Epigenetic variation in maize agronomical traits for breeding and trait improvement

Epigenetics-mediated breeding (epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels...

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Published in	Journal of genetics and genomics Vol. 52; no. 3; pp. 307 - 318
Main Authors	Zhang, Daolei, Gan, Yujun, Le, Liang, Pu, Li
Format	Journal Article
Language	English
Published	China Elsevier Ltd 01.03.2025
Subjects	agricultural productivity Agronomical traits chromatin corn CRISPR-Cas Systems crop yield Crops, Agricultural - genetics DNA Epibreeding Epigenesis, Genetic Epigenetic variation epigenetics epigenome Epigenome editing Gene Editing gene expression Gene Expression Regulation, Plant Genetic Variation genomics histone code non-coding RNA Plant Breeding - methods Quantitative Trait Loci Quantitative Trait, Heritable Synthetic epigenetics Zea mays - genetics Zea mays - growth & development Synthetic epigenetics Epigenome editing Epigenetic variation Epibreeding Agronomical traits
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ISSN	1673-8527
DOI	10.1016/j.jgg.2024.01.006

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Abstract	Epigenetics-mediated breeding (epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.
AbstractList	Epigenetics-mediated breeding (Epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding. Epigenetics-mediated breeding (epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.Epigenetics-mediated breeding (epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.
Author	Gan, Yujun Zhang, Daolei Le, Liang Pu, Li
Author_xml	– sequence: 1 givenname: Daolei surname: Zhang fullname: Zhang, Daolei organization: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China – sequence: 2 givenname: Yujun orcidid: 0009-0001-5148-1110 surname: Gan fullname: Gan, Yujun organization: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China – sequence: 3 givenname: Liang orcidid: 0000-0002-4148-0122 surname: Le fullname: Le, Liang email: leliang@caas.cn organization: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China – sequence: 4 givenname: Li surname: Pu fullname: Pu, Li email: puli@caas.cn organization: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/38310944$$D View this record in MEDLINE/PubMed
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Cites_doi	10.1016/j.plaphy.2021.01.024 10.1093/pcp/pcv023 10.1101/gr.155879.113 10.1007/s11120-016-0271-9 10.1038/s41587-022-01470-4 10.1111/nph.14688 10.1104/pp.103.025403 10.1104/pp.15.00075 10.1534/g3.114.014670 10.1126/sciadv.adh8990 10.1016/j.devcel.2016.06.008 10.1093/nar/28.17.3250 10.1016/j.molp.2018.01.010 10.1111/tpj.15527 10.1105/tpc.112.107219 10.1016/S0006-291X(87)80181-X 10.1038/225948a0 10.1105/tpc.113.114793 10.1007/s11427-021-2131-6 10.3390/genes8100274 10.1007/s00122-022-04055-6 10.1128/IAI.69.12.7197-7204.2001 10.1534/genetics.117.300625 10.1126/science.1191078 10.1016/j.xplc.2022.100453 10.1038/s41467-020-14746-7 10.1105/tpc.106.042549 10.1038/s41598-020-72464-y 10.4161/epi.4.1.7371 10.1016/j.pbi.2022.102297 10.3390/agronomy10101484 10.1016/j.molcel.2020.02.018 10.1073/pnas.1002720107 10.1371/journal.pgen.1003437 10.1007/s10681-013-0901-7 10.1038/s41576-019-0106-6 10.1007/s00709-019-01364-4 10.1038/cr.2017.55 10.1104/pp.113.233312 10.1371/journal.pgen.1002366 10.1111/pbi.12919 10.1093/jxb/eraa052 10.1126/science.aai8898 10.1007/s00425-019-03145-y 10.1101/gr.146985.112 10.1007/s11103-018-0751-8 10.1105/tpc.109.067256 10.1038/ng.3636 10.1007/s13238-020-00733-7 10.1016/j.molp.2018.11.005 10.1016/j.jgg.2012.02.009 10.1016/j.molp.2016.10.007 10.1016/j.molp.2022.08.009 10.1038/nrm4043 10.1105/tpc.114.133140 10.1104/pp.15.00155 10.1016/j.cell.2021.03.025 10.1007/s00122-009-1099-x 10.1111/jipb.13208 10.1111/nph.17882 10.1111/j.1364-3703.2010.00621.x 10.1016/j.devcel.2020.03.009 10.1038/s41467-019-08736-7 10.1101/gr.152538.112 10.1104/pp.18.00034 10.1111/pbi.13734 10.1007/s11427-023-2361-1 10.1007/s00299-021-02807-0 10.1126/science.abg7985 10.1016/j.cell.2019.01.029 10.1073/pnas.91.8.2905 10.1002/jcp.20869 10.1104/pp.19.00987 10.3390/v10120664 10.1007/s00122-020-03549-5 10.1111/jipb.12873 10.3835/plantgenome2015.07.0053 10.1038/s41467-022-28753-3 10.1038/s41586-019-1679-0 10.1111/jipb.12733 10.1111/nph.17630 10.1126/science.1063127 10.1105/tpc.16.00912 10.1016/j.jgg.2022.02.012 10.1093/aob/mcs293 10.1016/j.bbagrm.2011.07.001 10.1093/plcell/koab098 10.1105/tpc.113.115907 10.1186/s12870-014-0204-8 10.1016/j.agsy.2022.103541 10.1016/j.devcel.2018.03.012 10.1111/tpj.15669 10.1093/mp/ssp022 10.1016/j.tplants.2014.08.005 10.1002/pld3.337 10.3389/fpls.2022.925688 10.3389/fgene.2022.876987 10.1371/journal.pone.0033834 10.1093/plphys/kiad625 10.1105/tpc.15.00269 10.1016/j.tig.2020.07.011 10.1007/s13258-021-01189-7 10.1371/journal.pgen.1008291 10.1186/s13059-022-02641-x 10.1016/j.molp.2017.09.013 10.1371/journal.pgen.1008120 10.1093/jxb/eraa565 10.3389/fgene.2020.603920 10.1016/S1673-8527(08)60006-5 10.1101/gr.153510.112 10.1105/tpc.17.00833 10.1186/1471-2229-10-178 10.1105/tpc.108.058883 10.1016/j.cell.2021.04.007 10.1105/tpc.16.00751 10.1093/pcp/pcs008 10.1186/s13059-019-1771-7 10.1038/175336a0 10.1126/science.aad8711 10.1111/tpj.12009 10.1104/pp.19.00323 10.3389/fpls.2020.00052 10.1105/tpc.109.065714 10.1038/srep38504 10.1093/jxb/erab227 10.1105/tpc.107.056457 10.1111/tpj.15043 10.1016/j.molp.2019.12.007 10.3390/ijms20071754 10.1186/s13059-021-02578-7 10.1016/j.bbagrm.2016.08.009 10.3389/fpls.2022.986940 10.3390/ijms23094968 10.1111/pbi.13329 10.1038/s41587-021-00982-9 10.1093/plphys/kiab073 10.1111/gcb.12069 10.1038/s41580-019-0168-5 10.1371/journal.pgen.1009326
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Keywords	Synthetic epigenetics Epigenome editing Epigenetic variation Epibreeding Agronomical traits
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References	Du, Wang, Zou, Xu, Li (bib23) 2018; 177 Cui, Liang, Shen, Zhang, Bao, Geng, Zhang, Leo, Vardy, Lu (bib12) 2017; 10 Liu, Cook, Melia-Hancock, Guill, Bottoms, Garcia, Ott, Nelson, Recker, Balint-Kurti (bib57) 2016; 9 Zhao, Zhou (bib142) 2012; 39 Hawkins, Fricker, Challinor, Ferro, Ho, Osborne (bib41) 2013; 19 Zhang, Wang, Pan (bib132) 2007; 210 Wang, Elling, Li, Li, Peng, He, Sun, Qi, Liu, Deng (bib114) 2009; 21 Dalakouras, Vlachostergios (bib13) 2021; 72 Yang, Yang, Sun, Chen, Xu, Lai, Li, Wang, Bhattarai, Xiao (bib125) 2017; 27 Bonasio, Tu, Reinberg (bib5) 2010; 330 Xiong, Mei, Kim, Mukherjee, Hassanein, Barbazuk, Sung, Kolaczkowski, Kang (bib120) 2014; 14 Kim, Kim, Cho (bib48) 2022; 44 Chen, Chen, Zhang, Yang, Guo, Wang, Ji, Zhao, Yin, Cai (bib11) 2022; 375 Liang, Riaz, Chachar, Ding, Du, Gu (bib53) 2020; 13 Luo, Zhang, Liu, Liu, Li, Chen, Peng, Jin, Wei, Jian (bib64) 2022; 234 Messmer, Fracheboud, Bänziger, Vargas, Stamp, Ribaut (bib73) 2009; 119 Papikian, Liu, Gallego-Bartolomé, Jacobsen (bib81) 2019; 10 Alvarez, Nota, Cambiagno (bib1) 2010; 11 Centore, Sandoval, Soares, Kadoch, Chan (bib10) 2020; 36 Dou, Han, Cao, Ku, Liu, Su, Ren, Zhang, Zeng, Dong (bib21) 2021; 72 Wang, Zhao, Mao, Ma, Su (bib108) 2020; 11 Middeljans, Wan, Jansen, Sharma, Stunnenberg, Logie (bib75) 2012; 7 Mercé, Bayer, Fernandez, Batley, Edwards (bib72) 2020; 10 Steward, Kusano, Sano (bib98) 2000; 28 Liu, Sretenovic, Fan, Cheng, Li, Qi, Tang, Xu, Guo, Zhong (bib56) 2022; 3 Rossi, Locatelli, Varotto, Donn, Pirona, Henderson, Hartings, Motto (bib88) 2007; 19 David, Burgess, Parker, Li, Pulsford, Sibbritt, Preiss, Searle (bib14) 2017; 29 Forestan, Farinati, Rouster, Lassagne, Lauria, Dal Ferro, Varotto (bib29) 2018; 208 Gawra, Valdivieso, Roux, Laporte, de Lorgeril, Gueguen, Saccas, Escoubas, Montagnani, Destoumieux-Garzόn (bib33) 2023; 9 Sun, Hu, Mu, Zhao, Qin, Gong, Qiu (bib99) 2022; 135 Zhang, Zhang, Liao, Yu, Zhou, Feng, Yang, Lei, Bai, Wu (bib134) 2019; 15 Zhong, Li, Bodi, Button, Vespa, Herzog, Fray (bib145) 2008; 20 Yang, Kundariya, Xu, Sandhu, Yu, Hutton, Zhang, Mackenzie (bib126) 2015; 168 Guo, Wang, Lisch (bib38) 2021; 17 Zhou, Tian, Qin (bib147) 2019; 20 Wang, Yang, Wang, Li, Guo, Zhang, Ma, Song, Zhao, Xu (bib149) 2017; 215 Niederhuth, Schmitz (bib78) 2017; 1860 Nuñez, Chen, Pommier, Cogan, Replogle, Adriaens, Ramadoss, Shi, Hung, Samelson (bib80) 2021; 184 Deng, Zhai, Xie, Yang, Zhu, Liu, Wang, Qin, Yang, Zhang (bib16) 2017; 355 Long, Liu, Xia, Springer, He (bib59) 2021; 33 Yu, Jiang, Wu, Meng, Zhang, Li, Xia, Qi, Pang, Xu (bib129) 2016; 6 Erdmann, Souza, Clish, Gehring (bib27) 2014; 5 Miao, Zhang, Qi, Song, Han, Ma (bib74) 2020; 182 Duan, Wei, Zhang, Wang, Chen, Lu, Chen, He, Jia (bib24) 2017; 29 Dunn, Smith (bib25) 1955; 175 Park, Williams, Turpin, Wiggins, Tsolova, Onokpise, Bass (bib82) 2021; 5 Peterson, Dingwall, Scott (bib83) 1994; 91 Pintor-Toro (bib84) 1987; 147 Zhang, Wang, Chachar, Tian, Gu (bib138) 2020; 18 Gu, Jiang, Yang, Jacob, Michaels, He (bib36) 2011; 7 Meng, Yu, Wu, Kim, Nan, Cong, Wang, Liu, Xu (bib71) 2020; 11 Feng, Cokus, Zhang, Chen, Bostick, Goll, Hetzel, Jain, Strauss, Halpern (bib28) 2010; 107 Wang, Wang, Liu, Ferjani, Li, Yan, Yang, Qin (bib115) 2016; 48 Shen, Xu (bib95) 2009; 2 Zhang, Bodi, Mackinnon, Zhong, Archer, Mongan, Simpson, Fray (bib136) 2022; 13 Gent, Ellis, Guo, Harkess, Yao, Zhang, Dawe (bib34) 2013; 23 Regulski, Lu, Kendall, Donoghue, Reinders, Llaca, Deschamps, Smith, Levy, McCombie (bib87) 2013; 23 Luo, Han, Qian, Li (bib65) 2019; 250 Sang, Silva-Ortega, Wu, Yamaguchi, Wu, Pfluger, Gillmor, Gallagher, Wagner (bib90) 2012; 72 Lu, Rong, Cao (bib62) 2008; 35 Jia, Li, Li, Liu, Jian, Yang, Shen, Ning, Du, Zhao (bib46) 2020; 11 Hao, Wu, Cui, Zhu, Tan, Dou, Hsu, Lin, Peng, Zhang (bib40) 2020; 78 Arribas-Hernández, Bressendorff, Hansen, Poulsen, Erdmann, Brodersen (bib2) 2018; 30 Lieberman-Lazarovich, Kaiserli, Bucher, Mladenov (bib55) 2022; 70 Yang, Zhang, Li, Huang, Wen, Ma, Zhou, Li (bib123) 2010; 10 Zhou (bib146) 2009; 4 Saze, Tsugane, Kanno, Nishimura (bib91) 2012; 53 Silveira, Trontin, Cortijo, Barau, Del Bem, Loudet, Colot, Vincentz (bib97) 2013; 9 Sun, Xiang, Dou, Zhang, Pei, Franco, Menon, Monier, Ferebee, Liu (bib100) 2023; 41 Wang, Sheng, Liu, Zhang, Cheng, Duan, Pan, Qiao, Liu, Gao (bib118) 2019; 47 Zheng (bib144) 2022; 41 Li, Li, Sun, Peng, Liu, Liu, Yang, Li, Tan, Zhang (bib50) 2013; 193 Verkest, Byzova, Martens, Willems, Verwulgen, Slabbinck, Rombaut, Van de Velde, Vandepoele, Standaert (bib106) 2015; 168 Dong, Li, Chao, Shen, Gong, Zhao, Wang (bib19) 2016; 129 Guo, Liu, Wang, Zhang, Li, Liu, Zhang, Yang, Pu, Tian (bib37) 2022; 49 