The first polyploid cells were observed after the third day of culture in both genotypes of explants. Polyploid cells were the result of pre-existing mixoploidy in explants of A. thaliana. Other factors such as endoreduplication, endomitosis, abnormal microtubules arrangement and DNA damage may have induced polyploidization during early stages of callogenesis.

Contribution of anaphase B to chromosome separation in higher plant cells estimated by image processing

Anaphase can be categorized into the two subphases of anaphase A and B, but anaphase B has not been clearly described in higher plant cells. In this study, we time-sequentially followed the dynamics of chromosome segregation and spindle elongation in tobacco BY-2 cells using histone-red fluorescent protein (RFP) and green fluorescent protein (GFP)-tubulin, respectively. Construction of kymographs and determination of the positions of chromosomes and spindle edges by image processing revealed that anaphase B contributed to about 40% of the chromosome separation in distance, which is comparable with that in animal cells. These results suggest that higher plant cells potentially possess the process of anaphase B.

OsRAD21-3, an orthologue of yeast RAD21, is required for pollen development in Oryza sativa

In contrast to animals, in which products of meiosis differentiate directly into sperm, flowering plants employ a specific mechanism to give rise to functional sperm cells, the specifics of which remain largely unknown. A previous study revealed that, compared to yeast and vertebrates, which have two proteins (Rad21 and its meiosis-specific variant Rec8) that play a vital role in sister chromatid cohesion and segregation for mitosis and meiosis, respectively, the rice genome encodes four Rad21/Rec8 proteins (OsRad21s). In this paper, phylogenetic and immunostaining analyses reveal that OsRad21-3 is an orthologue of yeast Rad21. OsRAD21-3 transcript and protein accumulated preferentially in flowers, with low levels in vegetative tissues. In flowers, they persisted from the stamen and carpel primordia stages until the mature pollen stage. OsRAD21-3-deficient RNAi lines showed arrested pollen mitosis, aberrant pollen chromosome segregation and aborted pollen grains, which led to disrupted pollen viability. However, male meiosis in these RNAi lines did not appear to be severely disrupted, which suggests that the main involvement of OsRAD21-3 is in post-meiotic pollen development by affecting pollen mitosis. Furthermore, of the four OsRAD21 genes in the rice genome, only OsRAD21-3 was expressed in pollen grains. Given that the mechanism involving generation of sperm cells differs between flowering plants and metozoans, this study shows, in part, why flowering plants of rice and Arabidopsis have four Rad21/Rec8 proteins, as compared with two in yeast and metozoans, and gives some clues to the functional differentiation of Rad21/Rec8 proteins during evolution.

Sex chromosome-linked genes in plants

Recent studies of plant sex chromosome-linked genes have revealed many interesting characteristics, although there are limited reports about heteromorphic sex chromosomes in flowering plants. Sex chromosome-linked genes in angiosperms have been characterized mainly in the dioecious plant Silene latifolia. Although all such genes were isolated from transcripts of male flower buds of S. latifolia, most seem to be housekeeping genes except for the petal- and stamen-specific MADS box gene on the Y chromosome (SlAP3Y) and the male reproductive organ-specific gene on the X chromosome (MROS3X). Recent evolutionary studies have revealed at least three evolutionary strata on the X chromosome that are related to stepwise loss of recombination between the sex chromosomes. Moreover, genetic maps showed conservation of gene organization on the X chromosome in the genus Silene and substantial pericentric inversion between the X and Y chromosomes of S. latifolia during evolution. A comparison between paralogs on the sex chromosomes revealed that introns of the Y-linked genes are longer than those of X-linked paralogs. Although analyses of sex chromosome-linked genes suggest that degeneration of the Y chromosome has occurred, the Y chromosome in flowering plants remains the largest in the male genome, unlike that of mammals. Accumulation of repetitive sequences and the entire chloroplast genome on the Y chromosome appear to have contributed to this large size. However, more detailed studies will be required to help explain the basis for the fact that heteromorphic sex chromosomes in angiosperms are large.

