Neocentric activity of rye 5RL chromosome in wheat

Analytical Methodology of Meiosis in Autopolyploid and Allopolyploid Plants

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

Towards a whole-genome sequence for rye (Secale cereale L.)

We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.

Characterization of wheat-Secale africanum chromosome 5R(a) derivatives carrying Secale specific genes for grain hardness

New wheat- Secale africanum chromosome 5R (a) substitution and translocation lines were developed and identified by fluorescence in situ hybridization and molecular markers, and chromosome 5R (a) specific genes responsible for grain hardness were isolated. The wild species, Secale africanum Stapf. (genome R(a)R(a)), serves as a valuable germplasm resource for increasing the diversity of cultivated rye (S. cereale L., genome RR) and providing novel genes for wheat improvement. In the current study, fluorescence in situ hybridization (FISH) and molecular markers were applied to characterize new wheat-S. africanum chromosome 5R(a) derivatives. Labeled rye genomic DNA (GISH) and the Oligo-probes pSc119.2 and pTa535 (FISH) were used to study a wheat-S. africanum amphiploid and a disomic 5R(a) (5D) substitution, and to identify a T5DL.5R(a)S translocation line and 5R(a)S and 5R(a)L isotelosome lines. Twenty-one molecular markers were mapped to chromosome 5R(a) arms which will facilitate future rapid identification of 5R(a) introgressions in wheat backgrounds. Comparative analysis of the molecular markers mapped on 5R(a) with homoeologous regions in wheat confirmed a deletion on the chromosome T5DL.5R(a)S, which suggests that the wheat-S. africanum Robertsonian translocation involving homologous group 5 may not be fully compensating. Complete coding sequences at the paralogous puroindoline-a (Pina) and grain softness protein gene (Gsp-1) loci from S. africanum were cloned and localized onto the short arm of chromosome 5R(a). The S. africanum chromosome 5R(a) substitution and translocation lines showed a reduction in the hardness index, which may be associated with the S. africanum- specific Pina and Gsp-1 gene sequences. The present study reports the production of novel wheat-S. africanum chromosome 5R(a) stripe rust resistant derivatives and new rye-specific molecular markers, which may find application in future use of wild Secale genome resources for grain quality studies and disease resistance breeding.

Franklin FC, Heckmann S. Atypical centromeres in plants-what they can tell us

The centromere, visible as the primary constriction of condensed metaphase chromosomes, is a defined chromosomal locus essential for genome stability. It mediates transient assembly of a multi-protein complex, the kinetochore, which enables interaction with spindle fibers and thus faithful segregation of the genetic information during nuclear divisions. Centromeric DNA varies in extent and sequence composition among organisms, but a common feature of almost all active eukaryotic centromeres is the presence of the centromeric histone H3 variant cenH3 (a.k.a. CENP-A). These typical centromere features apply to most studied species. However, a number of species display "atypical" centromeres, such as holocentromeres (centromere extension along almost the entire chromatid length) or neocentromeres (ectopic centromere activity). In this review, we provide an overview of different atypical centromere types found in plants including holocentromeres, de novo formed centromeres and terminal neocentromeres as well as di-, tri- and metapolycentromeres (more than one centromere per chromosomes). We discuss their specific and common features and compare them to centromere types found in other eukaryotic species. We also highlight new insights into centromere biology gained in plants with atypical centromeres such as distinct mechanisms to define a holocentromere, specific adaptations in species with holocentromeres during meiosis or various scenarios leading to neocentromere formation.

Painting the rye genome with genome-specific sequences

We used rye-specific repetitive DNA sequences in fluorescence in situ hybridization (FISH) to paint the rye genome and to identify rye DNA in a wheat background. A 592 bp fragment from the rye-specific dispersed repetitive family R173 (named UCM600) was cloned and used as a FISH probe. UCM600 is dispersed over the seven rye chromosomes, being absent from the pericentromeric and subtelomeric regions. A similar pattern of distribution was also observed on the rye B chromosomes, but with weaker signals. The FISH hybridization patterns using UCM600 as probe were comparable with those obtained with the genomic in situ hybridization (GISH) procedure. There were, however, sharper signals and less background with FISH. UCM600 was combined with the rye-specific sequences Bilby and pSc200 to obtain a more complete painting. With these probes, the rye chromosomes were labeled with distinctive patterns; thus, allowing the rye cultivar 'Imperial' to be karyotyped. It was also possible to distinguish rye chromosomes in triticale and alien rye chromatin in wheat-rye addition and translocation lines. The distribution of UCM600 was similar in cultivated rye and in the wild Secale species Secale vavilovii Grossh., Secale sylvestre Host, and Secale africanum Stapf. Thus, UCM600 can be used to detect Secale DNA introgressed from wild species in a wheat background.

Activation of rye 5RL neocentromere by an organophosphate pesticide

An interstitial constriction located on the long arm of rye chromosome 5R (5RL) shows neocentromeric activity at meiosis. In some meiocytes this region is strongly stretched orienting with the true centromere to opposite poles at metaphase I, and keeping sister chromatid cohesion at anaphase I. We found previously that the frequency of neocentric activity varied dramatically in different generations suggesting the effect of environmental factors. Here we studied the behavior of the 5RL neocentromere in mono- and ditelosomic 5RL, and mono-, and disomic 5R wheat-rye addition lines, untreated and treated with an organophosphate pesticide. The treated plants form neocentromeres with an about 4.5-fold increased frequency compared to untreated ones, demonstrating that the pesticide promotes neocentric activity. The neocentromere was activated irrespectively of the pairing configuration or the presence of a complete or truncated 5R centromere. Fluorescence in situ hybridization (FISH) with 2 repetitive sequences (UCM600 and pSc119.2) present at the constriction showed kinetic activity at several locations within this region. Immunostaining with anti-α-tubulin showed that treated plants have abnormal spindles in 46% of the metaphase I cells, indicating that disturbances in spindle formation might promote neocentromere activation.

