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Here, we confirm that tetraploid rice exhibits stronger cold tolerance than diploid rice. This improved tolerance is mediated by reduced malondialdehyde accumulation, elevated antioxidant enzyme activity, and epigenetic regulation of genes involved in abscisic acid biosynthesis and signaling. Under cold stress, tetraploid rice induces stress-responsive genes (especially in the abscisic acid pathway) more rapidly and to higher levels than diploid rice. This enhanced gene expression coincides with increased endogenous abscisic acid accumulation. Furthermore, polyploidization and cold stress synergistically induce high methylation at CG, CHG, and CHH sites in genes and transposons. Notably, the methylation level of class II transposons in tetraploid rice is significantly higher than in diploid rice under low temperatures. To suppress transposon activation in gene promoter regions under cold stress, tetraploid rice enhances the methylation level of abscisic acid pathway-related gene promoters, thereby silencing transposons and maintaining genome stability. Collectively, these results enrich the theoretical understanding of the strong stress tolerance in polyploid plants and provide theoretical support for breeding cold-tolerant polyploid rice varieties.<\/jats:p>","DOI":"10.1093\/plphys\/kiag671","type":"journal-article","created":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T13:51:38Z","timestamp":1788616298000},"source":"Crossref","is-referenced-by-count":0,"title":["DNA hypermethylation of abscisic-acid-related genes helps enhance the cold tolerance of tetraploid rice"],"prefix":"10.1093","volume":"202","author":[{"given":"Haiyi","family":"Chen","sequence":"first","affiliation":[{"name":"School of Life Sciences, Hubei University, No. 368 Youyi Avenue, Wuchang District, Wuhan City, Hubei Province 430062 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanqing","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Hubei University, No. 368 Youyi Avenue, Wuchang 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