Welcome to the IKCEST
Evolutionary and functional genomics of DNA methylation in maize domestication and improvement
  1. 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).

    Article  CAS  Google Scholar 

  2. 2.

    Robertson, K. D. DNA methylation and human disease. Nat. Rev. Genet. 6, 597–610 (2005).

    CAS  Article  Google Scholar 

  3. 3.

    Arand, J. et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 8, e1002750 (2012).

    CAS  Article  PubMed Central  Google Scholar 

  4. 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).

    Article  CAS  PubMed Central  Google Scholar 

  5. 5.

    Niederhuth, C. E. et al. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 17, 194 (2016).

    Article  CAS  PubMed Central  Google Scholar 

  6. 6.

    Li, Q. et al. Examining the causes and consequences of context-specific differential DNA methylation in maize. Plant Physiol. 168, 1262–1274 (2015).

    CAS  Article  PubMed Central  Google Scholar 

  7. 7.

    Schmitz, R. et al. Patterns of population epigenomic diversity. Nature 495, 193–198 (2013).

    ADS  CAS  Article  PubMed Central  Google Scholar 

  8. 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).

    CAS  Article  Google Scholar 

  9. 9.

    Springer, N. M. & Schmitz, R. J. Exploiting induced and natural epigenetic variation for crop improvement. Nat. Rev. Genet. 18, 563–575 (2017).

    CAS  Article  Google Scholar 

  10. 10.

    Deniz, Ö., Frost, J. M. & Branco, M. R. Regulation of transposable elements by DNA modifications. Nat. Rev. Genet. 20, 417–431 (2019).

    CAS  Article  Google Scholar 

  11. 11.

    Seymour, D. K. & Becker, C. The causes and consequences of DNA methylome variation in plants. Curr. Opin. Plant Biol. 36, 56–63 (2017).

    CAS  Article  Google Scholar 

  12. 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).

    CAS  Article  PubMed Central  Google Scholar 

  13. 13.

    Li, Q. et al. Genetic perturbation of the maize methylome. Plant Cell 26, 4602–4616 (2014).

    Article  CAS  PubMed Central  Google Scholar 

  14. 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).

    CAS  Article  PubMed Central  Google Scholar 

  15. 15.

    Shen, Y. T. et al. DNA methylation footprints during soybean domestication and improvement. Genome Biol. 19, 1–14 (2018).

    Article  CAS  Google Scholar 

  16. 16.

    Hernando-Herraez, I., Garcia-Perez, R., Sharp, A. J. & Marques-Bonet, T. DNA methylation: insights into human evolution. PLoS Genet. 11, e1005661 (2015).

    Article  CAS  PubMed Central  Google Scholar 

  17. 17.

    Kader, F. & Ghai, M. DNA methylation-based variation between human populations. Mol. Genet. Genomics 292, 5–35 (2017).

    CAS  Article  Google Scholar 

  18. 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).

    CAS  Article  Google Scholar 

  19. 19.

    Cortijo, S. et al. Mapping the epigenetic basis of complex traits. Science 343, 1145–1148 (2014).

    ADS  CAS  Article  Google Scholar 

  20. 20.

    Eichten, S. R. et al. Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 25, 2783–2797 (2013).

    CAS  Article  PubMed Central  Google Scholar 

  21. 21.

    Van der Graaf, A. et al. Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proc. Natl Acad. Sci. USA 112, 6676–6681 (2015).

    ADS  Article  CAS  Google Scholar 

  22. 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. 23.

    Charlesworth, B. & Jain, K. Purifying selection, drift, and reversible mutation with arbitrarily high mutation rates. Genetics 198, 1587–1602 (2014).

    Article  PubMed Central  Google Scholar 

  24. 24.

    Vidalis, A. et al. Methylome evolution in plants. Genome Biol. 17, 264 (2016).

    Article  CAS  PubMed Central  Google Scholar 

  25. 25.

    Stitzer, M. C. & Ross-Ibarra, J. Maize domestication and gene interaction. New Phytol. 220, 395–408 (2018).

