Numerical Chromosome Variation Research Articles

Progress on molecular composition and genetic mechanism of plant B chromosomes.

In addition to the standard set of chromosomes (A chromosomes, As), so-called supernumerary B chromosomes (Bs) have been found causing a numerical chromosome variation. Bs have been considered to be genetically inert elements without any functional genes for a long period, because of the limited experimental methods and its dispensable property. More recently, sequencing of dissected Bs from several organisms has revealed the DNA composition, a vast number of protein-coding genes have been found with the effects on the transcripts and protein expression of the host. In this review, we summarize current understanding of B chromosomes carrying plants including rye (Secale cereale L.), maize (Zea mays L.) and Aegilops (Aegilops speltoides Tausch.), with the emphasis on Bs phenotypic effects, the inheritance mechanism of Bs, the molecular composition of Bs, the effects on host transcription regulation and protein expression upon the presence of Bs. Besides, we discuss the current study state and potential application of B chromosomes, aim to provide a new venue for chromosome engineering and breeding research.

Chromosomal instability and phenotypic variation in a specific lineage derived from a synthetic allotetraploid wheat.

Newly formed plant allopolyploids usually have meiosis defect, resulting in chromosomal instability manifested as variation in chromosome number and/or structure. However, not all nascent allopolyploids are equally unstable. The wheat group (Aegilops/Triticum) contains 13 diploid species with distinct genome types. Many of these species can be artificially hybridized to produce viable but sterile inter-specific/intergeneric F1 hybrids, which can generate fertile synthetic allotetraploid wheats after whole genome doubling. Compared with synthetic allotetraploid wheats that contain genome combinations of AADD and S*S*DD (S* refers to related S genomes of a different species), those containing an S*S*AA genome are significantly more stable. However, robustness of the relative stability of S*S*AA genomes is unknown, nor are the phenotypic and fitness consequences during occurrences of secondary chromosomal instability. Here, we report a specific lineage originated from a single individual plant of a relatively stable synthetic allotetraploid wheat with genomes SlSlAA (Sl and A subgenomes were from Ae. longissima and T. urartu, respectively) that showed a high degree of transgenerational chromosomal instability. Both numerical chromosome variation (NCV) and structural chromosome variation (SCV) occurred widely. While substantial differences in frequencies of both NCV and SCV were detected across the different chromosomes, only NCV frequencies were significantly different between the two subgenomes. We found that NCVs and SCVs occurred primarily due to perturbed meiosis, allowing formation of multivalents and univalents as well as homoeologous exchanges. Thus, the combination of NCVs and SCVs affected multiple phenotypic traits, particularly those related to reproductive fitness.

Cell-mediated immunity and expression of MHC class I and class II molecules in dogs naturally infected by canine transmissible venereal tumor: Is there complete spontaneous regression outside the experimental CTVT?

The canine transmissible venereal tumor (CTVT) is a transplantable cancer with the ability evade the immune system, despite strict immune surveillance of the host; in this context, the relationship between inflammatory infiltrate and CTVT prognosis is not entirely understood. Natural canine transmissible venereal tumors of 22 dogs were evaluated for tumor/host interaction through clinical and epidemiological data, cyto-histopathological and cytogenetic findings and, mainly, cell-mediated immune response. We performed analysis on dogs with naturally acquired disease to provide information from the study of CTVT biology in its natural course, as the clinical evolution of the natural tumor in the host is not yet as well known as in the laboratory. Populations for T cell labeling (CD3+ CD4+ CD8+), B cells, NK cells, and macrophages were analyzed by flow cytometry in blood and tumor samples and expressions of MHC class I and class II molecules were quantified by immunohistochemistry and compared mainly between the phases of progression and regression in the natural CTVT. Dogs were also treated with vincristine sulfate and evaluated for chemotherapeutic response. Chemotherapy was effective in 88% of cases and there was no recurrence of the disease 12 months after the cure. Tumor cells displayed a numerical chromosomal variation between 54 and 72, not correlating with the host genotype. Although a greater expression of MHC molecules [18.6 ± 5.8% class I (P < 0.004) and 38.5 ± 6.5% class II (P < 0.003)] was observed in the regression phase, no significant effect was observed between the clinical phase of the tumor and cellular immune response in the analysis by flow cytometry (P > 0.05). We also found no correlation between cytological subtype of the tumor (plasmacytoid, lymphocytoid and mixed) and cellular immune response, suggesting that there is no difference in tumor immunogenicity. Here, we found no immunological evidence to support the theory of the immune-induced complete spontaneous regression in CTVT.

