LBA technique in the detection of chromosome variants

Summary In Part I of this communication, a technique (LBA) was described which used DNA replication in the evaluation of chromosome variants in man. It was shown that the method was very useful in the detection of variants in D-and G-group chromosomes. Results on pairs 3 and 4 were also presented.In Part II, the rest of chromosomes were examined. In the evaluation of qh variants in 1,9 and 16, the LBA technique proved itself to be a very effective implement. It was practically free of technical variables coherent with C-band technique and, therefore, it was possible to use the size of an euchromatic segment of a chromosome as a reference standard. LBA variants were observed in about 50% of the members of the remaining 12 pairs of chromosomes, i.e., 2, 5, 6, 7, 8, 10, 11, 12, 17, 18, 19, and 20.     

LBA technique in the detection of chromosome variants

Summary A method is described (LBA method) which uses DNA replication pattern in the detection of chromosome variants in man. In Part I, results on chromosomes with known sites of Q-variants, i.e., 5 pairs of acrocentrics, as well as 3 and 4, were presented.Fourty-one variants were detected in a total of 40 acrocentrics. Twentyeight of them were detected only by the LBA technique; 11 of them being in short arms and 17 of them in centromeres. Seven variants, including 4 of those in satellites, were detected only in QFQ-stained metaphases. Six short-arm variants were observed by both methods. It appears that a sequential QFQ-LBA technique is very useful in the detection of variants in D- or G-group chromosomes.     

A new approach in the evaluation of chromosome variants in man

Summary A new approach is proposed for the evaluation of chromosome variants, which uses a scanning microdensitometer in the determination of the area of a variant. Results are assigned into five classes based on the difference from an average in terms of standard deviation. In the first two papers of the present series, results obtained in C variants of 1, 9, and 16 and LBA variants in 12 pairs lacking an established variable site (e.g., nos. 2, 5, 6, etc.) were described.In the present communication, results obtained in pairs with a known Q-variable site are described. When a variable region outside of ±1 SD of the average is defined as a variant, 9, 11, 7, 10, and 10 variants are detected in pairs 13, 14, 15, 21, and 22, respectively, from 12 individuals by means of LBA preparations, in addition to Q variants, which can be detected by the standard QFQ technique.     

A POLYPLOID SPECIES COMPLEX IN SPIROGYRA MAXIMA (CHLOROPHYTA,ZYGNEMATACEAE), A SPECIES WITH LARGE CHROMOSOMES1

A species complex in Spirogyra consists of the series of filament morphotypes of various ploidal levels arising from an original morphotype within a clonal culture or in nature. A clonal culture of filaments identified as Spirogyra maxima (Hassall) Kützing produced several morphotypes, i.e. filament types of distinctly different widths and ploidal levels. Banding patterns and satellites were visible on chromosomes stained at mitotic prophase and metaphase. The original culture of S. maxima contained filaments averaging 127 μ wide. Vegetative cells of the original culture contained six large chromosomes (>4 μ long), identifiable as three distinct pairs based on banding patterns and presence of satellites: (1) one pair of short chromosomes (ca. 5.0 μ); (2) one pair of long chromosomes (ca. 8.0 μm); and (3) a second pair of long chromosomes (ca. 9.0 μm) including a nucleolar organizing region and satellite. A larger morphotype averaging 175 μm in width contained 12 chromosomes, with two pairs of short chromosomes and four pairs of long chromosomes (satellites were usually indistinct). Aneuploid chromosome numbers ranging from 5 to 13 were observed in a few cells. Binucleate and trinucleate cells were also observed. A twobanded chromosome fragment was observed in a few cells with 6 chromosomes and a few cells with 12 chromosomes. The variety of morphotypes derived in this study could be identified as four different species of Spirogyra by conventional taxonomic criteria. The banding patterns and satellites on chromosomes suggest that three pairs of homologous chromosomes are present in filaments of the original clonal culture and that these filaments are themselves autopolyploid (diploid) descendants of ancestral form with a base chromosome number of x = 3.     

Chromosome markers in 12 inbred strains of the Norway rat, Rattus norvegicus.

