Identification and comparative analysis of low phosphate tolerance-associated microRNAs in two maize genotypes

Low phosphate (Pi) availability is a major constraint on maize growth and productivity. MicroRNAs (miRNAs) are known to play critical roles in plant responses to various environmental conditions. The identification of low Pi tolerance-associated miRNAs will accelerate the development of Pi starvation tolerant maize plants. However, miRNAs associated with low Pi tolerance have not been identified. In this study, we compared deep sequencing small RNA reads from two maize genotypes, the wild type, Qi319, and the low Pi tolerant mutant, 99038, under normal and low Pi conditions. Six known miRNA families and seven novel miRNAs were found differently expressed by the two genotypes. All these miRNAs were confirmed by sequencing a second batch of small RNA libraries constructed in the same way as those used in the first sequencing. The expression profiles of some of these miRNAs were further confirmed by real-time PCR. The predicted target genes of the low Pi tolerance-associated miRNAs were involved in root development or stress responses. Expression levels of some of target genes were significantly different between Qi319 and 99038. These findings suggested that miRNAs may play important roles in low Pi tolerance in maize and may be a key factor in determining the level of low Pi tolerance in different maize genotypes. This study provides an approach for identifying low Pi tolerance-associated miRNAs and can help in the selection and manipulation of high performing maize genotypes under low Pi conditions.