SUPPLEMENTARY INFORMATION

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1 doi: /nature11968 Expanded section and Discussion Supplementary Fig. S1 to S30 Supplementary Tables 1-26 Expanded section and Discussion RdDM targeted genes are re-expressed in pollen The mqtl identified revealed that there is a strong association among some genetic variants and variation in DNA methylation, especially for C-DMRs. It is also well established that other genetic features, such as repeats, are important for guiding the RdDM machinery to target loci. For example, the intergenic sub-telomeric repeats 3 to the MEDEA locus and the repeated SINE elements and tandem repeats around the transcription start site of FWA are key regulatory sequences for controlling gene expression of these loci 1,2. Although these loci are under transcriptional control by genetic elements, these specific elements are present and invariably methylated in every accession examined. Therefore, to understand the potential role of regions of the epigenome that are less prone to natural epigenetic variation we searched for loci that contained methylated alleles (methylation level 10%) in greater than 90% of the accessions sequenced and identified a total of 283 genes and 255 transposons. Essentially, these loci represent invariably methylated loci in this population similar to FWA and MEDEA. Furthermore, the expression of these loci was specifically activated 1

2 during pollen development (Fig. 5a and b). A previous study demonstrated that DDM1 is not expressed in the pollen vegetative nucleus and that this results in release from epigenetic silencing and expression of transposons, providing a substrate to generate mobile small RNAs, which are transmitted to the germ line (sperm cells) 3. This mechanism is not restricted to transposons as we identify protein-coding genes that are under control of the RdDM pathway and invariably methylated across this population are also expressed specifically in pollen (Fig. 5b). This re-activation of gene expression is not a general feature of pollen development as a control set of genes that show no evidence of being targeted by RdDM within this population or preference for pollen re-expression (Fig. 5c). In fact, these loci are expressed at lower levels in pollen development consistent with previous transcriptome analyses that revealed pollen has the fewest number of expressed loci in comparison to other vegetative tissues 4 (Supplementary Table 26). A closer examination of these invariably methylated genes with gene ontology 5 revealed a significant enrichment for two major categories, cell wall biology and translation (Table 1). These enriched GO terms are related to the major functions of pollen. For example, germination of pollen upon making contact with the stigma requires cell wall fusion and pollen tube elongation requires rapid cell wall expansion and protein synthesis to reach the central and egg cells for double fertilization. Therefore, these data indicate that the invariably methylated, pollen expressed genes are not only released from epigenetic silencing to reinforce their repressed state in the germ line, but also to function in pollen development. Although these invariably methylated loci are under similar epigenetic control as transposons (Fig. 5a and b), it is likely that all RdDM-targeted loci are under control of 2

3 this mechanism regardless of their variability within this population. In fact, Col-0 genes targeted by RdDM and their corresponding expression levels are positively correlated (Spearman correlation; P Value 5.81e -27 ) specifically in pollen and seed development (Fig. 5d); whereas, all 55 other tissues tested revealed either a significant negative correlation or no correlation (Supplementary Table 18) between the loci targeted by RdDM and their corresponding expression levels (Fig. 5d). It is noteworthy that categories of genes showing positive correlations are stronger for loci that overlap transposon sequences (Fig. 5d). These data indicate that these loci have come under control of sequences that are evolutionarily silenced, which acts to restrict their expression to these specific stages of development (Fig. 5d). Conclusion Natural epigenomic variation is widespread within Arabidopsis thaliana and the population-based epigenomics approach used throughout this study has uncovered features of the DNA methylome that are not linked to underlying genetic variation such as all forms of SMPs and CG-DMRs. However, C-DMRs have positional association decay patterns similar to LD decay patterns for SNPs and in some cases are associated with local and distant genetic variants. Our combined analysis of genetic and methylation variation did not uncover a significant correlation between major effect mutations and genes silenced by the RdDM pathway suggesting that these genes may be targeted by this pathway for another purpose. In fact, our study identifies protein-coding genes that are under control of the RdDM pathway, which likely serves to enact two possible fates. The first fate is permanent silencing of these loci in vegetative tissues similar to transposons. In fact, 3