Maqbool, Hassan, Xia, York, Rasheed, He (bib68) 2022; 110 Zhang, An, Li, Wang, Zhou, Dong, Zhao, Wang, Li (bib135) 2019; 20 Gao, Cui, Liu, Wang, Lian, Bai, Zhu, Wu, Wang, Yang (bib31) 2022; 15 Noshay, Anderson, Zhou, Ji, Ricci, Lu, Stitzer, Crisp, Hirsch, Zhang (bib79) 2019; 15 Vanyushin, Tkacheva, Belozersky (bib103) 1970; 225 Zhang, Xie, Dong, Zhao, Zeng, Chen, Li, Yang, Zhao, Wang (bib137) 2014; 24 Raiber, Hardisty, van Delft, Balasubramanian (bib85) 2017; 1 Bailey-Serres, Parker, Ainsworth, Oldroyd, Schroeder (bib3) 2019; 575 Meister, Rajani, Ruzicka, Schachtman (bib70) 2014; 19 Xu, Kuo, Rosli, Liu, Wu, Chen, Fletcher, Sung, Pu (bib121) 2018; 11 Zhao, Su (bib143) 2019; 9 Xu, Wu, Luo, Zhang, Lai, Li, Springer, Li (bib122) 2022; 23 Deniz, Frost, Branco (bib17) 2019; 20 Shi, Zhou, Song, Liu, Wang, Wang, Zhang, Zhao, Ren (bib96) 2023; 66 Kang, Fan, Wu, Zhu, Shen (bib47) 2022; 13 Shen, Liang, Gu, Chen, Teo, Hou, Cai, Dedon, Liu, Yu (bib94) 2016; 38 Kong, Wang, Wang (bib49) 2020; 62 Zhang, Guo, Wang, Wang, Le, Xu, Wu, Wuriyanghan, Sung, Pu (bib133) 2022; 10 Gupta, Salgotra (bib39) 2022; 13 Wang, Zhang, Guo, Liu, Li, Zhang, Du, Hu, Han, Pu (bib116) 2021; 232 Zhu, Zhang, Xing, Li, Jiang, Wang, Xu (bib148) 2017; 8 Long, Xia, Liu, Jing, Wang, Qi, He (bib60) 2019; 61 Gallego-Bartolomé, Liu, Kuo, Feng, Ghoshal, Gardiner, Zhao, Park, Chory, Jacobsen (bib30) 2019; 176 Gilbert, Bell, Schaening (bib35) 2016; 352 Xia, Zhao, Jiao, Xu, Wu, Zhou, Fan (bib119) 2018; 10 Sallam, Moussa (bib89) 2021; 160 Yang, Zhang, Wang, Hu, Guo, Gu, Pu (bib124) 2022; 65 Yu, Xu, Wei, Zhang, Chen, Pu (bib127) 2020; 133 Cao, Zeng, Ku, Ren, Han, Su, Dou, Liu, Dong, Zhu (bib7) 2020; 71 Castelletti, Tuberosa, Pindo, Salvi (bib9) 2014; 4 Gautam, Singh, Yadav, Singh, Kumar, Das, Sarkar (bib32) 2021; 148 Moussa, Angstman, Khalil (bib76) 2021; 184 Lynch (bib67) 2013; 112 Wang, Ren, Zhang, Zhao, Liu, He, Li, Han, Zhang, Zhao (bib109) 2023; 204 Yu, Liu, Yu, Xiao, Zhang, Wang, Xu, Yu, Li, Yang (bib128) 2021; 39 Yu, Meng, Liu, Li, Zhang, Wang, Jiang, Pang, Zhao, Qi (bib130) 2018; 97 Schmitz, He, Valdés-López, Khan, Joshi, Urich, Nery, Diers, Xu, Stacey (bib92) 2013; 23 Wang, Zhao, Hou, Zhang, Huang, Wang, Li, Gao, Yan, Li (bib110) 2015; 56 Dhakate, Sehgal, Vaishnavi, Chandra, Singh, Raina, Rajpal (bib18) 2022; 13 Zaccara, Ries, Jaffrey (bib131) 2019; 20 Du, Johnson, Jacobsen, Patel (bib22) 2015; 16 Liang, Shen, Cui, Bao, Geng, Yu, Liang, Xie, Lu, Gu (bib54) 2018; 45 Vercruyssen, Verkest, Gonzalez, Heyndrickx, Eeckhout, Han, Jégu, Archacki, Van Leene, Andriankaja (bib105) 2014; 26 Li, Eichten, Hermanson, Zaunbrecher, Song, Wendt, Rosenbaum, Madzima, Sloan, Huang (bib51) 2014; 26 Tang, Lv, Li, Zhang, Li, Xu, Wu, Wang, Feng, Lu (bib101) 2022; 23 Dong, Zhang, Chen, Peng, Zhang, Wang, Lai (bib20) 2017; 10 Wang, Zhang, Jiang, Zhang, Zheng, Chen, Xu, Ul Ikram, Li, Xu (bib113) 2021; 108 Berr, Shafiq, Shen (bib4) 2011; 1809 Luo, Guo, Wang, Liu, Zheng, He (bib66) 2024; 194 Hu, Li, Weng, Liu, Yu, Liu, Xiao, Huang, Wang, Wei (bib44) 2021; 105 Zhang, Han, Guo, Liu, Zheng, Wu, Jin (bib140) 2014; 9 Varotto, Locatelli, Canova, Pipal, Motto, Rossi (bib104) 2003; 133 de Melo, Lourenço-Tessutti, Paixão, Noriega, Silva, de Almeida-Engler, Fontes, Grossi-de-Sa (bib15) 2020; 10 Low, Weyand, Mahan (bib61) 2001; 69 Tang, Gao, Gao, Yang, Shi, Yu, Lyu, Sun, Wang, Xu (bib102) 2020; 53 Wang, Yu, Zhang, Wang, Lu, Liu, Li, Zhang, Tan, Li (bib107) 2022; 20 Casati, Campi, Chu, Suzuki, Maltby, Guan, Burlingame, Walbot (bib8) 2008; 20 Locatelli, Piatti, Motto, Rossi (bib58) 2009; 21 Nelissen, Eeckhout, Demuynck, Persiau, Walton, van Bel, Vervoort, Candaele, De Block, Aesaert (bib77) 2015; 27 Raju, Shao, Sanchez, Xu, Sandhu, Graef, Mackenzie (bib86) 2018; 16 Liang, Anderson, Noshay, Crisp, Enders, Springer (bib52) 2021; 186 Hou, Zhao, Zheng, Gautam, Yue, Hou, Chen, Wang, Li (bib42) 2019; 256 Jenuwein, Allis (bib45) 2001; 293 Wang, Xie, Mao, Wang, Wang, Chen, Zhang, Xu, Xing, Cui (bib112) 2022; 23 Zhao, Song, Liu, Song, Yi (bib141) 2020; 11 Candaele, Demuynck, Mosoti, Beemster, Inzé, Nelissen (bib6) 2014; 164 Mascheretti, Battaglia, Mainieri, Altana, Lauria, Rossi (bib69) 2013; 25 Eichten, Briskine, Song, Li, Swanson-Wagner, Hermanson, Waters, Starr, West, Tiffin (bib26) 2013; 25 Luo, Wang, Wang, Zhang, Peng, Zhou, Jia, He (bib63) 2020; 182 Zhang, Liang, Cui, Ji, Li, Zhang, Liu, Riaz, Yao, Liu (bib139) 2018; 11 Shang, He (bib93) 2022; 64 Wang (10.1016/j.jgg.2024.01.006_bib149) 2017; 215 Moussa (10.1016/j.jgg.2024.01.006_bib76) 2021; 184 Deng (10.1016/j.jgg.2024.01.006_bib16) 2017; 355 Dong (10.1016/j.jgg.2024.01.006_bib19) 2016; 129 Feng (10.1016/j.jgg.2024.01.006_bib28) 2010; 107 Luo (10.1016/j.jgg.2024.01.006_bib63) 2020; 182 Mercé (10.1016/j.jgg.2024.01.006_bib72) 2020; 10 Wang (10.1016/j.jgg.2024.01.006_bib113) 2021; 108 Zhong (10.1016/j.jgg.2024.01.006_bib145) 2008; 20 Alvarez (10.1016/j.jgg.2024.01.006_bib1) 2010; 11 Mascheretti (10.1016/j.jgg.2024.01.006_bib69) 2013; 25 Zhou (10.1016/j.jgg.2024.01.006_bib147) 2019; 20 Jia (10.1016/j.jgg.2024.01.006_bib46) 2020; 11 Berr (10.1016/j.jgg.2024.01.006_bib4) 2011; 1809 Yang (10.1016/j.jgg.2024.01.006_bib126) 2015; 168 Gu (10.1016/j.jgg.2024.01.006_bib36) 2011; 7 Yang (10.1016/j.jgg.2024.01.006_bib125) 2017; 27 Hu (10.1016/j.jgg.2024.01.006_bib44) 2021; 105 Casati (10.1016/j.jgg.2024.01.006_bib8) 2008; 20 Gautam (10.1016/j.jgg.2024.01.006_bib32) 2021; 148 Wang (10.1016/j.jgg.2024.01.006_bib115) 2016; 48 Zhang (10.1016/j.jgg.2024.01.006_bib132) 2007; 210 Sun (10.1016/j.jgg.2024.01.006_bib100) 2023; 41 Nuñez (10.1016/j.jgg.2024.01.006_bib80) 2021; 184 Park (10.1016/j.jgg.2024.01.006_bib82) 2021; 5 Vercruyssen (10.1016/j.jgg.2024.01.006_bib105) 2014; 26 Liu (10.1016/j.jgg.2024.01.006_bib57) 2016; 9 Bonasio (10.1016/j.jgg.2024.01.006_bib5) 2010; 330 Guo (10.1016/j.jgg.2024.01.006_bib38) 2021; 17 Gupta (10.1016/j.jgg.2024.01.006_bib39) 2022; 13 Bailey-Serres (10.1016/j.jgg.2024.01.006_bib3) 2019; 575 Cao (10.1016/j.jgg.2024.01.006_bib7) 2020; 71 Long (10.1016/j.jgg.2024.01.006_bib60) 2019; 61 Gilbert (10.1016/j.jgg.2024.01.006_bib35) 2016; 352 Wang (10.1016/j.jgg.2024.01.006_bib116) 2021; 232 Nelissen (10.1016/j.jgg.2024.01.006_bib77) 2015; 27 Pintor-Toro (10.1016/j.jgg.2024.01.006_bib84) 1987; 147 Zhao (10.1016/j.jgg.2024.01.006_bib143) 2019; 9 Xia (10.1016/j.jgg.2024.01.006_bib119) 2018; 10 Miao (10.1016/j.jgg.2024.01.006_bib74) 2020; 182 Zaccara (10.1016/j.jgg.2024.01.006_bib131) 2019; 20 Yang (10.1016/j.jgg.2024.01.006_bib123) 2010; 10 Deniz (10.1016/j.jgg.2024.01.006_bib17) 2019; 20 Wang (10.1016/j.jgg.2024.01.006_bib108) 2020; 11 Liang (10.1016/j.jgg.2024.01.006_bib52) 2021; 186 Noshay (10.1016/j.jgg.2024.01.006_bib79) 2019; 15 Silveira (10.1016/j.jgg.2024.01.006_bib97) 2013; 9 Rossi (10.1016/j.jgg.2024.01.006_bib88) 2007; 19 Gawra (10.1016/j.jgg.2024.01.006_bib33) 2023; 9 Zheng (10.1016/j.jgg.2024.01.006_bib144) 2022; 41 Zhang (10.1016/j.jgg.2024.01.006_bib135) 2019; 20 Luo (10.1016/j.jgg.2024.01.006_bib66) 2024; 194 Verkest (10.1016/j.jgg.2024.01.006_bib106) 2015; 168 Gao (10.1016/j.jgg.2024.01.006_bib31) 2022; 15 Zhang (10.1016/j.jgg.2024.01.006_bib134) 2019; 15 Centore (10.1016/j.jgg.2024.01.006_bib10) 2020; 36 Wang (10.1016/j.jgg.2024.01.006_bib114) 2009; 21 Lynch (10.1016/j.jgg.2024.01.006_bib67) 2013; 112 Papikian (10.1016/j.jgg.2024.01.006_bib81) 2019; 10 Saze (10.1016/j.jgg.2024.01.006_bib91) 2012; 53 Zhang (10.1016/j.jgg.2024.01.006_bib133) 2022; 10 Lieberman-Lazarovich (10.1016/j.jgg.2024.01.006_bib55) 2022; 70 Peterson (10.1016/j.jgg.2024.01.006_bib83) 1994; 91 Niederhuth (10.1016/j.jgg.2024.01.006_bib78) 2017; 1860 Zhang (10.1016/j.jgg.2024.01.006_bib136) 2022; 13 Dunn (10.1016/j.jgg.2024.01.006_bib25) 1955; 175 Guo (10.1016/j.jgg.2024.01.006_bib37) 2022; 49 Luo (10.1016/j.jgg.2024.01.006_bib64) 2022; 234 Shang (10.1016/j.jgg.2024.01.006_bib93) 2022; 64 Li (10.1016/j.jgg.2024.01.006_bib50) 2013; 193 Maqbool (10.1016/j.jgg.2024.01.006_bib68) 2022; 110 Zhang (10.1016/j.jgg.2024.01.006_bib138) 2020; 18 Xu (10.1016/j.jgg.2024.01.006_bib121) 2018; 11 Yu (10.1016/j.jgg.2024.01.006_bib129) 2016; 6 de Melo (10.1016/j.jgg.2024.01.006_bib15) 2020; 10 Duan (10.1016/j.jgg.2024.01.006_bib24) 2017; 29 Wang (10.1016/j.jgg.2024.01.006_bib118) 2019; 47 Meister (10.1016/j.jgg.2024.01.006_bib70) 2014; 19 Du (10.1016/j.jgg.2024.01.006_bib23) 2018; 177 Varotto (10.1016/j.jgg.2024.01.006_bib104) 2003; 133 Vanyushin (10.1016/j.jgg.2024.01.006_bib103) 1970; 225 Tang (10.1016/j.jgg.2024.01.006_bib101) 2022; 23 Shi (10.1016/j.jgg.2024.01.006_bib96) 2023; 66 Gent (10.1016/j.jgg.2024.01.006_bib34) 2013; 23 Forestan (10.1016/j.jgg.2024.01.006_bib29) 2018; 208 Raju (10.1016/j.jgg.2024.01.006_bib86) 2018; 16 David (10.1016/j.jgg.2024.01.006_bib14) 2017; 29 Middeljans (10.1016/j.jgg.2024.01.006_bib75) 2012; 7 Raiber (10.1016/j.jgg.2024.01.006_bib85) 2017; 1 Liang (10.1016/j.jgg.2024.01.006_bib53) 2020; 13 Chen (10.1016/j.jgg.2024.01.006_bib11) 2022; 375 Wang (10.1016/j.jgg.2024.01.006_bib110) 2015; 56 Erdmann (10.1016/j.jgg.2024.01.006_bib27) 2014; 5 Yu (10.1016/j.jgg.2024.01.006_bib127) 2020; 133 Arribas-Hernández (10.1016/j.jgg.2024.01.006_bib2) 2018; 30 Candaele (10.1016/j.jgg.2024.01.006_bib6) 2014; 164 Kim (10.1016/j.jgg.2024.01.006_bib48) 2022; 44 Eichten (10.1016/j.jgg.2024.01.006_bib26) 2013; 25 Sallam (10.1016/j.jgg.2024.01.006_bib89) 2021; 160 Regulski (10.1016/j.jgg.2024.01.006_bib87) 2013; 23 Zhang (10.1016/j.jgg.2024.01.006_bib139) 2018; 11 Xu (10.1016/j.jgg.2024.01.006_bib122) 2022; 23 Hao (10.1016/j.jgg.2024.01.006_bib40) 2020; 78 Wang (10.1016/j.jgg.2024.01.006_bib109) 2023; 204 Zhu (10.1016/j.jgg.2024.01.006_bib148) 2017; 8 Jenuwein (10.1016/j.jgg.2024.01.006_bib45) 2001; 293 Zhang (10.1016/j.jgg.2024.01.006_bib140) 2014; 9 Wang (10.1016/j.jgg.2024.01.006_bib112) 2022; 23 Liang (10.1016/j.jgg.2024.01.006_bib54) 2018; 45 Shen (10.1016/j.jgg.2024.01.006_bib95) 2009; 2 Yu (10.1016/j.jgg.2024.01.006_bib128) 2021; 39 Li (10.1016/j.jgg.2024.01.006_bib51) 2014; 26 Messmer (10.1016/j.jgg.2024.01.006_bib73) 2009; 119 Liu (10.1016/j.jgg.2024.01.006_bib56) 2022; 3 Hawkins (10.1016/j.jgg.2024.01.006_bib41) 2013; 19 Dalakouras (10.1016/j.jgg.2024.01.006_bib13) 2021; 72 Low (10.1016/j.jgg.2024.01.006_bib61) 2001; 69 Du (10.1016/j.jgg.2024.01.006_bib22) 2015; 16 Zhang (10.1016/j.jgg.2024.01.006_bib137) 2014; 24 Zhao (10.1016/j.jgg.2024.01.006_bib142) 2012; 39 Sun (10.1016/j.jgg.2024.01.006_bib99) 2022; 135 Hou (10.1016/j.jgg.2024.01.006_bib42) 2019; 256 Locatelli (10.1016/j.jgg.2024.01.006_bib58) 2009; 21 Castelletti (10.1016/j.jgg.2024.01.006_bib9) 2014; 4 Shen (10.1016/j.jgg.2024.01.006_bib94) 2016; 38 Dong (10.1016/j.jgg.2024.01.006_bib20) 2017; 10 Dhakate (10.1016/j.jgg.2024.01.006_bib18) 2022; 13 Steward (10.1016/j.jgg.2024.01.006_bib98) 2000; 28 Zhao (10.1016/j.jgg.2024.01.006_bib141) 2020; 11 Lu (10.1016/j.jgg.2024.01.006_bib62) 2008; 35 Schmitz (10.1016/j.jgg.2024.01.006_bib92) 2013; 23 Yang (10.1016/j.jgg.2024.01.006_bib124) 2022; 65 Cui (10.1016/j.jgg.2024.01.006_bib12) 2017; 10 Yu (10.1016/j.jgg.2024.01.006_bib130) 2018; 97 Wang (10.1016/j.jgg.2024.01.006_bib107) 2022; 20 Kang (10.1016/j.jgg.2024.01.006_bib47) 2022; 13 Gallego-Bartolomé (10.1016/j.jgg.2024.01.006_bib30) 2019; 176 Sang (10.1016/j.jgg.2024.01.006_bib90) 2012; 72 Tang (10.1016/j.jgg.2024.01.006_bib102) 2020; 53 Xiong (10.1016/j.jgg.2024.01.006_bib120) 2014; 14 Meng (10.1016/j.jgg.2024.01.006_bib71) 2020; 11 Long (10.1016/j.jgg.2024.01.006_bib59) 2021; 33 Kong (10.1016/j.jgg.2024.01.006_bib49) 2020; 62 Dou (10.1016/j.jgg.2024.01.006_bib21) 2021; 72 Luo (10.1016/j.jgg.2024.01.006_bib65) 2019; 250 Zhou (10.1016/j.jgg.2024.01.006_bib146) 2009; 4
