Progeny analysis of the interspecific somatic hybrids: Nicotiana tabacum (CMS) + Nicotiana sylvestris with respect to nuclear and chloroplast markers

Summary The progeny of a fusion experiment involving N. sylvestris protoplasts and X-irradiated protoplasts of the cytoplasmic male sterile Line 92 (N. tabacum nucleus and alien, male-sterility inducing, cytoplasm) were analyzed. Three groups of somatic hybrid plants resulted: Type A, Type B-1 and Type B-2. These as well as their androgenic progenies and the progenies resulting from their pollination with N. tabacum or N. sylvestris were followed with respect to several nuclear and cytoplasmic traits. Those controlled by the nuclear genome were plant and flower morphologies; those controlled by genetic information in the cytoplasm were tentoxin sensitivity (affecting the coupling factor of chloroplast ATPase), the large subunit of ribulose bisphosphate carboxylase and the restriction endonuclease pattern of plastid DNA. A further cytoplasmic trait investigated (exact site of genetic control not known) was male sterility. The examinations of the somatic-hybrid groups and their respective progenies indicated that: Type A plants have N. sylvestris nuclei and Line 92 plastids; Type B-1 plants also have Line 92 plastids but their genome is composed of N. sylvestris and N. tabacum nuclei; Type B-2 plants with impaired male fertility had N. sylvestris plastids and N. sylvestris nuclei.     

Ethylene Production by Tobacco (Nicotiana tabacum) Callus

Tobacco callus cultures grown on defined agar-solidified media produced ethylene in differing amounts, which were related to cultural treatment and age of the callus. There was a close correlation between the rate of ethylene production and growth. In darkness, maximal rates occurred in the third week of growth with ethylene production in the range of 750 nl (callus piece)^?1 d^?1 (fr. wt. = 1.5 g), and in the light, maximal rates occurred in the first week of growth, 200 nl (callus piece)^?1 d^?1 (fr. wt. = 200 mg). Growth was also correlated with ethylene production when the latter was altered by exposure of the callus to inhibitors of ethylene synthesis, L-canaline, benzyl isothiocyanate, and 3,5-diiodo-4-hydroxy-benzoic acid. No correlation was found following treatment with AgNO₃, a presumptive inhibitor of ethylene action. The inhibition of growth and ethylene production by L-canaline was partially reversed by gassing the cultures with ethylene (1 μl/1). A mercuric perchlorate sink had no significant effect on growth. A possible relationship between ethylene evolution and growth is discussed.     

Phylogenetic relationships in the grass family (Poaceae) based on the nuclear single copy locus topoisomerase 6 compared with chloroplast DNA

Phylogenetic relationships within the grass family were studied using a newly obtained locus of the nuclear single copy gene topoisomerase 6 (Topo6) spanning the four exons 8–11 and the chloroplast matK gene. Data were evaluated using maximum parsimony, maximum likelihood and Bayesian methods. All analyses showed genera Streptochaeta and Anomochloa as early diverging, followed by Pharus as sister to the rest of the Poaceae, and monophyly of the subfamily Anomochlooideae was supported by the nuclear dataset. The remaining grasses formed a strongly supported and monophyletic group, which split into the major clades BEP and PACMAD in the Topo6 analyses. Monophyly of the BEP clade was strongly supported by the Topo6 data. The results showed clearly incongruity between the two sets of data, such as the different subfamilial relationships of Bambusoideae, Ehrhartoideae and Pooideae. Most of the analysed species are representatives of subfamily Pooideae, which was analysed in more detail by PCR fragment length differences of another Topo6 region spanning the exons 17–19. Monophyly of Pooideae was strongly supported by the matK data, whereas the nuclear data placed Brachyelytrum outside of the remaining Pooideae. Relationships within the early evolutionary lineages remained largely unresolved in the phylogenetic trees, but the ‘core’ Pooideae (Aveneae/Poeae tribe complex and Hordeeae) were highly supported in all analyses. The differences in amplification lengths illustrate the tribe and subtribe classification of Pooideae. The comparatively conserved structure of the newly studied Topo6 region makes it a promising marker from the nuclear genome that could be successfully PCR-amplified to study higher-level phylogenetic relationships within grasses and perhaps between families within the order Poales.     

The 2005 version of the chloroplast DNA sequence from tobacco (Nicotiana tabacum)

The complete nucleotide sequence of tobacco chloroplast DNA was first determined in 1986, and then its updated gene map was reported in 1998. During the course of sequencing the chloroplast DNA ofNicotiana sylvestris, the female progenitor of tobacco, we found some sequence errors and amended the 1998 version. The tobacco chloroplast DNA comprises 155,943 bp, 4 bp longer than the 1998 version.     

