Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

This study focuses on the growth and morpho-physiological responses of the Malaysian commercial variety MR219 rice to salinity stress during the early vegetative stages, specifically during germination and the five-leaf stage. For germination responses, MR219 seeds were grown for 10 days in different salt concentrations. Low salinity significantly improves seed germination and increases the total number of germinated seeds. However, higher salinity (160 mM NaCl) inhibits the germination of MR219 seeds and reduces the total number of germinated seeds by 93.3%. The effects of salinity on the five-leaf stage of MR219 were also determined and compared to the salinity-tolerant (Pokkali) and susceptible (IR64) varieties. There were significant reductions in the photosynthesis rate, transpiration rate, stomatal conductance, and leaf chlorophyll content by 28.1%, 58.6%, 81.1%, and 3.7%, respectively. These reductions could contribute to the significant decrease in growth parameters measured throughout the treatment period. Based on the principal component analysis (PCA) result, MR219 is more tolerant to salinity than IR64, but is less tolerant than Pokkali. Further investigation on stress-related gene expression suggests that significant changes in the transcript level of genes involved in gamma-aminobutyric acid (GABA) shunt, ion transport, and reactive oxygen species detoxification could be attributed to the adaptation and tolerance level of each variety to salinity stress.

MR219 transgenic rice line which overexpressed an auxin-binding protein (ABP57) and its wild-type cultivar, MR219, were screened under well-watered (WW) and drought stress (DS) conditions at the early reproductive stage. This study was conducted with the standard planting distance and under a normal environment to assess the yield advantages based on the field conditions. The aim of this study was to understand the response of these rice genotypes towards DS at morpho-physiological, biochemical, and agronomical levels. It was found that the DS had affected all these levels of the genotypes studied; however, the transgenic plant showed a higher number of tillers, flag leaf area, biomass, relative water content, total chlorophyll content, and antioxidative defense mechanism than the MR219 under DS. Compared to its wild-type, the transgenic plant showed an increased leaf photosynthetic rate by 7% under WW and 11% under DS. The transgenic plant also showed higher yields than MR219 under the WW (10%) and DS (59%). The results propose that drought tolerance is significantly improved in the MR219 transgenic rice line. It may develop a new opportunity for the drought-tolerant rice breeding programme via overexpression of ABP57.

This study investigates the submergence tolerance level of 14 rice genotypes by morpho-physiological and molecular analyses of Sub1 alleles. IR64-Sub1 was used as a submergence tolerant check. The submergence screenings were conducted by submerging 14-days-old seedlings in water tanks for 14 days while molecular analysis was conducted using 14 Sub1 linked markers. The results showed that 5 tested genotypes, namely Inpari 48 Blas, Mundam Putiah, Batang Piaman, Banang Pulau and Pulau Sijunjung, recorded high survival rates (SR) of 80% to 100% under submergence stress. PCR-based identification of the Sub1 alleles confirmed that several tested genotypes carry Sub1A and Sub1C, but not all were expressed in their phenotypic performance towards submergence. IR64-Sub1 and Batang Piaman not only showed well-adaptation towards submergence by maintaining lower elongation (<20%) and less chlorophyll content change (TCC) (<30%) but were also equipped with the Sub1A allele. These genotypes potentially provide good phenotypic and genotypic performance under submergence stress conditions. Additionally, based on population structure analysis, these genotypes were grouped into 3 clusters, of which 35.71% are pure accessions, while the remaining 64.29% have admixture ancestry between populations 1, 2 and 3. The data in model-based population structure and UPGMA dendrogram supported that rice genotypes in this study have 3 well-differentiated genetic populations and admixtures. Most genotypes have a close genetic relationship with Nei’s similarity index ranging from 0.571 to 0.893.