Genome-Wide Analysis of microRNAs and Their Target Genes in Dongxiang Wild Rice (Oryza rufipogon Griff.) Responding to Salt Stress.

Rice (Oryza sativa) is a staple food for more than half of the world's population, and its production is critical for global food security. Moreover, rice yield decreases when exposed to abiotic stresses, such as salinity, which is one of the most detrimental factors for rice production. According to recent trends, as global temperatures continue to rise due to climate change, more rice fields may become saltier. Dongxiang wild rice (Oryza rufipogon Griff., DXWR) is a progenitor of cultivated rice and has a high tolerance to salt stress, making it useful for studying the regulatory mechanisms of salt stress tolerance. However, the regulatory mechanism of miRNA-mediated salt stress response in DXWR remains unclear. In this study, miRNA sequencing was performed to identify miRNAs and their putative target genes in response to salt stress in order to better understand the roles of miRNAs in DXWR salt stress tolerance. A total of 874 known and 476 novel miRNAs were identified, and the expression levels of 164 miRNAs were found to be significantly altered under salt stress. The stem-loop quantitative real-time PCR (qRT-PCR) expression levels of randomly selected miRNAs were largely consistent with the miRNA sequencing results, suggesting that the sequencing results were reliable. The gene ontology (GO) analysis indicated that the predicted target genes of salt-responsive miRNAs were involved in diverse biological pathways of stress tolerance. This study contributes to our understanding of DXWR salt tolerance mechanisms regulated by miRNAs and may ultimately improve salt tolerance in cultivated rice breeding using genetic methods in the future.

MicroRNA2871b of Dongxiang Wild Rice (Oryza rufipogon Griff.) Negatively Regulates Cold and Salt Stress Tolerance in Transgenic Rice Plants.

Cold and salt stresses are major environmental factors that constrain rice production. Understanding their mechanisms is important to enhance cold and salt stress tolerance in rice. MicroRNAs (miRNAs) are a class of non-coding RNAs with only 21-24 nucleotides that are gene regulators in plants and animals. Previously, miR2871b expression was suppressed by cold stress in Dongxiang wild rice (DXWR, Oryza rufipogon Griff.). However, its biological functions in abiotic stress responses remain elusive. In the present study, miR2871b of DWXR was overexpressed to investigate its function under stress conditions. When miR2871b of DWXR was introduced into rice plants, the transgenic lines were more sensitive to cold and salt stresses, and their tolerance to cold and salt stress decreased. The increased expression of miR2871b in rice plants also increased the levels of reactive oxygen species (ROS) and malondialdehyde (MDA); however, it markedly decreased the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) and the contents of proline (Pro) and soluble sugar (SS). These data suggested that miR2871b of DXWR has negative regulatory effects on cold and salt stress tolerance. Meanwhile, 412 differentially expressed genes (DEGs) were found in rice transgenic plants using transcriptome sequencing, among which 266 genes were up-regulated and 146 genes were down-regulated. Furthermore, the upstream cis-acting elements and downstream targets of miR2871b were predicted and analyzed, and several critical acting elements (ABRE and TC-rich repeats) and potential target genes (LOC_Os03g41200, LOC_Os07g47620, and LOC_Os04g30260) were obtained. Collectively, these results generated herein further elucidate the vital roles of miR2871b in regulating cold and salt responses of DXWR.