End Of Long Arm Research Articles

Molecular and cytogenetic dissection of stripe rust resistance gene Yr83 from rye 6R and generation of resistant germplasm in wheat breeding.

Rye 6R-derived stripe rust resistance gene Yr83 in wheat background was physically mapped to fraction length (FL) 0.87-1.00 on the long arm by non-denaturing-fluorescence in situ hybridization (ND-FISH), Oligo-FISH painting and 6R-specific PCR markers.Stripe rust resistance gene Yr83 derived from chromosome 6R of rye (Secale cereale) “Merced” has displayed high resistance to both Australian and Chinese wheat stripe rust isolates. With the aim to physically map Yr83 to a more precise region, new wheat- 6R deletion and translocation lines were produced from derived progenies of the 6R(6D) substitution line. The non-denaturing fluorescence in situ hybridization (ND-FISH) patterns of 6R were established to precisely characterize the variations of 6R in different wheat backgrounds. Comparative ND-FISH analysis localized the breakpoints of 6RL chromosomes relative to Oligo-pSc200 and Oligo-pSc119.2 rich sites in deletion lines. Molecular marker and resistance analyses confirmed that Yr83 is physically located at the fraction length (FL) 0.87-1.00 of 6RL and covers the corresponding region of 806-881 Mb in the reference genome of Lo7. Oligo-FISH painting demonstrated that the region carrying Yr83 is syntenic to the distal end of long arm of homoeologous group 7 of the Triticeae genome. The developed wheat-6R lines carrying the Yr83 gene will be useful for breeding for rust resistance.

Karyotypic analysis and isolation of four DNA markers of the scleractinian coral Favitespentagona (Esper, 1795) (Scleractinia, Anthozoa, Cnidaria).

We performed conventional and molecular cytogenetic studies on the Favitespentagona Esper, 1795, a scleractinian coral mostly found along the west coast of Japan. Karyotype analysis of F.pentagona by G-banding revealed a karyogram containing a homogenously staining region (HSR) on chromosome 10 in more than 50% of the examined metaphase spreads. This HSR consisted of sequences from 18S ribosomal RNA (rRNA) genes, as demonstrated by fluorescence in situ hybridization (FISH) and DNA sequencing. We highlighted the development of four chromosomal FISH markers from repetitive genes such as U2 small nuclear RNA linked to 5S rRNA sequence (U2 snRNA-5S), 18S rRNA, histone H3, and uncharacterized gene FP-9X. The chromosomal locations of the U2 snRNA-5S and 18S RNA were on the terminal end of long arm of chromosomes 2 and 10, respectively, while the histone H3 and the uncharacterized gene were located near the centromeres of chromosomes 1 and 9, respectively. These FISH markers will improve the karyotyping of F.pentagona from mitotic preparations which helps in widening our understanding of coral genetic structure and chromosome organization. In addition, these improvements in karyotyping will provide the basis in constructing of chromosome-level genome assembly for F.pentagona.

First report of bicolour FISH of Berberis diaphana and B. soulieana reveals interspecific differences and co-localization of (AGGGTTT)3 and rDNA 5S in B. diaphana

BackgroundBerberis consists of approximately 500 species and is the largest genus in Berberidaceae. Most Berberis species lack cytological data, and bicolour fluorescence in situ hybridization (FISH) has never been performed on Berberis. In this work, a karyotype of Berberis diaphana, an alpine Berberis species obtained from an altitude of 3600 m in Wolong National Nature Reserve, China, was analysed and compared with Berberis soulieana Schneid. via FISH using oligonucleotide telomere probes for (AGGGTTT)3 and 5S rDNA (41 bp) for the first time.ResultsBerberis diaphana belonged to cytotype 2A and had the karyotype formula 2n = 2x = 28 = 26 m + 2 sm (2SAT). The mitotic metaphase chromosome lengths ranged from 1.82 ± 0.04 μm to 2.75 ± 0.00 μm. Clear (AGGGTTT)3 signals were detected at two telomeres in every chromosome and were co–localized with 5S rDNA at the terminal regions of the long arms in the 6th pair of chromosomes. One pair of (AGGGTTT)3 sites was localized in the satellites of the 7th pair of chromosomes, which are the only submetacentric chromosomes in this species. Totally 28 chromosomes with one pair of satellited chromosomes were observed in B. soulieana. This species had four 5S rDNA signals with two weak signals at the end of long arms in the 5th pair of chromosomes and another two strong signals detected in the interstitial region close to the end of short arms in the 6th pair of chromosomes. Each large signal consisted of two smaller signals with secondary constrictions around them.ConclusionsFISH physical mapping of B. diaphana suggested that (AGGGTTT)3 and rDNA 5S co-localize at the 6th pair of chromosomes. The density, location and number difference of 5S rDNA loci indicated structural differences among the chromosomes between B. diaphana and B. soulieana. Our results provide information that may contribute to future studies on the physical assembly of the Berberis genome and the evolution of rDNA and telomere FISH patterns in Berberis.

