Expression profiling of nitrogen responsive genes in rice varieties

Abstract

The study entitled “Expression profiling of nitrogen responsive genes in rice varieties” was conducted at the Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani during 2022-23 with an objective to compare the expression profiles of nitrogen responsive genes OsAMT1.2, OsAMT2.1, OsNRT2.3, and OsNAR2.2 in organic (Jaiva) and popular (Uma) rice varieties. The seeds of the rice variety Jaiva were collected from RARS, Pilicode, Kasaragod, and the seeds of the rice variety Uma were collected from RRS, Mancompu, Alappuzha for the study. The seeds were treated with Pseudomonas fluorescens through the wet seed treatment method. The sprouted seeds were transferred to a pot containing clayey soil, which was collected from the rice field of the College of Agriculture, Vellayani after checking pH and liming addition. The rice varieties Jaiva and Uma were provided with 2 nutrient treatment methods i.e., inorganic and organic management during the entire crop duration. The inorganic nutrient treatment included the application of urea, rajphos, and Muriate of Potash (MOP) in the ratio 90:45:45 kgNPKha-1 and the organic nutrient application included the application of neem cake (4:1:2 ratio NPK), and cow dung (0.5:0.2:0.5 ratio NPK), at nitrogen equivalent basis. The plant performance analysis was carried out by observing various growth and yield parameters. The expression profiles of four nitrogen responsive genes, namely OsAMT1.2, OsAMT2.1, OsNRT2.3 and OsNAR2.2 were analyzed at seedling and tillering stages by performing RT-qPCR with OsActin as reference gene. It was observed that the rice varieties Uma and Jaiva showed better performance when managed with inorganic nutrients except in the number of days to flowering and sterility percentage. The yield gap under the inorganic and organic nutrient management was 14.14% and 25.77% for Jaiva and Uma respectively. When managed with inorganic and

organic nutrients, the number of days to flowering differed by 2 and 9 days in Jaiva and Uma rice varieties respectively. The early flowering considered to be beneficial for higher yield. The sterility percentage in Jaiva was on par under both nutrient management whereas in Uma there was a 0.95% decrease under inorganic management. The gene expression analysis showed elevated levels of OsAMT1.2 (ammonium uptake gene) in the leaf and root samples of Jaiva at seedling (1.85 and 4 folds) and tillering stages (1.69 and 1.57 folds) under organic nutrient management. In the case of Uma, these tissues showed low expression of OsAMT1.2 at both seedling and tillering stages under organic management. A similar trend was observed for OsAMT2.1 (ammonium transporter) expression in these rice varieties under organic nutrient management. Both OsAMT1.2 and OsAMT.2 showed maximum expression in roots (4 folds). The nitrate transporter gene OsNRT2.3 showed 7-fold expression in roots at the tillering stage of Jaiva when managed with organic nutrients. The variety Uma showed elevated expression of OsNRT2.3 in the leaves and roots at both stages under inorganic nutrient management. In the rice variety Jaiva, the nitrate assimilating gene OsNAR2.2 showed higher expression under inorganic nutrient management in the seedling stage, but in the variety Uma the expression was higher under organic management. The relative expression levels of the nitrogen responsive genes in the rice varieties Uma and Jaiva reveal that Jaiva maintains a higher level of expression of OsAMT1.2, OsAMT.2 and OsNRT2.3 under organic nutrient management, which may be the reason for its better yield. These genes after further verification can be used for selecting or breeding rice varieties for organic cultivation