*4.1. Plant Materials for Sequencing*

For WGBS sequencing, we used the shoots of wild-type *Oryza sativa* L. ssp. *japonica* cv. Wuyujing7 (WYJ7), T0 plants regenerated from tissue culture (CK), T4-generation plants carrying an insertion of the *pOsNAR2.1-OsNAR2.1* construct (*pOsNAR2.1-OsNAR2.1*) as described as Ox1 in Chen et al. [33] (see Supplementary Figure S1 and Table S2 for the transformation construct and plant growth data), and T4-generation wild-type line lacking the transgene that derived from the segregation process of the T0 *pOsNAR2.1-OsNAR2.1* heterozygote line (SDWT, see Supplementary Tables S1 and S2). T1 generation of Ox1-1 (AA) and Ox1-3 (aa) lines shown in Supplementary Table S1 were renamed as *pOsNAR2.1*-*OsNAR2.1* and SDWT and their T4 plants were used for further WGBS experiment.

The WYJ7, SDWT, and *pOsNAR2.1-OsNAR2.1* were sterilized for 30 min with 10% (*v*/*v*) hydrogen peroxide, washed thoroughly with deionized water and then grown in water. CK lines were moved from root medium to water after germination. All samples were collected when all four lines grew to two leaves and one heart period. DNA from each plant was sequenced with three replicates. Before sequencing, we tested for the T-DNA insertion loci of *pOsNAR2.1-OsNAR2.1* (Supplementary Figure S1d). The primers used for TAIL-PCR are listed in Supplementary Table S5.

We used MeDIP-seq to examine three types of plants: wild-type of *Oryza sativa* L. ssp. *japonica* cv. Nipponbare (NP), the T8-generation plant of knockdown plant of *OsNAR2.1* by RNA interference (RNAi) (describe as r1 in Yan et al. [29]), and the T8-generation *pUbi-OsNAR2.1* overexpression plant. The transformation constructs and plant growth data are shown in Supplementary Figure S1 and Table S3. We harvested the mixed samples of the first leaf blade, culm and panicles at the anthesis stage for MeDIP-seq (Figure 4e). Details of the growth conditions of the plants in soil are listed in Supplementary Table S3. The level of *OsNAR2.1* expression was reduced in T8 generation RNAi plants to one half of the WT, whereas was five times higher in the *pUbi-OsNAR2.1* T8 generation transgenic line (Figure 4f). Other growth characteristics of RNAi and *pUbi-OsNAR2.1* transgenic lines are described in Supplementary Table S3. We tested for T-DNA insertion in three samples (Supplementary Figure S1e); the primers for TAIL-PCR are listed in Supplementary Table S5.