Morphological details of metaphase chromosomes were compared among 12 inbred strains of rats (Rattus norvegicus) by means of conventional Giemsa staining and by a sequential Q- and C-banding method. Inter-strain variations were found in seven pairs, as identified on the basis of size differences in the short arms and/or satellites of chromosomes 3 and 12 and the X chromosome and in the centromeric C-bands of chromosomes 4, 5, 7, and 9. All pairs were homomorphic in the inbred strains, while F1 hybrids between two inbred strains showed certain heteromorphic pairs expected from the parents. These chromosome markers appear to be useful for characterization of inbred strains as well as for various genetic studies, including linkage analyses.     

Development of Chromosome-specific Cytogenetic Markers and Merging of Linkage Fragments in Papaya

Carica papaya L. is a tropical and sub-tropical fruit-tree crop with a small genome and nine pairs of chromosomes. The transgenic cultivar ‘SunUp’ has been sequenced and three high-density genetic maps are available for mapping agronomically and economically-important traits. However, the small size and similar morphology of papaya chromosomes hinder their identification and few cytological resources are available for integration of genetic and cytogenetic information. Fluorescence in situ hybridization (FISH) was performed on mitotic metaphase chromosomes using BAC clones harboring mapped simple sequence repeat (SSR) markers as probes. A total of 104 BAC clones covering all 12 linkage groups (LGs) were tested and 12 of them, that gave a single specific signal, were chosen as representative of the 12 LGs of the SSR genetic map. This set of chromosome-specific DNA markers acted as a foundation for papaya chromosome karyotyping and re-assigning orientation of LGs. Chromosome-specific markers allowed us to assign the minor LGs 10, 11, and 12 to major LGs 8, 9, and 7, respectively. We thus reduced the number of LGs in the genetic map to nine, corresponding to the haploid number of papaya chromosomes. We also tested the relative order of DNA markers on minor LGs 10 and 11 to place them on top of LGs 8 and 9 in the correct orientation. Ribosomal DNAs (rDNAs), a set of major cytogenetic markers, were positioned on specific papaya chromosomes. The 25S rDNA showed strong signals at the constriction site of a single pair of chromosomes identified as LG 2 by LG 2-specific BAC clone. The 5S rDNA showed strong signals on two pairs of chromosomes that are syntenic with LG 4- and LG 5-specific BAC clones. This integrated map will facilitate genome assembly, quantitative trait locus (QTL) mapping, and the study of cytological, physical and genetic distance relationships between papaya chromosomes.     

Dual‐color oligo‐FISH can reveal chromosomal variations and evolution in Oryza species

Fluorescence in situ hybridization using probes based on oligonucleotides (oligo‐FISH) is a useful tool for chromosome identification and karyotype analysis. Here we developed two oligo‐FISH probes that allow the identification of each of the 12 pairs of chromosomes in rice (Oryza sativa). These two probes comprised 25 717 (green) and 25 215 (red) oligos (45 nucleotides), respectively, and generated 26 distinct FISH signals that can be used as a barcode to uniquely label each of the 12 pairs of rice chromosomes. Standard karyotypes of rice were established using this system on both mitotic and meiotic chromosomes. Moreover, dual‐color oligo‐FISH was used to characterize diverse chromosomal abnormalities. Oligo‐FISH analyses using these probes in various wild Oryza species revealed that chromosomes from the AA, BB or CC genomes generated specific and intense signals similar to those in rice, while chromosomes with the EE genome generated less specific signals and the FF genome gave no signal. Together, the oligo‐FISH probes we established will be a powerful tool for studying chromosome variations and evolution in the genus Oryza.     

Stratification by CARD15 variant genotype in a genome-wide search for inflammatory bowel disease susceptibility loci

Previously we have conducted a genome-wide search for inflammatory bowel disease susceptibility loci in a large European cohort. Results from this study demonstrated suggestive evidence of linkage to loci at chromosomes 1q, 6p, and 10p and replicated linkages on chromosomes 12 and 16. Recently, NOD2/CARD15 on chromosome 16q12 has been found to be strongly associated with Crohn's disease. In order to determine if there are other loci in the genome that interact with the three associated functional variants in CARD15 (R702W, G908R, 1007fs), we have stratified our large inflammatory bowel disease genome scan cohort by dividing pedigrees into two groups stratified by CARD15 variant genotype. The two pedigree groups were analysed using non-parametric allele sharing methods. The group of pedigrees that contained one of the three CARD15 variants had two suggestive linkage results occurring in 6p (lod = 3.06 at D6S197, IBD phenotype) and 10p (lod=2.29 at D10S197, CD phenotype). In addition, at 16q12 where CARD15 is located, the original genome scan had a peak lod score of 2.18 at D16S415 (CD phenotype). The stratified pedigree cohort containing one of three CARD15 variants had a peak lod score of 0.90 at D16S415 (CD phenotype), accounting for approximately less than half of the genetic evidence for linkage at this locus. This result is in agreement with the existence of a substantial number of private variants at the NOD2/CARD15 locus. Interaction with NOD2/CARD15 needs to be considered in future gene identification efforts on chromosomes 6 and 10.     