[Bouquet arrest and its consequences for asynaptic meiosis in cereals--haploids and wide hybrids F1]

Arrest of chromosomes at bouquet configuration at zygothene leads to meiotic restitution in some haploids and allohaploids in cereals: univalents are transported preferentially to one spindle pole in bipolar spindle because of their oriented position in the beginning of prometaphase.

Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata

In contrast to the situation described for mammals and Drosophila, chromosome territory (CT) arrangement and somatic homologous pairing in interphase nuclei of Arabidopsis thaliana (n = 5) are predominantly random except for a more frequent association of the chromosomes bearing a homologous nucleolus organizer region. To find out whether this chromosome arrangement is also characteristic for other species of the genus Arabidopsis, we investigated Arabidopsis lyrata ssp. lyrata (n = 8), one of the closest relatives of A. thaliana. First, we determined the size of each chromosome and chromosome arm, the sequence type of centromeric repeats and their distribution between individual centromeres and the position of the 5S/45S rDNA arrays in A. lyrata. Then we demonstrated that CT arrangement, homologous pairing and sister chromatid alignment of distinct euchromatic and/or heterochromatic regions within A. lyrata interphase nuclei are similar to that in A. thaliana nuclei. Thus, the arrangement of interphase chromosomes appears to be conserved between both taxa that diverged about 5 million years ago. Since the chromosomes of A. lyrata resemble those of the presumed ancestral karyotype, a similar arrangement of interphase chromosomes is also to be expected for other closely related diploid species of the Brassicaceae family.

Aurora kinase is required for chromosome segregation in tobacco BY-2 cells

Post-translational modifications of core histone tails play crucial roles in chromatin structure and function. Although phosphorylation of Ser10 and Ser28 (H3S10ph and H3S28ph) of histone H3 is ubiquitous among eukaryotes, the phosphorylation mechanism during the cell cycle remains unclear. In the present study, H3S10ph and H3S28ph in tobacco BY-2 cells were observed in the pericentromeric regions during mitosis. Moreover, the Aurora kinase inhibitor Hesperadin inhibited the kinase activity of Arabidopsis thaliana Aurora kinase 3 (AtAUR3) in phosphorylating both Ser10 and Ser28 of histone H3 in vitro. Consistently, Hesperadin inhibited both H3S10ph and H3S28ph during mitosis in BY-2 cells. These results indicate that plant Aurora kinases phosphorylate not only Ser10, but also Ser28 of histone H3 in vivo. Hesperadin treatment increased the ratio of metaphase cells, while the ratio of anaphase/telophase cells decreased, although the mitotic index was not affected in Hesperadin-treated cells. These results suggest that Hesperadin induces delayed transition from metaphase to anaphase, and early exit from mitosis after chromosome segregation. In addition, micronuclei were observed frequently and lagging chromosomes, caused by the delay and failure of sister chromatid separation, were observed at anaphase and telophase in Hesperadin-treated BY-2 cells. The data obtained here suggest that plant Aurora kinases and H3S10ph/H3S28ph may have a role in chromosome segregation and metaphase/anaphase transition.

The relationship between induction of embryogenesis and chromosome doubling in microspore cultures

The objective of this paper is to review the relationship between induction of microspore embryogenesis and chromosome doubling. It has been augmented with relative data on chromosome doubling by nuclear fusion. Some of the treatments used for induction of embryogenesis may also lead to doubling of the chromosome number, either through nuclear fusion or endomitosis. High frequencies of spontaneous chromosome doubling in cereal species appear to be induced by treatments that block cell wall formation during the first cell divisions, resulting in coenocytic cells in which the nuclei are able to fuse. The use of mannitol as a pretreatment for induction of embryogenesis in barley, wheat, and maize microspore cultures provides examples of nuclear fusion. The use of antimicrotubule agents for embryo induction via treatments during the first few hours of microspore culture has also resulted in high frequencies of chromosome doubling. Factors such as the doubling agent concentration, temperature during treatment, and duration of treatment may be critical for individual species. Actin filament as well as microtubule assembly studies related to new cell wall formation provide further evidence at the molecular level for the relationship between microspore embryogenesis and chromosome doubling.

