Salinity stress tolerance and omics approaches: revisiting the progress and achievements in major cereal crops

Abstract

Salinity stress adversely affects plant growth and causes considerable losses in cereal crops. Salinity stress tolerance is a complex phenomenon, imparted by the interaction of compounds involved in various biochemical and physiological processes. Conventional breeding for salt stress tolerance has had limited success. However, the availability of molecular marker-based high-density linkage maps in the last two decades boosted genomics-based quantitative trait loci (QTL) mapping and QTL-seq approaches for fine mapping important major QTL for salinity stress tolerance in rice, wheat, and maize. For example, in rice, 'Saltol' QTL was successfully introgressed for tolerance to salt stress, particularly at the seedling stage. Transcriptomics, proteomics and metabolomics also offer opportunities to decipher and understand the molecular basis of stress tolerance. The use of proteomics and metabolomics-based metabolite markers can serve as an efficient selection tool as a substitute for phenotype-based selection. This review covers the molecular mechanisms for salinity stress tolerance, recent progress in mapping and introgressing major gene/QTL (genomics), transcriptomics, proteomics, and metabolomics in major cereals, viz., rice, wheat and maize.

Fig. 1. Salinity stress acreage and thresholds in major cereal crops.

a Area under salinity for important cereal (wheat, maize and rice) producing countries; b Different thresholds for salinity sensitivity of various traits in different crops (refer Supplementary Tables 1 and 2 for data source).

Fig. 2. Key players in ion homeostasis in cereals under salt stress.

Non-selective cation channels (NSCC) and high-affinity potassium (HAK) transporters provide entry points for Na⁺ (huge influx) and K⁺ in roots, respectively. The role of voltage insensitive NSCC (VI-NSCC) in Na⁺ uptake under salt stress has been demonstrated in rye, barley, wheat, and several other plant species. HAK transporters work to balance the augmented Na⁺ levels by increasing K⁺uptake (for Na⁺/K⁺ homeostasis). Once inside root cells, salt overlay sensitive (SOS) homologs jump in to exclude Na⁺ from cells. SOS1 is a Na⁺/H⁺ antiporter belonging to the cation protein antiporter family with homologs in rice (OsSOS1), wheat (TaSOS1 and TdSOS1), and maize (ZmNHX7). It is primarily involved in Na⁺ exclusion in roots after activation by serine-threonine kinase (SOS2) and myristoylated calcium-binding protein (SOS3) complex. Na⁺ accumulated in the cytosol is routed to vacuoles through another set of transporters called Na⁺/H⁺ exchangers (NHX), which guide the vacuolar sequestration of Na⁺. NHX transporters are well characterized in roots and leaves of rice (OsNHX1 to OsNHX5), wheat (TaNHX1toTaNHX3 and TaNHX4-B), and maize (ZmNHX1toZmNHX6). HKT are high-affinity K⁺ transporters involved in excluding Na⁺ from xylem vessels and candidate genes for salt-tolerance-related QTL in rice, wheat, and maize. The exclusion of Cl^– ions is mediated by a set of transporters—cation chloride co-transporter (CCC) and chloride transporter (CLC) genes. CCC mediates the exclusion of Cl^– from roots, while CLC transport Cl^– and contributes to salt tolerance.