References_xml	– volume: 147 start-page: 1082 year: 1987 end-page: 1087 ident: bib84 article-title: Adenine methylation in zein genes publication-title: Biochem. Biophys. Res. Commun. – volume: 15 year: 2019 ident: bib134 article-title: The subunit of RNA publication-title: PLoS Genet. – volume: 20 start-page: 1754 year: 2019 ident: bib135 article-title: The miRNA-mediated post-transcriptional regulation of maize in response to high temperature publication-title: Int. J. Mol. Sci. – volume: 39 start-page: 307 year: 2012 end-page: 315 ident: bib142 article-title: Epigenomic modification and epigenetic regulation in rice publication-title: J. Genet. Genomics – volume: 4 start-page: 15 year: 2009 end-page: 18 ident: bib146 article-title: Regulatory mechanism of histone epigenetic modifications in plants publication-title: Epigenetics – volume: 47 start-page: 11771 year: 2019 end-page: 11789 ident: bib118 article-title: A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA publication-title: Nucleic Acids Res. – volume: 26 start-page: 4602 year: 2014 end-page: 4616 ident: bib51 article-title: Genetic perturbation of the maize methylome publication-title: Plant Cell – volume: 20 start-page: 156 year: 2019 ident: bib147 article-title: RNA methylomes reveal the m publication-title: Genome Biol. – volume: 48 start-page: 1233 year: 2016 end-page: 1241 ident: bib115 article-title: Genetic variation in publication-title: Nat. Genet. – volume: 182 start-page: 332 year: 2020 end-page: 344 ident: bib63 article-title: Natural variation in RNA m publication-title: Plant Physiol. – volume: 20 start-page: 608 year: 2019 end-page: 624 ident: bib131 article-title: Reading, writing and erasing mRNA methylation publication-title: Nat. Rev. Mol. Cell Biol. – volume: 352 start-page: 1408 year: 2016 end-page: 1412 ident: bib35 article-title: Messenger RNA modifications: form, distribution, and function publication-title: Science – volume: 41 start-page: 120 year: 2023 end-page: 127 ident: bib100 article-title: The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize publication-title: Nat. Biotechnol. – volume: 330 start-page: 612 year: 2010 end-page: 616 ident: bib5 article-title: Molecular signals of epigenetic states publication-title: Science – volume: 26 start-page: 210 year: 2014 end-page: 229 ident: bib105 article-title: ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development publication-title: Plant Cell – volume: 10 start-page: 664 year: 2018 ident: bib119 article-title: Virus-derived small interfering RNAs affect the accumulations of viral and host transcripts in maize publication-title: Viruses – volume: 375 year: 2022 ident: bib11 article-title: Convergent selection of a WD40 protein that enhances grain yield in maize and rice publication-title: Science – volume: 10 start-page: 178 year: 2010 ident: bib123 article-title: Trichostatin A and 5-azacytidine both cause an increase in global histone H4 acetylation and a decrease in global DNA and H3K9 methylation during mitosis in maize publication-title: BMC Plant Biol. – volume: 9 year: 2019 ident: bib143 article-title: Mapping quantitative trait loci for yield-related traits and predicting candidate genes for grain weight in maize publication-title: Sci. Rep. – volume: 27 start-page: 606 year: 2017 end-page: 625 ident: bib125 article-title: 5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader publication-title: Cell Res. – volume: 53 start-page: 766 year: 2012 end-page: 784 ident: bib91 article-title: DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation publication-title: Plant Cell Physiol. – volume: 29 start-page: 2995 year: 2017 end-page: 3011 ident: bib24 article-title: ALKBH10B is an RNA publication-title: Plant Cell – volume: 184 start-page: 2281 year: 2021 end-page: 2283 ident: bib76 article-title: Here to stay: writing lasting epigenetic memories publication-title: Cell – volume: 69 start-page: 7197 year: 2001 end-page: 7204 ident: bib61 article-title: Roles of DNA adenine methylation in regulating bacterial gene expression and virulence publication-title: Infect. Immun. – volume: 38 start-page: 186 year: 2016 end-page: 200 ident: bib94 article-title: -Methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis publication-title: Dev. Cell – volume: 250 start-page: 69 year: 2019 end-page: 78 ident: bib65 article-title: Circular RNAs exhibit extensive intraspecific variation in maize publication-title: Planta – volume: 208 start-page: 1443 year: 2018 end-page: 1466 ident: bib29 article-title: Control of maize vegetative and reproductive development, fertility, and rRNAs silencing by publication-title: Genetics – volume: 33 start-page: 2183 year: 2021 end-page: 2196 ident: bib59 article-title: Maize decrease in DNA methylation 1 targets RNA-directed DNA methylation on active chromatin publication-title: Plant Cell – volume: 20 start-page: 417 year: 2019 end-page: 431 ident: bib17 article-title: Regulation of transposable elements by DNA modifications publication-title: Nat. Rev. Genet. – volume: 9 start-page: 1 year: 2016 end-page: 11 ident: bib57 article-title: Expanding maize genetic resources with predomestication alleles: maize-teosinte introgression populations publication-title: Plant Genome – volume: 148 year: 2021 ident: bib32 article-title: Conserved publication-title: Development – volume: 168 start-page: 1338 year: 2015 end-page: 1350 ident: bib106 article-title: Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes publication-title: Plant Physiol. – volume: 17 year: 2021 ident: bib38 article-title: RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in publication-title: PLoS Genet. – volume: 15 start-page: 1558 year: 2022 end-page: 1574 ident: bib31 article-title: Natural variations of publication-title: Mol. Plant – volume: 108 start-page: 1597 year: 2021 end-page: 1608 ident: bib113 article-title: is involved in maize leaf inclination publication-title: Plant J. – volume: 25 start-page: 404 year: 2013 end-page: 420 ident: bib69 article-title: The WD40-repeat proteins NFC101 and NFC102 regulate different aspects of maize development through chromatin modification publication-title: Plant Cell – volume: 2 start-page: 600 year: 2009 end-page: 609 ident: bib95 article-title: Chromatin remodeling in stem cell maintenance in publication-title: Mol. Plant – volume: 24 start-page: 167 year: 2014 end-page: 176 ident: bib137 article-title: Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize publication-title: Genome Res. – volume: 110 start-page: 23 year: 2022 end-page: 42 ident: bib68 article-title: Root system architecture in cereals: progress, challenges and perspective publication-title: Plant J. – volume: 7 year: 2012 ident: bib75 article-title: SS18 Together with animal-specific factors defines human BAF-type SWI/SNF complexes publication-title: PLoS ONE – volume: 194 start-page: 2165 year: 2024 end-page: 2182 ident: bib66 article-title: RNA m publication-title: Plant Physiol. – volume: 11 year: 2020 ident: bib108 article-title: QTL analysis and fine mapping of a major QTL conferring kernel size in maize ( publication-title: Front. Genet. – volume: 91 start-page: 2905 year: 1994 end-page: 2908 ident: bib83 article-title: Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 129 start-page: 71 year: 2016 end-page: 83 ident: bib19 article-title: Analysis of gene expression and histone modification between C4 and non-C4 homologous genes of publication-title: Photosynth. Res. – volume: 72 start-page: 1782 year: 2021 end-page: 1794 ident: bib21 article-title: CLA4 regulates leaf angle through multiple hormone signaling pathways in maize publication-title: J. Exp. Bot. – volume: 78 start-page: 382 year: 2020 end-page: 395 ident: bib40 article-title: -deoxyadenosine methylation in mammalian mitochondrial DNA publication-title: Mol. Cell – volume: 10 year: 2020 ident: bib15 article-title: Transcriptional modulation of publication-title: Sci. Rep. – volume: 53 start-page: 272 year: 2020 end-page: 286 ident: bib102 article-title: OsNSUN2-mediated 5-methylcytosine mRNA modification enhances rice adaptation to high temperature publication-title: Dev. Cell – volume: 39 start-page: 1581 year: 2021 end-page: 1588 ident: bib128 article-title: RNA demethylation increases the yield and biomass of rice and potato plants in field trials publication-title: Nat. Biotechnol. – volume: 160 start-page: 218 year: 2021 end-page: 224 ident: bib89 article-title: DNA methylation changes stimulated by drought stress in ABA-deficient maize mutant publication-title: Plant Physiol. Biochem. – volume: 293 start-page: 1074 year: 2001 end-page: 1080 ident: bib45 article-title: Translating the histone code publication-title: Science – volume: 23 start-page: 628 year: 2013 end-page: 637 ident: bib34 article-title: CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize publication-title: Genome Res. – volume: 13 year: 2022 ident: bib39 article-title: Epigenetics and its role in effecting agronomical traits publication-title: Front. Plant Sci. – volume: 176 start-page: 1068 year: 2019 end-page: 1082 ident: bib30 article-title: Co-targeting RNA polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis publication-title: Cell – volume: 3 year: 2022 ident: bib56 article-title: Hypercompact CRISPR-Cas12j2 (CasΦ) enables genome editing, gene activation, and epigenome editing in plants publication-title: Plant