Characterization of B chromosomes in Lilium hybrids through GISH and FISH

Supernumerary (B) chromosomes and small aberrant chromosomes were detected in Lilium hybrids and characterized through genomic in situ hybridization (GISH) and florescence in situ hybridization (FISH). Two small, supernumerary or B chromosomes were detected as extra chromosomes in a tetraploid plant derived from chromosome doubling of a hybrid (2n = 2x = 24) between a cultivar of the Longiflorum (L) and the Trumpet (T) group. When this tetraploid LLTT hybrid was crossed with a triploid LLO hybrid (O = Oriental), the B chromosome was transmitted to 73.4 % of the progenies. Based on GISH and FISH characterization, it was shown that the B chromosome consisted of two identical arms, with 5S rDNA hybridizing to the majority of it, which were flanked by normal telomeres, suggesting that this is an isochromosome. In another population, which is a backcross progeny between a F1 hybrid of Longiflorum × Asiatic (LA) and its Asiatic parent, the former produced functional 2n gametes which resulted in a triploid LAA progeny (2n = 3x = 36), in which three exceptional plants possessed 35 normal chromosomes and a small aberrant chromosome instead of the expected normal number of 36. In all three cases, the small aberrant chromosomes were isochromosomes which had obviously originated during the first backcross generation. These three chromosomes showed normal telomeres and mitosis. In addition, one of the new generated chromosomes possessed two 45S rDNA sites in the proximal positions. These new arisen isochromosomes were proposed to originate from centric breakage and fusion of two short arms of the missing chromosome in three genotypes, respectively, based on the comparison of arm lengths as well as rDNA loci. Their relevance to the origin of Bs is discussed.     

芥菜型油菜与埃塞俄比亚芥杂种基因组原位杂交分析

原产于非洲的埃塞俄比亚芥(Brassica carinata,2n=34,BBCC)具有适应于炎热干旱地区种植等特点,是改良我国芥菜型油菜(B.juncea,2n=36,AABB)的重要种质资源。本研究用基因组原位杂交方法(GISH,Genomic in situ hybridization)分析了芥菜型油菜与埃塞俄比亚芥种间杂种花粉母细胞的染色体分离,发现在后期I染色体主要以17∶18类型分离,其次是16∶19,染色体落后现象偶然发生,其中B染色体组以8∶8的分离比率较高,表明不同来源的B染色体可正常配对分离。本研究表明,芥菜型油菜与埃塞俄比亚芥远缘杂交,通过染色体同源重组(B染色体间),以及部分同源染色体配对交换的方式(A、B、C基因组间),有可能将埃塞俄比亚芥优良遗传成分转移到芥菜型油菜中。     

Amphidiploid Brassica juncea contains conserved progenitor genomes.

To perform a detailed study of genome evolution in the natural Brassica amphidiploid B. juncea, we have constructed two linkage maps based on RFLP (restriction fragment length polymorphism) markers; one generated from a cross between a resynthesized B. juncea (a chromosome doubled interspecific B. rapa x B. nigra hybrid) and a natural B. juncea cultivar, the other from a cross between two B. juncea cultivars. By using a common cultivar in both crosses, the two maps could be unambiguously integrated. All loci exhibited disomic inheritance of parental alleles in the natural x resynthesized cross, showing that B. rapa chromosomes paired exclusively with their A-genome homologues in B. juncea and that B. nigra chromosomes likewise paired with their B-genome homologues. The maps derived from the two crosses were also perfectly collinear. Furthermore, these maps were collinear with maps of the diploid progenitor species (B. nigra and B. rapa) produced using the same set of RFLP probes. These data indicate that the genome of B. juncea has remained essentially unchanged since polyploid formation. Our observations appear to refute the suggestion that the formation of polyploid genomes is accompanied by rapid change in genome structure.     

Recombination between chloroplast genomes of Trachystoma ballii and Brassica juncea following protoplast fusion

We document here the presence of a recombinant plastome in a cytoplasmic male sterile (CMS) line of Brassica juncea developed from the somatic hybrid Trachystoma ballii?+?B. juncea. Restriction endonuclease digestion of the chloroplast (cp) DNA has revealed that the recombinant plastome gives rise to novel fragments in addition to the parent-specific fragments. Analysis of the 16S rRNA region by Southern hybridization shows no variation between B. juncea, T. ballii and the CMS line. The rbcL gene region of the recombinant plastome is identical to that in T. ballii. Analysis with probes for psbA and psbD using single and double DNA digests indicates that the hybridization patterns of the recombinant plastome are identical to those of the parents in digests obtained with some restriction enzymes, while novel bands hybridize to probes in other digests. In the psbA region, a B. juncea-specific PstI site and a T. ballii-specific EcoRI site are found in the recombinant plastome. The psbD region of the recombinant plastome contains a B. juncea-specific HindIII site and T. ballii-specific BamHI and HpaII sites. These results indicate the occurrence of intergenomic recombination between the chloroplasts of T. ballii and B. juncea in the somatic hybrid from which the CMS line was developed. The recombined plastome appears to be a mosaic of fragments specific to both parents and the recombination event has occurred in the single-copy regions. These recombinational events have not caused any imbalance in the recombinant plastome in terms of chloroplast-related functions, which have remained stable over generations.     

