B-chromosomes in inbred lines of rye (Secale cereale L.): I. Vigour and fertility

Identification of rye B chromosome-associated peptides by mass spectrometry

B chromosomes (Bs) are supernumerary dispensable components of the standard genome (A chromosomes, As) that have been found in many eukaryotes. So far, it is unkown whether the B-derived transcripts translate to proteins or if the host proteome is changed due to the presence of Bs. Comparative mass spectrometry was performed using the protein samples isolated from shoots of rye plants with and without Bs. We aimed to identify B-associated peptides and analyzed the effects of Bs on the total proteome. Our comparative proteome analysis demonstrates that the presence of rye Bs affects the total proteome including different biological function processes. We found 319 of 16 776 quantified features in at least three out of five +B plants but not in 0B plants; 31 of 319 features were identified as B-associated peptide features. According to our data mining, one B-specific protein fragment showed similarity to a glycine-rich RNA binding protein which differed from its A-paralogue by two amino acid insertions. Our result represents a milestone in B chromosome research, because this is the first report to demonstrate the existence of Bs changing the proteome of the host.

Nondisjunction and unequal spindle organization accompany the drive of Aegilops speltoides B chromosomes

B chromosomes (Bs) are supernumerary chromosomes, which are often preferentially inherited. When transmission rates of chromosomes are higher than 0.5, not obeying the Mendelian law of equal segregation, the resulting transmission advantage is collectively referred to as 'chromosome drive'. Here we analysed the drive mechanism of Aegilops speltoides Bs. The repeat AesTR-183 of A. speltoides Bs, which also can be detected on the Bs of Aegilops mutica and rye, was used to track Bs during pollen development. Nondisjunction of CENH3-positive, tubulin interacting B sister chromatids and an asymmetric spindle during first pollen grain mitosis are key for the accumulation process. A quantitative flow cytometric approach revealed that, independent of the number of Bs present in the mother plant, Bs accumulate in the generative nuclei to > 93%. Nine out of 11 tested (peri)centromeric repeats were shared by A and B chromosomes. Our findings provide new insights into the process of chromosome drive. Quantitative flow cytometry is a useful and reliable method to study the drive frequency of Bs. Nondisjunction and unequal spindle organization accompany during first pollen mitosis the drive of A. speltoides Bs. The prerequisites for the drive process seems to be common in Poaceae.

Transmission and Drive Involving Parasitic B Chromosomes

B chromosomes (Bs) are enigmatic additional elements in the genomes of thousands of species of plants, animals, and fungi. How do these non-essential, harmful, and parasitic chromosomes maintain their presence in their hosts, making demands on all the essential functions of their host genomes? The answer seems to be that they have mechanisms of drive which enable them to enhance their transmission rates by various processes of non-mendelian inheritance. It is also becoming increasingly clear that the host genomes are developing their own mechanisms to resist the impact of the harmful effects of the Bs.

Long-term monitoring of B-chromosome invasion and neutralization in a population of Prospero autumnale (Asparagaceae)

B chromosomes have been reported in about 15% of eukaryotes, but long-term dynamics of B chromosomes in a single natural population has rarely been analyzed. Prospero autumnale plants collected in 1981 and 1983 at Cuesta de La Palma population had shown the presence of B chromosomes. We analyze here seven additional samples collected between 1987 and 2015, and show that B frequency increased significantly during the 1980s and showed minor fluctuations between 2005 and 2015. A mother-offspring analysis of B chromosome transmission, at population level, showed significant drive on the male side (k_B  = 0.65) and significant drag on the female side (k_B  = 0.33), with average B transmission rate being very close to the Mendelian rate (0.5). No significant effects of B chromosomes were observed on a number of vigor and fertility-related traits. Within a parasite/host framework, these results suggest that B chromosomes' drive on the male side is the main pathway for B chromosome invasion, whereas B chromosome drag on the female side might be the main manifestation of host genome resistance in this species. Prospero autumnale thus illuminates a novel evolutionary pathway for B chromosome neutralization by means of a decrease in B transmission through the nondriving sex.