Genetic analysis and gene mapping of purple stigma in rice

A new double-haploid (rdh) rice plant with purple stigma and red seeds was discovered by tissue culture. Genetic analysis suggested that the trait of rdh purple stigma was controlled by a pair of dominant gene. Polymorphic analysis of microsatellite markers demonstrated that the purple stigma gene of rdh was located on rice chromosome 6 at 4.2 cM, 0.35 cM and 0.53 cM from microsatellite markers RM276, RM253 and RM111, respectively. It was believed that the purple stigma gene of rdh was the first mapped purple stigma gene on rice chromosome 6. This purple stigma gene was designated tentatively as Ps-4.

Direct comparison between genomic constitution and flavonoid contents in Allium multiple alien addition lines reveals chromosomal locations of genes related to biosynthesis from dihydrokaempferol to quercetin glucosides in scaly leaf of shallot (Allium cepa L.)

The extrachromosome 5A of shallot (Allium cepa L., genomes AA) has an important role in flavonoid biosynthesis in the scaly leaf of Allium fistulosum-shallot monosomic addition lines (FF+nA). This study deals with the production and biochemical characterisation of A. fistulosum-shallot multiple alien addition lines carrying at least 5A to determine the chromosomal locations of genes for quercetin formation. The multiple alien additions were selected from the crossing between allotriploid FFA (female symbol) and A. fistulosum (male symbol). The 113 plants obtained from this cross were analysed by a chromosome 5A-specific PGI isozyme marker of shallot. Thirty plants were preliminarily selected for an alien addition carrying 5A. The chromosome numbers of the 30 plants varied from 18 to 23. The other extrachromosomes in 19 plants were completely identified by using seven other chromosome markers of shallot. High-performance liquid chromatography analyses of the 19 multiple additions were conducted to identify the flavonoid compounds produced in the scaly leaves. Direct comparisons between the chromosomal constitution and the flavonoid contents of the multiple alien additions revealed that a flavonoid 3'-hydroxylase (F3'H) gene for the synthesis of quercetin from kaempferol was located on 7A and that an anonymous gene involved in the glucosidation of quercetin was on 3A or 4A. As a result of supplemental SCAR analyses by using genomic DNAs from two complete sets of A. fistulosum-shallot monosomic additions, we have assigned F3'H to 7A and flavonol synthase to 4A.

Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains

Biochemical and cytogenetic experiments have led to the hypothesis that eukaryotic chromatin is organized into a series of distinct domains that are functionally independent. Two expectations of this hypothesis are: (i) adjacent genes are more frequently co-expressed than is expected by chance; and (ii) co-expressed neighbouring genes are often functionally related. Here we report that over 10% of Arabidopsis thaliana genes are within large, co-expressed chromosomal regions. Two per cent (497/22,520) of genes are highly co-expressed (r > 0.7), about five times the number expected by chance. These genes fall into 226 groups distributed across the genome, and each group typically contains two to three genes. Among the highly co-expressed groups, 40% (91/226) have genes with high amino acid sequence similarity. Nonetheless, duplicate genes alone do not explain the observed levels of co-expression. Co-expressed, non-homologous genes are transcribed in parallel, share functions, and lie close together more frequently than expected. Our results show that the A. thaliana genome contains domains of gene expression. Small domains have highly co-expressed genes that often share functional and sequence similarity and are probably co-regulated by nearby regulatory sequences. Genes within large, significantly correlated groups are typically co-regulated at a low level, suggesting the presence of large chromosomal domains.