The genetic identity of alien chromosomes in potato breeding lines revealed by sequential GISH and FISH analyses using chromosome-specific cytogenetic DNA markers.

Genomic in situ hybridization (GISH) is one of the most popular and effective techniques for detecting alien chromatin introgressed into breeding lines; however, GISH analysis alone does not reveal the genetic identity of the alien chromosomes. We previously isolated a set of bacterial artificial chromosomes (BACs) specific to each of the 12 potato chromosomes. These BAC clones can be used as chromosome-specific cytogenetic DNA markers (CSCDMs) for potato chromosome identification. Here we demonstrate that GISH and fluorescence in situ hybridization (FISH), using CSCDMs, can be performed sequentially on the same chromosome preparations. Somatic metaphase chromosomes prepared using an enzymatic digestion and "flame-drying" procedure allows repeated probing up to five times without significant damage to chromosome morphology. The sequential GISH and FISH analyses reveal the genomic origin and genetic identity of the alien chromosomes in a single experiment and also determine whether an alien chromosome has been added to the genetic background of potato or is substituting for a homoeologous potato chromosome. The sequential GISH and FISH procedures should be widely applicable for germplasm characterization, especially in plant species with small-sized chromosomes.     

Physical mapping by FISH and GISH of rDNA loci and discrimination of genomes A and B inScilla scilloides complex distributed in Korea

The chromosomal locations of the 18S-26S (45S) and 5S rDNA loci in cytotypes AA, BB, and AABB ofScilla scilloides Complex from Korea were physically mapped using multicolor fluorescencein situ hybridization (McFISH). Genomicin situ hybridization (GISH) was also performed to distinguish between the AA and BB genomes in allotetraploid AABB plants. One 18S-26S rDNA locus was detected in both AA (a2) and BB (b1 ); one locus also was found in the allopolyploid AABB (b1 ). This demon-strated the loss of that locus in genome A. GISH with biotin-labeled DNA from the BB genome and digoxigenin-labeled 18S-26S rDNA probes revealed that the 18S-26S rDNA in AABB plants was localized in the nucleolus organizer region (NOR) of genome B. One and two 5S rDNA loci were found in diploids AA and BB, respectively. As expected, all three 5S rDNA loci were detected in the AABB plants. The sequence identities of the 5S rDNA genes among cytotypes AA and BB, AA and AABB, and BB and AABB were 99%, 95%, and 95%, respectively. These authors contributed equally to this paper     

Determination by GISH and FISH of hybrid status in Lilium

In the genus Lilium, plants obtained from crosses, especially between distant relatives, are not always hybrids because embryos can develop as a result of apomixis. These plants constitute genetic material of the maternal parent only. In this study, verification of hybrid status of plants which have been obtained from the crosses 'Marco Polo'xLilium henryi and 'Expression'xL. henryi was performed through the use of cytological and molecular cytogenetic methods. According to cytological analyses, all genotypes tested had 2n = 2x = 24 chromosomes. Genomic in situ hybridisation (GISH) was used for hybrid verification. In hybrid plants, this method distinguished all paternal and maternal chromosomes at the stage of somatic metaphase and prophase. For GISH, paternal genomic DNA was used as a probe and maternal DNAs were used as blocks. Fluorescence in situ hybridisation (FISH) with 5S rDNA and 25S rDNA probes was used as the second method of hybrid verification. Selected chromosome markers based on genome-specific localisation of rDNA loci were used for analysis of the F1 hybrids obtained from the crosses 'Marco Polo'xL. henryi and 'Expression'xL. henryi. The presence of marker chromosomes characteristic for each of the paternal genotypes was a confirmation that the plants obtained were hybrids.     

