Comparative RNA-Seq Analysis of Extremophile Plants in Native Habitats and Controlled Cabinets is a Viable Approach for Identifying Adaptive Traits

In their natural environments, plants are exposed to complex and variable stresses.  These stresses can be minimized by using controlled environment conditions. However the use of chambers can underestimate the full phenotypic and metabolic plasticity associated with adaptive traits. We used RNA-Seq to compare genetic variation among inbred Eutrema salsugineum (Thellungiella salsuginea) plants growing under controlled environment conditions with plants collected from a highly saline natural environment in the Yukon Territory, Canada.  Using SNP, InDel and transcriptome expression data we show that there was little genetic variation between plants of the Yukon accession inbred five generations by single seed descent and plants selected at random in the field. The greatest genetic diversity was found between two inbred natural accessions, one originating in the Yukon and the second from Shandong, China.  Despite the dynamic and variable nature of their habitat, the transcriptome data from the field plants were no more variable than the highly reproducible data of cabinet-grown plants.  Differentially expressed genes associated with the GO terms “defense response” and “response to stress” were significantly enriched for Yukon and Shandong plants grown under identical cabinet conditions.  Predictably, more GO terms distinguished Yukon plants in cabinets and those from the field and, consistent with the field conditions, enriched terms were dominated by associations with stress and photosynthesis. Thus we show that meaningful comparisons can be made using RNA-Seq data from inbred plants grown under tightly controlled cabinet settings and native plants collected in their complex and variable natural habitat.