尼罗罗非鱼和萨罗罗非鱼遗传生殖隔离的初步证据(英文)

罗非鱼类(Tilapiini)含3个属70余种,种间和属间颇易人工杂交,但尼罗罗非鱼(Oreochromis niloticus)和萨罗罗非鱼(Sarotherodon melanotheron)人工杂交难度大,产苗概率甚低,要获得数量足够的可用于生产的杂交子代相当困难。该文对这两种鱼及其正交(O.niloticus♀×S.melanotheron♂)和反交(S.melanotheron♀×O.niloticus♂)子代的头肾细胞的核型进行了比较。此外,采用同工酶电泳方法检测肾、肝、眼、肌肉、心中乳酸脱氢酶等4种同工酶的表型差异。4种遗传型罗非鱼具有相同的染色体二倍数(2n=44)和总臂数(NF=50),但各具不同的染色体类型,尼罗罗非鱼为3对近中着丝点染色体(sm)、12对近端着丝点染色体(st)和7对端着丝点染色体(t);萨罗罗非鱼为1对中间着丝点染色体(m)、2对sm、12对st和7对t;正反杂交子代表现为介于双亲之间的混合类型,为0.5对m、2.5对sm、12对st和7对t。在同工酶中,仅见肾脏乳酸脱氢酶电泳结果有清晰差异,尼罗罗非鱼出现5条谱带,萨罗罗非鱼3条,而杂交子代6条,且所有谱带的迁移率和活性均表现出多态性。据此初步认为,核型和同工酶方面的差异可能是导致这两种不同属罗非鱼生殖隔离的遗传原因,这些差异也可能为这两种(属)鱼的分类学提供新的遗传背景资料。     

Extensive polymorphism and chromosomal characteristics of ribosomal DNA in a loach fish, Cobitis vardarensis (Ostariophysi, Cobitidae) detected by different banding techniques and fluorescence in situ hybridization (FISH)

When surveying the karyotype diversity of European loaches of the genus Cobitis to identify species involved in hybrid polyploid complexes, an extensive polymorphism in number and location of NORs was discovered in C. vardarensis using Ag-staining, C-banding, CMA₃-fluorescence and fluorescence in situ hybridization (FISH). This species had 2n=50, the karyotype contained 13 pairs of metacentric, 10 pairs of submetacentric and two pairs of subtelocentric chromosomes. The NOR-bearing chromosomes included one medium-sized metacentric pair with a large CMA₃-positive heterochromatic pericentromeric block, one small metacentric as well as one large submetacentric pairs. Ribosomal sites were always located in telomeres of these chromosomes. Each of the pair of NOR-bearing chromosomes occurred in three variants – (1) presence and/or (2) absence of NORs on both homologues and (3) heterozygous combination where only one of the homologues bears NORs. Altogether, 10 different NOR cytotypes from 27 theoretically possible ones were discovered among 20 indviduals examined. The number of NORs ranged from two to five per specimen. The results regarding the number and locations of NORs as revealed by banding techniques were confirmed using FISH with rDNA probe. NOR sites were of CMA₃-positive, suggesting that ribosomal sites are associated with GC-rich DNA. Very similar structural polymorphism with multiple NORs is expressed in the Danubian loach C. elongatoides indicating a close relationship between both species.     

New cytogenetic information on Allium iranicum (Alliaceae) from Iran

Karyotype analysis and chromosome behaviour in tetraploid Allium iranicum is reported. The somatic karyotype 2n = 32, consists of 12 pairs of metacentric chromosomes, two pairs of submetacentric chromosomes and two pairs of submetacentric satellite chromosomes. Chromosome complement follows two sets of 16 pairs of homologous chromosomes. A detailed analysis of Pachytene, Diplotene and Metaphase I of meiosis in pollen mother cells in this taxon showed that the most common chromosome configurations were bivalents at all subphases mentioned. It is concluded that A. iranicum is most likely a natural allotetraploid and certainly differs from related species A. ampeloprasum, A. commutatum and A. porrum.     