4 ectopic expression of some of these genes in vegetative tissues results in pleiotropic phenotypes 6,7 indicating the importance of restricting their expression from vegetative development. A possible second fate of being targeted by the RdDM pathway could be the coordinated expression specifically to pollen and endosperm to ensure proper development. An example of this phenomenon is illustrated by the FWA locus, which reaches its peak expression in young carpels 4 where the central cell is developing and FWA is specifically expressed 8. It reaches its second highest peak expression in pollen, a tissue in which it has no known functional role and thus its expression in this tissue likely serves to reinforce silencing in the sperm cells and ultimately vegetative tissues in a fashion analogous to transposon silencing 3. Of the loci targeted by RdDM in Col-0, most are repressed in vegetative tissues and some have clear roles in pollen tube growth and elongation, such as RIC5 and PPME1 9, or seed development, such as the MADS box transcription factors (AGL23, 28, 34, 36, 42, 90, 92) and MEE15, 23, 38 1,10,11,12,13,14,15. In fact, seven members of the ARF gene family (ARF12, 14, 15, 20-23) are targeted by the RdDM pathway and all seven are found specifically expressed in the endosperm and not detected in vegetative tissues 16. Together, these data support a role for some RdDMtargeted loci in both pollen and endosperm development. RNA silencing machinery is an evolutionarily conserved process found across eukaryotes, but the recent evolution of RNA polymerases, PolIV and PolV, is specific to flowering plants 17. These two components have enabled the assembly of the RdDM pathway, which uses small RNAs to guide DNA methylation to target loci. This pathway targets transposon sequences to ensure their silenced state is maintained throughout vegetative tissues and the germline 3. Animals also use small RNA directed DNA 4

5 methylation and heterochromatin formation mechanisms to maintain the epigenome of the germline through the use of Piwi-interacting RNAs 18,19,20. In both plants and animals these small RNAs are derived from the genome of companion cells, which are terminal in nature and thus can afford widespread reactivation of gene expression of transposon and repeat sequences as they are not passed on to the next generation. Our study provides evidence that protein-coding genes have co-opted this transposon silencing mechanism to maintain their silenced state in vegetative tissues and transgenerationally as well as to ensure proper expression of genes important for pollen, seed, and germ line development. References 1 Kinoshita, T. et al. One- way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303, (2004). 2 Xiao, W. et al. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev. Cell 5, (2003). 3 Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, (2009). 4 Schmid, M. et al. A gene expression map of Arabidopsis thaliana development. Nature Genetics (2005). 5 Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, (2009). 6 Soppe, W. J. et al. The late flowering phenotype of fwa mutants is caused by gain- of- function epigenetic alleles of a homeodomain gene. Mol. Cell 6, (2000). 7 Yoo, S. K., Lee, J. S. & Ahn, J. H. Overexpression of AGAMOUS- LIKE 28 (AGL28) promotes flowering by upregulating expression of floral promoters within the autonomous pathway. Biochem Biophys Res Commun 348, (2006). 8 Kinoshita, T. et al. One- way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303, (2003). 9 Tian, G. W., Chen, M. H., Zaltsman, A. & Citovsky, V. Pollen- specific pectin methylesterase involved in pollen tube growth. Dev Biol 294, (2006). 10 Colombo, M. et al. AGL23, a type I MADS- box gene that controls female gametophyte and embryo development in Arabidopsis. Plant J 54, (2008). 5

6 11 Dubreucq, B. et al. The Arabidopsis AtEPR1 extensin- like gene is specifically expressed in endosperm during seed germination. Plant J 23, (2000). 12 Nishimura, N. et al. ABA hypersensitive germination2-1 causes the activation of both abscisic acid and salicylic acid responses in Arabidopsis. Plant Cell Physiol 50, (2009). 13 Pagnussat, G. C. et al. Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis. Development 132, (2005). 14 Shirzadi, R. et al. Genome- wide transcript profiling of endosperm without paternal contribution identifies parent- of- origin- dependent regulation of AGAMOUS- LIKE36. PLoS Genet 7, e (2011). 15 You, W. et al. Atypical DNA methylation of genes encoding cysteine- rich peptides in Arabidopsis thaliana. BMC Plant Biol 12, 51 (2012). 16 Rademacher, E. H. et al. A cellular expression map of the Arabidopsis AUXIN RESPONSE FACTOR gene family. Plant J 68, (2011). 17 Luo, J. & Hall, B. D. A multistep process gave rise to RNA polymerase IV of land plants. J Mol Evol 64, (2007). 18 Carmell, M. A. et al. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell 12, (2007). 19 Vagin, V. V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, (2006). 20 Watanabe, T. et al. Role for pirnas and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science 332, (2011). 6

