Genome-wide association studies of Arabidopsis dark-induced senescence reveals signatures of autophagy in metabolic reprogramming.

Macroautophagy/autophagy is a conserved mechanism responsible for the degradation of unnecessary or dysfunctional components and recycling of the nutrients they contain in order to promote cellular or organismal longevity. In plants photosynthesis is massively impaired under extended darkness stress and the transition to heterotrophic metabolism results in carbon and nitrogen starvation which induces metabolic and autophagic shifts to recycle nutrients for plant survival. The majority of research concerning dark-induced senescence focuses on single genes or pathways, and the global characterization of primary and lipid metabolites and autophagy remains limited. To address these aspects we recently developed a time-resolved genome-wide association-based approach to analyze these shifts following 0 d, 3 d and 6 d of darkness. Six patterns of metabolic shifts and 215 associations with enzymes, transcriptional regulators and autophagy genes (such as AT2G31260/ATG9, AT4G16520/ATG8F, AT5G45900/ATG7 and AT2G05630/ATG8D) were identified. Furthermore detailed characterization of candidate genes further demonstrated that the metabolic and autophagic shifts in response to dark-induced senescence is under tightly coordinated genetic regulation.