实时荧光定量PCR(TaqMan)法测定外源基因的拷贝数

实时荧光定量PCR是近年新兴的一项技术,因其快速、方便、便宜,需要DNA样品量少,无需放射性检测等优点被广泛应用于基因的定量分析。该文就实时荧光定量PCR(TaqMan)技术的发展、基本原理及测定外源基因拷贝数的技术流程做一介绍。     

A Broad Spectrum Tissue Culture Experiment with Tobacco (Nicotiana tabacum) Pith Tissue Callus

The composition and rationale of a broad spectrum tissue culture experiment involving 81 different media are described. Tobacco calluses sub-cultured on media in this experiment were induced to form six main types of callus depending on the concentration levels of minerals, auxins, cytokinins, and sucrose, growth factors and amino acids in the medium. Only nine of the 81 media inhibited callus growth, and growth (increase in mass divided by initial mass of fresh matter) varied considerably reaching a maximum of nearly 200 after eight weeks on a medium high in minerals, cytokinins, sucrose, growth factors and amino acids and low in auxins. Five media induced regeneration from the calluses. This experiment is suggested as a potentially fruitful introductory test for many new or unresolved tissue culture situations.     

Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization

The European rabbit (Oryctolagus cuniculus) is relevant in a large spectrum of fields: it is a livestock, a pet, a biomedical model and a biotechnology tool, a wild resource and a pest. The sequencing of the rabbit genome has opened new perspectives to study this lagomorph at the genome level. We herein investigated for the first time the O. cuniculus genome by array comparative genome hybridization (aCGH) and established a first copy number variation (CNV) genome map in this species comprising 155 copy number variation regions (CNVRs; 95 gains, 59 losses, 1 with both gain and loss) covering ~0.3% of the OryCun2.0 version. About 50% of the 155 CNVRs identified spanned 139 different protein coding genes, 110 genes of which were annotated or partially annotated (including Major Histocompatibility Complex genes) with 277 different gene ontology terms. Many rabbit CNVRs might have a functional relevance that should be further investigated.     

Identification of copy number variation of CAPN10 in Thais with type 2 diabetes by multiplex PCR and denaturing high performance liquid chromatography (DHPLC)

Copy number variations (CNVs) have been shown to be associated with several diseases. They can cause deviation of genotypes from Hardy-Weinberg Equilibrium (HWE). Genetic case-control association studies in Thais revealed that genotype distribution of CAPN10 Indel19 was deviated from HWE after correction of genotyping error. Therefore, we aim to identify CNVs within CAPN10 Indel19 region. The semi-quantitative denaturating high performance liquid chromatography (DHPLC) method was used to detect CNVs in the region of CAPN10 Indel19 marker in cohort of 305 patients with type 2 diabetes and 250 control subjects without diabetes. CNVs in the region of CAPN10 Indel19 was successfully detected by DHPLC. After correction of genotype calling based on the status of identified CNVs, CAPN10 Indel19 genotypes were well-fitted for HWE (p>0.05). However, we did not find association between CNV genotypes and risk of type 2 diabetes in our population. CNVs in CAPN10 have been identified in Thais. These CNVs lead to deviation from HWE of CAPN10 Indel19 genotypes. After excluding identified CNVs from the analysis, CAPN10 Indel19 was associated with type 2 diabetes. The information obtained from our study would be helpful for genotyping accuracies of SNPs residing in the CNVs region.     