7 La_0 Di_G Kondara Neo_6 Westkar_4 Zal_1 Sus_1 Kar_1 Dja_1 Ler_1 Sorbo Altai_5 Kas_1 Kz_9 Rubezhnoe_1 Ms_0 Anholt_1 Bd_0 Sp_0 Jm_0 Je_0 Ting_1 Cvi_0 Ta_0 Tac_0 Da_1_12 Dra_0 Stw_0 En_D Li_2_1 Zdr_1 Gr_1 Dr_0 Pu2_7 Pu2_23 Bor_1 Krot_0 Uod_1 Ga_0 Er_0 Bl_1 Ber Ws_2 Ragl_1 Gre_0 Gifu_2 RRS_10 Tul_0 Kin_0 Seattle_0 Tu_0 Be_0 Abd_0 Ema_1 Tol_0 En_2 Ak_1 Bs_1 Pi_0 Vind_1 Cnt_1 Rld_1 Rd_0 Per_1 Chi_0 Se_0 Pla_0 Yo_0 Pna_17 Lip_0 Ra_0 Kyoto Jl_3 Lp2_2 Bor_4 In_0 Est Ha_0 Hh_0 Hau_0 Sei_0 Tamm_2 Es_0 Bla_1 Ts_1 Wa_1 Litva Ko_2 Ty_0 Mc_0 Tha_1 Got_7 Cal_0 RRS_7 Utrecht Wl_0 Tscha_1 Ann_1 Wei_0 Uk_1 Sg_1 Ang_0 Durh_1 Rou_0 HR_5 Alst_1 Rmx_A02 Knox_18 Et_0 Ag_0 Van_0 Rome_1 Br_0 Cerv_1 Pro_0 Gy_0 Lm_2 Pog_0 Com_1 Chat_1 Boot_1 Rennes_1 Le_0 Bu_0 Aa_0 Kelsterbach_4 Gu_0 Nz_1 Kro_0 Db_1 Co_1 Anz_0 Lan_0 Col_0 Bsch_0 Is_0 Kl_5 Mz_0 Mh_0 Ob_0 Nw_0 Ca_0 Ba_1 Hey_1 Baa_1 Fi_0 Ei_2 Do_0 Si_0 Wt_5 Nc_1 Benk_1 Ven_1 Nok_3 Sq_8 Su_0 Amel_1 Rhen_1 Pt_0 Gie_0 Np_0 Ove_0 Wc_1 Gel_1 Hn_0 Kil_0 Mnz_0 Old_1 Hs_0 Bch_1 Qar_8a Bik_1 An_1 Appt_1 El_0 Fr_2 Etna_2 Cluster Dendrogram for SNPs Supplementary Fig. 1. Clustering accessions using SNPs Height

8 Cluster Dendrogram based on CG-SMPs Is_0 Is_0_bud Fr_2 Fr_2_bud Ag_0 Ag_0_bud Ragl_1_bud Rd_0 Zdr_1 Zdr_1_bud Kin_0 Kin_0_bud Litva Litva_bud Ema_1 Ema_1_bud Uk_1 Uk_1_bud Pu2_23 Pu2_23_bud Er_0 Er_0_bud Bor_4 Bor_4_bud Ws_2_bud Di_G Ler_1 Seattle_0 La_0 Col_0 Lan_0 Neo_6_bud Westkar_4_bud Rubezhnoe_1_bud Altai_5 Kondara Kz_9 Sus_1_bud Kas_1 Sorbo_bud Rennes_1_bud Rmx_A02_bud Ty_0_bud Co_1_bud Pro_0_bud Bik_1 RRS_7 Anz_0 Sp_0_bud Pog_0_bud Rld_1_bud Cal_0 Benk_1 Et_0 El_0 Gy_0 Knox_18 Chat_1 Ragl_1 Boot_1 Db_1 Fi_0 Ra_0 Si_0 Aa_0 Gr_1 Kro_0 Je_0 Gie_0 HR_5_bud Wt_5 Got_7 Baa_1 Su_0 Nc_1_bud Bsch_0 Ob_0_bud Hs_0 Gel_1 An_1 Appt_1 Kil_0 Tu_0_bud Bu_0 Abd_0 Chi_0 Per_1 Est Hey_1 Cnt_1 Vind_1 Gre_0 Tol_0_bud Gifu_2 Bs_1 Pi_0 En_D Stw_0 Mz_0_bud Gu_0 Ba_1 Ca_0 Kelsterbach_4 Anholt_1 Bl_1 Uod_1_bud Sq_8_bud Wa_1 Bla_1 Pla_0_bud Se_0_bud Mh_0_bud Br_0_bud Old_1_bud Li_2_1_bud Ta_0_bud Ove_0_bud Kl_5 Jm_0 Kyoto Ei_2 Com_1 Ha_0 Lm_2 Van_0_bud Pna_17_bud Pt_0 Rome_1_bud Yo_0 Ms_0_bud Utrecht_bud Sei_0_bud Dja_1 Tamm_2_bud Nw_0_bud Amel_1 Np_0_bud Wl_0_bud In_0 Tscha_1_bud Ak_1 Ann_1 Lp2_2 Ga_0 Da_1_12 Krot_0 Mc_0 Sg_1 Es_0 Nok_3_bud Pu2_7_bud Cvi_0 Supplementary Fig. 2. Clustering accessions using CG-SMPs Height 8

