[1]

Hochholdinger F, Hoecker N. 2007. Towards the molecular basis of heterosis. Trends in Plant Science 12:427−432

doi: 10.1016/j.tplants.2007.08.005
[2]

Ma X, Xing F, Jia Q, Zhang Q, Hu T, et al. 2021. Parental variation in CHG methylation is associated with allelic-specific expression in elite hybrid rice. Plant Physiology 186:1025−1041

doi: 10.1093/plphys/kiab088
[3]

Springer NM, Stupar RM. 2007. Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Research 17:264−275

doi: 10.1101/gr.5347007
[4]

Shen Y, Sun S, Hua S, Shen E, Ye C, et al. 2017. Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs. The Plant Journal 91:874−893

doi: 10.1111/tpj.13605
[5]

Li B, Howe GT, Wu R. 1998. Developmental factors responsible for heterosis in aspen hybrids (Populus tremuloides × P. tremula). Tree Physiology 18:29−36

doi: 10.1093/treephys/18.1.29
[6]

Dale G, Dieters M. 2007. Economic returns from environmental problems: Breeding salt- and drought-tolerant eucalypts for salinity abatement and commercial forestry. Ecological Engineering 31:175−182

doi: 10.1016/j.ecoleng.2007.03.004
[7]

Liu J, Li M, Zhang Q, Wei X, Huang X. 2020. Exploring the molecular basis of heterosis for plant breeding. Journal of Integrative Plant Biology 62:287−298

doi: 10.1111/jipb.12804
[8]

Hochholdinger F, Baldauf JA. 2018. Heterosis in plants. Current Biology 28:R1089−R1092

doi: 10.1016/j.cub.2018.06.041
[9]

Liu W, Zhang Y, He H, He G, Deng XW. 2022. From hybrid genomes to heterotic trait output: challenges and opportunities. Current Opinion in Plant Biology 66:102193

doi: 10.1016/j.pbi.2022.102193
[10]

He G, Zhu X, Elling AA, Chen L, Wang X, et al. 2010. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. The Plant Cell 22:17−33

doi: 10.1105/tpc.109.072041
[11]

Shao L, Xing F, Xu C, Zhang Q, Che J, et al. 2019. Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis. Proceedings of the National Academy of Sciences of the United States of America 116:5653−5658

doi: 10.1073/pnas.1820513116
[12]

Sinha P, Singh VK, Saxena RK, Kale SM, Li Y, et al. 2020. Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea. Plant Biotechnology Journal 18:1697−1710

doi: 10.1111/pbi.13333
[13]

Crisp PA, Hammond R, Zhou P, Vaillancourt B, Lipzen A, et al. 2020. Variation and inheritance of small RNAs in maize inbreds and F1 hybrids. Plant Physiology 182:318−331

doi: 10.1101/692400
[14]

Li D, Lu X, Zhu Y, Pan J, Zhou S, et al. 2022. The multi-omics basis of potato heterosis. Journal of Integrative Plant Biology 64:671−687

doi: 10.1111/jipb.13211
[15]

Gao M, Huang Q, Chu Y, Ding C, Zhang B, et al. 2014. Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides. BMC Genetics 15:S8

doi: 10.1186/1471-2156-15-s1-s8
[16]

Yang H, Wang X, Wei Y, Deng Z, Liu H, et al. 2018. Transcriptomic analyses reveal molecular mechanisms underlying growth heterosis and weakness of rubber tree seedlings. BMC Plant Biology 18:10

doi: 10.1186/s12870-017-1203-3
[17]

Li J, Yang DL, Huang H, Zhang G, He L, et al. 2020. Epigenetic memory marks determine epiallele stability at loci targeted by de novo DNA methylation. Nature Plants 6:661−674

doi: 10.1038/s41477-020-0671-x
[18]

Takahashi Y, Morales Valencia M, Yu Y, Ouchi Y, Takahashi K, et al. 2023. Transgenerational inheritance of acquired epigenetic signatures at CpG islands in mice. Cell 186:715−731.e19

doi: 10.1016/j.cell.2022.12.047
[19]

Shen H, He H, Li J, Chen W, Wang X, et al. 2012. Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. The Plant Cell 24:875−892

doi: 10.1105/tpc.111.094870
[20]

Greaves IK, Groszmann M, Ying H, Taylor JM, Peacock WJ, et al. 2012. Trans chromosomal methylation in Arabidopsis hybrids. Proceedings of the National Academy of Sciences of the United States of America 109:3570−3575

doi: 10.1073/pnas.1201043109
[21]

