MdATG5a positively regulates nitrogen uptake under low nitrogen conditions by enhancing the accumulation of flavonoids and auxin in apple roots

Nitrogen (N) deficiency limits the production of apple (Malus domestica) on the Loess Plateau, which is the largest apple-producing region in China. Autophagy is a conserved degradation and recycling pathway in eukaryotes that has been reported to play a key role in the responses of plants to N deficiency. We previously identified the core autophagy-related gene MdATG5a from apple and showed that overexpression of this gene improves the drought tolerance of apple plants. Here, we showed that MdATG5a overexpression enhances root growth and the root N uptake of apple plants under low-N conditions and contributes to improving N use efficiency. MdATG5a positively regulated root N uptake by activating the shikimate pathway to increase levels of phenylalanine and tryptophan, which promoted the accumulation of flavonoids and IAA in apple roots under low-N conditions. In addition, MdATG5a was demonstrated to affect the expression of genes involved in root development in response to N deficiency. Moreover, we also found that autophagy activity was higher in the roots of MdATG5a-overexpressing apple plants compared with wild-type plants under low-N conditions. Overall, the results of our study provide new insights into the association between MdATG5a-mediated autophagy and the root N uptake of apple plants under low-N conditions.