Endoplasmic reticulum targeted GFP reveals ER organization in tobacco NT-1 cells during cell division

The endoplasmic reticulum (ER) of plant cells undergoes a drastic reorganization during cell division. In tobacco NT-1 cells that stably express a GFP construct targeted to the ER, we have mapped the reorganization of ER that occurs during mitosis and cytokinesis with confocal laser scanning microscopy. During division, the ER and nuclear envelope do not vesiculate. Instead, tubules of ER accumulate around the chromosomes after the nuclear envelope breaks down, with these tubules aligning parallel to the microtubules of the mitotic spindle. In cytokinesis, the phragmoplast is particularly rich in ER, and the transnuclear channels and invaginations present in many interphase cells appear to develop from ER tubules trapped in the developing phragmoplast. Drug studies, using oryzalin and latrunculin to disrupt the microtubules and actin microfilaments, respectively, demonstrate that during division, the arrangement of ER is controlled by microtubules and not by actin, which is the reverse of the situation in interphase cells.

Mitotic Microtubule Development and Histone H3 Phosphorylation in the Holocentric Chromosomes of Rhynchospora Tenuis (Cyperaceae)

In the present work we report the phosphorylation pattern of histone H3 and the development of microtubular structures using immunostaining techniques, in mitosis of Rhynchospora tenuis (2n = 4), a Cyperaceae with holocentric chromosomes. The main features of the holocentric chromosomes of R. tenuis coincide with those of other species namely: the absence of primary constriction in prometaphase and metaphase, and the parallel separation of sister chromatids at anaphase. Additionaly, we observed a highly conserved chromosome positioning at anaphase and early telophase sister nuclei. Four microtubule arrangements were distinguished during the root tip cell cycle. Interphase cells showed a cortical microtubule arrangement that progressively forms the characteristic pre-prophase band. At prometaphase the microtubules were homogeneously distributed around the nuclear envelope. Metaphase cells displayed the spindle arrangement with kinetochore microtubules attached throughout the entire chromosome extension. At anaphase kinetochoric microtubules become progressively shorter, whereas bundles of interzonal microtubules became increasingly broader and denser. At late telophase the microtubules were observed equatorially extended beyond the sister nuclei and reaching the cell wall. Immunolabelling with an antibody against phosphorylated histone H3 revealed the four chromosomes labelled throughout their entire extension at metaphase and anaphase. Apparently, the holocentric chromosomes of R. tenuis function as an extended centromeric region both in terms of cohesion and H3 phosphorylation.

Three-dimensional modelling of wheat endosperm development

We have developed methods, based on confocal microscopy and three-dimensional (3D) modelling, for the analysis of complex tissues and individual nuclei. These methods were used to study the development of early wheat (Triticum aestivum) endosperm as a whole and of endosperm nuclei undergoing polyploidization. Fixed sections of immature caryopses were either stained with SYTOX Green or used for fluorescence in situ hybridization (FISH) to visualize centromeres, telomeres and a rye chromosome arm substitution. Each section was imaged as a confocal image stack. By using Amira 3.0 for computer image processing, rendered models were produced of the whole endosperm and of individual nuclei. We followed endosperm development up to the formation of a complete syncytium, which develops via a dorsal and a ventral plate of nuclei in the central cell. Modelling of nuclei showed that wheat chromosomes are not anchored to the nuclear membrane and become more randomly positioned in endoreduplicated nuclei. This analysis produced a precise description of the positioning of nuclei throughout the developing endosperm and of chromosomal domains in single nuclei.

Control of conformation changes associated with homologue recognition during meiosis

During early meiosis, chromosomes pair via their telomeres and centromeres. This pairing induces a conformational change which propagates from these regions along each chromosome, making the chromatin of the partners accessible for intimate pairing. In the present study, we show by exploiting wheat-rye hybrids that the signal is initiated in both the presence and absence of either the Ph1 or Ph2 locus. However, the chromatin change only continues to propagate through rye telomeric heterochromatin when Ph1 is absent. This failure to propagate the chromatin change through the rye heterochromatin in the absence of Ph2 correlates with a subsequent lack of wheat-rye chromosome association at metaphase I.