Somatic and Meiotic Instabilities Cause Hypo-aneuploidy in Synthesized Wheat–Aegilops triuncialis Amphiploids

In newly formed allopolyploids, meiotic instability in early generations contributes to reduced fertility, but less is known about their mitotic accuracy and somatic instability. Here, the authors report somatic numerical chromosome variation (somatic aneuploidy) among different individuals of newly synthesized wheat–Aegilops triuncialis amphiploids (AABBDDUtUtCtCt genome) over three successive generations. In total, 21 seeds in the F2 to F4 generations descended from three different F1 hybrids (2n = 5x = 35, ABDUtCt genome) were analyzed by chromosome counting and fluorescent in situ hybridization. Somatic aneuploidy was detected in 17 (81%) investigated individuals. Somatic chromosome numbers of the cells (among and within the evaluated individuals) ranged from 62 to 70. Furthermore, flow cytometry revealed variation in genome size within and between individual amphiploids that may be due to variable chromosome numbers. There was no evidence that somatic aneuploidy leads to stable cytotypes, at least in the early generations. The authors conclude that both newly formed status and large genome sizes may contribute to somatic and meiotic instability in synthetic wheat–Aegilops triuncialis amphiploids.

Aneuvis: web-based exploration of numerical chromosomal variation in single cells

BackgroundNumerical chromosomal variation is a hallmark of populations of malignant cells. Identifying the factors that promote numerical chromosomal variation is important for understanding mechanisms of carcinogenesis. However, the ability to quantify and visualize differences in chromosome number between experimentally-defined groups (e.g. control vs treated) obtained from single-cell experiments is currently limited by the lack of user-friendly software.ResultsAneuvis is a web application that allows users to determine whether numerical chromosomal variation exists between experimental treatment groups. The web interface allows users to upload molecular cytogenetic or processed single cell whole-genome sequencing data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of numeric chromosomal variability.ConclusionsAneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote numerical chromosomal variation. Aneuvis is freely available as a web application at https://dpique.shinyapps.io/aneuvis/ and the source code for the application is available at https://github.com/dpique/aneuvis.

B Chromosomes in the Tree FrogHypsiboas albopunctatus(Anura: Hylidae)

Supernumerary or B chromosomes are one of the main causes for numerical chromosomal variation in higher eukaryotes. These extragenetic elements have been studied for more than a century, with the goal of trying to understand their origin, and how they survive as a polymorphism in natural populations. Hypsiboas albopunctatus is a nocturnal hylid frog distributed in the central-eastern part of South America. Previously, variation in chromosome numbers was described for a population from Rio Claro, Sao Paulo, Brazil, in which a single small-sized, metacentric B chromosome was present in ca. 40% of the analyzed individuals (n ¼ 17). We herein describe the presence of B chromosomes in populations of H. albopunctatus from northeastern Argentina (Corrientes and Misiones provinces), with unusual morphological and structural characteristics. The frequency of B chromosomes varied significantly among analyzed populations. We found four diploid numbers (2N ¼ 22, 22 þ 1B, 22 þ 2B, and 22 þ 3B), and in a few individuals mitotic instability occurred. C banding revealed variations in the heterochromatin (DAPIþ) pattern between Bs with similar morphology, indicating the existence of two new structural variants of these supernumerary elements in H. albopunctatus (B1 and B2). Nucleolar organizer regions marked positively on the eighth pair, coincident with the location of ribosomal DNA as demonstrated with fluorescent in situ hybridization, but Bs did not mark positive with these two techniques. Also, fluorescent in situ hybridization with telomeric probes showed no differences in location and intensity between Bs and autosomal chromosomes. The present communication is the first case of B chromosome polymorphisms in hylid frogs and the sixth reported in Anura.