9 Cluster Dendrogram based on CHG-SMPs Litva Litva_bud Nw_0_bud Pog_0_bud Mh_0_bud Old_1_bud Tamm_2_bud Pla_0_bud Se_0_bud Ms_0_bud Rld_1_bud Br_0_bud Co_1_bud Nok_3_bud Ty_0_bud Pna_17_bud Ag_0_bud Pu2_7_bud Fr_2 Fr_2_bud Wl_0_bud Utrecht_bud Np_0_bud Nc_1_bud Tol_0_bud Ta_0_bud Van_0_bud Pro_0_bud Uk_1 Uk_1_bud Sq_8_bud Com_1 Vind_1 Chat_1 Sei_0_bud Rmx_A02_bud Rubezhnoe_1_bud Tscha_1_bud Bor_4 Bor_4_bud Wa_1 Bsch_0 Hs_0 Lm_2 Tu_0_bud Er_0_bud Ha_0 Is_0_bud Mz_0_bud Li_2_1_bud RRS_7 Pu2_23 Pu2_23_bud Zdr_1 Zdr_1_bud Krot_0 Sg_1 Cal_0 Knox_18 Yo_0 Kin_0_bud Kin_0 Seattle_0 Ei_2 Abd_0 Ema_1 Ema_1_bud Gel_1 Rome_1_bud Sp_0_bud Gifu_2 Ob_0_bud Dja_1 Kondara Sorbo_bud Neo_6_bud Sus_1_bud Westkar_4_bud Altai_5 Kz_9 Anz_0 Cvi_0 Di_G Ler_1 Rd_0 Ws_2_bud Amel_1 Pi_0 Jm_0 Kyoto An_1 Rennes_1_bud Bla_1 Pt_0 Aa_0 Da_1_12 Baa_1 Wt_5 Je_0 Ca_0 Kro_0 El_0 In_0 Kil_0 Lp2_2 Gre_0 Got_7 En_D Ba_1 Kelsterbach_4 Appt_1 HR_5_bud Anholt_1 La_0 Is_0 Db_1 Gy_0 Ragl_1_bud Est Hey_1 Ak_1 Benk_1 Gr_1 Gu_0 Fi_0 Su_0 Ragl_1 Lan_0 Kl_5 Stw_0 Ove_0_bud Gie_0 Et_0 Ga_0 Col_0 Chi_0 Bu_0 Bl_1 Es_0 Si_0 Ra_0 Kas_1 Mc_0 Per_1 Uod_1_bud Bik_1 Bs_1 Boot_1 Ag_0 Ann_1 Cnt_1 Er_0 Supplementary Fig. 3. Clustering accessions using CHG-SMPs. Height 9