    Article  Google Scholar 

  26. 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. 27.

    Swarts, K. et al. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357, 512–515 (2017).

    ADS  CAS  Article  Google Scholar 

  28. 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).

    Article  CAS  Google Scholar 

  29. 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).

    CAS  Article  Google Scholar 

  30. 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).

    CAS  Article  Google Scholar 

  31. 31.

    Bukowski, R. et al. Construction of the third-generation Zea mays haplotype map. Gigascience 7, gix134 (2017).

    PubMed Central  Google Scholar 

  32. 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).

    Article  CAS  PubMed Central  Google Scholar 

  33. 33.

    Li, E. et al. Long-range interactions between proximal and distal regulatory regions in maize. Nat. Commun. 10, 2633 (2019).

    ADS  Article  CAS  PubMed Central  Google Scholar 

  34. 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. 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).

    CAS  Article  Google Scholar 

  36. 36.

    Zhang, Y. et al. Differentially regulated orthologs in sorghum and the subgenomes of maize. Plant Cell 29, 1938–1951 (2017).

    CAS  Article  PubMed Central  Google Scholar 

  37. 37.

    West, P. T. et al. Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLoS ONE 9, e105267 (2014).

  38. 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. 39.

    Ross-Ibarra, J., Tenaillon, M. & Gaut, B. S. Historical divergence and gene flow in the genus Zea. Genetics 181, 1397–1409 (2009).

    Article  CAS  Google Scholar 

  40. 40.

    Beissinger, T. M. et al. Recent demography drives changes in linked selection across the maize genome. Nat. Plants 2, 1–7 (2016).

    Article  Google Scholar 

  41. 41.

    Hahn, M. W. Molecular Population Genetics (Sinauer Associates/Oxford Univ. Press, 2018).

  42. 42.

    Wallace, J. G. et al. Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genet. 10, e1004845 (2014).

    Article  PubMed Central  Google Scholar 

  43. 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).

    CAS  Article  PubMed Central  Google Scholar 

  44. 44.

    Jühling, F. et al. metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 26, 256–262 (2016).

    Article  CAS  PubMed Central  Google Scholar 

  45. 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).

    Article  CAS  Google Scholar 

  46. 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).

    ADS  CAS  Article  Google Scholar 

  47. 47.

    Zemach, A. et al. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl Acad. Sci. USA 107, 18729–18734 (2010).

    ADS  CAS  Article  Google Scholar 

  48. 48.

    Gardiner, L. J. et al. A genome-wide survey of DNA methylation in hexaploid wheat. Genome Biol. 16, 273 (2015).

    Article  CAS  PubMed Central  Google Scholar 

  49. 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).

    Article  CAS  PubMed Central  Google Scholar 

  50. 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).

    CAS  Article  PubMed Central  Google Scholar 

  51. 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. 52.

    Sosso, D. et al. Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport. Nat. Genet 47, 1489 (2015).

    CAS  Article  Google Scholar 

  53. 53.

    Sigmon, B. & Vollbrecht, E. Evidence of selection at the ramosa1 locus during maize domestication. Mol. Ecol. 19, 1296–1311 (2010).

    CAS  Article  Google Scholar 

  54. 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).

    ADS  CAS  Article  Google Scholar 

  55. 55.

    Candaele, J. et al. Differential methylation during maize leaf growth targets developmentally regulated genes. Plant Physiol. 164, 1350–1364 (2014).

    CAS  Article  PubMed Central  Google Scholar 

  56. 56.

    Galli, M. et al. The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family. Nat. Commun. 9, 1–14 (2018).

    CAS  Article  Google Scholar 

  57. 57.

    Xue, S., Bradbury, P. J., Casstevens, T. & Holland, J. B. Genetic architecture of domestication-related traits in maize. Genetics 204, 99–113 (2016).

    Article  PubMed Central  Google Scholar 

  58. 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).

    CAS  Article  Google Scholar 

  59. 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).

    CAS  Article  Google Scholar 

  60. 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).