Commun. – volume: 97 start-page: 451 year: 2018 end-page: 465 ident: bib130 article-title: The chromatin remodeler ZmCHB101 impacts expression of osmotic stress-responsive genes in maize publication-title: Plant Mol. Biol. – volume: 23 start-page: 1651 year: 2013 end-page: 1662 ident: bib87 article-title: The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA publication-title: Genome Res. – volume: 13 start-page: 1127 year: 2022 ident: bib136 article-title: Two zinc finger proteins with functions in m publication-title: Nat. Commun. – volume: 1860 start-page: 149 year: 2017 end-page: 156 ident: bib78 article-title: Putting DNA methylation in context: from genomes to gene expression in plants publication-title: Biochim. Biophys. Acta Gene Regul. Mech. – volume: 21 start-page: 1053 year: 2009 end-page: 1069 ident: bib114 article-title: Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize publication-title: Plant Cell – volume: 20 start-page: 827 year: 2008 end-page: 842 ident: bib8 article-title: Histone acetylation and chromatin remodeling are required for UV-B-dependent transcriptional activation of regulated genes in maize publication-title: Plant Cell – volume: 215 start-page: 1503 year: 2017 end-page: 1515 ident: bib149 article-title: A transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize publication-title: New Phytol. – volume: 168 start-page: 222 year: 2015 end-page: 232 ident: bib126 article-title: MutS HOMOLOG1-derived epigenetic breeding potential in Tomato publication-title: Plant Physiol. – volume: 36 start-page: 936 year: 2020 end-page: 950 ident: bib10 article-title: Mammalian SWI/SNF chromatin remodeling complexes: emerging mechanisms and therapeutic strategies publication-title: Trends Genet. – volume: 13 year: 2022 ident: bib47 article-title: Histone modification and chromatin remodeling in plant response to pathogens publication-title: Front. Plant Sci. – volume: 11 start-page: 659 year: 2018 end-page: 677 ident: bib121 article-title: Trithorax group proteins act together with a polycomb group protein to maintain chromatin integrity for epigenetic silencing during seed germination in Arabidopsis publication-title: Mol. Plant – volume: 16 start-page: 519 year: 2015 end-page: 532 ident: bib22 article-title: DNA methylation pathways and their crosstalk with histone methylation publication-title: Nat. Rev. Mol. Cell Biol. – volume: 21 start-page: 1410 year: 2009 end-page: 1427 ident: bib58 article-title: Chromatin and DNA modifications in the publication-title: Plant Cell – volume: 232 start-page: 880 year: 2021 end-page: 897 ident: bib116 article-title: A deep learning approach to automate whole-genome prediction of diverse epigenomic modifications in plants publication-title: New Phytol. – volume: 225 start-page: 948 year: 1970 end-page: 949 ident: bib103 article-title: Rare bases in animal DNA publication-title: Nature – volume: 23 start-page: 77 year: 2022 ident: bib122 article-title: DNA demethylation affects imprinted gene expression in maize endosperm publication-title: Genome Biol. – volume: 41 start-page: 1171 year: 2022 end-page: 1180 ident: bib144 article-title: Molecular mechanisms of maize endosperm transfer cell development publication-title: Plant Cell Rep. – volume: 71 start-page: 2943 year: 2020 end-page: 2955 ident: bib7 article-title: ZmIBH1-1 regulates plant architecture in maize publication-title: J. Exp. Bot. – volume: 49 start-page: 514 year: 2022 end-page: 517 ident: bib37 article-title: SMOC: a smart model for open chromatin region prediction in rice genomes publication-title: J. Genet. Genomics – volume: 234 start-page: 513 year: 2022 end-page: 526 ident: bib64 article-title: Genetic variation in publication-title: New Phytol. – volume: 133 start-page: 606 year: 2003 end-page: 617 ident: bib104 article-title: Expression profile and cellular localization of maize Rpd3-type histone deacetylases during plant development publication-title: Plant Physiol. – volume: 45 start-page: 406 year: 2018 end-page: 416 ident: bib54 article-title: DNA publication-title: Dev. Cell – volume: 11 start-page: 1492 year: 2018 end-page: 1508 ident: bib139 article-title: -methyladenine DNA methylation in publication-title: Mol. Plant – volume: 23 start-page: 4968 year: 2022 ident: bib101 article-title: Characteristics of microRNAs and target genes in maize root under drought stress publication-title: Int. J. Mol. Sci. – volume: 11 start-page: 792 year: 2020 end-page: 808 ident: bib141 article-title: Mapping the epigenetic modifications of DNA and RNA publication-title: Protein Cell – volume: 175 start-page: 336 year: 1955 end-page: 337 ident: bib25 article-title: Occurrence of a new base in the deoxyribonucleic acid of a strain of publication-title: Nature – volume: 10 start-page: 1484 year: 2020 ident: bib72 article-title: Induced methylation in plants as a crop improvement tool: progress and perspectives publication-title: Agronomy – volume: 56 start-page: 965 year: 2015 end-page: 976 ident: bib110 article-title: Epigenetic changes are associated with programmed cell death induced by heat stress in seedling leaves of publication-title: Plant Cell Physiol. – volume: 61 start-page: 749 year: 2019 end-page: 764 ident: bib60 article-title: ( publication-title: J. Integr. Plant Biol. – volume: 1809 start-page: 567 year: 2011 end-page: 576 ident: bib4 article-title: Histone modifications in transcriptional activation during plant development publication-title: Biochim. Biophys. Acta – volume: 28 start-page: 3250 year: 2000 end-page: 3259 ident: bib98 article-title: Expression of publication-title: Nucleic Acids Res. – volume: 5 start-page: e337 year: 2021 ident: bib82 article-title: Differential nuclease sensitivity profiling uncovers a drought responsive change in maize leaf chromatin structure for two large retrotransposon derivatives, publication-title: Plant Direct – volume: 18 start-page: 1642 year: 2020 end-page: 1644 ident: bib138 article-title: eRice: a refined epigenomic platform for japonica and indica rice publication-title: Plant Biotechnol. J. – volume: 9 year: 2014 ident: bib140 article-title: Identification of maize long non-coding RNAs responsive to drought stress publication-title: PLoS ONE – volume: 7 year: 2011 ident: bib36 article-title: Arabidopsis homologs of retinoblastoma-associated protein 46/48 associate with a histone deacetylase to act redundantly in chromatin silencing publication-title: PLoS Genet. – volume: 16 start-page: 1836 year: 2018 end-page: 1847 ident: bib86 article-title: An epigenetic breeding system in soybean for increased yield and stability publication-title: Plant Biotechnol. J. – volume: 64 start-page: 499 year: 2022 end-page: 515 ident: bib93 article-title: Chromatin-remodeling complexes: conserved and plant-specific subunits in Arabidopsis publication-title: J. Integr. Plant Biol. – volume: 13 year: 2022 ident: bib18 article-title: Comprehending the evolution of gene editing platforms for crop trait improvement publication-title: Front. Genet. – volume: 10 start-page: 729 year: 2019 ident: bib81 article-title: Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems publication-title: Nat. Commun. – volume: 164 start-page: 1350 year: 2014 end-page: 1364 ident: bib6 article-title: Differential methylation during maize leaf growth targets developmentally regulated genes publication-title: Plant Physiol. – volume: 256 start-page: 1245 year: 2019 end-page: 1256 ident: bib42 article-title: Dynamic changes in histone modification are associated with upregulation of publication-title: Protoplasma – volume: 355 start-page: 962 year: 2017 end-page: 965 ident: bib16 article-title: Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance publication-title: Science – volume: 44 start-page: 259 year: 2022 end-page: 266 ident: bib48 article-title: Harnessing epigenetic variability for crop improvement: current status and future prospects publication-title: Genes Genomics – volume: 186 start-page: 420 year: 2021 end-page: 433 ident: bib52 article-title: Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize publication-title: Plant Physiol. – volume: 13 start-page: 14 year: 2020 end-page: 30 ident: bib53 article-title: Epigenetic modifications of mRNA and DNA in plants publication-title: Mol. Plant – volume: 11 start-page: 563 year: 2010 end-page: 576 ident: bib1 article-title: Epigenetic control of plant immunity publication-title: Mol. Plant Pathol. – volume: 30 start-page: 952 year: 2018 end-page: 967 ident: bib2 article-title: An m publication-title: Plant Cell – volume: 105 start-page: 108 year: 2021 end-page: 123 ident: bib44 article-title: Coordinated regulation of starch synthesis in maize endosperm by microRNAs and DNA methylation publication-title: Plant J. – volume: 193 start-page: 303 year: 2013 end-page: 316 ident: bib50 article-title: Quantitative trait loci mapping for yield components and kernel-related traits in multiple connected RIL populations in maize publication-title: Euphytica – volume: 9 year: 2013 ident: bib97 article-title: Extensive natural epigenetic variation at a de novo originated gene publication-title: PLoS Genet. – volume: 65 start-page: 2191 year: 2022 end-page: 2204 ident: bib124 article-title: Plant synthetic epigenomic engineering for crop improvement publication-title: Sci. China Life Sci. – volume: 11 start-page: 52 year: 2020 ident: bib71 article-title: Chromatin remodeling protein ZmCHB101 regulates nitrate-responsive gene expression in maize publication-title: Front. Plant Sci. – volume: 112 start-page: 347 year: 2013 end-page: 357 ident: bib67 article-title: Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems publication-title: Ann. Bot. – volume: 184 start-page: 2503 year: 2021 end-page: 2519 ident: bib80 article-title: Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing publication-title: Cell – volume: 210 start-page: 279 year: 2007 end-page: 289 ident: bib132 article-title: MicroRNAs and their regulatory roles in animals and plants publication-title: J. Cell. Physiol. – volume: 5 start-page: 1 year: 2014 end-page: 8 ident: bib27 article-title: 5-hydroxymethylcytosine is not present in appreciable quantities in Arabidopsis DNA publication-title: G3 (Bethesda) – volume: 204 year: 2023 ident: bib109 article-title: A sustainable approach to narrowing the summer maize yield gap experienced by smallholders in the North China Plain publication-title: Agric. Syst. – volume: 15 year: 2019 ident: bib79 article-title: Monitoring the interplay between