Identification of candidate genes related to salt tolerance of the secretohalophyte Atriplex canescens by transcriptomic analysis

Abstract

Background: Atriplex canescens is a typical C₄ secretohalophyte with salt bladders on the leaves. Accumulating excessive Na⁺ in tissues and salt bladders, maintaining intracellular K⁺ homeostasis and increasing leaf organic solutes are crucial for A. canescens survival in harsh saline environments, and enhanced photosynthetic activity and water balance promote its adaptation to salt. However, the molecular basis for these physiological mechanisms is poorly understood. Four-week-old A. canescens seedlings were treated with 100 mM NaCl for 6 and 24 h, and differentially expressed genes in leaves and roots were identified, respectively, with Illumina sequencing.

Results: In A. canescens treated with 100 mM NaCl, the transcripts of genes encoding transporters/channels for important nutrient elements, which affect growth under salinity, significantly increased, and genes involved in exclusion, uptake and vacuolar compartmentalization of Na⁺ in leaves might play vital roles in Na⁺ accumulation in salt bladders. Moreover, NaCl treatment upregulated the transcripts of key genes related to leaf organic osmolytes synthesis, which are conducive to osmotic adjustment. Correspondingly, aquaporin-encoding genes in leaves showed increased transcripts under NaCl treatment, which might facilitate water balance maintenance of A. canescens seedlings in a low water potential condition. Additionally, the transcripts of many genes involved in photosynthetic electron transport and the C₄ pathway was rapidly induced, while other genes related to chlorophyll biosynthesis, electron transport and C₃ carbon fixation were later upregulated by 100 mM NaCl.

Conclusions: We identified many important candidate genes involved in the primary physiological mechanisms of A. canescens salt tolerance. This study provides excellent gene resources for genetic improvement of salt tolerance of important crops and forages.

Keywords: Atriplex canescens; Differentially expressed gene; Halophyte; Salt tolerance; Transcriptomic analysis.

Fig. 1

Numbers of differentially expressed genes (DEGs) in leaves and roots of A. canescens under 100 mM NaCl for 6 and 24 h. A FDR < 0.001 and an absolute value of the log₂Ratio > 1 were used as the thresholds to determine significant differences in gene expression

Fig. 2

The DEGs related to ion transport in leaves of A. canescens under 100 mM NaCl for 6 (a) and 24 h (b). NHX: tonoplast Na⁺/H⁺ antiporter, SOS1: plasma membrane Na⁺/H⁺ antiporter, HKT: high-affinity K⁺ transporter, KEA: K⁺ efflux antiporter, KCO: calcium-activated outwardly rectifying potassium channel, SKOR: stelar K⁺ outwardly rectifying channel, AKT: inwardly rectifying K⁺ channel, KT/HAK/KUP: K⁺ transporter, CNGC: cyclic nucleotide-gated channel, CCX: cation/Ca²⁺ exchanger, P-Ca²⁺ ATPase: plasma membrane Ca²⁺ ATPase, V-CAX: vacuolar cation/H⁺ exchanger, P-H⁺ ATPase: plasma membrane H⁺ ATPase, V-H⁺ PPase: vacuolar H⁺ PPase, MGT: Mg²⁺ transporter, AMT: NH₄⁺ transporter, NRT: NO₃⁻ transporter, STAS: SO₄²⁻ transporter, PHT: PO₄³⁻ transporter, CLC: vacuolar Cl⁻/H⁺ exchanger, SLAH: Slow type anion channel, CTR: Cu²⁺ transporter, BOR: BO³⁻ transporter, ZnT: Zn³⁺ transporter, MOT: MoO₄²⁻ transporter. The up and down arrows indicate the total number of up and downregulated DEGs, respectively. The same below

Fig. 3

Heatmap of DEGs related to Na⁺, H⁺, glucose transporters and hemoglobin in leaves of A. canescens under 100 mM NaCl for 6 and 24 h

Fig. 4

The DEGs related to ion transport in roots of A. canescens under 100 mM NaCl for 6 (a) and 24 h (b)

Fig. 5

The DEGs related to organic osmolytes synthesis in leaves of A. canescens under 100 mM NaCl for 6 (a) and 24 h (b). P5CS: Δ1-pyrroline-5-carboxylate synthetase, OAT: ornithine aminotransferase, GDH: glutamate dehydrogenase, GOGAT: glutamate synthase, BADH: betaine aldehyde dehydrogenase, CMO: choline monooxygenase, PEAMT: phosphoethanolamine N-methyltransferase, INV: invertase, SuSy: sucrose synthase, SPS: sucrose-phosphate synthase, TPS: trehalose-phosphate synthase, AMS: amylase, SS: starch synthase, MD: mannitol dehydrogenase. The up and down arrows indicate the total number of up and downregulated DEGs, respectively

Fig. 6

Heatmap of the transcript level of genes related to aquaporin in A. canescens under 100 mM NaCl treatment for 6 and 24 h. NIP: nodulin-like intrinsic protein, SIP: small basic intrinsic protein, PIP: plasma membrane intrinsic protein, TIP: tonoplast intrinsic protein. The same below

Fig. 7

The DEGs related to photosynthesis of A. canescens under 100 mM NaCl for 6 (a) and 24 h (b)