Characterization ofArabidopsis thalianaSMC1 and SMC3: evidence that AtSMC3 may function beyond chromosome cohesion

Structural maintenance of chromosome (SMC) proteins are conserved in most prokaryotes and all eukaryotes examined. SMC proteins participate in many different aspects of chromosome folding and dynamics. They play essential roles in complexes that are responsible for sister chromatid cohesion, chromosome condensation and DNA repair. As part of studies to better understand SMC proteins and sister chromatid cohesion in plants we have characterized Arabidopsis SMC1 and SMC3. Although transcripts for AtSMC1 and AtSMC3 are present throughout the plant, transcript levels for the two genes vary between different tissues. Cell fractionation and immunolocalization results showed that AtSMC3 was present in the nucleus and cytoplasm. In the nucleus, it is primarily associated with the nuclear matrix during interphase and with chromatin from prophase through anaphase in both somatic and meiotic cells. During mitosis and meiosis the protein also co-localized with the spindle from metaphase to telophase. The distribution of AtSMC3 in syn1 mutant plants indicated that SYN1 is required for the proper binding of AtSMC3 to meiotic chromosomes, but not the spindle. Data presented here represent the first detailed cytological study of a plant SMC protein and suggest that SMC3 may have multiple functions in plants.

Production and characterization of alien chromosome additions in shallot (Allium cepa L. Aggregatum group) carrying extra chromosome(s) of Japanese bunching onion (A. fistulosum L.)

First and second backcrosses of amphidiploid hybrids (2n = 4x = 32, genomes AAFF) between shallot (Allium cepa Aggregatum group) and A. fistulosum were conducted to produce A. cepa - A. fistulosum alien addition lines. When shallot (A. cepa Aggregatum group) was used as a pollinator, the amphidiploids and allotriploids set germinable BC(1) and BC(2) seeds, respectively. The 237 BC(1) plants mainly consisted of 170 allotriploids (2n = 3x = 24, AAF) and 42 hypo-allotriploids possessing 23 chromosomes, i.e., single-alien deletions (2n = 3x-1 = 23, AAF-nF). The single-alien deletions in the BC(1) progeny showed dwarfing characteristics and were discriminated from the allotriploids (2n = 24) and hyper-allotriploids (2n = 25) by means of flow cytometric analysis. The chromosome numbers of 46 BC(2) seedlings varied from 16 to 24. Eight monosomic additions (2n = 2x+1 = 17, AA+nF) and 20 single-alien deletions were found in these BC(2) seedlings. Consequently, six kinds of A. cepa - A. fistulosum alien chromosome additions possessing different chromosome numbers (2n = 17, 18, 20, 21, 22, 23) were recognized in the BC(1) and BC(2) populations. A total of 79 aneuploids, including 62 single-alien deletions, were analyzed by a chromosome 6F-specific isozyme marker (Got-2) in order to recognize its existence in their chromosome complements. This analysis revealed that two out of 62 single-alien deletions did not possess 6F. One (AAF-6F) out of the possible eight single-alien deletions could be identified at first. The present study is a first step toward the development of a useful tool, such as a complete set of eight different single-alien deletions, for the rapid chromosomal assignment of genes and genetic markers in A. fistulosum.