transposable element families and DNA methylation in maize publication-title: PLoS Genet. – volume: 1 year: 2017 ident: bib85 article-title: Mapping and elucidating the function of modified bases in DNA publication-title: Nat. Rev. Chem. – volume: 25 start-page: 2783 year: 2013 end-page: 2797 ident: bib26 article-title: Epigenetic and genetic influences on DNA methylation variation in maize populations publication-title: Plant Cell – volume: 62 start-page: 394 year: 2020 end-page: 397 ident: bib49 article-title: and publication-title: J. Integr. Plant Biol. – volume: 19 start-page: 779 year: 2014 end-page: 788 ident: bib70 article-title: Challenges of modifying root traits in crops for agriculture publication-title: Trends Plant Sci. – volume: 4 start-page: 805 year: 2014 end-page: 812 ident: bib9 publication-title: A MITE transposon insertion is associated with differential methylation at the maize flowering time QTL – volume: 29 start-page: 445 year: 2017 end-page: 460 ident: bib14 article-title: Transcriptome-wide mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and noncoding RNAs publication-title: Plant Cell – volume: 66 start-page: 1903 year: 2023 end-page: 1914 ident: bib96 article-title: Trash to treasure: lactate and protein lactylation in maize root impacts response to drought publication-title: Sci. China Life Sci. – volume: 72 start-page: 5356 year: 2021 end-page: 5371 ident: bib13 article-title: Epigenetic approaches to crop breeding: current status and perspectives publication-title: J. Exp. Bot. – volume: 182 start-page: 345 year: 2020 end-page: 360 ident: bib74 article-title: Evolution of the RNA publication-title: Plant Physiol. – volume: 575 start-page: 109 year: 2019 end-page: 118 ident: bib3 article-title: Genetic strategies for improving crop yields publication-title: Nature – volume: 10 start-page: 1387 year: 2017 end-page: 1399 ident: bib12 article-title: 5-methylcytosine RNA methylation in publication-title: Mol. Plant – volume: 11 start-page: 988 year: 2020 ident: bib46 article-title: A serine/threonine protein kinase encoding gene publication-title: Nat. Commun. – volume: 72 start-page: 1000 year: 2012 end-page: 1014 ident: bib90 article-title: Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects publication-title: Plant J. – volume: 10 year: 2022 ident: bib133 article-title: RNA 5-methylcytosine modification regulates vegetative development associated with H3K27 trimethylation in Arabidopsis publication-title: Adv. Sci. – volume: 20 start-page: 1278 year: 2008 end-page: 1288 ident: bib145 article-title: MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor publication-title: Plant Cell – volume: 10 start-page: 442 year: 2017 end-page: 455 ident: bib20 article-title: Dynamic and antagonistic allele-specific epigenetic modifications controlling the expression of imprinted genes in maize endosperm publication-title: Mol. Plant – volume: 8 start-page: 274 year: 2017 ident: bib148 article-title: Transcriptomic analysis of long non-coding RNAs and coding genes uncovers a complex regulatory network that is involved in maize seed development publication-title: Genes – volume: 135 start-page: 1579 year: 2022 end-page: 1589 ident: bib99 article-title: Identification of a candidate gene underlying publication-title: Theor. Appl. Genet. – volume: 107 start-page: 8689 year: 2010 end-page: 8694 ident: bib28 article-title: Conservation and divergence of methylation patterning in plants and animals publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 20 start-page: 526 year: 2022 end-page: 537 ident: bib107 article-title: ZmTE1 promotes plant height by regulating intercalary meristem formation and internode cell elongation in maize publication-title: Plant Biotechnol. J. – volume: 6 year: 2016 ident: bib129 article-title: The core subunit of a chromatin-remodeling complex, ZmCHB101, plays essential roles in maize growth and development publication-title: Sci. Rep. – volume: 119 start-page: 913 year: 2009 end-page: 930 ident: bib73 article-title: Drought stress and tropical maize: QTL-by-environment interactions and stability of QTLs across environments for yield components and secondary traits publication-title: Theor. Appl. Genet. – volume: 70 year: 2022 ident: bib55 article-title: Natural and induced epigenetic variation for crop improvement publication-title: Curr. Opin. Plant Biol. – volume: 9 year: 2023 ident: bib33 article-title: Epigenetic variations are more substantial than genetic variations in rapid adaptation of oyster to Pacific oyster mortality syndrome publication-title: Sci. Adv. – volume: 27 start-page: 1605 year: 2015 end-page: 1619 ident: bib77 article-title: Dynamic changes in ANGUSTIFOLIA3 complex composition reveal a growth regulatory mechanism in the maize leaf publication-title: Plant Cell – volume: 19 start-page: 937 year: 2013 end-page: 947 ident: bib41 article-title: Increasing influence of heat stress on French maize yields from the 1960s to the 2030s publication-title: Glob. Chang. Biol. – volume: 23 start-page: 1663 year: 2013 end-page: 1674 ident: bib92 article-title: Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population publication-title: Genome Res. – volume: 35 start-page: 41 year: 2008 end-page: 48 ident: bib62 article-title: Analysis of DNA methylation in different maize tissues publication-title: J. Genet. Genomics – volume: 14 start-page: 204 year: 2014 ident: bib120 article-title: Adaptive expansion of the maize publication-title: BMC Plant Biol. – volume: 23 start-page: 5 year: 2022 ident: bib112 article-title: -acetyldeoxycytosine DNA modification marks euchromatin regions in publication-title: Genome Biol. – volume: 19 start-page: 1145 year: 2007 end-page: 1162 ident: bib88 article-title: Maize histone deacetylase hda101 is involved in plant development, gene transcription, and sequence-specific modulation of histone modification of genes and repeats publication-title: Plant Cell – volume: 177 start-page: 1743 year: 2018 end-page: 1753 ident: bib23 article-title: The publication-title: Plant Physiol. – volume: 133 start-page: 1467 year: 2020 end-page: 1489 ident: bib127 article-title: Epigenomic landscape and epigenetic regulation in maize publication-title: Theor. Appl. Genet. – volume: 160 start-page: 218 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib89 article-title: DNA methylation changes stimulated by drought stress in ABA-deficient maize mutant vp10 publication-title: Plant Physiol. Biochem. doi: 10.1016/j.plaphy.2021.01.024 – volume: 1 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib85 article-title: Mapping and elucidating the function of modified bases in DNA publication-title: Nat. Rev. Chem. – volume: 56 start-page: 965 year: 2015 ident: 10.1016/j.jgg.2024.01.006_bib110 article-title: Epigenetic changes are associated with programmed cell death induced by heat stress in seedling leaves of Zea mays publication-title: Plant Cell Physiol. doi: 10.1093/pcp/pcv023 – volume: 9 year: 2014 ident: 10.1016/j.jgg.2024.01.006_bib140 article-title: Identification of maize long non-coding RNAs responsive to drought stress publication-title: PLoS ONE – volume: 24 start-page: 167 year: 2014 ident: 10.1016/j.jgg.2024.01.006_bib137 article-title: Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize publication-title: Genome Res. doi: 10.1101/gr.155879.113 – volume: 129 start-page: 71 year: 2016 ident: 10.1016/j.jgg.2024.01.006_bib19 article-title: Analysis of gene expression and histone modification between C4 and non-C4 homologous genes of PPDK and PCK in maize publication-title: Photosynth. Res. doi: 10.1007/s11120-016-0271-9 – volume: 41 start-page: 120 year: 2023 ident: 10.1016/j.jgg.2024.01.006_bib100 article-title: The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize publication-title: Nat. Biotechnol. doi: 10.1038/s41587-022-01470-4 – volume: 215 start-page: 1503 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib149 article-title: A transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize publication-title: New Phytol. doi: 10.1111/nph.14688 – volume: 133 start-page: 606 year: 2003 ident: 10.1016/j.jgg.2024.01.006_bib104 article-title: Expression profile and cellular localization of maize Rpd3-type histone deacetylases during plant development publication-title: Plant Physiol. doi: 10.1104/pp.103.025403 – volume: 168 start-page: 222 year: 2015 ident: 10.1016/j.jgg.2024.01.006_bib126 article-title: MutS HOMOLOG1-derived epigenetic breeding potential in Tomato publication-title: Plant Physiol. doi: 10.1104/pp.15.00075 – volume: 5 start-page: 1 year: 2014 ident: 10.1016/j.jgg.2024.01.006_bib27 article-title: 5-hydroxymethylcytosine is not present in appreciable quantities in Arabidopsis DNA publication-title: G3 (Bethesda) doi: 10.1534/g3.114.014670 – volume: 9 year: 2023 ident: 10.1016/j.jgg.2024.01.006_bib33 article-title: Epigenetic variations are more substantial than genetic variations in rapid adaptation of oyster to Pacific oyster mortality syndrome publication-title: Sci. Adv. doi: 10.1126/sciadv.adh8990 – volume: 38 start-page: 186 year: 2016 ident: 10.1016/j.jgg.2024.01.006_bib94 article-title: N6-Methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis publication-title: Dev. Cell doi: 10.1016/j.devcel.2016.06.008 – volume: 28 start-page: 3250 year: 2000 ident: 10.1016/j.jgg.2024.01.006_bib98 article-title: Expression of ZmMET1, a gene encoding a DNA methyltransferase from maize, is associated not only with DNA replication in actively proliferating cells, but also with altered DNA methylation status in cold-stressed quiescent cells publication-title: Nucleic Acids Res. doi: 10.1093/nar/28.17.3250 – volume: 11 start-page: 659 year: 2018 ident: 10.1016/j.jgg.2024.01.006_bib121 article-title: Trithorax group proteins act together with a polycomb group protein to maintain chromatin integrity for epigenetic silencing during seed germination in Arabidopsis publication-title: Mol. Plant doi: 10.1016/j.molp.2018.01.010 – volume: 108 start-page: 1597 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib113 article-title: SDG128 is involved in maize leaf inclination publication-title: Plant J. doi: 10.1111/tpj.15527 – volume: 25 start-page: 404 year: 2013 ident: 10.1016/j.jgg.2024.01.006_bib69 article-title: The WD40-repeat proteins NFC101 and NFC102 regulate different aspects of maize development through chromatin modification publication-title: Plant Cell doi: 10.1105/tpc.112.107219 – volume: 147 start-page: 1082 year: 1987 ident: 