Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum

Abstract

Cotton is an important economic crop affected by different abiotic stresses at different developmental stages. Salinity limits the growth and productivity of crops worldwide. Na⁺/H⁺ antiporters play a key role during the plant development and in its tolerance to salt stress. The aim of the present study was a genome-wide characterization and expression pattern analysis under the salinity stress of the sodium-proton antiporter (NHX) of <i>Gossypium barbadense</i> in comparison with <i>Gossypium hirsutum</i>. In <i>G. barbadense</i>, 25 <i>NHX</i> genes were identified on the basis of the Na⁺_H⁺ exchanger domain. All except one of the <i>G. barbadense</i><i>NHX</i> transporters have an Amiloride motif that is a known inhibitor of Na⁺ ions in plants. A phylogenetic analysis inferred three classes of <i>GbNHX</i> genes-viz., Vac (<i>GbNHX1</i>, <i>2</i> and <i>4</i>), Endo (<i>GbNHX6</i>), and PM (<i>GbNHX7</i>). A high number of the stress-related <i>cis</i>-acting elements observed in promoters show their role in tolerance against abiotic stresses. The Ka/Ks values show that the majority of <i>GbNHX</i> genes are subjected to strong purifying selection under the course of evolution. To study the functional divergence of <i>G. barbadense</i><i>NHX</i> transporters, the real-time gene expression was analyzed under salt stress in the root, stem, and leaf tissues. In <i>G. barbadense</i>, the expression was higher in the stem, while in <i>G. hirsutum</i> the leaf and root showed a high expression. Moreover, our results revealed that <i>NHX2</i> homologues in both species have a high expression under salinity stress at higher time intervals, followed by <i>NHX7</i>. The protein-protein prediction study revealed that <i>GbNHX7</i> is involved in the CBL-CIPK protein interaction pathway. Our study also provided valuable information explaining the molecular mechanism of Na⁺ transport for the further functional study of Gossypium <i>NHX</i> genes.