烤烟SSR标记多样性及与致香物质的关联分析

了解烤烟品种的遗传多样性,寻找与烤烟致香物质含量关联的分子标记,挖掘高致香物质含量的优异等位变异与种质,对香气品质分子标记辅助育种具有重要意义。本研究检测了山东和四川2个生态区60份烤烟种质中76种致香物质的含量;筛选覆盖全基因组的1914个SSR标记,利用得到的390对多态性引物扩增供试群体。用基于Nei's(1983)遗传距离的邻接法(Neighor-joining,NJ)进行聚类分析。在分析群体结构的基础上,利用混合线性模型进行关联分析,并进一步发掘极显著关联标记的优异等位变异和种质。结果检测到928个等位变异,平均每个位点2.38个等位变异,变化范围为2~5个。PIC值的变化范围分别为0.141~0.733,平均值0.332。这说明供试群体遗传多样性较丰富。聚类分析将该群体划分为2个亚群,划分结果体现了烤烟品种间的亲缘关系;群体结构分析与聚类结果基本一致。关联分析结果显示:共有56个SSR标记位点与41种致香物质同时在2个生态区显著关联(P0.05)。共5个标记与6个性状在2个生态区极显著关联(P0.01),6种致香物质为草酸、肉豆蔻酸、2,4-庚二烯醛、芳樟醇、a-松油醇和gamma-壬内酯,关联标记分别为PT50662、PT60191、PT52263、PT60597、PT60597和PT52722。关联位点表型解释率为12.54%~42.20%。进一步分析发掘了14种致香物质的优异等位变异,并筛选出含增效等位变异较多的种质:净叶黄、抗9201、单育二号、满屋香、金星6007、秦烟95等。这对香气品质分子标记辅助选择育种以及亲本材料选配等奠定了基础。     

Attempted Transformation of Wheat (Triticum aestivum) and Tobacco (Nicotiana tabacum) by Plasmid DNA Uptake Via the Pollen-tube Pathway

Plasmid DNA (CaMVGUS, containing β-glucuronldase gene) was used to transform developing seed of wheat and tobacco through pollen-tube pathway. The DNA was applied on the ovule end of excised styles and stigmas of wheat and tobacco after pollination. None of the 272 wheat and 13,567 tobacco plants obtained after application of the isolated DNA showed β-glucuronidase activity suggesting that the pollen-tube pathway may not be effective for transformation of plants.     

Phylogeny of Crocus (Iridaceae) based on one chloroplast and two nuclear loci: Ancient hybridization and chromosome number evolution

Crocus consists of about 100 species distributed from western Europe and northern Africa to western China, with the center of diversity on the Balkan Peninsula and in Asia Minor. Our study focuses on clarifying phylogenetic relationships and chromosome number evolution within the genus using sequences of the chloroplast trnL-F region, the nuclear ribosomal DNA internal transcribed spacer (ITS) region, and a part of the nuclear single-copy gene pCOSAt103.In a combined dataset of ITS and trnL-F sequences, 115 individuals representing 110 taxa from both subgenera and all sections and series of Crocus were analyzed with Bayesian phylogenetic inference. For pCOSAt103 79 individuals representing 74 Crocus taxa were included, and for the majority of them PCR amplicons were cloned and up to eight clones per individual were sequenced to detect allopolyploidization events. Romulea species were included as outgroup in both analyses. Characteristics of seed surface structures were evaluated by scanning electron microscopy.Phylogenetic analysis of ITS/trnL-F data resulted in a monophyletic genus Crocus, probably monophyletic sections Crocus and Nudiscapus, and inferred monophyly for eight of the 15 series of the genus. The C. biflorus aggregate, thought to be consisting of closely related subspecies, was found to be polyphyletic, the taxa occurring within three major clades in the phylogenetic tree. Cloning of pCOSAt103 resulted in the detection of homoeologous copies in about one third of the taxa of section Nudiscapus, indicating an allotetraploid origin of this section. Reconstruction of chromosome number evolution along the phylogenetic tree using a probabilistic and a parsimony approach arrived at partly contradictory results. Both analyses agreed however on the occurrence of multiple polyploidization and dysploidy events. B chromosomes evolved at least five times independently within the genus, preferentially in clades characterized by karyotype changes.     

Assimilation of Phytate-phosphorus by the Extracellular Phytase Activity of Tobacco (Nicotiana tabacum) is Affected by the Availability of Soluble Phytate

Phytate, the major organic phosphorus in soil, is not readily available to plants as a source of phosphorus (P). It is either complexed with cations or adsorbed to various soil components. The present study was carried out to investigate the extracellular phytase activities of tobacco (Nicotiana tabacum variety GeXin No.1) and its ability to assimilate external phytate-P. Whereas phytase activities in roots, shoots and growth media of P_i-fed 14-day-old seedlings were only 1.3–4.9% of total acid phosphatase (APase) activities, P starvation triggered an increase in phytase secretion up to 914.9 mU mg⁻¹ protein, equivalent to 18.2% of total APase activities. Much of the extracellular phytase activities were found to be root-associated than root-released. The plants were not able to utilize phytate adsorbed to sand, except when insoluble phytate salts were preformed with Mg²⁺ and Ca²⁺ ions for supplementation. Tobacco grew better in sand supplemented with Mg-phytate salts (31.9 mg dry weight plant⁻¹; 0.68% w/w P concentration) than that with Ca-phytate salts (9.5 mg plant⁻¹; 0.42%), presumably due to its higher solubility. We conclude that insolubility of soil phytate is the major constrain for its assimilation. Improving solubility of soil phytate, for example, by enhancement of citrate secretion, may be a feasible approach to improve soil phytate assimilation.     