Numerical chromosome variation and mitotic segregation defects in the adult brain of teleost fish

Teleost fish are distinguished by their enormous potential for the generation of new cells in both the intact and the injured adult brain. Here, we present evidence that these cells are a genetic mosaic caused by somatic genomic alteration. Metaphase chromosome spreads from whole brains of the teleost Apteronotus leptorhynchus revealed an euploid complement of 22 chromosomes in only 22% of the cells examined. The rate of aneuploidy is substantially higher in brain cells than in liver cells, as shown by both metaphase chromosome spreads and flow cytometric analysis. Among the aneuploid cells in the brain, approximately 84% had fewer, and the remaining 16% more, than 22 chromosomes. Typically, multiple chromosomes were lost or gained. The aneuploidy is putatively caused by segregation defects during mitotic division. Labeling of condensed chromosomes of M-phase cells by phosphorylated histone-H3 revealed laggards, anaphase bridges, and micronuclei, all three of which indicate displaced mitotic chromosomes. Quantitative analysis has shown that in the entire brain on average 14% of all phosphorylated histone-H3-labeled cells exhibit such signs of segregation defects. Together with the recent discovery of aneuploidy in the adult mammalian brain, the results of the present investigation suggest that the loss or gain of chromosomes might provide a mechanism to regulate gene expression during development of new cells in the adult vertebrate brain.

Numerical chromosome polymorphism in Mikania cordifolia Willd. (Asteraceae)

Cytogenetical analysis of Mikania cordifolia, from southeastern Brazil, using the conventional Feulgen method, showed a chromosome number of 2n = 36. Previous karyotypic descriptions for this species showed a numerical chromosome variation of 2n = 34 to 38. There was a secondary constriction in every metaphase in the first chromosome pair, which constitutes a cytological marker. Small extranumerary chromosomes with numerical variation in the same plant were found in the tenth chromosome pair.

Chromosomal rearrangements in a Somali wild ass pedigree, Equus africanus somaliensis (Perissodactyla, Equidae)

Chromosome analyses were conducted on 15 animals in a pedigree of Somali wild ass, Equus africanus somaliensis. G- and C-banded karyotypes are presented for the first time on this endangered species. The diploid number ranged from 62 to 64. Numerical chromosomal variation was the result of a centric fission which was accompanied by a heterochromatic deletion. The fission polymorphism involved acrocentric elements 19 and 21 as determined by G-banding. These autosomes are homologous to those involved in centric fission/fusion polymorphisms in other equids: E. asinus (domestic donkey), E. hemionus (onager), E. kiang (kiang), and E. burchelli (common zebra). Banding analyses also revealed a paracentric inversion polymorphism in submetacentric chromosome pair 2 of E. a. somaliensis. Both the centric fission and paracentric inversion polymorphisms involved heterochromatic regions. One individual was found to be heterozygous for two de novo chromosomal rearrangements: a centric fission (involving acrocentric elements 19 and 21) and a heterochromatic deletion of chromosome 2.

Effect of genotype on chromosome variation in tissue culture of inbred and outbred rye

To examine the effect of genotype on the nature of the cytological variation induced in culture, plants were regenerated from cultured immature embryos of six genotypes (lines A-F) of rye (Secale cereale L.). The variation observed differed among the six lines and was generally consistent with the donors. Regenerants of line A were consistent with the donor, cv. Ailes, in that chromosome translocations appeared at high frequencies. No structural or numerical variation was observed in the B chromosomes of line B. Two of the four inbred lines studied were very stable in culture. Inbred line D was also stable except for a translocation in the regenerants. In inbred line F, variation was observed in the donors and the regenerants. An examination of chiasma frequency and distribution indicated that the regenerated plants generally had higher chiasma frequencies and more distally localized chiasmata than the donors. Line F was exceptional in that the regenerants had more interstitial chiasmata. The elevation in chiasma frequency was not as great, or statistically as significant, as the change in distribution. These results provide further evidence that the nature of cytological variation observed in regenerated plants is genotype-dependent and that, in addition to numerical and structural chromosome variation, shifts in chiasma frequency and distribution, and therefore in genetic recombination, can occur as a result of somaclonal variation.