10 Cluster Dendrogram based on CHH-SMPs Kz_9 Neo_6_bud Rennes_1_bud Nok_3_bud Pna_17_bud Tamm_2_bud Pu2_7_bud Mh_0_bud Old_1_bud Rld_1_bud Ws_2_bud Ag_0_bud Bor_4 Sg_1 Gel_1 Gifu_2 Ema_1_bud Litva_bud Np_0_bud Mz_0_bud Pla_0_bud Co_1_bud Se_0_bud Ms_0_bud Br_0_bud Westkar_4_bud Pu2_23_bud Fr_2_bud Li_2_1_bud Sq_8_bud RRS_7 Uk_1_bud Wl_0_bud Utrecht_bud Is_0_bud Pog_0_bud Nw_0_bud Tol_0_bud Ty_0_bud Er_0_bud El_0 Amel_1 Pi_0 Ha_0 Pro_0_bud Rd_0 Kyoto Tscha_1_bud Rome_1_bud Rmx_A02_bud Bu_0 Zdr_1_bud Nc_1_bud Kin_0_bud Sus_1_bud Ta_0_bud Van_0_bud Litva Bs_1 Si_0 Ove_0_bud Stw_0 Mc_0 Zdr_1 Aa_0 Pu2_23 Ragl_1 Jm_0 Gy_0 Hey_1 Lp2_2 Chat_1 HR_5_bud Ca_0 Gu_0 Anholt_1 Ak_1 Je_0 En_D Altai_5 In_0 Lm_2 Cvi_0 Kondara Kelsterbach_4 Vind_1 Gr_1 Su_0 Kas_1 Fi_0 Et_0 Bl_1 Gre_0 Seattle_0 Krot_0 Kl_5 Kin_0 Knox_18 Kil_0 La_0 Es_0 Com_1 Gie_0 Tu_0_bud Is_0 Lan_0 Da_1_12 Fr_2 Est Wa_1 Dja_1 Ei_2 Di_G Ler_1 Ga_0 Bor_4_bud Ba_1 Appt_1 Benk_1 Yo_0 Cal_0 Baa_1 Kro_0 Wt_5 Uk_1 Anz_0 Hs_0 Ema_1 Abd_0 Bsch_0 Db_1 Got_7 Col_0 Pt_0 Bla_1 Cnt_1 Uod_1_bud Per_1 Ra_0 Sorbo_bud Sei_0_bud Sp_0_bud Ob_0_bud Rubezhnoe_1_bud Ragl_1_bud An_1 Bik_1 Chi_0 Ag_0 Boot_1 Er_0 Ann_1 Supplementary Fig. 4. Clustering accessions using CHH-SMPs Height 10

11 Conservation score Mb 5 Mb 10 Mb 15 Mb mcg mchg mchh Chromosome II position 20 Mb Conservation score Mb 5 Mb 10 Mb 15 Mb mcg mchg mchh 20 Mb Chromosome III position Conservation score Mb 5 Mb 10 Mb 15 Mb mcg mchg mchh Chromosome IV position Conservation score Mb 5 Mb 10 Mb 15 Mb 20 Mb mcg mchg mchh 25 Mb Chromosome V position Supplementary Fig. 5. Plots of the genome-wide distribution of methylation conservation across chromosomes II, III, IV, V. A methylation state conservation score was calculated across all SMPs in each nucleotide context (CG, CHG, and CHH) and averaged together into 100kb windows. A structural variant is visible on the top arm of chromosome II and in the centromere of chromosome IV. 11

12 CG DMR C DMR DMR size (bp) Supplementary Fig. 6. Size distribution of CG-DMRs (red line) and C-DMRs (black line). 12

13 CG DMRs chromosome I C DMRs chromosome I 0e+00 2e 08 4e 08 6e 08 8e 08 1e 07 0e+00 2e 08 4e 08 6e 08 8e 08 1e 07 0 Mb 10 Mb 20 Mb 30 Mb 0 Mb 10 Mb 20 Mb 30 Mb CG DMRs chromosome II C DMRs chromosome II 0.0e+002.0e 084.0e 086.0e 088.0e 081.0e 071.2e e+002.0e 084.0e 086.0e 088.0e 081.0e 071.2e 07 0 Mb 5 Mb 10 Mb 15 Mb 20 Mb 0 Mb 5 Mb 10 Mb 15 Mb 20 Mb 0.0e e e e e e e 07 CG DMRs chromosome III 0 Mb 5 Mb 10 Mb 15 Mb 20 Mb 0.0e e e e e e e 07 C DMRs chromosome III 0 Mb 5 Mb 10 Mb 15 Mb 20 Mb CG DMRs chromosome IV C DMRs chromosome IV 0.0e+002.0e 084.0e 086.0e 088.0e 081.0e 071.2e e+002.0e 084.0e 086.0e 088.0e 081.0e 071.2e 07 0 Mb 5 Mb 10 Mb 15 Mb 0 Mb 5 Mb 10 Mb 15 Mb 0e+00 2e 08 4e 08 6e 08 8e 08 1e 07 CG DMRs chromosome V 0 Mb 10 Mb 20 Mb 0e+00 2e 08 4e 08 6e 08 8e 08 1e 07 C DMRs chromosome V 0 Mb 10 Mb 20 Mb Supplementary Fig. 7. Genome-wide distribution of CG-DMRs and C-DMRs. CG-DMRs are enriched along the euchromatic gene-rich regions, whereas C-DMRs are enriched within the pericentromeric gene-poor, transposon-rich regions of the genome. 13