B chromosomes are associated with redistribution of genetic recombination towards lower recombination chromosomal regions in perennial ryegrass

Supernumerary 'B' chromosomes are non-essential components of the genome present in a range of plant and animal species-including many grasses. Within diploid and polyploid ryegrass and fescue species, including the forage grass perennial ryegrass (Lolium perenne L.), the presence of B chromosomes has been reported as influencing both chromosome pairing and chiasma frequencies. In this study, the effects of the presence/absence of B chromosomes on genetic recombination has been investigated through generating DArT (Diversity Arrays Technology) marker genetic maps for six perennial ryegrass diploid populations, the pollen parents of which contained either two B or zero B chromosomes. Through genetic and cytological analyses of these progeny and their parents, we have identified that, while overall cytological estimates of chiasma frequencies were significantly lower in pollen mother cells with two B chromosomes as compared with zero B chromosomes, the recombination frequencies within some marker intervals were actually increased, particularly for marker intervals in lower recombination regions of chromosomes, namely pericentromeric regions. Thus, in perennial ryegrass, the presence of two B chromosomes redistributed patterns of meiotic recombination in pollen mother cells in ways which could increase the range of allelic variation available to plant breeders.

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.

Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog

B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.

Similar Sister Chromatid Arrangement in Mono- and Holocentric Plant Chromosomes

Due to the X-shape formation at somatic metaphase, the arrangement of the sister chromatids is obvious in monocentric chromosomes. In contrast, the sister chromatids of holocentric chromosomes cannot be distinguished even at mitotic metaphase. To clarify their organization, we differentially labelled the sister chromatids of holocentric Luzula and monocentric rye chromosomes by incorporating the base analogue EdU during replication. Using super-resolution structured illumination microscopy (SIM) and 3D rendering, we found that holocentric sister chromatids attach to each other at their contact surfaces similar to those of monocentrics in prometaphase. We found that sister chromatid exchanges (SCEs) are distributed homogeneously along the whole holocentric chromosomes of Luzula, and that their occurrence is increased compared to monocentric rye chromosomes. The SCE frequency of supernumerary B chromosomes, present additionally to the essential A chromosome complement of rye, does not differ from that of A chromosomes. Based on these results, models of the sister chromatid arrangement in mono- and holocentric plant chromosomes are presented.

Rye B chromosomes influence the dynamics of histone H3 methylation during microgametogenesis

We have studied the trimethylation dynamics of lysines 4 and 27 of histone H3 in rye with and without B chromosomes (Bs) in root tip mitosis, meiosis, and pollen grain mitosis by immunostaining. In root meristems, H3K4me3 immunolabeling was homogeneous along the chromosome arms of the normal complement (As), with the exception of the pericentromeric and subtelomeric regions which were unlabeled. On the contrary, a signal was observed on the long arm of the B chromosome, in the region where most of the B-specific repeats are located. H3K27me3 immunosignals were observed on the subtelomeric heterochromatic region of the As and the Bs and some interstitial bands of the As. Thus, the terminal region of the Bs showed both signals, whereas the subtelomeric region of the As showed H3K27me3 immunosignals only. During meiosis and first pollen grain mitosis, the immunosignals were observed distributed as in the root tip mitosis in plants with or without Bs. However, we observed remarkable changes in the immunolabeling patterns during the second pollen grain mitosis between 0B and +B plants. In 0B plants, H3K4me3 immunosignals were similarly distributed in the vegetative and generative nuclei. In B-carrying plants, the vegetative nucleus showed a lighter signal than the generative one. In 0B plants, all nuclei of the microgametophyte showed H3K27me3 immunosignals. In B-carrying plants, the generative nucleus and, correspondingly, the second metaphase, anaphase, and sperm nuclei did not show any signal. When the Bs were lost as micronuclei, they did not show any H3K4me3 or H3K27me3 signal. Most remarkably, Bs are able to change the pattern of H3 methylation on K4 and K27 during the second pollen mitosis, resulting in differently labeled sperm nuclei in 0 and +B plants.

