Differential Evaluation of Basmati and Non-basmati Rice Varieties Under Salt Stress Conditions and in-silico Analysis of Salt Responsive Genes

Abstract

Rice (Oryza sativa L.), belonging to the family Gramineae, is also called the Grain of Life. India is one of the largest centres of diversity and the accessions of rice are a rich reservoir of useful genes with wide genetic variability, leaving a wide scope for the rice improvement programme. Salinity in soil or water rises in importance in agriculture because it causes stress conditions for cropping plants. The salt-affected soils are assessed to spread to an extent of over 6.73 million ha in India, with the conditions in Gujarat and Uttar Pradesh having more area under saline tracts of 2.23 m ha and 1.37 m ha, respectively. Maharashtra and West Bengal follow with 0.61 mha and 0.44 mha of salt-affected areas, respectively. Soils affected by salt have high soluble salts like sodium (Na+), magnesium (Mg2+), calcium (Ca2+), chloride (Cl–), and sulphate (SO4 2–). In this study, the response of salinity stress on different rice varieties (basmati and non-basmati) was studied with respect to the morphological, physiological, biochemical, and phytochemical characters along with in-silico and molecular analysis by salinity-specific SSR primers. For this study, a total of 8 germplasm was selected including four basmati and four non-basmati varieties. All genotypes were observed for various morphological characters viz. root length and shoot length; physiological characters viz. membrane stability index, relative water content, chlorophyll content, biochemical characters viz. proline content, peroxidase content and phytochemical characters viz. phenolic content under two levels of salinity stress T-1 (50 mM) and T-2 (100 mM). For root length point view, BPT-5204 is the highest length recorded, and for shoot length, VB-24 is the highest length recorded. After those physiological aspects like chlorophyll content, relative water content, and membrane stability indexes, BPT-5204 show the maximum growth compared to all the rice varieties. Biochemical parameters like proline (BPT-5204 maximum) show maximum values, peroxidase (VB-24) shows maximum values, and phenolics (VB-23) show maximum values. We selected two genes for in silico analysis, namely DHAR and OsMYB3R-2, which were reported for their role in abiotic stress and were selected to observe their patterns under salt stress in rice varieties. The in-silico analysis of each gene was done using different bioinformatic software and programmes, which gave much information regarding the selected genes. The molecular analysis of using different primers specific for the salinity stress to check the genetic variability among all basmati and non-basmati rice varieties and find the best varieties