14 Distribution of normalized expression values Gene body No mc Type of methylation in gene Supplementary Fig. 8. Distributions of the expression levels of genes with gene body methylation and those without methylation entirely. Gene body methylated genes in general are more highly expressed. 14

15 Distribution of normalized expression values > > > > > >1.0 Distribution of methylation levels (C-DMRs) Supplementary Fig. 9. Boxplot representation of expression values for genes containing C-DMRs. In this plot unlike in Fig. 2l, the 0.0 category is comprised of genes with no noncg methylation as genes with no methylation tend to be less expressed than those with gene body methylation. 15

16 Diversity Mb 5 Mb 10 Mb 15 Mb 0 Mb 5 Mb 10 Mb 15 Mb 20 Mb Position on chromosome II Position on chromosome III 0 Mb 5 Mb 10 Mb 15 Mb Diversity Diversity Mb 5 Mb 10 Mb 15 Mb 20 Mb 25 Mb Position on chromosome IV Position on chromosome V Supplementary Fig. 10. A plot of SNP, SMP, and C-DMR diversity across chromosomes II, III, IV, and V. The diversity for each data type was computed by calculating the Euclidean distances between the C-DMRs/SNPs/SMPs of all pairwise combinations of accessions in overlapping 500 kb windows offset by 100 kb (binary values for SNPs and SMPs, methylation levels for C-DMRs). Each diversity measure was normalized to have a mean of zero and a standard deviation of one. Pink shaded regions indicate the location of the pericentromere. Diversity 16

17 a r^ Genes CG SMPs CHG SMPs CHH SMPs b r^ Distance (bp) Transposons Distance (bp) c r^ Regions outside of genes and transposons Distance (bp) Supplementary Fig. 11. Assocation decay rates for CG-, CHG- and CHH-SMPs across genomic features. (a) The association decay rate for SMPs in genes. (b) the association decay rate of SMPs in transposons. (c) the association decay rate of SMPs in regions not containing genes or transposons. The rates of decay outside of genes for CG-SMPs indicate that these SMPs have different properties compared to CG-SMPs in transposons, which could be due to other factors such as nucleosome density, an important factor for maintenance of CG methylation. 17

18 a r^ Genes CG SMPs CHG SMPs CHH SMPs Distance (kb) b Transposons r^ Distance (kb) c r^ Regions outside of genes and transposons Distance (kb) Supplementary Fig. 12. Assocation decay rates for CG-, CHG- and CHH-SMPs across genomic features over long ranges. (a) The association decay rate for SMPs in genes. (b) the association decay rate of SMPs in transposons. (c) the association decay rate of SMPs in regions not containing genes or transposons. The rate of decay outside of genes for CHG-SMPs and for CG-SMPs in transposons eventually decreases, but the distance of decay is far greater than the linkage disequilibrium deteremined by using SNPs from these same accessions. CG-SMPs in genes decay at rates faster than LD and CHG-SMPs in genes and CG-SMPs in transposons decay at rates greater than LD indicating that SMPs can be unliked from genotype. 18

19 Col-0 Cvi-0 Ler-1 Bor-1 Bor-4 Da(12)-1 Knox-18 Wt-5 Yo-0 AT5G10130 AT5G10140 Supplementary Fig. 13. A selected screen shot of C-DMRs (red boxes) that overlap with the FLC locus. Within some of these C-DMRs there is a transposition event that has occurred and the methylation has spread from the transposon into the inserted locus. a -log(p-value) ChrI ChrII PAI1 ChrIII ChrIV ChrV ChrM b -log(p-value) ChrI ChrII PAI2 ChrIII ChrIV ChrV ChrM c -log(p-value) ChrI ChrII PAI3 ChrIII ChrIV ChrV ChrM Supplementary Fig. 14. Manhattan plots for the PAI-gene family. Each point represents an association test between a particular C-DMR, the location of which is indicated by a vertical line, and a SNP. The y-axis indicates the level of significance, which increases from the bottom to the top of the plot, and the x-axis denotes the position of the SNP being tested. An association test is deemed significant if the dot is above the horizontal line, which indicates a 1% FDR. 19