High-copy sequences reveal distinct evolution of the rye B chromosome

B chromosomes (Bs) are supernumerary chromosomes that vary in number among individuals of the same species. Because of their dispensable nature, their non-Mendelian inheritance and their origin from A chromosomes (As), one might assume that Bs followed a different evolutionary pathway from As, this being reflected in differences in their high-copy DNA constitution. We provide detailed insight into the composition and distribution of rye (Secale cereale) B-located high-copy sequences. A- and B-specific high-copy sequences were identified in silico. Mobile elements and satellite sequences were verified by fluorescence in situ hybridization (FISH). Replication was analyzed via EdU incorporation. Although most repeats are similarly distributed along As and Bs, several transposons are either amplified or depleted on the B. An accumulation of B-enriched satellites was found mostly in the nondisjunction control region of the B, which is transcriptionally active and late-replicating. All B-enriched sequences are not unique to the B but are also present in other Secale species, suggesting the origin of the B from As of the same genus. Our findings highlight the differences between As and Bs. Although Bs originated from As, they have since taken a separate evolutionary pathway.

Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences

Supernumerary B chromosomes are optional additions to the basic set of A chromosomes, and occur in all eukaryotic groups. They differ from the basic complement in morphology, pairing behavior, and inheritance and are not required for normal growth and development. The current view is that B chromosomes are parasitic elements comparable to selfish DNA, like transposons. In contrast to transposons, they are autonomously inherited independent of the host genome and have their own mechanisms of mitotic or meiotic drive. Although B chromosomes were first described a century ago, little is known about their origin and molecular makeup. The widely accepted view is that they are derived from fragments of A chromosomes and/or generated in response to interspecific hybridization. Through next-generation sequencing of sorted A and B chromosomes, we show that B chromosomes of rye are rich in gene-derived sequences, allowing us to trace their origin to fragments of A chromosomes, with the largest parts corresponding to rye chromosomes 3R and 7R. Compared with A chromosomes, B chromosomes were also found to accumulate large amounts of specific repeats and insertions of organellar DNA. The origin of rye B chromosomes occurred an estimated ∼1.1-1.3 Mya, overlapping in time with the onset of the genus Secale (1.7 Mya). We propose a comprehensive model of B chromosome evolution, including its origin by recombination of several A chromosomes followed by capturing of additional A-derived and organellar sequences and amplification of B-specific repeats.

Cytomolecular characterization of de novo formed rye B chromosome variants

BACKGROUND

B chromosomes (Bs) are dispensable elements which occur in many species including rye (Secale cereale). We determined the organization of B variants to obtain insights into the origin of B polymorphisms in rye.

RESULTS

The observed B variants were classified according to their morphology and in situ hybridization patterns with the B-specific repeats D1100 and CL11 into (I) long arm iso B, (II) D1100-deficient B and (III) small metacentric B variants. Long arm iso Bs are likely products of a meiotic centromere misdivision and subsequent duplication of the long arm, whereas small B variants are probably generated by chromosome breakage. Some deficient Bs experienced extensive amplification of CL11 repeats.

CONCLUSIONS

Both the pericentromere and the nondisjunction control region seem to be involved in the generation of rye B chromosome variants. However, due to the loss of the B-specific nondisjuction control region most of the variants generated are not capable to accumulate in a population.

CENH3 distribution and differential chromatin modifications during pollen development in rye (Secale cereale L.)

Microgametogenesis in angiosperms results in two structurally and functionally different cells, one generative cell, which subsequently forms the sperm cells, and the vegetative cell. We analysed the chromatin properties of both types of nuclei after first and second pollen mitosis in rye (Secale cereale). The condensed chromatin of generative nuclei is earmarked by an enhanced level of histone H3K4/K9 dimethylation and H3K9 acetylation. The less condensed vegetative nuclei are RNA polymerase II positive. Trimethylation of H3K27 is not involved in transcriptional downregulation of genes located in generative nuclei as H3K27me3 was exclusively detected in the vegetative nuclei. The global level of DNA methylation does not differ between both types of pollen nuclei. In rye, unlike in Arabidopsis thaliana (Ingouff et al. Curr Biol 17:1032-1037 2007; Schoft et al. EMBO Rep 10:1015-1021 2009), centromeric histone H3 is not excluded from the chromatin of the vegetative nucleus and the condensation degree of centromeric and subtelomeric regions did not differ between the generative and vegetative nuclei. Differences between rye and A. thaliana data suggest that the chromatin organization in mature nuclei of pollen grains is not universal across angiosperms.

