Nitrogen (N) strongly affects plant growth and metabolism. For shikonin biosynthesis, although the ammonium toxicity phenomenon has been reported, the effects of nitrogen on the shikonin synthesis remains obscure. In this study, we carried out four different concentrations of NH4+ treatments on Arnebia euchroma hairy roots (AEHR) to clarify the influence of NH4+ on the growth and shikonin accumulation in A. euchroma and the possible mechanism. The results showed that compared with the 0% NH4+ treatment (only nitrate as nitrogen source), 10% NH4+ treatment increased the fresh weight and the dry weight of AEHR, and promoted the synthesis of shikonins; 20% NH4+ treatment started to show the inhibition effects on growth and shikonin accumulation of AEHR and 30% NH4+ treatment exhibited the strongest inhibition effects. With increased percentage of NH4+, AEHRs became shorter and thicker with more branches. To further elucidate the mechanism, we analyzed the time-course of nitrogen assimilation, gene expression level of key enzymes involved in the shikonin biosynthesis pathway, and contents of various endogenous hormones under NH4+ toxicity condition. Results indicated that auxin and cytokinin might regulate the growth and architecture of AEHR under NH4+ toxicity, and jasmonate level was reduced along with the inhibition of shikonin biosynthesis. This first comprehensive investigation into the effects of ammonium/nitrate ratio on shikonin biosynthesis not only provided valuable data for optimizing the in vitro culture and shikonin production in A. euchroma, but also suggested potential fertilizer strategies for its cultivation.

Alfalfa, an important legume forage, is an ideal crop for sustainable agriculture and a potential bioenergy plant. Drought, one of the most common environmental stresses, substantially affects plants’ growth, development and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of 4 samples, each with 3 biological replicates. We identified 348 known miRNAs, belonging to 80 miRNA families, from the 12 libraries and 281 novel miRNAs using Mireap software. 18 known miRNAs in roots and 12 known miRNAs in leaves were screened out as drought-responsive miRNAs. Except for miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs were different between roots and leaves in alfalfa. This is the first study discovering miR157a, miR1507, miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 are drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.