    Article  PubMed Central  Google Scholar 

  61. 61.

    Ricci, W. A. et al. Widespread long-range cis-regulatory elements in the maize genome. Nat. Plants 5, 1237–1249 (2019).

    CAS  Article  PubMed Central  Google Scholar 

  62. 62.

    Arnold, C. D. et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074–1077 (2013).

    ADS  CAS  Article  Google Scholar 

  63. 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).

    ADS  CAS  Article  PubMed Central  Google Scholar 

  64. 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).

    ADS  CAS  Article  Google Scholar 

  65. 65.

    Hufford, M. B. et al. Comparative population genomics of maize domestication and improvement. Nat. Genet. 44, 808–811 (2012).

    CAS  Article  PubMed Central  Google Scholar 

  66. 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).

    CAS  Article  Google Scholar 

  67. 67.

    Oka, R. et al. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 18, 137 (2017).

    Article  CAS  PubMed Central  Google Scholar 

  68. 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).

    CAS  Article  Google Scholar 

  69. 69.

    Becker, C. et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245–249 (2011).

    ADS  CAS  Article  Google Scholar 

  70. 70.

    Jiao, Y. P. et al. Genome-wide genetic changes during modern breeding of maize. Nat. Genet. 44, 812–815 (2012).

    CAS  Article  Google Scholar 

  71. 71.

    Li, X. R. et al. Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res. 22, 2436–2444 (2012).

    CAS  Article  PubMed Central  Google Scholar 

  72. 72.

    Murray, M. G. & Thompson, W. F. Rapid isolation of high molecular-weight plant DNA. Nucleic Acids Res. 8, 4321–4325 (1980).

    CAS  Article  PubMed Central  Google Scholar 

  73. 73.

    Schnable, P. S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112–1115 (2009).

    ADS  CAS  Article  Google Scholar 

  74. 74.

    Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv:13033997 (2013).

  75. 75.

    Picard toolkit. http://broadinstitute.github.io/picard/ (2019).

  76. 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).

    CAS  Article  PubMed Central  Google Scholar 

  77. 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).

    Article  CAS  PubMed Central  Google Scholar 

  78. 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).

    CAS  Article  PubMed Central  Google Scholar 

  79. 79.

    Wang, H. et al. The origin of the naked grains of maize. Nature 436, 714–719 (2005).

    ADS  CAS  Article  PubMed Central  Google Scholar 

  80. 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).

    ADS  CAS  Article  Google Scholar 

  81. 81.

    Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393–402 (2010).

    CAS  Article  PubMed Central  Google Scholar 

  82. 82.

    Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    CAS  Article  PubMed Central  Google Scholar 

  83. 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).

    CAS  Article  PubMed Central  Google Scholar 

  84. 84.

    Mumbach, M. R. et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat. Methods 13, 919–922 (2016).

    CAS  Article  PubMed Central  Google Scholar 

  85. 85.

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).

    CAS  Article  PubMed Central  Google Scholar 

  86. 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).

    Article  CAS  PubMed Central  Google Scholar 

  87. 87.

    Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).

    Article  CAS  PubMed Central  Google Scholar 

  88. 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. 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).

    CAS  Article  PubMed Central  Google Scholar 

  90. 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).

    Article  CAS  PubMed Central  Google Scholar 

  91. 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).

    Article  PubMed Central  Google Scholar 

  92. 92.

    Buckler, E. S. et al. The genetic architecture of maize flowering time. Science 325, 714–718 (2009).

    ADS  CAS  Article  Google Scholar 

  93. 93.

    Bradbury, P. J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635 (2007).

    CAS  Article  PubMed Central  Google Scholar 

  94. 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).

    Article  CAS  PubMed Central  Google Scholar 

  95. 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).

    CAS  Article  Google Scholar 

Original Text (This is the original text for your reference.)

  1. 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).

    Article  CAS  Google Scholar 

  2. 2.

    Robertson, K. D. DNA methylation and human disease. Nat. Rev. Genet. 6, 597–610 (2005).

