RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions

BMC Genomics

Research Article

Wilson WL Sung¹  Susan A Dudley¹  Rupa Salwan¹  Elizabeth A Weretilnyk¹  Vasile Catana¹  Marc J Champigny¹  Peter S Summers¹  G Brian Golding¹  Robin K Cameron¹  Nicholas J Provart² 

[1] Department of Biology, McMaster University, L8S 4K1, Hamilton, Ontario, Canada;Department of Cell and Systems Biology, University of Toronto, M5S 3B2, Toronto, Ontario, Canada;

关键词: Eutrema salsugineum;    Thellungiella salsuginea;    Transcriptome profiling;    RNA-Seq;    Salt tolerance;    Natural plant populations;    Single nucleotide polymorphisms;    Phenotypic plasticity;    Ecological genomics;    Natural field conditions;    Halophyte;    Extremophile;    Plant stress tolerance traits;   

DOI  :  10.1186/1471-2164-14-578

 received in 2013-05-31, accepted in 2013-08-17,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions. Accordingly, transcriptome sequencing offers a powerful approach to address questions concerning the influence of natural habitat on the physiology of an organism. We used RNA sequencing of Eutrema salsugineum, an extremophile relative of Arabidopsis thaliana, to investigate the extent to which genetic variation and controlled versus natural environments contribute to differences between transcript profiles.ResultsUsing 10 million cDNA reads, we compared transcriptomes from two natural Eutrema accessions (originating from Yukon Territory, Canada and Shandong Province, China) grown under controlled conditions in cabinets and those from Yukon plants collected at a Yukon field site. We assessed the genetic heterogeneity between individuals using single-nucleotide polymorphisms (SNPs) and the expression patterns of 27,016 genes. Over 39,000 SNPs distinguish the Yukon from the Shandong accessions but only 4,475 SNPs differentiated transcriptomes of Yukon field plants from an inbred Yukon line. We found 2,989 genes that were differentially expressed between the three sample groups and multivariate statistical analyses showed that transcriptomes of individual plants from a Yukon field site were as reproducible as those from inbred plants grown under controlled conditions. Predicted functions based upon gene ontology classifications show that the transcriptomes of field plants were enriched by the differential expression of light- and stress-related genes, an observation consistent with the habitat where the plants were found.ConclusionOur expectation that comparative RNA-Seq analysis of transcriptomes from plants originating in natural habitats would be confounded by uncontrolled genetic and environmental factors was not borne out. Moreover, the transcriptome data shows little genetic variation between laboratory Yukon Eutrema plants and those found at a field site. Transcriptomes were reproducible and biological associations meaningful whether plants were grown in cabinets or found in the field. Thus RNA-Seq is a valuable approach to study native plants in natural environments and this technology can be exploited to discover new gene targets for improved crop performance under adverse conditions.

【 授权许可】

Unknown   
© Champigny et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.