Snow-Moderated Freeze–Thaw Cycles Prime Cold-Desert Shrub Seeds for Germination Through Metabolic Reprogramming and Phytohormone Regulation

Seed germination in cold deserts is constrained by winter conditions, yet the combined effects of snow cover and freeze–thaw cycles on seed metabolism remain unclear. We investigated their interactive influence on Seriphidium transiliense germination using four snow cover levels (P1: 0%, P2: 50%, P3: natural, P4: 200% natural) and five freeze–thaw cycles (C1: none; C2 to C5: daily fluctuations from −2/8 °C to 8/−2 °C) in a factorial design. Germination traits, physiology, and metabolomics were analyzed. Snow cover and freeze–thaw cycles significantly interacted. P4C5 treatment (200% snow cover, 8/−2 °C freeze–thaw regime) most strongly promoted germination, increasing the germination percentage, potential, index, and vigor index by 67.6–172.5% compared with P1C1. P4C5 treatment increased soluble sugars and proteins but reduced proline and malondialdehyde levels, indicating improved osmotic balance and membrane stability. Antioxidant enzyme activities rose alongside increased indole-3-acetic acid and gibberellin and decreased abscisic acid. Metabolomic profiling revealed reprogramming, with HexCer (17:2;02/16:1;0) as a key metabolite and enrichment in cofactor biosynthesis, ABC transporters, and flavonoid pathways. Greater snow cover combined with mild freeze–thaw regime primes S. transiliense seeds for germination by optimizing the microenvironment, strengthening physiological resilience, and activating coordinated metabolic networks.