The integrative expression of GUS gene driven by FCP promoter in the seaweed Laminaria japonica (Phaeophyta)

In this study, the background activity of β-glucuronidase (GUS) was analyzed histochemically and fluorometrically in the negative control of Laminaria japonica (Phaeophyta) thalli, showing low level of activity. GUS gene transformation without selectable gene in L. japonica was performed using four different promoters, i.e., Cauliflower mosaic virus 35S promoter (CaMV35S) from cauliflower mosaic virus, ubiquitin promoter (UBI) from maize, adenine-methyl transfer enzyme gene promoter (AMT) from virus in green alga Chlorella, and fucoxanthin chlorophyll a/c-binding protein gene promoter (FCP) from diatom Phaeodactylum tricornutum. The GUS transient activity was determined fluorometrically after bombarding sliced parthenogenetic sporophytes explants, and it was found that the activity resulting from CaMV35S and FCP promoters (in 114.3 and 80.6 pmol MU min⁻¹ (mg protein)⁻¹, respectively) was higher than for the other two promoters. The female gametophytes were bombarded and regenerated parthenogenetic sporophytes. FCP was the only promoter that resulted in detectable GUS chimeric expression activity during histochemical staining and polymerase chain reaction. Results of Southern blot showed that GUS gene was integrated with the L. japonica genome.     

Development of a fed-batch fermentation process to overproduce phosphoenolpyruvate carboxykinase using an expression vector with promoter and plasmid copy number controllable by heat

To effectively achieve tight regulation and high-level expression of cloned genes, a novel expression plasmid has been developed to contain the promoter and allow the plasmid copy number to be controlled by heat. The feasibility of the plasmid was tested by overproducing the pck gene product (Pck), a protein responsible for cell growth on gluconeogenic carbons and with potential toxicity. By fusing the pck gene with the promoter on the plasmid, the Escherichia coli strain harboring the composite vector was shown to produce various amounts of Pck in response to different degrees of heat shock. With the use of a 30 degrees -->41 degrees C stepwise upshift, the shake-flask culture of recombinant cells enabled production of maximal Pck in soluble form accounting for 20% of total cell protein. In sharp contrast, Pck production was undetectable in the uninduced cell, and this was further confirmed by the failed growth of strain JCL1305, defective in the essential genes for gluconeogenesis, carrying the composite vector on succinate at 30 degrees C. By exploiting the fed-batch fermentation approach, the recombinant cell batch initially kept at 30 degrees C in a lab-scale fermentor was exposed to 41 degrees C for 2 h at the batch fermentation stage, followed by a reduction in temperature to 37 degrees C throughout the remainder of the culturing process. Consequently, this resulted in Pck production equivalent to 15% of total cell protein. The total Pck yield thus calculated was amplified 1880-fold over that obtained at the shake-flask scale. Overall, there is great promise for this expression system due to its tight control, high production, simple thermomodulation, and feasible scale-up of recombinant proteins.     

Origin of the disjunct tetraploid Cardamine amporitana (Brassicaceae) assessed with nuclear and chloroplast DNA sequence data

Seventy-four nucleotide sequences from the ITS regions of nuclear ribosomal DNA and 76 from the trnL-trnF spacer of chloroplast DNA were used to address the origin of tetraploid Cardamine amporitana, the conspecifity of central Italian and northeastern Spanish populations, and the possible cause for such geographic disjunction. Because of the complex lineage relationships in Cardamine, the sampling included 22 taxa. In the results, both data sets are highly congruent in supporting a close relationship of C. amporitana to the widespread Eurasian C. amara. Low genetic variability in northeastern Spanish populations of C. amporitana suggests long-distance dispersal from central Italy. The interior position of the single northeastern Spanish haplotype in a statistical parsimony network of trnL-trnF haplotypes however does not support this scenario and invokes other plausible phylogeographic explanations. The disappearance of geographically intermediate populations and genetic impoverishment by migration and isolation, both probably associated with Quaternary climatic oscillations, appears as an alternative hypothesis to explain the phylogeographic pattern. A recent hybridization event is reported between C. amporitana and a diploid from the C. pratensis group in central Italy on the basis of additive polymorphisms in ITS for all the 22 distinguishing nucleotides.