Karyotype of Zea luxurians and Z. mays subsp. mays using FISH/DAPI, and analysis of meiotic behavior of hybrids

The karyotypes of Zea luxurians and a race of maize from northwestern Argentina are described and compared using 4′,6-diamidino-2-phenylindole (DAPI) banding and fluorescent in situ hybridization (FISH) to localize the 180 bp knobs. The meiotic behavior of the F₁ artificial hybrids Z. luxurians × maize is also analyzed to determine the genomic relationships between both species. Neocentromere activity at knobs in the meiosis of the hybrids is particularly discussed. The meiotic behavior and the high pollen sterility of the hybrid revealed genetical and (or) chromosomal divergences, leading to postzygotic reproductive isolation among their parents. Here, we propose that maize shows lower genomic affinity to Z. luxurians than to other species of the genus with 2n = 20.

Movement ability of rye terminal neocentromeres

Rye terminal neocentromeres were analyzed in various aspects. Plants with and without neocentromeres were crossed to determine the possible genetic control on their formation. The segregation obtained in our work is consistent with the hypothesis of two trans-acting genes determining neocentric activity in such a way that individuals with no neocentromeres at all would carry all non-activating alleles, whereas one activating allele might permit the activation of a few neocentromeres. Individuals with four activating alleles would show the maximum frequency of neocentromeres per cell. Anti-tubulin immunolabelling was used to visualize the interaction between the neocentromeres and the microtubules. In most cases an end-on interaction between neocentromeres and microtubules was observed, but a few neocentromeres were observed free of them. Spikes were irradiated at early meiosis to determine whether acentric fragments carrying subtelomeric heterochromatin were able to behave as neocentromeres. In no case were acentric fragments observed to form an extension polewards as they did in whole chromosomes. Broken chromosomes joined by a thin thread of chromatin to the centromeric region

Using Arabidopsis to understand centromere function: progress and prospects

Arabidopsis thaliana has emerged in recent years as a leading model for understanding the structure and function of higher eukaryotic centromeres. Arabidopsis centromeres, like those of virtually all higher eukaryotes, encompass large DNA domains consisting of a complex combination of unique, dispersed middle repetitive and highly repetitive DNA. For this reason, they have required creative analysis using molecular, genetic, cytological and genomic techniques. This synergy of approaches, reinforced by rapid progress in understanding how proteins interact with the centromere DNA to form a complete functional unit, has made Arabidopsis one the best understood centromere systems. Yet major problems remain to be solved: gaining a complete structural definition of the centromere has been surprisingly difficult, and developing synthetic mini-chromosomes in plants has been even more challenging.

Tandemly repeated DNA sequences and centromeric chromosomal regions of Arabidopsis species

Despite their common function, centromeric DNA sequences are not conserved between organisms. Most centromeres of animals and plants so far investigated have now been shown to consist of large blocks of tandemly repeated satellite sequences that are embedded in recombination-deficient heterochromatic regions. This central domain of satellite sequences that is postulated to mediate spindle attachment is surrounded by pericentromeric sequences incorporating various classes of repetitive sequences often including retroelements. The centromeric satellite DNA sequences are amongst the most rapidly evolving sequences and pose some fundamental problems of maintaining function. In this overview, we will discuss work on centromeric repetitive sequences in Arabidopsis thaliana and its relatives, and highlight some of the common features that are emerging when analysing closely related species.

A tandem repetitive sequence located in the centromeric region of common wheat (Triticum aestivum) chromosomes

Although Tail-family sequences are present in the subtelomeric region of Leymus racemosus, it became apparent in the present study that such sequences are also present in the centromeric region of common wheat (Triticum aestivum). These sequences hybridized to all chromosomes with various degrees of signal strength. FISH using Tail and Ty3/gypsy, a conservative sequence in cereal centromeres, revealed a complicated arrangement of both sequences in all wheat chromosomes at once. Unlike the Arabidopsis centromeres characterized by massive tandem arrays of 180-bp family with flanking paracentromeric retrotransposons in all chromosomes, wheat chromosomes showed various arrangement patterns of Tail and Ty3/gypsy sequences depending on the chromosome; Tail-family sequences were scattered in many wheat centromeres as isolated colonies instead of forming uninterrupted solid tandem arrays. This pattern may have resulted from retrotransposon insertion within pre-existing Tail-tandem arrays or a two-step amplification mechanism of the Tail family where each Tail colony was amplified to form arrays independently after the insertion of Tail-family sequences along the entire centromere. Although sequence analysis of centromeric Tail repeats in wheat and subtelomeric Tail repeats in L. racemosus showed variable and conservative regions between the two repeats, they did not show a distinctive difference phylogenically. The widespread presence of tandem repetitive sequences in the eucaryotic centromere suggests a significant role for them in centromeric formation.