Abstract

Soil salinization is a serious problem for cultivation of rice, as among cereals rice is the most salt sensitive crop, and more than 40% of the total agricultural land amounting to approximately 80 million ha the world over is salt affected. Salinity affects a plant in a varieties of ways, including ion toxicity, osmotic stress and oxidative damage. Since miRNAs occupy the top place in biochemical events determining a trait, understanding their role in salt tolerance is highly desirable, which may allow introduction of the trait in the rice cultivars of choice through biotechnological interventions. High throughput sequencing of sRNAs in the root and shoot tissues of the seedlings of the control and NaCl treated Pokkali, a salt-tolerant rice variety, identified 75 conserved miRNAs and mapped 200 sRNAs to the rice genome as novel miRNAs. Expression of nine novel miRNAs and two conserved miRNAs were confirmed by Northern blotting. Several of both conserved and novel miRNAs that expressed differentially in root and/or shoot tissues targeted transcription factors like AP2/EREBP domain protein, ARF, NAC, MYB, NF-YA, HD-Zip III, TCP and SBP reported to be involved in salt tolerance or in abiotic stress tolerance in general. Most of the novel miRNAs expressed in the salt tolerant wild rice Oryza coarctata, suggesting conservation of miRNAs in taxonomically related species. One of the novel miRNAs, osa-miR12477, also targeted L-ascorbate oxidase (LAO), indicating build-up of oxidative stress in the plant upon salt treatment, which was confirmed by DAB staining. Thus, salt tolerance might involve miRNA-mediated regulation of 1) cellular abundance of the hormone signaling components like EREBP and ARF, 2) synthesis of abiotic stress related transcription factors, and 3) antioxidative component like LAO for mitigation of oxidative damage. The study clearly indicated importance of osa-miR12477 regulated expression of LAO in salt tolerance in the plant.

Highlights

  • Rice, undisputedly, is one of the most important crops in the world, because of its importance as staple food, and because of several other features like vast availability of germplasm, including landraces and wild progenitors varying in innumerable characters, a comparatively smaller genome size and ease of transformation and regeneration that makes it a model cereal system

  • Regulation of gene expression by miRNAs has emerged as an important molecular process determining functioning of several metabolic pathways, including the biochemical events involved in salt tolerance in plants [20,21,40]

  • Among the conserved miRNAs, precursors of several of them were different from those available at miRBase 22.1 for rice, and these precursors could be considered as novel (S5 File)

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Summary

Introduction

Rice is one of the most important crops in the world, because of its importance as staple food, and because of several other features like vast availability of germplasm, including landraces and wild progenitors varying in innumerable characters, a comparatively smaller genome size and ease of transformation and regeneration that makes it a model cereal system It has been genetically modified successfully for nutritional quality and resistance to various diseases [1]. Increasing salinization of cultivable land is in contrast to the demand for rice production in future, which should must increase from the current production of approximately 500 million tons to at least 800 million tons [10] to meet the demand of estimated 9.6 billion people by 2050 [11] This requirement is in the backdrop of challenges being faced by the staple food crops from abiotic stresses, including salinity, that negatively influence their biomass production and yield [12]. The option left is to introduce the trait in the rice cultivar of choice through biotechnological intervention

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