RNA-seq reveals sucrose-responsive and sucrose-independent crosstalk between early nutrient-deficiency responses in white lupin

Phosphate (Pi) starvation is a major issue that affects crop production worldwide. Pienriched fertilizer is used to compensate; however, the world’s mined rock phosphate is a limited and non-renewable resource that is expected to deplete in the next 100-300 years. In order to improve Pi uptake in plants, we study white lupin as a model organism for its exceptional ability to thrive in low-nutrient conditions. Much research has been done to understand long-term nutrient starvation responses in white lupin. However, the molecular mechanisms underlying early nutrient starvation responses remain poorly understood. Independent studies have hypothesized that sucrose acts as a signal of both Pi and Fe deficiency, raising the question if plants can distinguish between both nutrient deficiencies, and to what degree sucrose is involved in potential crosstalk between nutrient deficiency responses. To investigate these questions, we performed RNA-seq of white lupin roots in response to short-term phosphate (–Pi) or iron deficiency (–Fe), or addition of sucrose, compared to a nutrient-sufficient control. Using a white lupin reference transcriptome, we assembled 380 million Illumina reads from 8 cDNA libraries (2 biological replicates x 4 conditions) into 51,713 contigs. A total of 3099 contigs were upregulated in response to Pi deficiency; 32% of these were upregulated in both –Pi and –Fe. Of this overlap, about 40% was sucrose-responsive, meaning that gene expression changed even under nutrientsufficient conditions when sucrose was added. Taken together, these findings indicate the existence of sucrose-responsive and sucrose-independent crosstalk in early Pi and Fe deficiency responses. Among the upregulated genes shared between -Pi and -Fe responses, 15 and 18 GO (Gene Ontology) terms were significantly enriched in sucrose-responsive and sucrose-independent groups, respectively. Phosphate and nitrogen metabolism pathways were most notably enriched in all treatments, while vesicle-mediated transport and lipid metabolism were exclusively enriched in sucrose-responsive conditions.