Polyploidy in a Cultivar of Black Pepper(Piper nigrum L.) and Its Open Pollinated Progenies.

Polyploidy in a cultivar (Collection No: 1344) of black pepper (Piper nigrum L.) and numerical chromosomal variation in its twenty progenies were identified by cytological analysis. The plant was a triploid with chromosome number 2n=78, and the progenies showed a range of variation from 2n=52 to 2n=104. Morphological types were observed with variation in chromosome number. Possible origin of the mother plant is also discussed.

Chromosomal variation in dividing protoplasts derived from cell suspensions of barley (Hordeum vulgare L.)

Numerical and structural chromosome variation was analysed in dividing protoplasts isolated from suspension cells of barley. Five cell lines exhibited distribution patterns in chromosome number with different peaks and ranges. Embryogenic/morphogenic cell lines showed a peak at 2n = 14 (ca. 50%) after 6-7 months in culture, while older non-embryogenic cell lines had peaks at aneuploid or polyploid chromosome numbers. Culture duration had a clear effect on numerical and structural chromosome variation in embryogenic cell lines. With ageing of the cultures chromosome variation accumulated and the proportion of 2n = 14 cells decreased. The effect of protoplast isolation and culture on chromosome variation was examined; more cells with normal chromosome sets (12%) were maintained in protoplast-derived colonies than in source suspension cells (4%) of the same culture age.

A sequence specific to B chromosomes of Brachycome dichromosomatica

Supernumerary B chromosomes represent one of many causes of numerical chromosome variation that exist in higher plants and animals. Sequences of DNA unique to B chromosomes of Brachycome dichromosomatica were enriched prior to cloning and resultant clones hybridizing only to plants containing B chromosomes were further investigated. Sequences of DNA that were characterised include members of a family of 176-bp tandem repeats that are specific to the B chromosomes of B. dichromosomatica, an annual Australian native plant species with only two pairs of A chromosomes and up to three dispensable B chromosomes. Sequence analysis of these six related clones indicated that some regions of the sequence are more highly conserved than others or, alternatively, that some adenine residues at the NdeII site are methylated. The repeat is homologous to DNA from Brachycome ciliaris var. languinosa but not to DNA from other related taxa growing in the vicinity of the B. dichromosomatica populations.

Evolutionary genomic change paralleled by differential responses of 2× and 4× calli cultures

A comparative account of numerical chromosome variation in 2× and 4× callus cultures ofHyoscyamus muticus examined at monthly intervals reveals that both types of calli tend to attain a genomic flux around 4×. Parallels apparently exist between the course of ploidy change and chromosomal flow in culture and evolutionary processes in nature, suggesting the utility of the in vitro system as a rapid approach for recognizing trends in genome evolution.

Variability in potato tissue culture

Tissue culture systems in potato (Solanum tuberosum L.) that involve a callus phase, such as regeneration of plants from protoplasts or expiants, can be accompanied by phenotypic variability, or somaclonal variation. The extent of this variability appears to be greatest in protoplast-derived potato plants. Cytological studies have shown that some of the variation observed in regenerated potato plants arises from numerical and structural chromosome variation. Aneuploidy is particularly a problem in regeneration from protoplasts. Factors affecting the degree of chromosome instability include the genotype and ploidy of the starting material, the regeneration system adopted, the source of the plant cells and the composition of the tissue culture media. Studies at the molecular level have indicated that changes in the potato genome, other than those associated with chromosomes, also occur. The implications of somaclonal variation in potato, particularly with regard to its potential usefulness for plant breeding are discussed.

Heritable somaclonal variation in wild barley (Hordeum spontaneum)

Progenies of H. spontaneum plants regenerated from immature embryo derived calli were analysed for somaclonal variation on the following traits: (1) organization of the intergenic spacer of the rRNA genes; (2) B and C hordein pattern on SDS-PAGE; (3) genomic organization of the B and C hordein coding sequences; (4) mitochondrial DNA organization assayed by hybridization of Southern blots of total DNA with mitochondrial coding genes; (5) cytology. One out of twelve progeny plants was characterized as variant for two traits: (a) a loss of 1.8 and 2.5 kb Taq I intergenic rDNA spacer fragments and (b) a variant pattern of hordeins on 1-D SDS-PAGE. No numerical or structural chromosome variation was detected among the control plants therefore it is assumed that the variation was caused by the in vitro culture and transmitted, through sexual reproduction, to the analysed progeny.