    CAS  Article  Google Scholar 

  3. 3.

    Arand, J. et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 8, e1002750 (2012).

    CAS  Article  PubMed Central  Google Scholar 

  4. 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).

    Article  CAS  PubMed Central  Google Scholar 

  5. 5.

    Niederhuth, C. E. et al. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 17, 194 (2016).

    Article  CAS  PubMed Central  Google Scholar 

  6. 6.

    Li, Q. et al. Examining the causes and consequences of context-specific differential DNA methylation in maize. Plant Physiol. 168, 1262–1274 (2015).

    CAS  Article  PubMed Central  Google Scholar 

  7. 7.

    Schmitz, R. et al. Patterns of population epigenomic diversity. Nature 495, 193–198 (2013).

    ADS  CAS  Article  PubMed Central  Google Scholar 

  8. 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).

    CAS  Article  Google Scholar 

  9. 9.

    Springer, N. M. & Schmitz, R. J. Exploiting induced and natural epigenetic variation for crop improvement. Nat. Rev. Genet. 18, 563–575 (2017).

    CAS  Article  Google Scholar 

  10. 10.

    Deniz, Ö., Frost, J. M. & Branco, M. R. Regulation of transposable elements by DNA modifications. Nat. Rev. Genet. 20, 417–431 (2019).

    CAS  Article  Google Scholar 

  11. 11.

    Seymour, D. K. & Becker, C. The causes and consequences of DNA methylome variation in plants. Curr. Opin. Plant Biol. 36, 56–63 (2017).

    CAS  Article  Google Scholar 

  12. 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).

    CAS  Article  PubMed Central  Google Scholar 

  13. 13.

    Li, Q. et al. Genetic perturbation of the maize methylome. Plant Cell 26, 4602–4616 (2014).

    Article  CAS  PubMed Central  Google Scholar 

  14. 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).

    CAS  Article  PubMed Central  Google Scholar 

  15. 15.

    Shen, Y. T. et al. DNA methylation footprints during soybean domestication and improvement. Genome Biol. 19, 1–14 (2018).

    Article  CAS  Google Scholar 

  16. 16.

    Hernando-Herraez, I., Garcia-Perez, R., Sharp, A. J. & Marques-Bonet, T. DNA methylation: insights into human evolution. PLoS Genet. 11, e1005661 (2015).

    Article  CAS  PubMed Central  Google Scholar 

  17. 17.

    Kader, F. & Ghai, M. DNA methylation-based variation between human populations. Mol. Genet. Genomics 292, 5–35 (2017).

    CAS  Article  Google Scholar 

  18. 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).

    CAS  Article  Google Scholar 

  19. 19.

    Cortijo, S. et al. Mapping the epigenetic basis of complex traits. Science 343, 1145–1148 (2014).

    ADS  CAS  Article  Google Scholar 

  20. 20.

    Eichten, S. R. et al. Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 25, 2783–2797 (2013).

    CAS  Article  PubMed Central  Google Scholar 

  21. 21.

    Van der Graaf, A. et al. Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proc. Natl Acad. Sci. USA 112, 6676–6681 (2015).

    ADS  Article  CAS  Google Scholar 

  22. 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. 23.

    Charlesworth, B. & Jain, K. Purifying selection, drift, and reversible mutation with arbitrarily high mutation rates. Genetics 198, 1587–1602 (2014).

    Article  PubMed Central  Google Scholar 

  24. 24.

    Vidalis, A. et al. Methylome evolution in plants. Genome Biol. 17, 264 (2016).

    Article  CAS  PubMed Central  Google Scholar 

  25. 25.

    Stitzer, M. C. & Ross-Ibarra, J. Maize domestication and gene interaction. New Phytol. 220, 395–408 (2018).

    Article  Google Scholar 

  26. 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. 27.

    Swarts, K. et al. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357, 512–515 (2017).

    ADS  CAS  Article  Google Scholar 

  28. 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).

    Article  CAS  Google Scholar 

  29. 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).

    CAS  Article  Google Scholar 

  30. 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).