Sex Differences in Recombination in Sticklebacks.

Recombination often differs markedly between males and females. Here we present the first analysis of sex-specific recombination in Gasterosteus sticklebacks. Using whole-genome sequencing of 15 crosses between G. aculeatus and G. nipponicus, we localized 698 crossovers with a median resolution of 2.3 kb. We also used a bioinformatic approach to infer historical sex-averaged recombination patterns for both species. Recombination is greater in females than males on all chromosomes, and overall map length is 1.64 times longer in females. The locations of crossovers differ strikingly between sexes. Crossovers cluster toward chromosome ends in males, but are distributed more evenly across chromosomes in females. Suppression of recombination near the centromeres in males causes crossovers to cluster at the ends of long arms in acrocentric chromosomes, and greatly reduces crossing over on short arms. The effect of centromeres on recombination is much weaker in females. Genomic differentiation between G. aculeatus and G. nipponicus is strongly correlated with recombination rate, and patterns of differentiation along chromosomes are strongly influenced by male-specific telomere and centromere effects. We found no evidence for fine-scale correlations between recombination and local gene content in either sex. We discuss hypotheses for the origin of sexual dimorphism in recombination and its consequences for sexually antagonistic selection and sex chromosome evolution.

Detection of QTL for exudation rate at ripening stage in rice and its contribution to hydraulic conductance

Dry matter production of crops is determined by how much light they intercept and how efficiently they use it for carbon fixation; i.e., photosynthesis. The high-yielding rice cultivar, Akenohoshi, maintains a high photosynthetic rate in the middle of the day owing to its high hydraulic conductance in comparison with the elite commercial rice cultivar, Koshihikari. We developed 94 recombinant inbred lines derived from Akenohoshi and Koshihikari and measured their exudation rate to calculate hydraulic conductance to osmotic water transport in a paddy field. A quantitative trait locus (QTL) for exudation rate was detected on the long arm of chromosome 2 at the heading and ripening stages. We developed chromosome segment substitution lines which carried Akenohoshi segments in the Koshihikari genetic background, and measured hydraulic conductance to both osmotic and passive water transport. The QTL was confirmed to be located within a region of about 4.2Mbp on the distal end of long arm of chromosome 2. The Akenohoshi allele increased root surface area and hydraulic conductance, but didn't increase hydraulic conductivity of a plant.

Karyotype of the Eichwald’s Toad, Bufo eichwaldi (Amphibia: Bufonidae)

For the first time the karyotype of Bufo eichwaldi was described (2n = 22). It consists of 12 large metacentric (V), 8 small metacentric (v), and 2 small submetacentric chromosomes (sv): 12 V + 8 v + 2 sv, NF = 44. According to the number of chromosomes and arrangement of NORs (in the end of long arms of pairs 6), the karyotype of B. eichwaldi has no differences from karyotypes of close related B. bufo and B. verrucosissimus. The main difference is wide heterochromatin C-blocks in long arms of pair 10, which is present in B. eichwaldi and lacking in B. bufo and B. verrucosissimus. Moreover, in the Eichwald’s toad the pair 1 has, as a rule, larger size if compare with other two species. Additionally, these two species had two submetacentric chromosomes (pairs 4 and 7), but B. eichwaldi had only one (pair 7).

Alkaline phosphatase: an overview.

Alkaline phosphatase (ALP; E.C.3.I.3.1.) is an ubiquitous membrane-bound glycoprotein that catalyzes the hydrolysis of phosphate monoesters at basic pH values. Alkaline phosphatase is divided into four isozymes depending upon the site of tissue expression that are Intestinal ALP, Placental ALP, Germ cell ALP and tissue nonspecific alkaline phosphatase or liver/bone/kidney (L/B/K) ALP. The intestinal and placental ALP loci are located near the end of long arm of chromosome 2 and L/B/K ALP is located near the end of the short arm of chromosome 1. Although ALPs are present in many mammalian tissues and have been studied for the last several years still little is known about them. The bone isoenzyme may be involved in mammalian bone calcification and the intestinal isoenzyme is thought to play a role in the transport of phosphate into epithelial cells of the intestine. In this review, we tried to provide an overview about the various forms, structure and functions of alkaline phosphatase with special focus on liver/bone/kidney alkaline phosphatase.