Chromosome variation in dividing protoplasts and cell suspensions of wheat

The cytology of bread wheat (Triticum aestivum) suspension lines, recycled lines (selected for high division frequency) and their dividing protoplasts, have been examined. Extensive numerical and structural chromosome variation was present in all the lines. The most frequently observed chromosome numbers were around 2n=32, indicating that considerable chromosome loss from the normal wheat complement (2n=6x=42) had occurred during selection of the lines. Chromosome aberrations also indicated loss of chromosome arms and chromosome segments. The implications of this variation for studies on transformation and for the potential regeneration of whole plants from protoplasts of bread wheat are discussed.

Structural and numerical chromosomal polymorphism in natural populations ofAlopecurus (Poaceae)

Considerable structural and numerical chromosomal variation has been found in natural populations ofAlopecurus. Interchange heterozygotes, identified by multivalent formation during meiosis, have been recovered in four out of six species studied and are reported for the first time in the diploidsA. bulbosus, andA. myosuroides, and the tetraploidA. pratensis. B chromosomes have been found in two species,A. pratensis andA. myosuroides and also in inter-specific hybrids betweenA. pratensis andA. arundinaceus. The characteristics, distribution and meiotic behaviour of both interchange heterozygotes and B chromosomes are described.

Association Between Congenital Heart Malformation and Chromosomal Variations1

SummaryA family is described in which mother rind son both displayed auricular septal defects of the secundum type while father and daughter had no cardiovascular disorders. The karyotypes of these individuals were analysed by the cell culture method using biopsies from bone marrow and skin. The majority of the cells from the mother had 47 chromosomes and she was apparently trisomic [19–20]. A similar additional chromosome of group [19–20] was found in the cells derived from the son.However, he lacked one of the smallest acrocentric chromosomes. His chromosome number was 46. The father and daughter both had normal karyotypes. The significance of numerical and/or structural chromosome variation in the etiology of congenital heart malformation is discussed with regard to recent developments in clinical cytogenetics.

Hybridisation in a wild population of eleocharis palustris

1. Twenty-nine inflorescences from plants of Eleocharis palustris in a small area of Port Meadow, Oxford, were found to include four types. Two of these were the recognised sub-species E. p. vulgaris (2n=38) and E. p. microcarpa (2n=16). 2. The former was represented by seven inflorescences one of which was abnormal showing delayed or non-disjunction of the chromosomes at PGM I in approximately 8% of the cells. 3. The latter was represented by ten inflorescence two of which were abnormal showing a failure in 40% of the cells of the nuclear differentiation which normally precedes PGM. 4. In four of the other inflorescences the chromosome number at PGM I ranged from 11 to 18 with a modal value of 14. Plants with 2n=27 chromosomes in the root tips have also been found. We consider these to be F1 hybrids between the two subspecies. 5. In the remaining seven inflorescences, the chromosome number at PGM I ranged from 16 to 21 with a modal value of 18/19. These may be plants of E. p. vulgaris with an abnormal meiosis or hybrid derivatives. 6. The survival of the hybrid material in this population is attributed to the fact that sexual fertility is not at a premium. The meadow has been subjected to continuous grazing for centuries and under these curcumstances survival depends on vegetative vigour and propagation. Presumably the presence of fertility-affecting abnormalities in the parental types can be explained on the same basis as indeed, may the occurrence of hybridisation. 7. Numerical chromosome variation in the genus appears to be due to a variety of causes. a) Aneuploidy. α) Non-disjunction at meiosis (especially in hybrids or hybrid derivatives) or at pollen grain mitosis. β) Fragmentation, perhaps following inversion loop crossing over in structural hybrids—a source of variation which is excluded in most groups by the localisation of centromeres. b) Polyploidy. α) Restitution at meiosis (diploid self-fertilisation). β) Restitution at pollen grain mitosis (formation of homozygous diploid gametes).