Extended Data Fig. 7: Methylation and expression of epigenetic flowering and relative fitness QTLs.

(a) FLC expression change in met1 lines of accessions with either gbM or unmethylated (UM) FLC epialleles in wild-type (WT), assessed by RNA-seq⁷⁵. Numbers of accessions within each group are indicated. (b) Tripartite association between intragenic DNA methylation (mCG), gene expression (GE), and relative MLP fitness (rFMLP) in the entire population and after accounting (acc.) for structural variation (SV). Associations between the three variables are shown in two independent haplogroups of PROT1 (PROT1-23 and PROT1-4) and AT1G19410 (AT1G19410-1 and AT1G19410-21) before and after accounting for SV. *P < 0.05, Pearson’s correlation test. (c) Transcript levels of PROT1 relative to UBQ10 in Col-0 and met1-6, assessed by qRT-PCR in six biological replicates. P, two-tailed Student’s t-test. (d) PROT1 expression change in met1 lines of accessions with either gbM or UM PROT1 epialleles in WT, assessed by RNA-seq⁷⁵. Numbers of accessions within each group are indicated. (e) DRM and CMT methyltransferases control teM of AT1G19410. Fractional methylation in CG, CHG, and CHH sequence contexts is shown in indicated genotypes. (f) Transcript levels of AT1G19410 (ANH) relative to UBQ10 in Col-0 and ddcc, assessed by qRT-PCR in five biological replicates. P, two-tailed Student’s t-test. Center lines within box plots represent sample medians and plus signs correspond to means. Box limits indicate the 25th and 75th percentiles, whiskers extend to 1.5 times the interquartile range.