Identification of phosphate-stress responsive microRNAs in tropical maize

Abstract

Low phosphorus availability poses major constrain to crop yield by limiting plant growth in many Indian soil types (acidic, alkaline and calcareous). Cropping system is dependent on external application of phosphate fertilizers that is mainly (~90%) imported. Phosphorus is non-renewable natural resource and its global supply would start tapering off after 2030, thereby triggering a massive agricultural crisis. Phosphorus (P) is essential for normal growth and maturity as it plays important role in photosynthesis, respiration, energy storage and transfer, cell division, cell enlargement and several other processes in plants. Modern cereal genotypes, like, the single cross maize hybrids require a high dose of phosphate for optimum production. However, the plant is capable of utilizing only about 10% of the applied phosphorus. Due to its precipitation as aluminium phosphate, phosphorus availability is even more severely constrained in acidic soil of eastern and north-eastern India, where large acreage of maize is grown under upland with very low productivity. Thus, phosphorus availability is one of the most important production constraints in maize, especially in north eastern parts of India. Owing its emergence as an industrial, feed and food crop, improvement in phosphorus use efficiency (PUE) is highly essential in maize for sustainable use of phosphate containing fertilizers. Identification of key genes and their regulatory elements playing pivotal role in acquisition, transportation and utilization of phosphorus in maize can help in developing phosphorus efficient maize genotypes. MicroRNA-mediated gene regulation plays a crucial role in controlling low phosphorus stress adaptation and tolerance in plants. In this endeavour, the present study was undertaken to identify differentially expressed miRNAs under low phosphorus stress in tropical maize through NGS and expression profiling. The HKI-163 maize inbred line was grown hydroponically under sufficient (1mM KH2PO4) and deficient (5µM KH2PO4) phosphate conditions for 21 days. Observations were recorded on all important shoot and root physiological parameters. The phosphate content was measured in shoots and roots of the maize plants growing in both phosphate stressed and unstressed condition. The root and shoot samples were deep sequenced for miRNA study. The expression analysis revealed 35 known miRNAs (12 up & 23 down-regulated) in shoot and 27 known miRNAs (15 up & 12 down-regulated) in root expressed differentially under low phosphate stress. Among these, 10 miRNAs were common in roots and shoot/leaf tissue. We also identified 40 (18 up & 22 down-regulated) and 46 (37 up & 9 down-regulated) novel miRNAs in shoots and roots respectively. The deep sequencing result is being validated through stem-loop RT-PCR. This study will provide valuable insight into the role of miRNA in phosphate use efficiency in maize. The expression of key miRNA(s) identified from this study could be modulated / engineered to enhance phosphate utilization efficiency in maize plants.