中国云南果蝇属暗果蝇种组的核型分化

观察了新近发现于我国云南的果蝇属暗果蝇种组(Drosophila obscura species group)种类D．luguensis、D．dianensis和D．limingi的有丝分裂中期核型,并将3个种的核型与各自的近缘种类进行了比较。D．luguensis具2n=12条染色体,包括3对中央着丝粒(V形)染色体、2对近端着丝粒(棒状)染色体以及1对微小(点状)染色体。其中X和Y染色体均为中央着丝粒染色体。D．dianensis和D．limingi具2n=10条染色体,包括1对大的V形常染色体,1对小的V形常染色体,2对J形(亚中着丝粒型)常染色体和1对点状染色体。其中X染色体为J形,Y染色体为短棒状。基于核型比较的结果以及D．sinobscura亚组地理分布的资料,结合种间系统发育关系研究结果,认为D．luguensis可能保留了该亚组祖先种类的核型。D．sinobscum的核型(2n=12：2V,1J,2R,1D)可能由一个pre-“sinobscura-hubeiensis”谱系的一个分支通过臂间倒位演化而来,而D．hubeiensis的核型(2n=10：4V,1D)可能由该谱系的另一分支通过着丝粒融合(2对近端着丝粒常染色体的融合)而形成。推测在D．dianensis和近缘欧洲种D．subsilvestris(2n=12：3V,2R,1D)间、D．limingi和东亚近缘种D．tsukubaensis(2n=12：3V,2R,1D)间的物种分化过程中,可能有相似的染色体变异类型发生。     

Types and frequencies of Q-variant chromosomes in a Japanese population

Summary The types of Q-variant bands were determined by a combination of numerical designations setting five levels for both the size of bands and the intensity of fluorescence. This scoring system was used in a study of the frequencies of Q variants in 400 Japanese individuals: variant bands were observed in seven specific autosome pairs of Nos. 3,4,13,14,15,21, and 22. The number of variants per individual ranged from 0 to 8, and the mean was 3.83±1.86. The incidence of Q variants according to the types of variant bands was determined in specific chromosomes.A low frequency of No. 3 chromosome variants and a high frequency of a long Y in males seems to be characteristic for Japanese populations.Variation in the length of the long arm of Y (Yq) was analyzed in a total of 157 men. The relative length of Yq, which was determined by a ratio of Yq/21q, ranged from 0.98 to 2.27, with an average of 1.56±0.25. The length of pale band Yq11 was relatively constant between individuals, with an average of 0.64±0.08. Therefore, it was clear that the variation in the Yq length was the result mainly of a variation in the length of the brilliant band Yq12. However, a slight tendency for the length of band Yq11 to increase in proportionally to the total length of the Yq was revealed. In this study special consideration was paid to the reliable analysis of Q-band heteromorphism, and the factors or obstacles preventing such analysis have been discussed briefly.     

Occurrence of macro B chromosomes in Astyanax scabripinnis paranae (Pisces,Characiformes, Characidae)

B chromosomes occur in several Neotropical fish species. Cytogenetic analysis of 27 specimens (15 females and 12 males) of Astyanax scabripinnis paranae from the Araquá river (a small headwater tributary of the Tietê river) shows that this population has 2n=50 chromosomes (4M+30 SM+4ST+12A), two chromosome pairs with NORs and conspicuous C-band positive blocks in the terminal position of the long arm of four chromosome pairs. In this population, eight females presented 2n=51 chromosomes and the extra chromosome was a large metacentric similar in size and morphology to the first chromosome pair in the karotype. This accessory chromosome is entirely heterochromatic in C-banded metaphases and shows a late replication pattern evidenced by BrdU incorporation. There was no significant correlation between the presence of B chromosomes and increased NOR activity at the P>0.05 level. Some aspects related to these B chromosomes are discussed.     

Chromosome studies on capsicum (Solanaceae) I. Karyotype analysis in C. Chacoënse

The somatic chromosomes and karyotypes of two Argentine populations of Capsicum chacoënse A. T. Hunz. have been studied, both of which have 2n=24. The karyotypes are symmetrical, being composed of 11 m paris + one st pair; two pairs of chromosomes are satellied: pairs 1 and 12 in one population and pairs 11 and 12 in the other one. A heteromorphic pair of satellited chromosomes in one individual suggests a spontaneous reciprocal translocation. Results are compared with previous reports for the species and genus. Data show an intraspecific karyotype variation.     