Histone deacetylation is required for progression through mitosis in tobacco cells

Post-translational modifications of core histone proteins play a key role in chromatin structure and function. Here, we study histone post-translational modifications during reentry of protoplasts derived from tobacco mesophyll cells into the cell cycle and evaluate their significance for progression through mitosis. Methylation of histone H3 at lysine residues 4 and 9 persisted in chromosomes during all phases of the cell cycle. However, acetylation of H4 and H3 was dramatically reduced during mitosis in a stage-specific manner; while deacetylation of histone H4 commenced at prophase and persisted up to telophase, histone H3 remained acetylated up to metaphase but was deacetylated at anaphase and telophase. Phosphorylation of histone H3 at serine 10 was initiated at prophase, concomitantly with deacetylation of histone H4, and persisted up to telophase. Preventing histone deacetylation by the histone deacetylase inhibitor trichostatin A (TSA) led to accumulation of protoplasts at metaphase-anaphase, and reduced S10 phosphorylation during anaphase and telophase; in cultured tobacco cells, TSA significantly reduced the frequency of mitotic figures. Our results indicate that deacetylation of histone H4 and H3 in tobacco protoplasts occurs during mitosis in a phase-specific manner, and is important for progression through mitosis.

Meiotic pairing in the hybrid (Zea diploperennis x Zea perennis) x Zea mays and its reciprocal

Genomic formulae, fertility, chromosome pairing, and the cryptic intergenomic pairing (induced by using diluted colchicine solution) were analysed in the tri-hybrid (MDP), obtained by crossing DP40 (2n=40, which was inferred in previous studies to have originated from the fusion of an unreduced gamete of Zea diploperennis with a normal gamete of Z. perennis) with the maize inbred line Zm40 (2n=40). MDP (2n=40) showed a higher fertility (90% of the seeds are viable) than Zm40 (60%) and DP40 (80%). A regular migration of 20 chromosomes to each pole occurred in 92% of the cells in anaphase I, while bridges were observed in the other 8% of the cells. When Zm40 was used as female of the crossing (Zm40 x DP40), ears were similar to corn. Conversely, ears resembled those of the wild species when cytoplasm was donoured by Zd. Then, it can be stated the existence of cytoplasmic influence on MDP ear type. MDP had almost no I or III, with an average of 0.04I + 10.90II + 0.01III + 4.50IV. The most frequent meiotic configuration was 10II + 5IV (43.93% of the cells). On average, 33.81 chiasmata/cell were observed (17.34, 0.05 and 16.42 average numbers of chiasmata/cell in bivalents, trivalents and tetravalents, respectively). It can be inferred that the 5IV were the product of homoeologous chromosome pairing of A genomes from the three species. On the other hand, the 10II configuration suggests separate pairing of the 5 homologous B chromosomes from maize and the 5 homoeologous B chromosomes from Zp and Zd.

The Arabidopsis MutS homolog AtMSH4 functions at an early step in recombination: evidence for two classes of recombination in Arabidopsis

MSH4, a meiosis-specific member of the MutS-homolog family of genes, is required for normal levels of recombination and fertility in budding yeast, mouse, and Caenorhabditis elegans. In this paper, we report the identification and characterization of the Arabidopsis homolog of MSH4 (AtMSH4). We demonstrate that AtMSH4 expression can only be detected in floral tissues, consistent with a role in reproduction. Immunofluorescence studies indicate that its expression is limited to early meiotic prophase I, preceding the synapsis of homologous chromosomes. A T-DNA insertional mutant (Atmsh4) exhibited normal vegetative growth but a severe reduction in fertility, consistent with a meiotic defect; this was confirmed by cytological analysis of meiosis. RNAi-induced down-regulation of the MSH4 gene resulted in a similar fertility and meiotic phenotype. We demonstrate that prophase I chromosome synapsis is delayed and may be incomplete in Atmsh4, and metaphase I chiasma frequency is greatly reduced to approximately 15% of wild type, leading to univalence and nondisjunction. We show that these residual chiasmata are randomly distributed among cells and chromosomes. These features of chiasma frequency and distribution in Atmsh4 show close parallels to MSH4-independent crossovers in budding yeast that have been proposed to originate by a separate pathway. Furthermore, the characteristics of the MSH4-independent chiasmata in the Atmsh4 mutant closely parallel those of second-pathway crossovers that have been postulated from Arabidopsis crossover analysis and mathematical modeling. Taken together, this evidence strongly indicates that Arabidopsis possesses two crossover pathways.