Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective

Abstract

Improvement of salinity tolerance in rice can minimize the stress-induced yield losses. Rice (Oryza sativa) is one of Asia's most widely consumed crops, native to the subtropical regions, and is generally associated with sensitivity to salinity stress episodes. Salt-tolerant rice genotypes have been developed using conventional breeding methods; however, the success ratio is limited because of the complex nature of the trait and the high cost of development. The narrow genetic base of rice limited the success of conventional breeding methods. Hence, it is critical to launch the molecular tools for screening rice novel germplasm for salt-tolerant genes. In this regard, the latest molecular techniques like quantitative trait loci (QTL) mapping, genetic engineering (GE), transcription factors (TFs) analysis, and clustered regularly interspaced short palindromic repeats (CRISPR) are reliable for incorporating the salt tolerance in rice at the molecular level. Large-scale use of these potent genetic approaches leads to identifying and editing several genes/alleles, and QTL/genes are accountable for holding the genetic mechanism of salinity tolerance in rice. Continuous breeding practices resulted in a huge decline in rice genetic diversity, which is a great worry for global food security. However, molecular breeding tools are the only way to conserve genetic diversity by exploring wild germplasm for desired genes in salt tolerance breeding programs. In this review, we have compiled the logical evidences of successful applications of potent molecular tools for boosting salinity tolerance in rice, their limitations, and future prospects. This well-organized information would assist future researchers in understanding the genetic improvement of salinity tolerance in rice.

Keywords: CRISPR/Cas9; genes; rice; salinity stress; tolerance.

Figure 1

Effects of salinity stress on rice. Salinity stress affects rice seed germination, growth, and photosynthesis. Salinity stress induces ions toxicity, osmotic pressure, dehydration, and alteration in reproduction organs. Salinity stress also reduces roots hairs number, root volume, diameter, root area, length, root dry weight, spikelet’s fertility, grain yield, and nutrients uptake.

Figure 2

Graphical display of the different types of salt tolerance mechanisms in rice. It involves the activation of different salt-responsive TFs and genes which encode different proteins and enzymes. Besides this rice plant also activates the antioxidants defense system, maintains ions homeostasis, and synthesizes osmoprotectants and compatible solutes to counter the toxic effects of salinity stress.

Figure 3

Key steps of CRISPR/Cas9 mediated gene editing for salinity tolerance in rice. CRISPR/Cas9 has the ability to edit the gene of interest for salinity tolerance by a complex mechanism. Mutants plants with salinity tolerance character are exposed to salinity stress to confirm the targeted gene expression.

Figure 4

Role of TFs in the development of salt-tolerant rice cultivars. It is obvious that the expression of TFs is induced by salt stress. TFs are overexpressed in leaves and roots and increase salt tolerance via ABA synthesis regulation, improving seed germination and increasing the activity of antioxidant enzymes. These TFs are transformed into rice cultivars via genetic engineering or targeted using the CRISPR/Cas9 gene-editing tool.