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Background  Low temperature influences the development and latex production of rubber trees ( Hevea brasiliensis ) when extension to suboptimal high-latitude areas. The successful extension of  Hevea brasiliensis  cultivation to high-latitude areas has long believed to benefit from the breeding of cold-tolerant cultivars. A puzzling incongruity is the variation in cold tolerance among the cultivated clones despite their similar genetic make-up.    Results  To investigate this, we first transferred cultivar Reyan 7–33-97 to short-term cold treatment, and showed that cold-related genes (such as  HbICE1  and  HbCBF2 ), cold-responsive ( COR ) genes, and DNA-methylation related genes (such as  HbMET1 ) were induced by cold treatment. Furthermore, long-term cold treatment not only elevated the transcriptional activities of the  HbICE1 ,  HbCBF2 , and  HbMET , but also induced DNA demethylation of their promoters. Cold treatment increased the transcriptional activities of demethylation-related genes such as the  HbDME ,  HbROS , and  HbDML  genes, but did not alter the promoter methylation status. Furthermore, the  HbICE1  and  HbMET  promoters showed hypomethylation status in samples collected at the end of winter from 12 different cultivars grown in four geographical locations, but switched to hypermethylation status at the end of summer. Expression of  COR  was correlated with the low temperature. Given that little genetic diversity exists in the  HbICE1  and  HbMET  promoters among different cultivars, the DNA demethylation induced by cold was highly correlated with low temperature, but not with the genetic backgrounds of cultivars.    Conclusion  Cold-induced epigenetic modification might play an important role in cold tolerance of  H. brasiliensis.Electronic supplementary material  The online version of this article (10.1186/s12870-018-1276-7) contains supplementary material, which is available to authorized users.

Chilling-induced DNA Demethylation is associated with the cold tolerance of Hevea brasiliensis