20 a All C DMRs chromosome I b C DMRs tested in GWAS chromosome I 0.0e e e e e e e e e e e e e e+07 c C DMRs with an mqtl chromosome I d C DMRs with no mqtl chromosome I 0.0e e e e e e e e e e e e e e+07 Supplementary Fig. 15. Chromosome I mqtl anlaysis. (a) a histogram representing the distribution of C-DMRs along the chromosome. (b) a histogram representing the distribution of C-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of C-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of C-DMRs with no significantly associated mqtl along the chromosome. 20

21 a All CG DMRs chromosome I b CG DMRs tested in GWAS chromosome I 0.0e e e e e e e e e e e e e e e e e e e e e e+07 c CG DMRs with an mqtl chromosome I d CG DMRs with no mqtl chromosome I 0.0e e e e e e e e e e e e e e e e e e e e e e+07 Supplementary Fig. 16. Chromosome I mqtl anlaysis. (a) a histogram representing the distribution of CG-DMRs along the chromosome. (b) a histogram representing the distribution of CG-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of CG-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of CG-DMRs with no significantly associated mqtl along the chromosome. 21

22 a All C DMRs chromosome II b C DMRs tested in GWAS chromosome II 0e+00 1e 07 2e 07 3e 07 4e 07 0e+00 1e 07 2e 07 3e 07 4e e e e e e e e e e e+07 c C DMRs with an mqtl chromosome II d C DMRs with no mqtl chromosome II 0e+00 1e 07 2e 07 3e 07 4e 07 0e+00 1e 07 2e 07 3e 07 4e e e e e e e e e e e+07 Supplementary Fig. 17. Chromosome II mqtl anlaysis. (a) a histogram representing the distribution of C-DMRs along the chromosome. (b) a histogram representing the distribution of C-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of C-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of C-DMRs with no significantly associated mqtl along the chromosome. 22

23 a All CG DMRs chromosome II b CG DMRs tested in GWAS chromosome II 0.0e e e e e e e e e e+07 c CG DMRs with an mqtl chromosome II d CG DMRs with no mqtl chromosome II 0.0e e e e e e e e e e+07 Supplementary Fig. 18. Chromosome II mqtl anlaysis. (a) a histogram representing the distribution of CG-DMRs along the chromosome. (b) a histogram representing the distribution of CG-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of CG-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of CG-DMRs with no significantly associated mqtl along the chromosome. 23

24 a All C DMRs chromosome III b C DMRs tested in GWAS chromosome III 0.0e e e e e e e e e e+07 c C DMRs with an mqtl chromosome III d C DMRs with no mqtl chromosome III 0.0e e e e e e e e e e+07 Supplementary Fig. 19. Chromosome III mqtl anlaysis. (a) a histogram representing the distribution of C-DMRs along the chromosome. (b) a histogram representing the distribution of C-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of C-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of C-DMRs with no significantly associated mqtl along the chromosome. 24

25 a All CG DMRs chromosome III b CG DMRs tested in GWAS chromosome III 0.0e e e e e e e e e e e e e e e e e e e e+07 c CG DMRs with an mqtl chromosome III d CG DMRs with no mqtl chromosome III 0.0e e e e e e e e e e e e e e e e e e e e+07 Supplementary Fig. 20. Chromosome III mqtl anlaysis. (a) a histogram representing the distribution of CG-DMRs along the chromosome. (b) a histogram representing the distribution of CG-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of CG-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of CG-DMRs with no significantly associated mqtl along the chromosome. 25

26 a All C DMRs chromosome IV b C DMRs tested in GWAS chromosome IV 0e+00 1e 07 2e 07 3e 07 0e+00 1e 07 2e 07 3e e e e e e e e e+07 c C DMRs with an mqtl chromosome IV d C DMRs with no mqtl chromosome IV 0e+00 1e 07 2e 07 3e 07 0e+00 1e 07 2e 07 3e e e e e e e e e+07 Supplementary Fig. 21. Chromosome IV mqtl anlaysis. (a) a histogram representing the distribution of C-DMRs along the chromosome. (b) a histogram representing the distribution of C-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of C-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of C-DMRs with no significantly associated mqtl along the chromosome. 26