10.1016/j.jgg.2024.01.006_bib84 article-title: Adenine methylation in zein genes publication-title: Biochem. Biophys. Res. Commun. doi: 10.1016/S0006-291X(87)80181-X – volume: 225 start-page: 948 year: 1970 ident: 10.1016/j.jgg.2024.01.006_bib103 article-title: Rare bases in animal DNA publication-title: Nature doi: 10.1038/225948a0 – volume: 25 start-page: 2783 year: 2013 ident: 10.1016/j.jgg.2024.01.006_bib26 article-title: Epigenetic and genetic influences on DNA methylation variation in maize populations publication-title: Plant Cell doi: 10.1105/tpc.113.114793 – volume: 65 start-page: 2191 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib124 article-title: Plant synthetic epigenomic engineering for crop improvement publication-title: Sci. China Life Sci. doi: 10.1007/s11427-021-2131-6 – volume: 8 start-page: 274 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib148 article-title: Transcriptomic analysis of long non-coding RNAs and coding genes uncovers a complex regulatory network that is involved in maize seed development publication-title: Genes doi: 10.3390/genes8100274 – volume: 135 start-page: 1579 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib99 article-title: Identification of a candidate gene underlying qHKW3, a QTL for hundred-kernel weight in maize publication-title: Theor. Appl. Genet. doi: 10.1007/s00122-022-04055-6 – volume: 69 start-page: 7197 year: 2001 ident: 10.1016/j.jgg.2024.01.006_bib61 article-title: Roles of DNA adenine methylation in regulating bacterial gene expression and virulence publication-title: Infect. Immun. doi: 10.1128/IAI.69.12.7197-7204.2001 – volume: 208 start-page: 1443 year: 2018 ident: 10.1016/j.jgg.2024.01.006_bib29 article-title: Control of maize vegetative and reproductive development, fertility, and rRNAs silencing by HISTONE DEACETYLASE 108 publication-title: Genetics doi: 10.1534/genetics.117.300625 – volume: 330 start-page: 612 year: 2010 ident: 10.1016/j.jgg.2024.01.006_bib5 article-title: Molecular signals of epigenetic states publication-title: Science doi: 10.1126/science.1191078 – volume: 3 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib56 article-title: Hypercompact CRISPR-Cas12j2 (CasΦ) enables genome editing, gene activation, and epigenome editing in plants publication-title: Plant Commun. doi: 10.1016/j.xplc.2022.100453 – volume: 11 start-page: 988 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib46 article-title: A serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield publication-title: Nat. Commun. doi: 10.1038/s41467-020-14746-7 – volume: 19 start-page: 1145 year: 2007 ident: 10.1016/j.jgg.2024.01.006_bib88 article-title: Maize histone deacetylase hda101 is involved in plant development, gene transcription, and sequence-specific modulation of histone modification of genes and repeats publication-title: Plant Cell doi: 10.1105/tpc.106.042549 – volume: 10 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib15 article-title: Transcriptional modulation of AREB-1 by CRISPRa improves plant physiological performance under severe water deficit publication-title: Sci. Rep. doi: 10.1038/s41598-020-72464-y – volume: 4 start-page: 15 year: 2009 ident: 10.1016/j.jgg.2024.01.006_bib146 article-title: Regulatory mechanism of histone epigenetic modifications in plants publication-title: Epigenetics doi: 10.4161/epi.4.1.7371 – volume: 70 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib55 article-title: Natural and induced epigenetic variation for crop improvement publication-title: Curr. Opin. Plant Biol. doi: 10.1016/j.pbi.2022.102297 – volume: 10 start-page: 1484 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib72 article-title: Induced methylation in plants as a crop improvement tool: progress and perspectives publication-title: Agronomy doi: 10.3390/agronomy10101484 – volume: 78 start-page: 382 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib40 article-title: N6-deoxyadenosine methylation in mammalian mitochondrial DNA publication-title: Mol. Cell doi: 10.1016/j.molcel.2020.02.018 – volume: 107 start-page: 8689 year: 2010 ident: 10.1016/j.jgg.2024.01.006_bib28 article-title: Conservation and divergence of methylation patterning in plants and animals publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1002720107 – volume: 148 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib32 article-title: Conserved LBL1-ta-siRNA and miR165/166-RLD1/2 modules regulate root development in maize publication-title: Development – volume: 9 year: 2013 ident: 10.1016/j.jgg.2024.01.006_bib97 article-title: Extensive natural epigenetic variation at a de novo originated gene publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1003437 – volume: 193 start-page: 303 year: 2013 ident: 10.1016/j.jgg.2024.01.006_bib50 article-title: Quantitative trait loci mapping for yield components and kernel-related traits in multiple connected RIL populations in maize publication-title: Euphytica doi: 10.1007/s10681-013-0901-7 – volume: 20 start-page: 417 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib17 article-title: Regulation of transposable elements by DNA modifications publication-title: Nat. Rev. Genet. doi: 10.1038/s41576-019-0106-6 – volume: 256 start-page: 1245 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib42 article-title: Dynamic changes in histone modification are associated with upregulation of Hsf and rRNA genes during heat stress in maize seedlings publication-title: Protoplasma doi: 10.1007/s00709-019-01364-4 – volume: 27 start-page: 606 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib125 article-title: 5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader publication-title: Cell Res. doi: 10.1038/cr.2017.55 – volume: 164 start-page: 1350 year: 2014 ident: 10.1016/j.jgg.2024.01.006_bib6 article-title: Differential methylation during maize leaf growth targets developmentally regulated genes publication-title: Plant Physiol. doi: 10.1104/pp.113.233312 – volume: 7 year: 2011 ident: 10.1016/j.jgg.2024.01.006_bib36 article-title: Arabidopsis homologs of retinoblastoma-associated protein 46/48 associate with a histone deacetylase to act redundantly in chromatin silencing publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1002366 – volume: 16 start-page: 1836 year: 2018 ident: 10.1016/j.jgg.2024.01.006_bib86 article-title: An epigenetic breeding system in soybean for increased yield and stability publication-title: Plant Biotechnol. J. doi: 10.1111/pbi.12919 – volume: 71 start-page: 2943 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib7 article-title: ZmIBH1-1 regulates plant architecture in maize publication-title: J. Exp. Bot. doi: 10.1093/jxb/eraa052 – volume: 355 start-page: 962 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib16 article-title: Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance publication-title: Science doi: 10.1126/science.aai8898 – volume: 250 start-page: 69 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib65 article-title: Circular RNAs exhibit extensive intraspecific variation in maize publication-title: Planta doi: 10.1007/s00425-019-03145-y – volume: 23 start-page: 628 year: 2013 ident: 10.1016/j.jgg.2024.01.006_bib34 article-title: CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize publication-title: Genome Res. doi: 10.1101/gr.146985.112 – volume: 97 start-page: 451 year: 2018 ident: 10.1016/j.jgg.2024.01.006_bib130 article-title: The chromatin remodeler ZmCHB101 impacts expression of osmotic stress-responsive genes in maize publication-title: Plant Mol. Biol. doi: 10.1007/s11103-018-0751-8 – volume: 21 start-page: 1410 year: 2009 ident: 10.1016/j.jgg.2024.01.006_bib58 article-title: Chromatin and DNA modifications in the Opaque2-mediated regulation of gene transcription during maize endosperm development publication-title: Plant Cell doi: 10.1105/tpc.109.067256 – volume: 48 start-page: 1233 year: 2016 ident: 10.1016/j.jgg.2024.01.006_bib115 article-title: Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings publication-title: Nat. Genet. doi: 10.1038/ng.3636 – volume: 11 start-page: 792 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib141 article-title: Mapping the epigenetic modifications of DNA and RNA publication-title: Protein Cell doi: 10.1007/s13238-020-00733-7 – volume: 11 start-page: 1492 year: 2018 ident: 10.1016/j.jgg.2024.01.006_bib139 article-title: N6-methyladenine DNA methylation in Japonica and Indica rice genomes and its association with gene expression, plant development, and stress responses publication-title: Mol. Plant doi: 10.1016/j.molp.2018.11.005 – volume: 39 start-page: 307 year: 2012 ident: 10.1016/j.jgg.2024.01.006_bib142 article-title: Epigenomic modification and epigenetic regulation in rice publication-title: J. Genet. Genomics doi: 10.1016/j.jgg.2012.02.009 – volume: 10 start-page: 442 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib20 article-title: Dynamic and antagonistic allele-specific epigenetic modifications controlling the expression of imprinted genes in maize endosperm publication-title: Mol. Plant doi: 10.1016/j.molp.2016.10.007 – volume: 15 start-page: 1558 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib31 article-title: Natural variations of ZmSRO1d modulate the trade-off between drought resistance and yield by affecting ZmRBOHC-mediated stomatal ROS production in maize publication-title: Mol. Plant doi: 10.1016/j.molp.2022.08.009 – volume: 16 start-page: 519 year: 2015 ident: 10.1016/j.jgg.2024.01.006_bib22 article-title: DNA methylation pathways and their crosstalk with histone methylation publication-title: Nat. Rev. Mol. Cell Biol. doi: 10.1038/nrm4043 – volume: 26 start-page: 4602 year: 2014 ident: 10.1016/j.jgg.2024.01.006_bib51 article-title: Genetic perturbation of the maize methylome publication-title: Plant Cell doi: 10.1105/tpc.114.133140 – volume: 168 start-page: 1338 year: 2015 ident: 10.1016/j.jgg.2024.01.006_bib106 article-title: Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes publication-title: Plant Physiol. doi: 10.1104/pp.15.00155 – volume: 184 start-page: 2503 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib80 article-title: Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing publication-title: Cell doi: 10.1016/j.cell.2021.03.025 – volume: 119 start-page: 913 year: 2009 ident: 10.1016/j.jgg.2024.01.006_bib73 article-title: Drought stress and tropical maize: QTL-by-environment interactions and stability of QTLs across environments for yield components and secondary traits