Higher involvement of subtelomere regions for chromosome rearrangements in leukemia and lymphoma and in irradiated leukemic cell line

Importance of subtelomeric chromosome rearrangements associated with idiopathic mental retardation and with methylation of gene expression in neoplastic cells has been shown. In order to observe incidence of deletions or translocations involving subtelomere region in leukemias and lymphomas, 41 patients were observed precisely by chromosome metaphase fluorescent in situ hybridization (FISH) using subtelomere probes and so on, specially focus on the end of long arm of chromosome 11 or short arm of chromosome 17. The abnormalities of subtelomere region on chromosome 11 were frequently observed in 7 of 17 patients (41.6%) with 11q22-q25 abnormalities, which were 3 of 9 patients with add(11)(q23-q25) and 3 of 7 patients with del(11)(q22-25), and 16 of 24 patients (66.0%) with 17p13 abnormalities, which were 2 of 6 with translocation between 17 and other chromosome, 6 of 10 with add(17)(p13) and all of 8 with del(17)(p13). Lymphoid disease had slightly higher abnormalities of subtelomere region than myeloid disease in patients with 11q22-25 or 17p13 abnormalities. Chemo- or radiotherapy treated patients had also subtelomeric chromosomal rearrangements. These results indicate that leukemia and lymphomas have many abnormalities at subtelomere region and possible association of chromosome instability, relating to pathogenesis of these diseases especially after therapy. Furthermore, FISH and chromosome analyses were performed on long-term cultured HL-60 leukemic cell line after irradiation using three different sources, and the results confirmed the higher induction of chromosome instability involving subtelomere region after α-rays irradiation.

Higher involvement of subtelomere regions for chromosome rearrangements in leukemia and lymphoma and in irradiated leukemic cell line

Importance of subtelomeric chromosome rearrangements associated with idiopathic mental retardation and with methylation of gene expression in neoplastic cells has been shown. In order to observe incidence of deletions or translocations involving subtelomere region in leukemias and lymphomas, 41 patients were observed precisely by chromosome metaphase fluorescent in situ hybridization (FISH) using subtelomere probes and so on, specially focus on the end of long arm of chromosome 11 or short arm of chromosome 17. The abnormalities of subtelomere region on chromosome 11 were frequently observed in 7 of 17 patients (41.6%) with 11q22-q25 abnormalities, which were 3 of 9 patients with add(11)(q23-q25) and 3 of 7 patients with del(11)(q22-25), and 16 of 24 patients (66.0%) with 17p13 abnormalities, which were 2 of 6 with translocation between 17 and other chromosome, 6 of 10 with add(17)(p13) and all of 8 with del(17)(p13). Lymphoid disease had slightly higher abnormalities of subtelomere region than myeloid disease in patients with 11q22-25 or 17p13 abnormalities. Chemo- or radiotherapy treated patients had also subtelomeric chromosomal rearrangements. These results indicate that leukemia and lymphomas have many abnormalities at subtelomere region and possible association of chromosome instability, relating to pathogenesis of these diseases especially after therapy. Furthermore, FISH and chromosome analyses were performed on long-term cultured HL-60 leukemic cell line after irradiation using three different sources, and the results confirmed the higher induction of chromosome instability involving subtelomere region after α-rays irradiation. Keywords: Chromosome instability, subtelomere, telomere, radiation, α-rays, γ-rays, β-rays, leukemia cell line, FISH analysis

Screen of FISH marker of chromosomes at Gossypium D genome species

Appropriate centromere probes for fluorescence in situ hybridization (FISH) of cotton were screened and high density cytogenetic maps based on pachytene-FISH in D genome cotton were developed. A BAC library of Gossypium barbadense var. pima 90-53 was screened using two-dimensional PCR with molecular markers close to the centromere region and 12 BAC clones were identified by BAC-FISH. BAC clone 150D24 screened with SSR marker BNL3563,located at the end of long arm of Chromosome 10 was identified. Signals for BAC clone 150D24 were located in centromere regions of some shorter chromosomes in tetraploid cotton G. hirsutum (AD)1 and G. barbadense (AD)2. FISH conducted on diploid cotton demonstrated that there were clear signals in the centromere region of D genome diploid cotton species when BAC clone 150D24 was used as a probe. No signals were evident in A,C or E genome diploid cotton. This suggests that 150D24 contains repeat sequences,which are specific to D genome species centromere region; therefore,150D24 can be used as a specific FISH marker for centromere regions in D genome diploid cotton,including the D sub-genome.

