- 1.
Sánchez-Romero, M. A., Cota, I. & Casadesús, J. DNA methylation in bacteria: from the methyl group to the methylome. Curr. Opin. Microbiol. 25, 9–16 (2015).
- 2.
Robertson, K. D. DNA methylation and human disease. Nat. Rev. Genet. 6, 597–610 (2005).
- 3.
Arand, J. et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 8, e1002750 (2012).
- 4.
Alonso, C., Perez, R., Bazaga, P. & Herrera, C. M. Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in angiosperms. Front Genet. 6, 4 (2015).
- 5.
Niederhuth, C. E. et al. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 17, 194 (2016).
- 6.
Li, Q. et al. Examining the causes and consequences of context-specific differential DNA methylation in maize. Plant Physiol. 168, 1262–1274 (2015).
- 7.
Schmitz, R. et al. Patterns of population epigenomic diversity. Nature 495, 193–198 (2013).
- 8.
Zhang, H. M., Lang, Z. B. & Zhu, J. K. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489–506 (2018).
- 9.
Springer, N. M. & Schmitz, R. J. Exploiting induced and natural epigenetic variation for crop improvement. Nat. Rev. Genet. 18, 563–575 (2017).
- 10.
Deniz, Ö., Frost, J. M. & Branco, M. R. Regulation of transposable elements by DNA modifications. Nat. Rev. Genet. 20, 417–431 (2019).
- 11.
Seymour, D. K. & Becker, C. The causes and consequences of DNA methylome variation in plants. Curr. Opin. Plant Biol. 36, 56–63 (2017).
- 12.
Dorweiler, J. E. et al. mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci. Plant Cell 12, 2101–2118 (2000).
- 13.
Li, Q. et al. Genetic perturbation of the maize methylome. Plant Cell 26, 4602–4616 (2014).
- 14.
Fu, F. F., Dawe, R. K. & Gent, J. I. Loss of RNA-directed DNA methylation in maize chromomethylase and DDM1-type nucleosome remodeler mutants. Plant Cell 30, 1617–1627 (2018).
- 15.
Shen, Y. T. et al. DNA methylation footprints during soybean domestication and improvement. Genome Biol. 19, 1–14 (2018).
- 16.
Hernando-Herraez, I., Garcia-Perez, R., Sharp, A. J. & Marques-Bonet, T. DNA methylation: insights into human evolution. PLoS Genet. 11, e1005661 (2015).
- 17.
Kader, F. & Ghai, M. DNA methylation-based variation between human populations. Mol. Genet. Genomics 292, 5–35 (2017).
- 18.
Manning, K. et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38, 948–952 (2006).
- 19.
Cortijo, S. et al. Mapping the epigenetic basis of complex traits. Science 343, 1145–1148 (2014).
- 20.
Eichten, S. R. et al. Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 25, 2783–2797 (2013).
- 21.
Van der Graaf, A. et al. Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proc. Natl Acad. Sci. USA 112, 6676–6681 (2015).
- 22.
Shahryary, Y. et al. AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. Genome Biol. 21, 260 (2020).
- 23.
Charlesworth, B. & Jain, K. Purifying selection, drift, and reversible mutation with arbitrarily high mutation rates. Genetics 198, 1587–1602 (2014).
- 24.
Vidalis, A. et al. Methylome evolution in plants. Genome Biol. 17, 264 (2016).
- 25.
Stitzer, M. C. & Ross-Ibarra, J. Maize domestication and gene interaction. New Phytol. 220, 395–408 (2018).
- 26.
Gates, D. J. et al. Single-gene resolution of locally adaptive genetic variation in Mexican maize. Preprint at https://doi.org/10.1101/706739 (2019).
- 27.
Swarts, K. et al. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357, 512–515 (2017).
- 28.
Navarro, J. A. R. et al. A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat. Genet. 49, 476–480 (2017).
- 29.
Teixeira, J. et al. Hallauer’s Tuson: a decade of selection for tropical-to-temperate phenological adaptation in maize. Heredity 114, 229–240 (2015).
- 30.
