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Open Access Research article

Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties

Florian Martin1, Lucien Bovet1, Audrey Cordier1, Mario Stanke2, Irfan Gunduz3, Manuel C Peitsch1 and Nikolai V Ivanov1*

Author Affiliations

1 Philip Morris International R&D, Philip Morris Products SA, Neuchatel, 2000, Switzerland

2 Institut für Mathematik und Informatik, Greifswald, D-17487, Germany

3 Philip Morris International Operations, Neuchatel, 2000, Switzerland

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BMC Genomics 2012, 13:674  doi:10.1186/1471-2164-13-674

Published: 28 November 2012

Abstract

Background

For decades the tobacco plant has served as a model organism in plant biology to answer fundamental biological questions in the areas of plant development, physiology, and genetics. Due to the lack of sufficient coverage of genomic sequences, however, none of the expressed sequence tag (EST)-based chips developed to date cover gene expression from the whole genome. The availability of Tobacco Genome Initiative (TGI) sequences provides a useful resource to build a whole genome exon array, even if the assembled sequences are highly fragmented. Here, the design of a Tobacco Exon Array is reported and an application to improve the understanding of genes regulated by cadmium (Cd) in tobacco is described.

Results

From the analysis and annotation of the 1,271,256 Nicotiana tabacum fasta and quality files from methyl filtered genomic survey sequences (GSS) obtained from the TGI and ~56,000 ESTs available in public databases, an exon array with 272,342 probesets was designed (four probes per exon) and tested on two selected tobacco varieties.

Two tobacco varieties out of 45 accumulating low and high cadmium in leaf were identified based on the GGE biplot analysis, which is analysis of the genotype main effect (G) plus analysis of the genotype by environment interaction (GE) of eight field trials (four fields over two years) showing reproducibility across the trials. The selected varieties were grown under greenhouse conditions in two different soils and subjected to exon array analyses using root and leaf tissues to understand the genetic make-up of the Cd accumulation.

Conclusions

An Affymetrix Exon Array was developed to cover a large (~90%) proportion of the tobacco gene space. The Tobacco Exon Array will be available for research use through Affymetrix array catalogue. As a proof of the exon array usability, we have demonstrated that the Tobacco Exon Array is a valuable tool for studying Cd accumulation in tobacco leaves. Data from field and greenhouse experiments supported by gene expression studies strongly suggested that the difference in leaf Cd accumulation between the two specific tobacco cultivars is dependent solely on genetic factors and genetic variability rather than on the environment.

Keywords:
Tobacco plant; Nicotiana tabacum; Exon array; Gene expression; Cadmium accumulation