Banding patterns and chromosomal evolution in five species of neotropical Teiinae lizards (Squamata: Teiidae)

Karyotypes of five species of South American teiid lizards from subfamily Teiinae: Ameiva ameiva, Kentropyx calcarata, K. paulensis, K. vanzoi (2n = 50, all acrocentric), and Cnemidophorus ocellifer (2n = 50, all biarmed), are herein described and compared on the basis of conventional and silver staining, and CBG and RBG banding patterns. Meiotic data are also included. Karyotypes of K. paulensis, K. vanzoi, and C. ocellifer are reported here for the first time. Inter-generic variability in Ag-NORs location was detected with NORs occurring at the end of long arm of pair 1 in K. calcarata, K. paulensis, and K. vanzoi; pair 5 in C. ocellifer and pair 7 in A. ameiva. The location of NORs, along with the karyological differences between A. ameiva and the Central American species (A. auberi), corroboretes the molecular-based hypothesis that the genus Ameiva is paraphyletic. Inter-populational heteromorphism in Ag-NORs size was detected between populations of C. ocellifer. RBG and CBG banding data demonstrated that the biarmed condition of the C. ocellifer chromosomes is due to multiple pericentric inversion events instead of addition of constitutive heterochromatin. Differential-staining techniques used here revealed valuable information about Teiinae karyotypic diversity and made it possible to compare these species, contributing to both the better comprehension of their chromosomal evolution and issues on taxa systematics.

Fusion of two apparently intact human X chromosomes.

Cytological studies have been presented from a 15-year-old girl with short stature and failure of puberty. Buccal mucosa preparations revealed X-chromatin mass approximately double in size of that of a normal female. Leukocyte metaphases suggested a two cell line composition of the patient. One population of cells conformed with 45,X chromosome distribution. The chromosome complement of her other cell line had a modal number of 46. In this cell line a "C" chromosome was replaced by an exceptionally large submetacentric chromosome. This abnormal element exhibited late DNA replicating pattern. G-banding study revealed that the abnormal chromosome was produced as a result of fusion involving telomeric ends of long arms of 2 intact X chromosomes. This translocation X was bearing 2 C-banded areas; one around the centromere and the other at the distal end of the long arm. The distal C-band area did not show any evidence for centromeric function. It appears that a centromere becomes latent in the presence of another centromere in a translocation bearing 2 total chromosomes. Such a change of state in the additional centromere is vital for the stability of the translocation chromosome.

The value of fluorescence microscopy in studying abnormalities of G group chromosomes

Caspersson et al demonstrated that chromosomes stained with quinacrine mustard and examined under ultraviolet light had distinctive patterns of fluroescence. This technique has been used to study the G group chromosomes from 25 individuals.The pattern of fluorescence of the G group chromosomes from 10 normal individuals was determined. The very bright fluoresence on the distal end of long arm of the Y chromosome, as described by others, was apparent. The 4 autosomes could be separated into 2 distinct pairs. One pair had a broad band of fluorescence encompassing 2 3 of the proximal long arm. The second pair had a small area of increased fluorescence in the region of the centromere and short arm. The trisomic chromosome in 9 patients with Down's syndrome was the one with a broad band of fluorescence on the proximal 2 3 of the long arm. Chromosome #21 is smaller than chromosome #22. In a family with a G group marker, the fluorescence technique made identification of the marker chromosome, as #21, possible.Chromosomes from 2 phenotypic males with XX sex chromosomes were examined. the brightly fluorescent region of the long arm of a Y chromosome was not found translocated on any part of the genome. These data plus morphologic considerations indicate that if any Y material were present, it could only be short arm DNA. This is further evidence for male determinants being located on the short arm of the Y chromosome.Quinacrine mustard staining and UV microscopy is a new technique that enables us to identify specific chromosomes and regions within chromosomes.