牛蛙(Rana catesbeiana)染色体研究

对牛蛙（Rana catesbeiana,Shaw）的染色体组型进行了研究。观察骨髓的C-中期细胞,结果证明牛蛙的体细胞染色体数目2n=26,其中有5对大型染色体和8对小型染色体,可以分成A、B、C3个组,雌性和雄性个体间没有发现异型性染色体。上述结果与前人的研究结果基本一致。但是作者发现牛蛙骨髓细胞的第7、8、10、12号染色体上均有次缢痕。牛蛙的核型为2n：26=22m＋4sm。     

Description of the karyotype of Rhagomys rufescens Thomas, 1886 (Rodentia, Sigmodontinae) from Southern Brazil Atlantic forest

Rhagomys rufescens (Rodentia: Sigmodontinae) is an endemic species of the Atlantic forest from Southern and Southeastern Brazil. Some authors consider Rhagomys as part of the tribe Thomasomyini; but its phylogenetic relationships remain unclear. Chromosomal studies on eight specimens of Rhagomys rufescens revealed a diploid number of 2n = 36 and a number of autosome arms FN = 50. GTG, CBG and Ag-NOR banding and CMA(3) /DAPI staining were performed on metaphase chromosomes. Eight biarmed and nine acrocentric pairs were found in the karyotype of this species. The X and Y chromosomes were both acrocentric. Most of the autosomes and the sex chromosomes showed positive C-bands in the pericentromeric region. The X chromosome showed an additional heterochromatic block in the proximal region of the long arm. Nucleolus organizer regions (NORs) were located in the pericentromeric region of three biarmed autosomes (pairs 4, 6 and 8) and in the telomeric region of the short arm of three acrocentrics (pairs 10, 12 and 17). CMA (3) /DAPI staining produced fluorescent signals in many autosomes, especially in pairs 4, 6, and 8. This study presents cytogenetic data of Rhagomys rufescens for the first time.     

Karyotype,chromosomal characteristics of multiple rDNA clusters and intragenomic variability of ribosomal ITS2 in Caryophyllaeides fennica (Cestoda)

Karyotype and chromosomal characteristics, i.e. number and location of ribosomal DNA (rDNA) clusters, and sequence variation of the ribosomal internal transcribed spacer 2 (ITS2) were studied in a monozoic (unsegmented) tapeworm, Caryophyllaeides fennica (Caryophyllidea), using conventional and Ag-staining, fluorescent in situ hybridization (FISH) with 18S rDNA probe, and PCR amplification, cloning and sequencing of the complete ribosomal ITS2 spacer. The karyotype of this species was composed of ten pairs of metacentric (m) chromosomes (2n = 20). All chromosomes except the pair No. 2 displayed DAPI-positive heterochromatin in centromeric regions. In addition, two distinct interstitial DAPI-positive bands were identified on chromosome pair No. 7. FISH with 18S rDNA probe revealed four clusters of major ribosomal genes situated in the pericentromeric region of the short arms in two pairs of metacentric chromosomes Nos. 8 and 9. Hybridization signals were stronger in the pair No. 8, indicating a higher amount of rDNA repeats at this nucleolar organizer region (NOR). Analysis of 15 ITS2 rDNA sequences (five recombinant clones from each of three individuals) showed 13 structurally different ribotypes, distinguished by 26 nucleotide substitutions and variable numbers and combinations of short repetitive motifs that allowed sorting the sequences into four ITS2 variants. These results contribute to recently published evidence for the intraindividual ribosomal ITS sequence variability in basal tapeworms with multiple rDNA loci and imply that both phenomena may be mutually linked.     

黄鳝体内寄生胃瘤线虫的染色体核型及G-带分析

采用常规空气干燥法制片,对寄生于黄鳝(Monopterus albus)体腔内的胃瘤线虫(Eustrongylidesignotus)染色体核型进行分析。结果表明:胃瘤线虫体细胞有12条染色体,为二倍体,核型公式为2n=12=10 m+2 sm。由5对常染色体和1对性染色体组成,性别决定模式为XX-XY,其中X、Y和1～4号染色体都为中着丝粒染色体,5号为亚中着丝粒染色体。每对染色体都有特定的G-带带型。