publication-title: Theor. Appl. Genet. doi: 10.1007/s00122-009-1099-x – volume: 64 start-page: 499 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib93 article-title: Chromatin-remodeling complexes: conserved and plant-specific subunits in Arabidopsis publication-title: J. Integr. Plant Biol. doi: 10.1111/jipb.13208 – volume: 234 start-page: 513 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib64 article-title: Genetic variation in YIGE1 contributes to ear length and grain yield in maize publication-title: New Phytol. doi: 10.1111/nph.17882 – volume: 11 start-page: 563 year: 2010 ident: 10.1016/j.jgg.2024.01.006_bib1 article-title: Epigenetic control of plant immunity publication-title: Mol. Plant Pathol. doi: 10.1111/j.1364-3703.2010.00621.x – volume: 53 start-page: 272 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib102 article-title: OsNSUN2-mediated 5-methylcytosine mRNA modification enhances rice adaptation to high temperature publication-title: Dev. Cell doi: 10.1016/j.devcel.2020.03.009 – volume: 10 start-page: 729 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib81 article-title: Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems publication-title: Nat. Commun. doi: 10.1038/s41467-019-08736-7 – volume: 23 start-page: 1663 year: 2013 ident: 10.1016/j.jgg.2024.01.006_bib92 article-title: Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population publication-title: Genome Res. doi: 10.1101/gr.152538.112 – volume: 177 start-page: 1743 year: 2018 ident: 10.1016/j.jgg.2024.01.006_bib23 article-title: The PILNCR1-miR399 regulatory module is important for low phosphate tolerance in maize publication-title: Plant Physiol. doi: 10.1104/pp.18.00034 – volume: 20 start-page: 526 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib107 article-title: ZmTE1 promotes plant height by regulating intercalary meristem formation and internode cell elongation in maize publication-title: Plant Biotechnol. J. doi: 10.1111/pbi.13734 – volume: 66 start-page: 1903 year: 2023 ident: 10.1016/j.jgg.2024.01.006_bib96 article-title: Trash to treasure: lactate and protein lactylation in maize root impacts response to drought publication-title: Sci. China Life Sci. doi: 10.1007/s11427-023-2361-1 – volume: 41 start-page: 1171 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib144 article-title: Molecular mechanisms of maize endosperm transfer cell development publication-title: Plant Cell Rep. doi: 10.1007/s00299-021-02807-0 – volume: 9 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib143 article-title: Mapping quantitative trait loci for yield-related traits and predicting candidate genes for grain weight in maize publication-title: Sci. Rep. – volume: 375 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib11 article-title: Convergent selection of a WD40 protein that enhances grain yield in maize and rice publication-title: Science doi: 10.1126/science.abg7985 – volume: 176 start-page: 1068 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib30 article-title: Co-targeting RNA polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis publication-title: Cell doi: 10.1016/j.cell.2019.01.029 – volume: 91 start-page: 2905 year: 1994 ident: 10.1016/j.jgg.2024.01.006_bib83 article-title: Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.91.8.2905 – volume: 210 start-page: 279 year: 2007 ident: 10.1016/j.jgg.2024.01.006_bib132 article-title: MicroRNAs and their regulatory roles in animals and plants publication-title: J. Cell. Physiol. doi: 10.1002/jcp.20869 – volume: 182 start-page: 332 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib63 article-title: Natural variation in RNA m6A methylation and its relationship with translational status publication-title: Plant Physiol. doi: 10.1104/pp.19.00987 – volume: 10 start-page: 664 year: 2018 ident: 10.1016/j.jgg.2024.01.006_bib119 article-title: Virus-derived small interfering RNAs affect the accumulations of viral and host transcripts in maize publication-title: Viruses doi: 10.3390/v10120664 – volume: 133 start-page: 1467 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib127 article-title: Epigenomic landscape and epigenetic regulation in maize publication-title: Theor. Appl. Genet. doi: 10.1007/s00122-020-03549-5 – volume: 62 start-page: 394 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib49 article-title: UPA2 and ZmRAVL1: promising targets of genetic improvement of maize plant architecture publication-title: J. Integr. Plant Biol. doi: 10.1111/jipb.12873 – volume: 9 start-page: 1 year: 2016 ident: 10.1016/j.jgg.2024.01.006_bib57 article-title: Expanding maize genetic resources with predomestication alleles: maize-teosinte introgression populations publication-title: Plant Genome doi: 10.3835/plantgenome2015.07.0053 – volume: 13 start-page: 1127 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib136 article-title: Two zinc finger proteins with functions in m6A writing interact with HAKAI publication-title: Nat. Commun. doi: 10.1038/s41467-022-28753-3 – volume: 575 start-page: 109 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib3 article-title: Genetic strategies for improving crop yields publication-title: Nature doi: 10.1038/s41586-019-1679-0 – volume: 61 start-page: 749 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib60 article-title: Decrease in DNA methylation 1 (DDM1) is required for the formation of mCHH islands in maize publication-title: J. Integr. Plant Biol. doi: 10.1111/jipb.12733 – volume: 232 start-page: 880 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib116 article-title: A deep learning approach to automate whole-genome prediction of diverse epigenomic modifications in plants publication-title: New Phytol. doi: 10.1111/nph.17630 – volume: 293 start-page: 1074 year: 2001 ident: 10.1016/j.jgg.2024.01.006_bib45 article-title: Translating the histone code publication-title: Science doi: 10.1126/science.1063127 – volume: 29 start-page: 2995 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib24 article-title: ALKBH10B is an RNA N6-Methyladenosine demethylase affecting Arabidopsis floral transition publication-title: Plant Cell doi: 10.1105/tpc.16.00912 – volume: 49 start-page: 514 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib37 article-title: SMOC: a smart model for open chromatin region prediction in rice genomes publication-title: J. Genet. Genomics doi: 10.1016/j.jgg.2022.02.012 – volume: 112 start-page: 347 year: 2013 ident: 10.1016/j.jgg.2024.01.006_bib67 article-title: Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems publication-title: Ann. Bot. doi: 10.1093/aob/mcs293 – volume: 1809 start-page: 567 year: 2011 ident: 10.1016/j.jgg.2024.01.006_bib4 article-title: Histone modifications in transcriptional activation during plant development publication-title: Biochim. Biophys. Acta doi: 10.1016/j.bbagrm.2011.07.001 – volume: 33 start-page: 2183 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib59 article-title: Maize decrease in DNA methylation 1 targets RNA-directed DNA methylation on active chromatin publication-title: Plant Cell doi: 10.1093/plcell/koab098 – volume: 47 start-page: 11771 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib118 article-title: A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA N6-adenine methylation at the ApT dinucleotides as an epigenetic mark associated with transcription publication-title: Nucleic Acids Res. – volume: 26 start-page: 210 year: 2014 ident: 10.1016/j.jgg.2024.01.006_bib105 article-title: ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development publication-title: Plant Cell doi: 10.1105/tpc.113.115907 – volume: 14 start-page: 204 year: 2014 ident: 10.1016/j.jgg.2024.01.006_bib120 article-title: Adaptive expansion of the maize maternally expressed gene (Meg) family involves changes in expression patterns and protein secondary structures of its members publication-title: BMC Plant Biol. doi: 10.1186/s12870-014-0204-8 – volume: 4 start-page: 805 year: 2014 ident: 10.1016/j.jgg.2024.01.006_bib9 – volume: 10 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib133 article-title: RNA 5-methylcytosine modification regulates vegetative development associated with H3K27 trimethylation in Arabidopsis publication-title: Adv. Sci. – volume: 204 year: 2023 ident: 10.1016/j.jgg.2024.01.006_bib109 article-title: A sustainable approach to narrowing the summer maize yield gap experienced by smallholders in the North China Plain publication-title: Agric. Syst. doi: 10.1016/j.agsy.2022.103541 – volume: 45 start-page: 406 year: 2018 ident: 10.1016/j.jgg.2024.01.006_bib54 article-title: DNA N6-adenine methylation in Arabidopsis thaliana publication-title: Dev. Cell doi: 10.1016/j.devcel.2018.03.012 – volume: 110 start-page: 23 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib68 article-title: Root system architecture in cereals: progress, challenges and perspective publication-title: Plant J. doi: 10.1111/tpj.15669 – volume: 2 start-page: 600 year: 2009 ident: 10.1016/j.jgg.2024.01.006_bib95 article-title: Chromatin remodeling in stem cell maintenance in Arabidopsis thaliana publication-title: Mol. Plant doi: 10.1093/mp/ssp022 – volume: 19 start-page: 779 year: 2014 ident: 10.1016/j.jgg.2024.01.006_bib70 article-title: Challenges of modifying root traits in crops for agriculture publication-title: Trends Plant Sci. doi: 10.1016/j.tplants.2014.08.005 – volume: 5 start-page: e337 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib82 article-title: Differential nuclease sensitivity profiling uncovers a drought responsive change in maize leaf chromatin structure for two large retrotransposon derivatives, Uloh and Vegu publication-title: Plant Direct doi: 10.1002/pld3.337 – volume: 13 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib39 article-title: Epigenetics and its role in effecting agronomical traits publication-title: Front. Plant Sci. doi: 10.3389/fpls.2022.925688 – volume: 13 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib18 article-title: Comprehending the evolution of gene editing platforms for crop trait improvement publication-title: Front. Genet. doi: 10.3389/fgene.2022.876987 – volume: 7 year: 2012 ident: 10.1016/j.jgg.2024.01.006_bib75 article-title: SS18 Together with animal-specific factors defines human BAF-type SWI/SNF complexes publication-title: PLoS ONE doi: 10.1371/journal.pone.0033834 – volume: 194 start-page: 2165 year: 2024 ident: 10.1016/j.jgg.2024.01.006_bib66 article-title: RNA m6A modification facilitates DNA