Transcriptomics and metabolomics reveal that seed cold priming enhances cold tolerance in tobacco seedlings by activating lignin biosynthesis and auxin signaling pathways

Plants frequently encounter repeated cold stress throughout their life cycle. When subjected to future environmental stimulations, plants stress response can be activated after experiencing priming events during the seed stage. This study employed multi omics approaches to investigate the intricate response mechanisms to cold stress at five true leaves and one central bud in two tobacco varieties, resistant variety NC102 and sensitive variety PVH06, which underwent cold- (SC) and non-priming (CK) at the seed stage. After cold stress, NC102 in SC exhibited the strongest tolerance capacity, with relative water content 1.06 times that of CK. Superoxide dismutase and catalase activities, along with proline content, increased by 25 %, 42 %, and 50 %, respectively. Additionally, hydrogen peroxide and malondialdehyde decreased by 23 % and 12 %, respectively. Both the tricarboxylic acid cycle and amino acid metabolism in NC102 seed priming (NS) and PVH06 seed priming (PS) reacted positive responses to cold stress, with NS accumulating higher levels of unsaturated fatty acids and jasmonic acid. The co-expression network identified three hub genes TAR3 , ABP19A , and psb28 that were enriched in PS and associated with auxin regulation. PS might enhance cold tolerance by upregulating the early auxin responsive genes GH3 and SAUR . Additionally, genes and intermediate metabolites involved in the lignin biosynthetic pathway were significantly expressed in both NS and PS, with a more pronounced response observed in NS. Key metabolites of the lignin biosynthetic pathway were regulated to increase in response to cold stress, and the expression levels of structural genes associated with this pathway were detected via qRT-PCR. This work advances understanding of cold stress tolerance, aiding breeding research. • Cold priming during seed stage enhanced plant resistance when exposed to stress. • Metabolites in TCA cycle and amino acid metabolic were increased for stress response. • Auxin early response genes were upregulated in PS to enhance cold tolerance. • Lignin biosynthesis genes in NS were upregulated enhancing content and resistance.