Climate-dependent variation in cold tolerance of weedy rice and rice mediated by OsICE1 promoter methylation

The mechanisms by which weedy rice (Oryza sativa f. spontanea) has adapted to endure low-temperature stress in northern latitudes remain unresolved. In this study, we assessed cold tolerance of 100 rice varieties and 100 co-occurring weedy rice populations, which were sampled across a broad range of climates in China. A parallel pattern of latitude-dependent variation in cold tolerance was detected in cultivated rice and weedy rice. At the molecular level, differential cold tolerance was strongly correlated with relative expression levels of CBF cold response pathway genes and with methylation levels in the promoter region of OsICE1, a regulator of this pathway. Among all methylated cytosine sites of the OsICE1 promoter, levels of CHG and CHH methylation were found to be significantly correlated with cold tolerance among accessions. Furthermore, within many of the collection locales, weedy rice shared identical or near-identical OsICE1 methylation patterns with co-occurring cultivated rice. These findings provide new insights on the possible roles that methylation variation in the OsICE1 promoter may play in cold tolerance, and they suggest that weedy rice can rapidly acquire cold tolerance via methylation patterns that are shared with co-occurring rice cultivars.