Dual-Direction of DNA Methylome Reprogramming During Rice Domestication

doi:10.1016/j.rsci.2026.02.005

Rice Science ›› 2026, Vol. 33 ›› Issue (3): 287-291.DOI: 10.1016/j.rsci.2026.02.005

• Letters • Previous Articles Next Articles

Dual-Direction of DNA Methylome Reprogramming During Rice Domestication

Yu Xiaoman¹^,²^,^#, Cheng Xiang²^,^#, Li Yilin²^,^#, Yu Ruoqian¹, Liu Jiajia¹, Yang Lingwei¹, He Huiying², Wei Hua², Shang Lianguang²^,³(), Wang Yuexing¹(), Liu Xiangpei²()

¹ State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
² State Key Laboratory of Genome and Multi-Omics Technologies, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
³ Nanfan Research Institute, Chinese Academy of Agriculture Science, Sanya 572024, China

Received:2025-12-04 Accepted:2026-02-02 Online:2026-05-28 Published:2026-06-02
Contact: Liu Xiangpei (doris6364@163.com); Wang Yuexing (wangyuexing@caas.cn); Shang Lianguang (shanglianguang@caas.cn)
About author:^#These authors contributed equally to this work

Abstract

Yu Xiaoman, Cheng Xiang, Li Yilin, Yu Ruoqian, Liu Jiajia, Yang Lingwei, He Huiying, Wei Hua, Shang Lianguang, Wang Yuexing, Liu Xiangpei. Dual-Direction of DNA Methylome Reprogramming During Rice Domestication[J]. Rice Science, 2026, 33(3): 287-291.

Figures/Tables 1

References 27

[1]	Bewick A J, Schmitz R J. 2017. Gene body DNA methylation in plants. Curr Opin Plant Biol, 36: 103-110.
[2]	Doebley J F, Gaut B S, Smith B D. 2006. The molecular genetics of crop domestication. Cell, 127(7): 1309-1321.
[3]	Dong Z B, Hu G Y, Chen Q Y, et al. 2024. A regulatory network controlling developmental boundaries and meristem fates contributed to maize domestication. Nat Genet, 56(11): 2528-2537.
[4]	Hasan S, Furtado A, Henry R. 2023. Analysis of domestication loci in wild rice populations. Plants, 12(3): 489.
[5]	Huang X H, Kurata N, Wei X H, et al. 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature, 490: 497-501.
[6]	Jones P A. 2012. Functions of DNA methylation: Islands, start sites, gene bodies and beyond. Nat Rev Genet, 13(7): 484-492.
[7]	Konishi S, Izawa T, Lin S Y, et al. 2006. An SNP caused loss of seed shattering during rice domestication. Science, 312: 1392-1396.
[8]	Kumar A, Daware A, Kumar A, et al. 2020. Genome-wide analysis of polymorphisms identified domestication-associated long low-diversity region carrying important rice grain size/weight quantitative trait loci. Plant J, 103(4): 1525-1547.
[9]	Law J A, Jacobsen S E. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet, 11(3): 204-220.
[10]	Lev Maor G, Yearim A, Ast G. 2015. The alternative role of DNA methylation in splicing regulation. Trends Genet, 31(5): 274-280.
[11]	Li C B, Zhou A L, Sang T. 2006. Rice domestication by reducing shattering. Science, 311: 1936-1939.
[12]	Luo W K, Gao J Y, Leng L C, et al. 2025. Population genomic analysis unravels the repeated trait evolution after the centric origin of African cultivated rice. Mol Plant, 18(10): 1672-1687.
[13]	Meyer R S, Purugganan M D. 2013. Evolution of crop species: Genetics of domestication and diversification. Nat Rev Genet, 14(12): 840-852.
[14]	Rao X L, Yang S L, Lü S Y, et al. 2024. DNA methylation dynamics in response to drought stress in crops. Plants, 13(14): 1977.
[15]	Shang L G, Li X X, He H Y, et al. 2022. A super pan-genomic landscape of rice. Cell Res, 32(10): 878-896.
[16]	Shomura A, Izawa T, Ebana K, et al. 2008. Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet, 40(8): 1023-1028.
[17]	Song X W, Tang S J, Liu H, et al. 2025. Inheritance of acquired adaptive cold tolerance in rice through DNA methylation. Cell, 188(16): 4213-4224.e12.
[18]	Song Y G, Ji D D, Li S, et al. 2012. The dynamic changes of DNA methylation and histone modifications of salt responsive transcription factor genes in soybean. PLoS One, 7(7): e41274.
[19]	Tan L B, Li X R, Liu F X, et al. 2008. Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet, 40(11): 1360-1364.
[20]	Wang J, Nan N, Li N, et al. 2020. A DNA methylation reader-chaperone regulator-transcription factor complex activates OsHKT1;5 expression during salinity stress. Plant Cell, 32(11): 3535-3558.
[21]	Wang J D, Wang J, Huang L C, et al. 2024. ABA-mediated regulation of rice grain quality and seed dormancy via the NF-YB1-SLRL2-bHLH 144 module. Nat Commun, 15(1): 4493.
[22]	Xu G, Lyu J, Li Q, et al. 2020. Evolutionary and functional genomics of DNA methylation in maize domestication and improvement. Nat Commun, 11(1): 5539.
[23]	Xu F, Tang J Y, Wang S X, et al. 2022. Antagonistic control of seed dormancy in rice by two bHLH transcription factors. Nat Genet, 54(12): 1972-1982.
[24]	Xu R, Sun C Q. 2021. What happened during domestication of wild to cultivated rice. Crop J, 9(3): 564-576.
[25]	Yang N, Wang Y B, Liu X G, et al. 2023. Two teosintes made modern maize. Science, 382: eadg8940.
[26]	Zhao L, Xie L, Zhang Q, et al. 2020. Integrative analysis of reference epigenomes in 20 rice varieties. Nat Commun, 11(1): 2658.
[27]	Zhu G T, Wang S C, Huang Z J, et al. 2018. Rewiring of the fruit metabolome in tomato breeding. Cell, 172(1/2): 249-261.e12.

Dual-Direction of DNA Methylome Reprogramming During Rice Domestication

RichHTML

PDF

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 1

References 27

Related Articles 0

Recommended Articles

Metrics