methylation during maize kernel development publication-title: Plant Physiol. doi: 10.1093/plphys/kiad625 – volume: 27 start-page: 1605 year: 2015 ident: 10.1016/j.jgg.2024.01.006_bib77 article-title: Dynamic changes in ANGUSTIFOLIA3 complex composition reveal a growth regulatory mechanism in the maize leaf publication-title: Plant Cell doi: 10.1105/tpc.15.00269 – volume: 36 start-page: 936 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib10 article-title: Mammalian SWI/SNF chromatin remodeling complexes: emerging mechanisms and therapeutic strategies publication-title: Trends Genet. doi: 10.1016/j.tig.2020.07.011 – volume: 44 start-page: 259 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib48 article-title: Harnessing epigenetic variability for crop improvement: current status and future prospects publication-title: Genes Genomics doi: 10.1007/s13258-021-01189-7 – volume: 15 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib79 article-title: Monitoring the interplay between transposable element families and DNA methylation in maize publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1008291 – volume: 23 start-page: 77 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib122 article-title: DNA demethylation affects imprinted gene expression in maize endosperm publication-title: Genome Biol. doi: 10.1186/s13059-022-02641-x – volume: 10 start-page: 1387 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib12 article-title: 5-methylcytosine RNA methylation in Arabidopsis thaliana publication-title: Mol. Plant doi: 10.1016/j.molp.2017.09.013 – volume: 15 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib134 article-title: The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1008120 – volume: 72 start-page: 1782 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib21 article-title: CLA4 regulates leaf angle through multiple hormone signaling pathways in maize publication-title: J. Exp. Bot. doi: 10.1093/jxb/eraa565 – volume: 11 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib108 article-title: QTL analysis and fine mapping of a major QTL conferring kernel size in maize (Zea mays) publication-title: Front. Genet. doi: 10.3389/fgene.2020.603920 – volume: 35 start-page: 41 year: 2008 ident: 10.1016/j.jgg.2024.01.006_bib62 article-title: Analysis of DNA methylation in different maize tissues publication-title: J. Genet. Genomics doi: 10.1016/S1673-8527(08)60006-5 – volume: 23 start-page: 1651 year: 2013 ident: 10.1016/j.jgg.2024.01.006_bib87 article-title: The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA publication-title: Genome Res. doi: 10.1101/gr.153510.112 – volume: 30 start-page: 952 year: 2018 ident: 10.1016/j.jgg.2024.01.006_bib2 article-title: An m6A-YTH module controls developmental timing and morphogenesis in Arabidopsis publication-title: Plant Cell doi: 10.1105/tpc.17.00833 – volume: 10 start-page: 178 year: 2010 ident: 10.1016/j.jgg.2024.01.006_bib123 article-title: Trichostatin A and 5-azacytidine both cause an increase in global histone H4 acetylation and a decrease in global DNA and H3K9 methylation during mitosis in maize publication-title: BMC Plant Biol. doi: 10.1186/1471-2229-10-178 – volume: 20 start-page: 1278 year: 2008 ident: 10.1016/j.jgg.2024.01.006_bib145 article-title: MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor publication-title: Plant Cell doi: 10.1105/tpc.108.058883 – volume: 184 start-page: 2281 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib76 article-title: Here to stay: writing lasting epigenetic memories publication-title: Cell doi: 10.1016/j.cell.2021.04.007 – volume: 29 start-page: 445 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib14 article-title: Transcriptome-wide mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and noncoding RNAs publication-title: Plant Cell doi: 10.1105/tpc.16.00751 – volume: 53 start-page: 766 year: 2012 ident: 10.1016/j.jgg.2024.01.006_bib91 article-title: DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation publication-title: Plant Cell Physiol. doi: 10.1093/pcp/pcs008 – volume: 20 start-page: 156 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib147 article-title: RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening publication-title: Genome Biol. doi: 10.1186/s13059-019-1771-7 – volume: 175 start-page: 336 year: 1955 ident: 10.1016/j.jgg.2024.01.006_bib25 article-title: Occurrence of a new base in the deoxyribonucleic acid of a strain of Bacterium coli publication-title: Nature doi: 10.1038/175336a0 – volume: 352 start-page: 1408 year: 2016 ident: 10.1016/j.jgg.2024.01.006_bib35 article-title: Messenger RNA modifications: form, distribution, and function publication-title: Science doi: 10.1126/science.aad8711 – volume: 72 start-page: 1000 year: 2012 ident: 10.1016/j.jgg.2024.01.006_bib90 article-title: Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects publication-title: Plant J. doi: 10.1111/tpj.12009 – volume: 182 start-page: 345 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib74 article-title: Evolution of the RNA N6-methyladenosine methylome mediated by genomic duplication publication-title: Plant Physiol. doi: 10.1104/pp.19.00323 – volume: 11 start-page: 52 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib71 article-title: Chromatin remodeling protein ZmCHB101 regulates nitrate-responsive gene expression in maize publication-title: Front. Plant Sci. doi: 10.3389/fpls.2020.00052 – volume: 21 start-page: 1053 year: 2009 ident: 10.1016/j.jgg.2024.01.006_bib114 article-title: Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize publication-title: Plant Cell doi: 10.1105/tpc.109.065714 – volume: 6 year: 2016 ident: 10.1016/j.jgg.2024.01.006_bib129 article-title: The core subunit of a chromatin-remodeling complex, ZmCHB101, plays essential roles in maize growth and development publication-title: Sci. Rep. doi: 10.1038/srep38504 – volume: 72 start-page: 5356 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib13 article-title: Epigenetic approaches to crop breeding: current status and perspectives publication-title: J. Exp. Bot. doi: 10.1093/jxb/erab227 – volume: 20 start-page: 827 year: 2008 ident: 10.1016/j.jgg.2024.01.006_bib8 article-title: Histone acetylation and chromatin remodeling are required for UV-B-dependent transcriptional activation of regulated genes in maize publication-title: Plant Cell doi: 10.1105/tpc.107.056457 – volume: 105 start-page: 108 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib44 article-title: Coordinated regulation of starch synthesis in maize endosperm by microRNAs and DNA methylation publication-title: Plant J. doi: 10.1111/tpj.15043 – volume: 13 start-page: 14 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib53 article-title: Epigenetic modifications of mRNA and DNA in plants publication-title: Mol. Plant doi: 10.1016/j.molp.2019.12.007 – volume: 20 start-page: 1754 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib135 article-title: The miRNA-mediated post-transcriptional regulation of maize in response to high temperature publication-title: Int. J. Mol. Sci. doi: 10.3390/ijms20071754 – volume: 23 start-page: 5 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib112 article-title: N4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana publication-title: Genome Biol. doi: 10.1186/s13059-021-02578-7 – volume: 1860 start-page: 149 year: 2017 ident: 10.1016/j.jgg.2024.01.006_bib78 article-title: Putting DNA methylation in context: from genomes to gene expression in plants publication-title: Biochim. Biophys. Acta Gene Regul. Mech. doi: 10.1016/j.bbagrm.2016.08.009 – volume: 13 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib47 article-title: Histone modification and chromatin remodeling in plant response to pathogens publication-title: Front. Plant Sci. doi: 10.3389/fpls.2022.986940 – volume: 23 start-page: 4968 year: 2022 ident: 10.1016/j.jgg.2024.01.006_bib101 article-title: Characteristics of microRNAs and target genes in maize root under drought stress publication-title: Int. J. Mol. Sci. doi: 10.3390/ijms23094968 – volume: 18 start-page: 1642 year: 2020 ident: 10.1016/j.jgg.2024.01.006_bib138 article-title: eRice: a refined epigenomic platform for japonica and indica rice publication-title: Plant Biotechnol. J. doi: 10.1111/pbi.13329 – volume: 39 start-page: 1581 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib128 article-title: RNA demethylation increases the yield and biomass of rice and potato plants in field trials publication-title: Nat. Biotechnol. doi: 10.1038/s41587-021-00982-9 – volume: 186 start-page: 420 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib52 article-title: Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize publication-title: Plant Physiol. doi: 10.1093/plphys/kiab073 – volume: 19 start-page: 937 year: 2013 ident: 10.1016/j.jgg.2024.01.006_bib41 article-title: Increasing influence of heat stress on French maize yields from the 1960s to the 2030s publication-title: Glob. Chang. Biol. doi: 10.1111/gcb.12069 – volume: 20 start-page: 608 year: 2019 ident: 10.1016/j.jgg.2024.01.006_bib131 article-title: Reading, writing and erasing mRNA methylation publication-title: Nat. Rev. Mol. Cell Biol. doi: 10.1038/s41580-019-0168-5 – volume: 17 year: 2021 ident: 10.1016/j.jgg.2024.01.006_bib38 article-title: RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1009326
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Snippet	Epigenetics-mediated breeding (epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features... Epigenetics-mediated breeding (Epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features...
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SubjectTerms	agricultural productivity Agronomical traits chromatin corn CRISPR-Cas Systems crop yield Crops, Agricultural - genetics DNA Epibreeding Epigenesis, Genetic Epigenetic variation epigenetics epigenome Epigenome editing Gene Editing gene expression Gene Expression Regulation, Plant Genetic Variation genomics histone code non-coding RNA Plant Breeding - methods Quantitative Trait Loci Quantitative Trait, Heritable Synthetic epigenetics Zea mays - genetics Zea mays - growth & development
Title	Epigenetic variation in maize agronomical traits for breeding and trait improvement
URI	https://dx.doi.org/10.1016/j.jgg.2024.01.006 https://www.ncbi.nlm.nih.gov/pubmed/38310944 https://www.proquest.com/docview/2922446035 https://www.proquest.com/docview/3153622769
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