Dataset Information

A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development.

ABSTRACT: Tobacco (Nicotiana tabacum L.) is a species in the large family of the Solanaceae and is important as an agronomic crop and as a model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available that can be used for genome analysis, genetic mapping and breeding. We report here on the development and characterization of 5,119 new and functional microsatellite markers and on the generation of a high-resolution genetic map for the tetraploid tobacco genome. The genetic map was generated using an F2 mapping population derived from the intervarietal cross of Hicks Broadleaf × Red Russian and merges the polymorphic markers from this new set with those from a smaller set previously used to produce a lower density map. The genetic map described here contains 2,317 microsatellite markers and 2,363 loci, resulting in an average distance between mapped microsatellite markers which is less than 2 million base pairs or 1.5 cM. With this new and expanded marker resource, a sufficient number of markers are now available for multiple applications ranging from tobacco breeding to comparative genome analysis. The genetic map of tobacco is now comparable in marker density and resolution with the best characterized genomes of the Solanaceae: tomato and potato.

SUBMITTER: Bindler G

PROVIDER: S-EPMC3114088 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development.

Bindler Gregor G Plieske Jörg J Bakaher Nicolas N Gunduz Irfan I Ivanov Nikolai N Van der Hoeven Rutger R Ganal Martin M Donini Paolo P

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 20110402 2

Tobacco (Nicotiana tabacum L.) is a species in the large family of the Solanaceae and is important as an agronomic crop and as a model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available that can be used for genome analysis, genetic mapping and breeding. We report here on the development and characterization of 5,119 new and functional microsatellite markers and on the generation of a high-resolution genetic map for the tetraploid tobacco ...[more]

PMID: 21461649

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Project description:BackgroundPollen tube growth is essential for plant reproduction and represents a widely employed model to investigate polarized cell expansion, a process important for plant morphogenesis and development. Cellular and regulatory mechanisms underlying pollen tube elongation are under intense investigation, which stands to greatly benefit from a comprehensive understanding of global gene expression profiles in pollen and pollen tubes. Here, RNA sequencing technology was applied to de novo assemble a Nicotiana tabacum male gametophytic transcriptome and to compare transcriptome profiles at two different stages of gametophyte development: mature pollen grains (MPG) and pollen tubes grown for six hours in vitro (PT6).ResultsDe novo assembly of data obtained by 454 sequencing of a normalized cDNA library representing tobacco pollen and pollen tube mRNA (pooled mRNA isolated from mature pollen grains [MPG] and from pollen tubes grown in vitro for 3 [PT3] or 6 [PT6] hours) resulted in the identification of 78,364 unigenes. Among these unigenes, which mapped to 24,933 entries in the Sol Genomics Network (SGN) N. tabacum unigene database, 24,672 were predicted to represent full length cDNAs. In addition, quantitative analyses of data obtained by Illumina sequencing of two separate non-normalized MPG and PT6 cDNA libraries showed that 8979 unigenes were differentially expressed (differentially expressed unigenes: DEGs) between these two developmental stages at a FDR q-value of <0.0001. Interestingly, whereas most of these DEGs were downregulated in PT6, the minor fraction of DEGs upregulated in PT6 was enriched for GO (gene ontology) functions in pollen tube growth or fertilization.ConclusionsA major output of our study is the development of two different high-quality databases representing the tobacco male gametophytic transcriptome and containing encompassing information about global changes in gene expression after pollen germination. Quantitative analyses of these databases 1) indicated that roughly 30% of all tobacco genes are expressed in the male gametophyte, and 2) support previous observations suggesting a global reduction of transcription after pollen germination. Interestingly, a small number of genes, many of which predicted to function in pollen tube growth or fertilization, were found to be upregulated in elongating pollen tubes despite globally reduced transcription.