Yang, C. J. et al. The genetic architecture of teosinte catalyzed and constrained maize domestication. Proc. Natl Acad. Sci. USA 116, 5643–5652 (2019).
- 31.
Bukowski, R. et al. Construction of the third-generation Zea mays haplotype map. Gigascience 7, gix134 (2017).
- 32.
Lemmon, Z. H., Bukowski, R., Sun, Q. & Doebley, J. F. The role of cis regulatory evolution in maize domestication. PLoS Genet. 10, e1004745 (2014).
- 33.
Li, E. et al. Long-range interactions between proximal and distal regulatory regions in maize. Nat. Commun. 10, 2633 (2019).
- 34.
Wulfridge, P., Langmead, B., Feinberg, A. P. & Hansen, K. D. Choice of reference genome can introduce massive bias in bisulfite sequencing data. Nucleic Acid Res. 47, e117 (2019).
- 35.
Bertioli, D. J. et al. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat. Genet. 48, 438–446 (2016).
- 36.
Zhang, Y. et al. Differentially regulated orthologs in sorghum and the subgenomes of maize. Plant Cell 29, 1938–1951 (2017).
- 37.
West, P. T. et al. Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLoS ONE 9, e105267 (2014).
- 38.
Benaglia, T., Chauveau, D. S., Hunter, D. R. & Young, D. S. mixtools: An R package for analyzing finite mixture models. J. Stat. Softw. 32, 1–29 (2009).
- 39.
Ross-Ibarra, J., Tenaillon, M. & Gaut, B. S. Historical divergence and gene flow in the genus Zea. Genetics 181, 1397–1409 (2009).
- 40.
Beissinger, T. M. et al. Recent demography drives changes in linked selection across the maize genome. Nat. Plants 2, 1–7 (2016).
- 41.
Hahn, M. W. Molecular Population Genetics (Sinauer Associates/Oxford Univ. Press, 2018).
- 42.
Wallace, J. G. et al. Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genet. 10, e1004845 (2014).
- 43.
Speed, D., Hemani, G., Johnson, M. R. & Balding, D. J. Improved heritability estimation from genome-wide SNPs. Am. J. Hum. Genet. 91, 1011–1021 (2012).
- 44.
Jühling, F. et al. metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 26, 256–262 (2016).
- 45.
Sun, Y. et al. 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize. Genome Biol. 21, 1–25 (2020).
- 46.
Zhang, M. et al. Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm. Proc. Natl Acad. Sci. USA 108, 20042–20047 (2011).
- 47.
Zemach, A. et al. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl Acad. Sci. USA 107, 18729–18734 (2010).
- 48.
Gardiner, L. J. et al. A genome-wide survey of DNA methylation in hexaploid wheat. Genome Biol. 16, 273 (2015).
- 49.
Song, Q., Zhang, T., Stelly, D. M. & Chen, Z. J. Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons. Genome Biol. 18, 99 (2017).
- 50.
Studer, A., Zhao, Q., Ross-Ibarra, J. & Doebley, J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat. Genet. 43, 1160–1163 (2011).
- 51.
Zhao, D. P., Huang, Z. C., Umino, N., Hasegawa, A. & Kanamori, H. Structural heterogeneity in the megathrust zone and mechanism of the 2011 Tohoku-oki earthquake (Mw 9.0). Geophys. Res. Lett. 38 (2011).
- 52.
Sosso, D. et al. Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport. Nat. Genet 47, 1489 (2015).
- 53.
Sigmon, B. & Vollbrecht, E. Evidence of selection at the ramosa1 locus during maize domestication. Mol. Ecol. 19, 1296–1311 (2010).
- 54.
Whitt, S. R., Wilson, L. M., Tenaillon, M. I., Gaut, B. S. & Buckler, E. S. Genetic diversity and selection in the maize starch pathway. Proc. Natl Acad. Sci. USA 99, 12959–12962 (2002).
- 55.
Candaele, J. et al. Differential methylation during maize leaf growth targets developmentally regulated genes. Plant Physiol. 164, 1350–1364 (2014).
- 56.
Galli, M. et al. The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family. Nat. Commun. 9, 1–14 (2018).
- 57.