Gene transfer in plants of Brassica juncea using Agrobacterium tumefaciens-mediated transformation

An efficient system for gene transfer into plants of Brassica juncea var. India Mustard, mediated by Agrobacterium tumefaciens. was developed through the manipulation of the culture medium and the use of the appropriate Agrobacterium strain. High frequency shoot regeneration (90–100%) was obtained from hypocotyl explants grown on medium containing 0.9% agarose, 3.3 mg/L AgNO₃ and 0.5–2 mg/L BA in combination with 0.01–0.05 mg/L 2,4-D or 0.1–1 mg/L NAA. Of all the Agrobacterium strains tested, A. tumefaciens A208-SE, carrying the disarmed Ti plasmid and a binary vector pROA93, was the most effective for B. juncea transformation. pROA93 carries the coding sequences of the NPTII and the GUS genes, both driven by a common CaMV 35S promoter in two divergent directions. Inoculated explants grown on the selection medium in the presence of 0.5 mg/L BA and 0.1 mg/L NAA gave rise to transgenic shoots at the highest frequency (9%). All R_o transgenic plants were phenotypically normal, but variation in expression patterns of the GUS gene occurred among the transgenic plants in an organ- and tissue-specific manner. Both the NPTII and the GUS genes were transmitted to the R₁ seed progeny and showed co-segregation.Abbreviations BA benzyladenine - 2,4-D 2,4-dichlorophenoxyacetic acid - NAA naphthaleneacetic acid - NPTII neomycin phosphotransferase type II - GUS -glucuronidase - CaMV cauliflower mosaic virus - MS Murashige and Skoog - X-Gluc 5-bromo-4-chloro-3-indolyl-D--glucuronic acid - IBA indolebutyric acid - SDS sodium dodecyl sulfate     

Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana

We review here the progress that has been achieved using molecular cytogenetics to analyze the genome structure of sugarcane (Saccharum spp) and banana (Musa spp), two crops that are polyploid, of interspecific origin and with chromosomes not distinguishable by their gross morphology. In Saccharum, molecular cytogenetics enabled us to determine the basic chromosome number of two species, Saccharum officinarum and S. spontaneum, involved in the origin of modern cultivars, to quantify the proportion of chromosomes of these species in the genome of modern cultivars, to assess the extent of interspecific chromosome recombination and to clarify the origin of the related species S. barberi. These techniques are also used to monitor introgression with related genera. In Musa, GISH enabled us to differentiate the four genomes involved in banana cultivars and allowed us to determine the genome constitution of several cultivars. FISH was used to analyze the distribution of repeated sequences along the genome.     

The use of combined FISH/GISH in conjuction with DAPI counterstaining to identify chromosomes containing transgene inserts in amphidiploid tobacco

We have used combined fluorescent and genomic in situ hybridization (FISH/GISH) together with 4′,6-diamidino-2-phenylindole (DAPI) counterstaining to determine simultaneously the chromosomal integration site and subgenomic allocation of a transgene insert in amphidiploid tobacco (Nicotiana tabacum, 2n=4x=48). The procedure provides sufficient information on physical markers to identify at least 20 out of 24 chromosome pairs of two tobacco cultivars commonly used in studies on transgene expression and silencing (cv. Petit Havana SR1 and cv. Gatersleben). The chromosomes can be distinguished on the basis of diploid parental ancestry, size, morphology, the presence of rDNA loci and/or intergenomic exchanges, and the DAPI banding pattern, which is shown here for the first time forN. tabacum. From a single ISH experiment, it should now be possible in most cases to identify a tobacco chromosome carrying a transgene insert, thus permitting systematic studies of how the chromosomal location of transgenes influences expression levels. Edited by: D. Schweizer     

Identification of sesame (Sesamum indicum L.) chromosomes using the BAC‐FISH system

• Sesame (Sesamum indicum L.; Pedaliaceae) is a commercially valuable oilseed crop with high oil content. Its small genome size favours the genomic analysis of key biological processes, such as oil synthesis and metabolism. However, the 13 chromosome pairs of sesame have not been characterised because of technological limitations and their small size.
• We constructed a BAC library comprising 57,600 BAC clones for sesame. The estimated genome coverage of the sesame BAC library was 13.8×. The successive double colour fluorescence in situ hybridisation (FISH) with bacterial artificial chromosomes (BACs) for sesame was established in this study.
• Subsequently, the 13 sesame chromosome pairs were individually differentiated using 17 specific BACs for the first time. The schematic of the sesame chromosome set was drawn according to the chromosome relative length and relative position of the BAC signal. The cytogenetic characteristics of sesame chromosomes were also explored.
• The results provide the technical background required for further cytogenetic map construction, genome assembly and localisation of the DNA sequence in sesame.