27 a All CG DMRs chromosome IV b CG DMRs tested in GWAS chromosome IV 0.0e e e e e e e e+07 c CG DMRs with an mqtl chromosome IV d CG DMRs with no mqtl chromosome IV 0.0e e e e e e e e+07 Supplementary Fig. 22. Chromosome IV mqtl anlaysis. (a) a histogram representing the distribution of CG-DMRs along the chromosome. (b) a histogram representing the distribution of CG-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of CG-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of CG-DMRs with no significantly associated mqtl along the chromosome. 27

28 a All C DMRs chromosome V b C DMRs tested in GWAS chromosome V 0.0e e e e e e e e e e e e+07 c C DMRs with an mqtl chromosome V d C DMRs with no mqtl chromosome V 0.0e e e e e e e e e e e e+07 Supplementary Fig. 23. Chromosome V mqtl anlaysis. (a) a histogram representing the distribution of C-DMRs along the chromosome. (b) a histogram representing the distribution of C-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of C-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of C-DMRs with no significantly associated mqtl along the chromosome. 28

29 a All CG DMRs chromosome V b CG DMRs tested in GWAS chromosome V 0.0e e e e e e e e e e e e e e e e e e e e+07 c CG DMRs with an mqtl chromosome V d CG DMRs with no mqtl chromosome V 0.0e e e e e e e e e e e e e e e e e e e e+07 Supplementary Fig. 24. Chromosome V mqtl anlaysis. (a) a histogram representing the distribution of CG-DMRs along the chromosome. (b) a histogram representing the distribution of CG-DMRs that passed the required thresholds for association mapping.along the chromosome. (c) a histogram representing the distribution of CG-DMRs with an mqtl along the chromosome. (d) a histogram representing the distribution of CG-DMRs with no significantly associated mqtl along the chromosome. 29

30 Fraction of signi cant C-DMRs 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% Not signi cant in MLMM Monogenic/Polygenic Polygenic/Monogenic Monogenic/Monogenic Polygenic/Polygenic Supplementary Fig. 25. A summary of the comparison of the results from using EMMAX or MLMM for the C-DMR GWA. THe word before the slash indicates the state of the C-DMR when run with EMMAX, and the word after the slash indicates the state of the C-DMR when run with MLMM. 30

31 30.00% Fraction of normalized count 25.00% 20.00% 15.00% 10.00% 5.00% 0.00% Distant Distance (kb) from mqtl to CG-DMR Supplementary Fig. 26. The distribution of distances of significant mqtl from their CG-DMRs normalized for the base pair space covered by each range of distances. A distant mqtl is defined as any mqtl that is more than 100 kb from its CG-DMR. 31

32 % % % % Number of DMRs % 30.00% 20.00% Fraction gained % 40.00% 30.00% 20.00% % % Number of Samples 0.00% % C-DMRs % % % % Number of DMRs % 40.00% 30.00% 20.00% Fraction gained Number of DMRs % 8.00% 6.00% 4.00% 2.00% Fraction gained % % Number of Samples 0.00% Number of Samples -2.00% CHG-DMRs CHH-DMRs Supplementary Fig. 27. Plots of the number of DMRs in various nucleotide contexts found after randomly subsampling the data. The blue line represents the mean number of DMRs found in a particular context for a particular number of samples and the red line represents the precent of additional DMRs found over the last number of samples. Error bars represent the s.e.m. Although CHH DMRs seemed to have reaached a saturation point, this analysis indicates that there are still other kinds of DMRs to be found. 32

33 25.00% Fraction of normalized count 20.00% 15.00% 10.00% 5.00% 0.00% Distant Distance from mqtl to DMR (kb) Supplementary Fig. 28. The distribution of distances of significant mqtl from the randomization method from their C-DMRs for the base pair space covered by each range of distances. A distant mqtl is defined as any mqtl that is more than 100 kb from its CG-DMR. 33

34 Median of normalized expression value (0.0,0.1) [0.1,0.2) [0.2,0.3) [0.3,0.4) [0.4,0.5) [0.5,1.0] Distribution of methylation levels CG DMRs Supplementary Fig. 29. The median normalized expression values from Figure 2j. Error bars indicate the bootstrap confidence intervals around the median. 34

35 Median of normalized expression value (0.0,0.1) [0.1,0.2) [0.2,0.3) [0.3,0.4) [0.4,0.5) [0.5,1.0] Distribution of methylation levels C DMRs Supplementary Fig. 30. The median normalized expression values from Figure 2k. Error bars indicate the bootstrap confidence intervals around the median. 35

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