Project description:The ability of tobacco (Nicotiana tabacum L. cv. Badischer Geudertheimer) for phytomanaging and remediating soil ecological functions at a contaminated site was assessed with a potted soil series made by fading an uncontaminated sandy soil with a contaminated sandy soil from the Borifer brownfield site, Bordeaux, SW France, at the 0%, 25%, 50%, 75%, and 100% addition rates. Activities of sandblasting and painting with metal-based paints occurred for decades at this urban brownfield, polluting the soil with metal(loid)s and organic contaminants, e.g., polycyclic aromatic hydrocarbons, in addition to past backfilling. Total topsoil metal(loid)s (e.g., 54,700 mg Zn and 5060 mg Cu kg-1) exceeded by seven- to tenfold the background values for French sandy soils, but the soil pH was 7.9, and overall, the 1M NH4NO3 extractable soil fractions of metals were relatively low. Leaf area, water content of shoots, and total chlorophyll (Chl) progressively decreased with the soil contamination, but the Chl fluorescence remained constant near its optimum value. Foliar Cu and Zn concentrations varied from 17.8 ± 4.2 (0%) to 27 ± 5 mg Cu kg-1 (100%) and from 60 ± 15 (0%) to 454 ± 53 mg Zn kg-1 (100%), respectively. Foliar Cd concentration peaked up to 1.74 ± 0.09 mg Cd kg-1, and its bioconcentration factor had the highest value (0.2) among those of the metal(loid)s. Few nutrient concentrations in the aboveground plant parts decreased with the soil contamination, e.g., foliar P concentration from 5972 ± 1026 (0%) to 2861 ± 334 mg kg-1 (100%). Vulnerability to drought-induced embolism (P50) did not differ for the tobacco stems across the soil series, whereas their hydraulic efficiency (Ks) declined significantly with increasing soil contamination. Overall, this tobacco cultivar grew relatively well even in the Borifer soil (100%), keeping its photosynthetic system healthy under stress, and contaminant exposure did not increase the vulnerability of the vascular system to drought. This tobacco had a relevant potential to annually phytoextract a part of the bioavailable soil Zn and Cd, i.e., shoot removals representing here 8.8% for Zn and 43.3% for Cd of their 1M NH4NO3 extractable amount in the potted Borifer soil.

Project description:BACKGROUND:Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with coding RNAs in modulating and controlling of cellular process in plants is largely unknown. Using a diverse group of high-throughput sequencing strategies, the mRNA, miRNA, lncRNA and circRNA compositions of tobacco (Nicotiana tabacum) roots determined and their alteration and potential biological functions in response to topping treatment analyzed. RESULTS:A total of 688 miRNAs, 7423 non-redundant lncRNAs and 12,414 circRNAs were identified, among which, some selected differentially expressed RNAs were verified by quantitative real-time PCR. Using the differentially expressed RNAs, a co-expression network was established that included all four types of RNAs. The number of circRNAs identified were higher than that of miRNAs and lncRNAs, but only two circRNAs were present in the co-expression network. LncRNAs appear to be the most active ncRNAs based on their numbers presented in the co-expression network, but none of them seems to be an eTM (endogenous Target Mimicry) of miRNAs. Integrated with analyses of sequence interaction, several mRNA-circRNA-miRNA interaction networks with a potential role in the regulation of nicotine biosynthesis were uncovered, including a QS-circQS-miR6024 interaction network. In this network miR6024 was significantly down-regulated, while the expression levels of its two targets, circQS and its host gene QS, were sharply increased following the topping treatment. CONCLUSIONS:These results illustrated the transcriptomic profiles of tobacco roots, the organ responsible for nicotine biosynthesis. mRNAs always play the most important roles, while ncRNAs are also expressed extensively for topping treatment response, especially circRNAs are the most activated in the ncRNA pool. These studies also provided insights on the coordinated regulation module of coding and non-coding RNAs in a single plant biological sample. The findings reported here indicate that ncRNAs appear to form interaction complex for the regulation of stress response forming regulation networks with transcripts involved in nicotine biosynthesis in tobacco.

Dataset Information

A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development.

Publications

A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development.

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