Conceptual review on the conventional and genome-wide association analysis towards developing salinity tolerance in rice

Abstract

Salinity is the major abiotic stress which predominantly affects the productivity of rice worldwide. Conventional breeding programs to develop stress-tolerant varieties showed only marginal success. Marker-assisted selection can improve the efficiency of salinity tolerance as they are growth stage and environment independent. However, physiological response due to ionic and osmotic stresses caused by salt accumulation in the soil hinders plant growth and development. Genetic engineering strategy was adopted to tailor the selection and incorporation of candidate salt-tolerant genes in rice. Understanding the genomics of salinity tolerance remains a complex phenomenon since several genes and pathways control them. Genome-wide association studies revealing the information of SNP's variants and functional effects appear to be a future for breeding salinity-tolerant rice. Therefore, this review provides scientific insights into the mechanisms and approaches to enhance salinity tolerance, genome-wide association analysis, and the CRISPR/Cas technology as an efficient tool for genome modifications. Genome-wide association analysis showed the presence of major QTL region SalTol in chromosome 1, containing potential salt tolerant responsive genes in indica varieties. The distribution of SNP and InDels was highest in the Chromosome 1 of Godawee, Pokkali, and Nona Bokra. The SNP and InDels density was not consistent among the varieties. Genome-wide association analysis of SNPs and InDels data highlighted the importance of genomic variants in regulating the salinity tolerance that could be useful for future crop improvements.