Integrated physiological, transcriptomic and metabolomic analysis reveals differential cold response in wheat seedlings across varieties

Abstract Background Cold stress severely constrains global wheat productivity, yet the molecular basis for differential cold tolerance in genetically similar cultivars remains poorly understood. This study employed integrated physiological, transcriptomic, and metabolomic analyses to dissect cold adaptation mechanisms in cold-tolerant "Luyan951" and cold-sensitive "Luyan955" wheat sister lines, which share a close genetic background but exhibit contrasting cold responses. Results Physiological assays demonstrated that Luyan951 exhibited a 52.67% survival rate under cold stress—significantly higher than Luyan955 (20.67%)—alongside enhanced antioxidant enzyme activities (SOD, CAT, POD) and superior osmotic adjustment (elevated proline and soluble sugars). Pathway enrichment analysis revealed that phenylpropanoid biosynthesis and jasmonic acid (JA) signaling pathways are critical for cold adaptation, with the cultivar "Luyan951" exhibiting stronger activation of these pathways. Key genes ( CAD , 4CL , JAZ , MYC2 ) and JA metabolism-related genes were significantly upregulated in "Luyan951", which was validated by qRT-PCR. Bioinformatic analysis indicated that these pathways may be regulated by AP2/ERF transcription factors. Subcellular localization and transcriptional activation experiments confirmed the nuclear localization and transactivation function of three AP2/ERF genes ( TraesCS5D02G318400 , TraesCS6A02G381000, TraesCS6D02G366100 ). Conclusions This study provides the first evidence in wheat that phenylpropanoid biosynthesis contributes to cold tolerance, and together with jasmonate signaling, constitutes a core regulatory network for freezing resistance by enabling ROS scavenging, osmotic homeostasis, and metabolic stability; we further speculate this pathway is potentially regulated by upstream ERF transcription factors, offering multi-faceted evidence to elucidate cold adaptation mechanisms and advance precision breeding in wheat.