In Silico Characterisation and Determination of Gene Expression Levels of the CPK Family Under Saline Stress Conditions in Chenopodium quinoa Willd

TL;DR

This study identifies and evaluates CPK genes in quinoa under salt stress, finding specific genes linked to salt tolerance and antioxidant activity.

Contribution

The study identifies specific CPK genes (CqCPK12, CqCPK17, CqCPK20, CqCPK32) associated with salt tolerance in quinoa through in silico and experimental analysis.

Findings

Sixteen CPK family sequences with conserved domains were identified in quinoa.

Salt-tolerant accession UNSA_VP033 showed overexpression of CqCPK12, CqCPK17, CqCPK20, and CqCPK32 with higher antioxidant activity.

Promoter analysis revealed cis-elements related to stress and hormonal responses in CPK genes.

Abstract

Quinoa (Chenopodium quinoa Willd.) is a highly nutritious crop known for its tolerance to salt stress; however, the molecular mechanisms underlying this trait remain poorly understood. This study aims to perform the in silico characterisation of calcium-dependent protein kinase (CPK) gene family sequences and to evaluate their expression profiles under salt stress conditions. Using bioinformatics tools, CPK family gene sequences were identified and in silico-characterised, including conserved domains, cis-regulatory motifs, and physicochemical properties. Experimentally, two contrasting accessions were compared: a salt-tolerant one (UNSA_VP033) and a salt-sensitive one (UNSA_VP021). Salt tolerance indices were determined during germination, gene expression levels were quantified by RT-qPCR, and antioxidant enzyme activities, along with malondialdehyde (MDA) content, were evaluated under different NaCl concentrations. Sixteen sequences with characteristic CPK family domains were identified. Promoter analysis revealed cis-elements associated with hormonal and stress responses. Physicochemical parameters predicted proteins of 50–60 kDa with variable isoelectric points. Experimentally, UNSA_VP033 showed the significant overexpression of CqCPK12, CqCPK17, CqCPK20, and CqCPK32, correlated with the higher antioxidant activity of superoxide dismutase (SOD) and peroxidase (POD), and lower MDA levels at 200 mM NaCl. In contrast, the sensitive accession exhibited significant reductions in gene expression and antioxidant activity. In conclusion CPK genes play a key role in the salt stress response in quinoa, particularly CqCPK12, CqCPK17, CqCPK20, and CqCPK32 in the tolerant accession. These findings may contribute to the development of more salt-tolerant varieties, thereby enhancing agricultural sustainability in saline soils.

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