    CAS  Article  Google Scholar 

  31. 31.

    Bukowski, R. et al. Construction of the third-generation Zea mays haplotype map. Gigascience 7, gix134 (2017).

    PubMed Central  Google Scholar 

  32. 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).

    Article  CAS  PubMed Central  Google Scholar 

  33. 33.

    Li, E. et al. Long-range interactions between proximal and distal regulatory regions in maize. Nat. Commun. 10, 2633 (2019).

    ADS  Article  CAS  PubMed Central  Google Scholar 

  34. 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. 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).

    CAS  Article  Google Scholar 

  36. 36.

    Zhang, Y. et al. Differentially regulated orthologs in sorghum and the subgenomes of maize. Plant Cell 29, 1938–1951 (2017).

    CAS  Article  PubMed Central  Google Scholar 

  37. 37.

    West, P. T. et al. Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLoS ONE 9, e105267 (2014).

  38. 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. 39.

    Ross-Ibarra, J., Tenaillon, M. & Gaut, B. S. Historical divergence and gene flow in the genus Zea. Genetics 181, 1397–1409 (2009).

    Article  CAS  Google Scholar 

  40. 40.

    Beissinger, T. M. et al. Recent demography drives changes in linked selection across the maize genome. Nat. Plants 2, 1–7 (2016).

    Article  Google Scholar 

  41. 41.

    Hahn, M. W. Molecular Population Genetics (Sinauer Associates/Oxford Univ. Press, 2018).

  42. 42.

    Wallace, J. G. et al. Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genet. 10, e1004845 (2014).

    Article  PubMed Central  Google Scholar 

  43. 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).

    CAS  Article  PubMed Central  Google Scholar 

  44. 44.

    Jühling, F. et al. metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 26, 256–262 (2016).

    Article  CAS  PubMed Central  Google Scholar 

  45. 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).

    Article  CAS  Google Scholar 

  46. 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).

    ADS  CAS  Article  Google Scholar 

  47. 47.

    Zemach, A. et al. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl Acad. Sci. USA 107, 18729–18734 (2010).

    ADS  CAS  Article  Google Scholar 

  48. 48.

    Gardiner, L. J. et al. A genome-wide survey of DNA methylation in hexaploid wheat. Genome Biol. 16, 273 (2015).

    Article  CAS  PubMed Central  Google Scholar 

  49. 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).

    Article  CAS  PubMed Central  Google Scholar 

  50. 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).

    CAS  Article  PubMed Central  Google Scholar 

  51. 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. 52.

    Sosso, D. et al. Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport. Nat. Genet 47, 1489 (2015).

    CAS  Article  Google Scholar 

  53. 53.

    Sigmon, B. & Vollbrecht, E. Evidence of selection at the ramosa1 locus during maize domestication. Mol. Ecol. 19, 1296–1311 (2010).

    CAS  Article  Google Scholar 

  54. 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).

    ADS  CAS  Article  Google Scholar 

  55. 55.

    Candaele, J. et al. Differential methylation during maize leaf growth targets developmentally regulated genes. Plant Physiol. 164, 1350–1364 (2014).

    CAS  Article  PubMed Central  Google Scholar 

  56. 56.

    Galli, M. et al. The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family. Nat. Commun. 9, 1–14 (2018).

    CAS  Article  Google Scholar 

  57. 57.

    Xue, S., Bradbury, P. J., Casstevens, T. & Holland, J. B. Genetic architecture of domestication-related traits in maize. Genetics 204, 99–113 (2016).

    Article  PubMed Central  Google Scholar 

  58. 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).

    CAS  Article  Google Scholar 

  59. 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).

    CAS  Article  Google Scholar 

  60. 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).

    Article  PubMed Central  Google Scholar 

  61. 61.

    Ricci, W. A. et al. Widespread long-range cis-regulatory elements in the maize genome. Nat. Plants 5, 1237–1249 (2019).

    CAS  Article  PubMed Central  Google Scholar 

  62. 62.

    Arnold, C. D. et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074–1077 (2013).

