Background Drought has become the major abiotic stress that causes losses in rice yields and consequently is one of the main environmental factors threatening food security. Long non-coding RNA (lncRNA) is known to play an important role in plant response to drought stress, while the mechanisms of competing endogenous RNA (ceRNA) in drought resistance in upland rice have been rarely reported. Results In our study, a total of 191 lncRNAs, 2115 mRNAs and 32 miRNAs (microRNAs) were found by strand-specific sequencing and small RNA sequencing to be differentially expressed in drought-stressed rice. Functional analysis of results indicate that they play important roles in hormone signal transduction, chlorophyll synthesis, protein synthesis and other pathways. Construction of a ceRNA network revealed that MSTRG.28732.3 may interact with miR171 in the chlorophyll biosynthesis pathway and affect the ability of plants to withstand drought stress by regulating Os02g0662700, Os02g0663100 and Os06g0105350. The accuracy of the regulatory network was verified by qRT-PCR. Conclusion Our results provide a theoretical basis for future studies on the potential function of lncRNA in plant drought resistance, and they provide new genetic resources for drought-resistant rice breeding.

Shanlan upland rice is a kind of upland rice and is suitable for planting in the mountains and in hilly terrain. It is mainly found in China’s Hainan province. To discover the drought-resistant genes in Shanlan upland rice, two representative varieties—Baishanuo (BSN) and Dongfang Manpoxiang (MPX)—were selected for transcriptome sequencing, after which gene expression analysis was used to confirm their gene expression patterns. The results demonstrated that 2791 and 829 differentially expressed genes (DEGs) were identified for each variety, including 184 and 58 transcriptional factors, respectively. Expression analysis demonstrated that some genes with unknown functions, such as Os10g0505900, were highly expressed under drought stress treatment. The transcriptomic data and digital gene expression profiling data obtained in this study provide a basis for studying the drought-resistant mechanism in Shanlan upland rice.

Background LEA proteins are widely distributed in the plant and animal kingdoms, as well as in micro-organisms. LEA genes make up a large family and function in plant protection against a variety of adverse conditions. Results Bioinformatics approaches were adopted to identify LEA genes in the flax genome. In total, we found 50 LEA genes in the genome. We also conducted analyses of the physicochemical parameters and subcellular location of the genes and generated a phylogenetic tree. LuLEA genes were unevenly mapped among 15 flax chromosomes and 90% of the genes had less than two introns. Expression profiles of LuLEA showed that most LuLEA genes were expressed at a late stage of seed development. Functionally, the LuLEA1 gene reduced seed size and fatty acid contents in LuLEA1-overexpressed transgenic Arabidopsis lines. Conclusion Our study adds valuable knowledge about LEA genes in flax which can be used to improve related genes of seed development.