Rye B chromosomes are weakly transcribed and might alter the transcriptional activity of A chromosome sequences

B chromosomes (Bs) are dispensable components of the genomes of numerous species. To test whether the transcriptome of a host is influenced by Bs, we looked for differences in expression in response to additional Bs. Comparative complementary DNA amplified fragment length polymorphism experiments resulted in the identification of 16 putative B-chromosome-associated transcripts. This comprises 0.7% of the total transcript number and indicates a low activity of Bs. We also provide evidence that B chromosome influences in trans the transcription of A chromosome sequences. The B-specific transcribed sequences B1334, B8149, and B2465 belong to high-copy families with similarity to mobile elements. For all analyzed B-chromosome-derived transcripts, similar A chromosome-encoded sequences were found which supports an A-derived origin of rye B chromosomes.

Rye Bs disclose ancestral sequences in cereal genomes with a potential role in gametophyte chromatid segregation

Two sequence families, E3900 and D1100, are amplified on the subtelomeric domain of the long arm of rye B chromosomes, the region that controls its drive mechanism. In this work, polymerase chain reaction (PCR) with a number of primers spanning E3900 shows that the organization and nucleotide sequence of E3900-related portions are present and highly conserved on rye A chromosomes as well as in other cereals. Quantitative Real-Time PCR estimates two E3900 sequences to be represented in 100-150 copies on Bs and at least as single copies on As. A novel E3900-related sequence, with a deletion that results in a frameshift and subsequently an open reading frame with putative DNA binding motifs, is identified. Expression analysis of E3900 indicates identical transcription levels in leaves from plants with and without Bs, showing that the expression of these sequences must be silenced on Bs and tightly regulated on As in leaves. In contrast, E3900 transcription is upregulated during meiosis exclusively in plants with Bs, maintaining a high level of transcription in the gametophyte. Interestingly, Bs not only influence their own chromatid segregation but also that of the regular chromosome complement of both rye and wheat. There is a drastic increase in frequency of disrupted metaphase and anaphase cells in the first mitosis of pollen grains carrying Bs, which appears to be due to anomalous adherences between sister chromatids. Taken together, this work provides insight into how E3900 sequences are potentially associated with important evolutionary mechanisms involved in basic cellular processes.

Chromosomes with a life of their own

B chromosomes (Bs) can be described as 'passengers in the genome', a term that has been used for the repetitive DNA which comprises the bulk of the genome in large genome species, except that Bs have a life of their own as independent chromosomes. As with retrotransposons they can accumulate in number, but in this case by various processes of mitotic or meiotic drive, based on their own autonomous ways of using spindles, especially in the gametophyte phase of the life cycle of flowering plants. This selfish property of drive ensures their survival and spread in natural populations, even against a gradient of harmful effects on the host plant phenotype. Bs are inhabitants of the nucleus and they are subject to control by 'genes' in the A chromosome (As) complement. This interaction with the As, together with the balance between drive and harmful effects makes a dynamic system in the life of a B chromosome, notwithstanding the fact that we are only now beginning to unravel the story in a few favoured species. In this review we concentrate mainly on recent developments in the Bs of rye and maize, two of the species currently receiving most attention. We focus on their population dynamics and on the molecular basis of their structural organisation and mechanisms of drive, as well as on their mode of origin and potential applications in plant biotechnology.

B chromosomes in plants

This review of supernumerary B chromosome systems in flowering plants deals mainly with work published in the last 15 yr, hut also includes older material which has not hitherto been presented systematically. The term B chromosome (B) is defined, and there is an introductory overview dealing with general characteristics and the significance of Bs as a widespread chromosome polymorphism. Detailed sections are then presented covering the occurrence of Bs in different taxa, their structure and molecular organization, their irregular modes of inheritance, their phenotypic effects, population dynamics and origin. Particular attention is paid to the research growth points in molecular analysis of the structure and genome organization of Bs, and to transmission genotypes in the context of their adaptive versus their selfish properties. Where appropriate, reference is also made to likely future lines of research, and also to the usefulness of B chromosomes in genetic analysis and as model systems to study general phenomena of genome organization and evolution, nuclear physiology and architecture, chromosome polymorphism and selfish DNA. CONTENTS Summary 411 I. Introduction 411 II. Occurrence 411 III. Structure and organization 415 IV. Inheritance 422 V. Phenotypic effects 426 VI. Populations 429 VII. Applications 430 VIII. Origin 430 Acknowiedgements 430 References 431.