    ADS  CAS  Article  Google Scholar 

  63. 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).

    ADS  CAS  Article  PubMed Central  Google Scholar 

  64. 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).

    ADS  CAS  Article  Google Scholar 

  65. 65.

    Hufford, M. B. et al. Comparative population genomics of maize domestication and improvement. Nat. Genet. 44, 808–811 (2012).

    CAS  Article  PubMed Central  Google Scholar 

  66. 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).

    CAS  Article  Google Scholar 

  67. 67.

    Oka, R. et al. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 18, 137 (2017).

    Article  CAS  PubMed Central  Google Scholar 

  68. 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).

    CAS  Article  Google Scholar 

  69. 69.

    Becker, C. et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245–249 (2011).

    ADS  CAS  Article  Google Scholar 

  70. 70.

    Jiao, Y. P. et al. Genome-wide genetic changes during modern breeding of maize. Nat. Genet. 44, 812–815 (2012).

    CAS  Article  Google Scholar 

  71. 71.

    Li, X. R. et al. Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res. 22, 2436–2444 (2012).

    CAS  Article  PubMed Central  Google Scholar 

  72. 72.

    Murray, M. G. & Thompson, W. F. Rapid isolation of high molecular-weight plant DNA. Nucleic Acids Res. 8, 4321–4325 (1980).

    CAS  Article  PubMed Central  Google Scholar 

  73. 73.

    Schnable, P. S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112–1115 (2009).

    ADS  CAS  Article  Google Scholar 

  74. 74.

    Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv:13033997 (2013).

  75. 75.

    Picard toolkit. http://broadinstitute.github.io/picard/ (2019).

  76. 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).

    CAS  Article  PubMed Central  Google Scholar 

  77. 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).

    Article  CAS  PubMed Central  Google Scholar 

  78. 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).

    CAS  Article  PubMed Central  Google Scholar 

  79. 79.

    Wang, H. et al. The origin of the naked grains of maize. Nature 436, 714–719 (2005).

    ADS  CAS  Article  PubMed Central  Google Scholar 

  80. 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).

    ADS  CAS  Article  Google Scholar 

  81. 81.

    Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393–402 (2010).

    CAS  Article  PubMed Central  Google Scholar 

  82. 82.

    Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    CAS  Article  PubMed Central  Google Scholar 

  83. 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).

    CAS  Article  PubMed Central  Google Scholar 

  84. 84.

    Mumbach, M. R. et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat. Methods 13, 919–922 (2016).

    CAS  Article  PubMed Central  Google Scholar 

  85. 85.

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).

    CAS  Article  PubMed Central  Google Scholar 

  86. 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).

    Article  CAS  PubMed Central  Google Scholar 

  87. 87.

    Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).

    Article  CAS  PubMed Central  Google Scholar 

  88. 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. 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).

    CAS  Article  PubMed Central  Google Scholar 

  90. 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).

    Article  CAS  PubMed Central  Google Scholar 

  91. 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).

    Article  PubMed Central  Google Scholar 

  92. 92.

    Buckler, E. S. et al. The genetic architecture of maize flowering time. Science 325, 714–718 (2009).

    ADS  CAS  Article  Google Scholar 

  93. 93.

    Bradbury, P. J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635 (2007).

    CAS  Article  PubMed Central  Google Scholar 

  94. 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).

    Article  CAS  PubMed Central  Google Scholar 

  95. 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).

    CAS  Article  Google Scholar 

Comments

    Something to say?

    Log in or Sign up for free

    Disclaimer: The translated content is provided by third-party translation service providers, and IKCEST shall not assume any responsibility for the accuracy and legality of the content.
    Translate engine
    Article's language
    English
    中文
    Pусск
    Français
    Español
    العربية
    Português
    Kikongo
    Dutch
    kiswahili
    هَوُسَ
    IsiZulu
    Action
    Related

    Report

    Select your report category*



    Reason*



    By pressing send, your feedback will be used to improve IKCEST. Your privacy will be protected.

    Submit
    Cancel