Xue, S., Bradbury, P. J., Casstevens, T. & Holland, J. B. Genetic architecture of domestication-related traits in maize. Genetics 204, 99–113 (2016).
- 58.
Li, Y. X. et al. Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. Plant J. 86, 391–402 (2016).
- 59.
Xu, C. et al. Genome-wide association study dissects yield components associated with low-phosphorus stress tolerance in maize. Theor. Appl. Genet. 131, 1699–1714 (2018).
- 60.
Li, C. H. et al. Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations. BMC Genomics 17, 894 (2016).
- 61.
Ricci, W. A. et al. Widespread long-range cis-regulatory elements in the maize genome. Nat. Plants 5, 1237–1249 (2019).
- 62.
Arnold, C. D. et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074–1077 (2013).
- 63.
Dong, Z. S. et al. A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling. PLoS ONE 7, e43450 (2012).
- 64.
Salvi, S. et al. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc. Natl Acad. Sci. USA 104, 11376–11381 (2007).
- 65.
Hufford, M. B. et al. Comparative population genomics of maize domestication and improvement. Nat. Genet. 44, 808–811 (2012).
- 66.
Rodgers-Melnick, E., Vera, D. L., Bass, H. W. & Buckler, E. S. Open chromatin reveals the functional maize genome. Proc. Natl Acad. Sci. USA 113, E3177–E3184 (2016).
- 67.
Oka, R. et al. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 18, 137 (2017).
- 68.
Splinter, E., de Wit, E., van de Werken, H. J. G., Klous, P. & De Laat, W. Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation. Methods 58, 221–230 (2012).
- 69.
Becker, C. et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245–249 (2011).
- 70.
Jiao, Y. P. et al. Genome-wide genetic changes during modern breeding of maize. Nat. Genet. 44, 812–815 (2012).
- 71.
Li, X. R. et al. Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res. 22, 2436–2444 (2012).
- 72.
Murray, M. G. & Thompson, W. F. Rapid isolation of high molecular-weight plant DNA. Nucleic Acids Res. 8, 4321–4325 (1980).
- 73.
Schnable, P. S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112–1115 (2009).
- 74.
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv:13033997 (2013).
- 75.
Picard toolkit. http://broadinstitute.github.io/picard/ (2019).
- 76.
McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
- 77.
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
- 78.
Schultz, M. D., Schmitz, R. J. & Ecker, J. R. ‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes. Trends Genet. 28, 583–585 (2012).
- 79.
Wang, H. et al. The origin of the naked grains of maize. Nature 436, 714–719 (2005).
- 80.
Tian, F., Stevens, N. M. & Buckler, E. S. Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10. Proc. Natl Acad. Sci. USA 106, 9979–9986 (2009).
- 81.
Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393–402 (2010).
- 82.
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
- 83.
Tian, T. et al. agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 45, W122–W129 (2017).
- 84.
Mumbach, M. R. et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat. Methods 13, 919–922 (2016).
- 85.
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).
- 86.
Ramírez, F., Dündarm, F., Diehl, S., Grüning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–W191 (2014).
- 87.
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
- 88.
Lareau, C. A. & Aryee, M. J. hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data. Nat. Methods 15, 155–156 (2018).
- 89.
Phanstiel, D. H., Boyle, A. P., Heidari, N. & Snyder, M. P. Mango: a bias-correcting ChIA-PET analysis pipeline. Bioinformatics 31, 3092–3098 (2015).
- 90.
Raviram, R. et al. 4C-ker: a method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments. PLoS Comput. Biol. 12, e1004780 (2016).
- 91.
Yu, J. M., Holland, J. B., McMullen, M. D. & Buckler, E. S. Genetic design and statistical power of nested association mapping in maize. Genetics 178, 539–551 (2008).
- 92.
Buckler, E. S. et al. The genetic architecture of maize flowering time. Science 325, 714–718 (2009).
- 93.
Bradbury, P. J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635 (2007).
- 94.
Hellens, R. P. et al. Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants. Plant Methods 1, 13 (2005).
- 95.
Yoo, S. D., Cho, Y. H. & Sheen, J. Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat. Protoc. 2, 1565–1572 (2007).
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