Linking the Salt Transcriptome with Physiological Responses of a Salt-Resistant Populus Species as a Strategy to Identify Genes Important for Stress Acclimation

Abstract

To investigate early salt acclimation mechanisms in a salt-tolerant poplar species (Populus euphratica), the kinetics of molecular, metabolic, and physiological changes during a 24-h salt exposure were measured. Three distinct phases of salt stress were identified by analyses of the osmotic pressure and the shoot water potential: dehydration, salt accumulation, and osmotic restoration associated with ionic stress. The duration and intensity of these phases differed between leaves and roots. Transcriptome analysis using P. euphratica-specific microarrays revealed clusters of coexpressed genes in these phases, with only 3% overlapping salt-responsive genes in leaves and roots. Acclimation of cellular metabolism to high salt concentrations involved remodeling of amino acid and protein biosynthesis and increased expression of molecular chaperones (dehydrins, osmotin). Leaves suffered initially from dehydration, which resulted in changes in transcript levels of mitochondrial and photosynthetic genes, indicating adjustment of energy metabolism. Initially, decreases in stress-related genes were found, whereas increases occurred only when leaves had restored the osmotic balance by salt accumulation. Comparative in silico analysis of the poplar stress regulon with Arabidopsis (Arabidopsis thaliana) orthologs was used as a strategy to reduce the number of candidate genes for functional analysis. Analysis of Arabidopsis knockout lines identified a lipocalin-like gene (AtTIL) and a gene encoding a protein with previously unknown functions (AtSIS) to play roles in salt tolerance. In conclusion, by dissecting the stress transcriptome of tolerant species, novel genes important for salt endurance can be identified.

Genomic insights into salt adaptation in a desert poplar

“…Populus euphratica is an excellent candidate for the analysis of salt tolerance 22 , as it displays apoplastic sodium accumulation and develops leaf succulence after prolonged salt exposure 8 . Consequently, in the last decade it has become a model for elucidating both physiological and molecular mechanisms of salt tolerance in tree species [5][6][7][8][9][10][11] . Using a newly developed fosmid-pooling strategy 14 , we sequenced and assembled the complex genome of P. euphratica with high heterozygosity and compared it with the closely related salt-sensitive model plant, P. trichocarpa.…”

“…More than 30 wild Populus species occur across diverse habitats over a wide geographical range, thereby providing an excellent system for unravelling the genetic bases of adaptive divergence 4 . Populus euphratica Oliv., which is native to desert regions ranging from western China to North Africa, is characterized by extraordinary adaptation to salt stress [5][6][7][8] . Notably, at high salinity it maintains higher growth and photosynthetic rates than other poplar species 9,10 and can survive concentrations of NaCl in nutrient solution up to 450 mM 11 .…”

Identification of Differentially Expressed Genes by cDNA-AFLP Technique in Response to Drought Stress in Triticum durum

“…A wide range of techniques and strategies are being employed these days to identify genes involved in stress responses (14). Although DNA microarrays are currently the standard tool for genome-wide expression analysis, their application also is limited to organisms for which the complete genome sequence or large collections of known transcript sequences are available (23,24). Next generation sequencing, such as RNAseq are also valuable tools for transcriptional studies, especially when working with organisms that do not have completely sequenced genomes.…”

Plant Abiotic Stress: Insights from the Genomics Era

“…Ultimately two genes, a lipocalin-like gene and a gene encoding a protein with previously unknown functions were identified and shown to display salt-sensitive phenotypes in Arabidopsis knockout mutants, suggesting these genes play roles in salt tolerance. These results are quite exciting, since they demonstrate saltsusceptible plants harbor genes important for salt tolerance that cannot be identified by conventional salt screens relying on differential gene expression (Brinker et al 2010). Foxtail millet (Setaria italica) is a food and fodder grain crop grown in arid and semi-arid regions (Puranik et al, 2011) and is a self-pollinating, diploid, C4 grass.…”

“…A recent microarray study of P. euphratica by Brinker et al (2010) noted three distinct transcriptome phase changes associated with salt stress, with the duration and intensity of these phases differing between the leaf and root tissues sampled. Key factors initially involved with salinity-stress are molecular chaperones, namely the dehydrins and osmotin, which assist with protein stabilization.…”