Lauss K, Wardenaar R, Oka R, van Hulten MHA, Guryev V, et al. 2018. Parental DNA methylation states are associated with heterosis in epigenetic hybrids. Plant Physiology 176:1627−1645

doi: 10.1104/pp.17.01054
[22]

Fei Q, Xia R, Meyers BC. 2013. Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. The Plant Cell 25:2400−2415

doi: 10.1105/tpc.113.114652
[23]

Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics 11:204−220

doi: 10.1038/nrg2719
[24]

Zhang H, Lang Z, Zhu JK. 2018. Dynamics and function of DNA methylation in plants. Nature Reviews Molecular Cell Biology 19:489−506

doi: 10.1038/s41580-018-0016-z
[25]

Zhang H, Zhu JK. 2011. RNA-directed DNA methylation. Current Opinion in Plant Biology 14:142−147

doi: 10.1016/j.pbi.2011.02.003
[26]

Zhai J, Bischof S, Wang H, Feng S, Lee TF, et al. 2015. A one precursor one siRNA model for Pol IV-dependent siRNA biogenesis. Cell 163:445−455

doi: 10.1016/j.cell.2015.09.032
[27]

Shivaprasad PV, Dunn RM, Santos BA, Bassett A, Baulcombe DC. 2012. Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs. The EMBO Journal 31:257−266

doi: 10.1038/emboj.2011.458
[28]

Matzke MA, Mosher RA. 2014. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nature Reviews Genetics 15:394−408

doi: 10.1038/nrg3683
[29]

Groszmann M, Greaves IK, Albertyn ZI, Scofield GN, Peacock WJ, et al. 2011. Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proceedings of the National Academy of Sciences of the United States of America 108:2617−2622

doi: 10.3410/f.9116956.9699058
[30]

Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, et al. 2016. Novel meiotic miRNAs and indications for a role of phasiRNAs in meiosis. Frontiers in Plant Science 7:762

doi: 10.3389/fpls.2016.00762
[31]

Zhang M, Ma X, Wang C, Li Q, Meyers BC, et al. 2021. CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers. New Phytologist 229:2984−2997

doi: 10.1111/nph.17060
[32]

Liu C, Shen Y, Qin B, Wen H, Cheng J, et al. 2020. Oryza sativa RNA-dependent RNA polymerase 6 contributes to double-strand break formation in meiosis. The Plant Cell 32:3273−3289

doi: 10.1105/tpc.20.00213
[33]

Li SW, Zhang Z, He CZ, An XM, Yu ZS, et al. 2005. Variation analysis of seed and seedling traits of cross combination progenies in Populus. Forestry Studies in China 7:61−69

doi: 10.1007/s11632-005-0034-8
[34]

Apuli RP, Richards T, Rendón-Anaya M, Karacic A, Rönnberg-Wästljung AC, et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr & Gray). Science 313:1596−1604

doi: 10.1126/science.1128691
[35]

Zhang W, Yuan Z, Zhang J, Su X, Huang Q, et al. 2023. Identification and functional prediction of circRNAs in leaves of F1 hybrid poplars with different growth potential and their parents. International Journal of Molecular Sciences 24:2284

doi: 10.3390/ijms24032284
[36]

Zhang J, Zhang W, Ding C, Chu Y, Su X, et al. 2025. 美洲黑杨亲本及其不同林龄及生长势子代叶片糖代谢的差异 [Differences in leaf sugar metabolism of Populus deltoides parents and their hybrids with different growth potentials and different forest ages]. 林业科学 [Scientia Silvae Sinicae] 61:131−145 (in Chinese)

doi: 10.11707/j.1001-7488.LYKX20240636
[37]

Zhang J, Zhang W, Ding C, Zhao J, Su X, et al. 2025. Non-additive gene expression in carbon and nitrogen metabolism drives growth heterosis in Populus deltoides. Plant, Cell & Environment 48:3529−3543

doi: 10.1111/pce.15371
[38]

Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 38:1767−1771

doi: 10.1093/nar/gkp1137
[39]

Krueger F, Andrews SR. 2011. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571−1572

doi: 10.1093/bioinformatics/btr167
[40]

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315−322

doi: 10.1038/nature08514
[41]

Catoni M, Tsang JM, Greco AP, Zabet NR. 2018. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Research 46:e114

doi: 10.1093/nar/gky602
[42]

Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841−842

doi: 10.1093/bioinformatics/btq033
[43]

Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3):R25

doi: 10.1186/gb-2009-10-3-r25
[44]

Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550

doi: 10.1186/s13059-014-0550-8
[45]

Kanehisa M, Furumichi M, Sato Y, Matsuura Y, Ishiguro-Watanabe M. 2025. KEGG: biological systems database as a model of the real world. Nucleic Acids Research 53(D1):D672−D677

doi: 10.1093/nar/gkae909
[46]

Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCᴛ method. Methods 25:402−408

doi: 10.1006/meth.2001.1262
[47]

Wang L, Wu LM, Greaves IK, Zhu A, Dennis ES, et al. 2017. PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 114:E3555−E3562

doi: 10.1073/pnas.1703179114
[48]

Li H, Yuan J, Wu M, Han Z, Li L, et al. 2018. Transcriptome and DNA methylome reveal insights into yield heterosis in the curds of broccoli (Brassica oleracea L var. italic). BMC Plant Biology 18:168

doi: 10.1186/s12870-018-1384-4
[49]

Zhou G, Chen Y, Yao W, Zhang C, Xie W, et al. 2012. Genetic composition of yield heterosis in an elite rice hybrid. Proceedings of the National Academy of Sciences of the United States of America 109:15847−15852

doi: 10.1073/pnas.1214141109
[50]

Greaves IK, Eichten SR, Groszmann M, Wang A, Ying H, et al. 2016. Twenty-four-nucleotide siRNAs produce heritable trans-chromosomal methylation in F1 Arabidopsis hybrids. Proceedings of the National Academy of Sciences of the United States of America 113:6895−6902

doi: 10.1073/pnas.1613623113
[51]

Zhang Q, Wang D, Lang Z, He L, Yang L, et al. 2016. Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation. Proceedings of the National Academy of Sciences of the United States of America 113:4248−4256

doi: 10.1073/pnas.1607851113
[52]

Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2007. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics 39(1):61−69

doi: 10.1038/ng1929
[53]

Bewick AJ, Schmitz RJ. 2017. Gene body DNA methylation in plants. Current Opinion in Plant Biology 36:103−110

doi: 10.1016/j.pbi.2016.12.007
[54]

Yang L, Liu P, Wang X, Jia A, Ren D, et al. 2021. A central circadian oscillator confers defense heterosis in hybrids without growth vigor costs. Nature Communications 12:2317

doi: 10.1038/s41467-021-22268-z
[55]

Raju SKK, Shao MR, Sanchez R, Xu YZ, Sandhu A, et al. 2018. An epigenetic breeding system in soybean for increased yield and stability. Plant Biotechnology Journal 16:1836−1847

doi: 10.1111/pbi.12919
[56]

Ng DW, Miller M, Yu HH, Huang TY, Kim ED, et al. 2014. A role for CHH methylation in the parent-of-origin effect on altered circadian rhythms and biomass heterosis in Arabidopsis intraspecific hybrids. The Plant Cell 26:2430−2440

doi: 10.1105/tpc.113.115980
[57]

Barber WT, Zhang W, Win H, Varala KK, Dorweiler JE, et al. 2012. Repeat associated small RNAs vary among parents and following hybridization in maize. Proceedings of the National Academy of Sciences of the United States of America 109:10444−10449

doi: 10.1073/pnas.1202073109
[58]

Xia R, Chen C, Pokhrel S, Ma W, Huang K, et al. 2019. 24-nt reproductive phasiRNAs are broadly present in angiosperms. Nature Communications 10:627

doi: 10.1038/s41467-019-08543-0
[59]

Durand M, Brehaut V, Clement G, Kelemen Z, Macé J, et al. 2023. The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply. The Plant Cell 35:1429−1454

doi: 10.1093/plcell/koad025
[60]

Che Y, Kusama S, Matsui S, Suorsa M, Nakano T, et al. 2020. Arabidopsis PsbP-like protein 1 facilitates the assembly of the photosystem II supercomplexes and optimizes plant fitness under fluctuating light. Plant and Cell Physiology 61:1168−1180

doi: 10.1093/pcp/pcaa045
[61]

Xiong HB, Wang J, Huang C, Rochaix JD, Lin FM, et al. 2020. mTERF8, a member of the mitochondrial transcription termination factor family, is involved in the transcription termination of chloroplast gene psbJ. Plant Physiology 182:408−423

doi: 10.1104/pp.19.00906
[62]

Weis BL, Kovacevic J, Missbach S, Schleiff E. 2015. Plant-specific features of ribosome biogenesis. Trends in Plant Science 20:729−740

doi: 10.1016/j.tplants.2015.07.003