     

The use of combined FISH/GISH in conjunction with DAPI counterstaining to identify chromosomes containing transgene inserts in amphidiploid tobacco

We have used combined fluorescent and genomic in situ hybridization (FISH/GISH) together with 4′,6-diamidino-2-phenylindole (DAPI) counterstaining to determine simultaneously the chromosome integration site and subgenomic allocation of a transgene in-sert in amphidiploid tobacco (Nicotiana tabacum, 2n = 4x = 48). The procedure provides sufficient information on physical markers to identify at least 20 out of 24 chromosome pairs of two tobacco cultivars commonly used in studies on transgene expression and silencing (cv. Petit Havana SR1 and cv. Gatersleben). The chromosomes can be distinguished on the basis of diploid parental ancestry, size, morphology, the presence of rDNA loci and/or intergenomic exchanges, and the DAPI banding pattern, which is shown here for the first time for N. tabacum. From a single ISH experiment, it should now be possible in most cases to identify a tobacco chromosome carrying a transgene insert, thus permitting systematic studies of how the chromosome location of transgenes influences expression levels. Received: 23 April 1996; in revised form: 11 June 1996 / Accepted: 18 June 1996     

FISH and GISH analysis of the genomic relationships amongPanax species

Ginseng is a well-known medicinal plant that has been used as an anti-aging agent for many years in East Asia. In the genusPanax, only three species,P. ginseng (Oriental ginseng),P. quinquefolius (American ginseng) andP. notoginseng (Chinese ginseng), are currently considered to be important medicinal herbs. Despite the increase in their breeding value, molecular cytogenetic information on the species is not available. To analyze the genomic relationships among thePanax species, FISH (fluorescencein situ hybridization) and GISH (genomicin situ hybridization) techniques were applied. FISH analysis revealed that the 45S and 5S rRNA genes ofP. notoginseng (2n=2x=24) andP. ginseng (2n=4x=48) cluster on a single locus on different chromosomes, whileP. quinquefolius (2n=4x=48),P. japonicus (2n=4x=48), and Korean wild ginseng (2n =4x= 48) had one locus of the 45S rRNA gene and two loci of the 5S rRNA gene, respectively. GISH analysis using genomic DNA as a probe detected strong cross-hybridization of genomes betweenP. ginseng andP. quinquefolius. GISH analysis of other species showed weak or no distinct signals on the chromosomes. Our data revealed thatP. ginseng andP. quinquefolius showed the highest degree of homology, indicating that these species diverged in most recent years.     

豇豆胰蛋白酶抑制剂基因转化芥菜及抗虫鉴定

用农杆菌介导将豇豆胰蛋白酶抑制剂 (CpTI)基因导入芥菜 ,获得了Kan抗性植株 .经PCR扩增、PCR Southern印迹和Northern印迹分析 ,转化再生植株大部分呈阳性 ,而非转化的再生植株均为阴性 ,证明CpTI基因已存在于芥菜基因组中 .在室内进行了喂虫试验 ,结果表明转基因芥菜抗虫性明显高于对照 ,转基因植株之间存在抗虫性差异     

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC‐by‐BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high‐resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high‐resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome‐scale analysis of repetitive sequences and revealed a ~800‐kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone‐by‐clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC‐contig physical map and validate sequence assembly on a chromosome‐arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome‐by‐chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.     

芥菜型油菜种质资源研究进展

本文从收集保存、鉴定、研究、创新和利用5个方面介绍了芥菜型油菜种质资源研究进展。芥菜型油菜起源于亚洲,印度、中国收集的资源最多。芥菜型油菜可以分为中国-东欧类型和中国-印度类型2大类,每一类中均存在较大的遗传变异,许多具有优良性状的种质已经鉴定出来,并对其进行了生理学、遗传学研究。通过远缘杂交、诱变和遗传转化已创造出芥菜型油菜新种质。已鉴定、培育的芥菜型油菜优异种质资源在油菜育种上得到广泛利用。     

Identification of alien chromosomes through GISH and RFLP analysis and the potential for establishing potato lines with monosomic additions of tomato chromosomes.

To increase the potential for establishing a complete series of tomato chromosome addition-sbstitution lines in a potato background, six new BC1 progeny were produced. All of them originated from crosses between three different hexaploid potato (+) tomato fusion hybrids. Three different somatic hybrids, viz., C31-17-5, C31-17-24, and C31-17-51, were used as female parents, and four different tetraploids, viz., Katahdin, Frieslander, 6704-1, and AM66.42 were used as male parents. A characterisation of the genomes of the three fusion hybrids and the six BC1 progenies (6739, 2001, 2002, 2003, 2004, and 2005) through genomic in situ hybridization and restriction fragment length polymorphism (RFLP) analysis indicated that there was preferential tomato chromosome elimination in the fusion hybrids. Similar analyses of the six BC1 progeny indicated that a variable number of the alien tomato chromosomes (6-11) were present in individual plants. RFLP analysis using chromosome specific DNA probes indicated that BC1 progenies had retained all 12 tomato chromosomes, albeit in different individual plants. This means that the available BC1 progenies have the potential for establishing a complete series of tomato chromosome addition-substitution lines in a potato background.