[1]

Bao JP, Zhang SL. 2010. Effects of seed coat, chemicals and hormones on breaking dormancy in pear rootstock seeds (Pyrus betulaefolia Bge. and Pyrus calleryana Dcne.). Seed Science and Technology 38:348−357

doi: 10.15258/sst.2010.38.2.08
[2]

Bao J, Sha S, Zhang S. 2011. Changes in germinability, lipid peroxidation, and antioxidant enzyme activities in pear stock (Pyrus betulaefolia Bge.) seeds during room- and low-temperature storage. Acta Physiologiae Plantarum 33:2035−2040

doi: 10.1007/s11738-011-0728-6
[3]

Kan J, Yuan N, Lin J, Li H, Yang Q, et al. 2023. Seed germination and growth improvement for early maturing pear breeding. Plants 12:4120

doi: 10.3390/plants12244120
[4]

Qi KJ, Wu X, Xie ZH, Sun XJ, Gu C, et al. 2019. Seed coat removal in pear accelerates embryo germination by down-regulating key genes in ABA biosynthesis. The Journal of Horticultural Science and Biotechnology 94:718−725

doi: 10.1080/14620316.2019.1602001
[5]

Qi KJ, Wu X, Gao X, Li LF, Xie ZH, et al. 2022. Metabolome and transcriptome analyses unravel the inhibition of embryo germination by abscisic acid in pear. Scientia Horticulturae 292:110652

doi: 10.1016/j.scienta.2021.110652
[6]

Singh P, Dave A, Vaistij FE, Worrall D, Holroyd GH, et al. 2017. Jasmonic acid-dependent regulation of seed dormancy following maternal herbivory in Arabidopsis. New Phytologist 214:1702−1711

doi: 10.1111/nph.14525
[7]

Stirk WA, Václavíková K, Novák O, Gajdošová S, Kotland O, et al. 2012. Involvement of cis-zeatin, dihydrozeatin, and aromatic cytokinins in germination and seedling establishment of maize, oats, and lucerne. Journal of Plant Growth Regulation 31:392−405

doi: 10.1007/s00344-011-9249-1
[8]

Kazmi RH, Willems LAJ, Joosen RVL, Khan N, Ligterink W, et al. 2017. Metabolomic analysis of tomato seed germination. Metabolomics 13:145

doi: 10.1007/s11306-017-1284-x
[9]

Zhao H, He Y, Zhang K, Li S, Chen Y, et al. 2023. Rewiring of the seed metabolome during Tartary buckwheat domestication. Plant Biotechnology Journal 21:150−164

doi: 10.1111/pbi.13932
[10]

Gu EJ, Kim DW, Jang GJ, Song SH, Lee JI, et al. 2017. Mass-based metabolomic analysis of soybean sprouts during germination. Food Chemistry 217:311−319

doi: 10.1016/j.foodchem.2016.08.113
[11]

Han C, Zhen S, Zhu G, Bian Y, Yan Y. 2017. Comparative metabolome analysis of wheat embryo and endosperm reveals the dynamic changes of metabolites during seed germination. Plant Physiology and Biochemistry 115:320−327

doi: 10.1016/j.plaphy.2017.04.013
[12]

Fu XZ, Zhang XY, Qiu JY, Zhou X, Yuan M, et al. 2019. Whole-transcriptome RNA sequencing reveals the global molecular responses and ceRNA regulatory network of mRNAs, lncRNAs, miRNAs and circRNAs in response to copper toxicity in Ziyang Xiangcheng (Citrus junos Sieb. Ex Tanaka). BMC Plant Biology 19:509

doi: 10.1186/s12870-019-2087-1
[13]

Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, et al. 2008. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Research 18:610−621

doi: 10.1101/gr.7179508
[14]

Solofoharivelo MC, van der Walt AP, Stephan D, Burger JT, Murray SL. 2014. MicroRNAs in fruit trees: discovery, diversity and future research directions. Plant Biology 16:856−865

doi: 10.1111/plb.12153
[15]

Zaman F, Zhang M, Wu R, Zhang Q, Luo Z, et al. 2023. Recent research advances of small regulatory RNA in fruit crops. Horticulturae 9:294

doi: 10.3390/horticulturae9030294
[16]

Herman AB, Tsitsipatis D, Gorospe M. 2022. Integrated lncRNA function upon genomic and epigenomic regulation. Molecular Cell 82:2252−2266

doi: 10.1016/j.molcel.2022.05.027
[17]

Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. 2011. A ceRNA hypothesis: the rosetta stone of a hidden RNA language? Cell 146:353−358

doi: 10.1016/j.cell.2011.07.014
[18]

He X, Guo S, Wang Y, Wang L, Shu S, et al. 2020. Systematic identification and analysis of heat-stress-responsive lncRNAs, circRNAs and miRNAs with associated co-expression and ceRNA networks in cucumber (Cucumis sativus L.). Physiologia Plantarum 168:736−754

doi: 10.1111/ppl.12997
[19]

Xu P, Li H, Wang X, Zhao G, Lu X, et al. 2022. Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut. BMC Genomics 23:239

doi: 10.1186/s12864-022-08470-3
[20]

Dey SS, Sharma PK, Munshi AD, Jaiswal S, Behera TK, et al. 2022. Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.). Frontiers in Plant Science 13:884476

doi: 10.3389/fpls.2022.884476
[21]

Yang S, Yang T, Tang Y, Aisimutuola P, Zhang G, et al. 2020. Transcriptomic profile analysis of non-coding RNAs involved in Capsicum chinense Jacq. fruit ripening. Scientia Horticulturae 264:109158

doi: 10.1016/j.scienta.2019.109158
[22]

Zuo J, Grierson D, Courtney LT, Wang Y, Gao L, et al. 2020. Relationships between genome methylation, levels of non-coding RNAs, mRNAs and metabolites in ripening tomato fruit. The Plant Journal 103:980−994

doi: 10.1111/tpj.14778
[23]

Wu X, Chen Y, Wang X, Qi K, Qiao X, et al. 2023. New insights into aroma regulation in pear peel and flesh under methyl jasmonate treatment obtained by metabolite and whole-transcriptome RNA sequencing analyses. Postharvest Biology and Technology 201:112347

doi: 10.1016/j.postharvbio.2023.112347
[24]

Yuan Y, Chen Y, Wu W, Qi K, Xie Z, et al. 2024. Regulatory network analysis reveals gene-metabolite relationships in pear fruit treated with methyl jasmonate. Plant Physiology and Biochemistry 216:109176

doi: 10.1016/j.plaphy.2024.109176
[25]

Gu C, Pei MS, Guo ZH, Wu L, Qi KJ, et al. 2024. Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism. Genome Biology 25:70

doi: 10.1186/s13059-024-03200-2
[26]

Gu C, Xu HY, Zhou YH, Yao JL, Xie ZH, et al. 2020. Multiomics analyses unveil the involvement of microRNAs in pear fruit senescence under high- or low-temperature conditions. Horticulture Research 7:196

doi: 10.1038/s41438-020-00420-y
[27]

Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. 2016. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 11:1650−1667

doi: 10.1038/nprot.2016.095
[28]

Zhou Y, Wang X, Qi K, Bao J, Zhang S, et al. 2023. Involvement of long non-coding RNAs in pear fruit senescence under high- and low-temperature conditions. Horticultural Plant Journal 9:224−236

doi: 10.1016/j.hpj.2022.08.004
[29]

Xue C, Yao JL, Qin MF, Zhang MY, Allan AC, et al. 2019. PbrmiR397a regulates lignification during stone cell development in pear fruit. Plant Biotechnology Journal 17:103−117

doi: 10.1111/pbi.12950
[30]

Miransari M, Smith DL. 2014. Plant hormones and seed germination. Environmental and Experimental Botany 99:110−121

doi: 10.1016/j.envexpbot.2013.11.005
[31]

Vaistij FE, Gan Y, Penfield S, Gilday AD, Dave A, et al. 2013. Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA. Proceedings of the National Academy of Sciences of the United States of America 110:10866−10871

doi: 10.1073/pnas.1301647110
[32]

Shu K, Liu XD, Xie Q, He ZH. 2016. Two faces of one seed: hormonal regulation of dormancy and germination. Molecular Plant 9:34−45

doi: 10.1016/j.molp.2015.08.010
[33]

Graeber K, Nakabayashi K, Miatton E, Leubner-Metzger G, Soppe WJJ. 2012. Molecular mechanisms of seed dormancy. Plant, Cell & Environment 35:1769−1786

doi: 10.1111/j.1365-3040.2012.02542.x
[34]

Liu X, Zhang H, Zhao Y, Feng Z, Li Q, et al. 2013. Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 110:15485−15490

doi: 10.1073/pnas.1304651110
[35]

Shuai H, Meng Y, Luo X, Chen F, Zhou W, et al. 2017. Exogenous auxin represses soybean seed germination through decreasing the gibberellin/abscisic acid (GA/ABA) ratio. Scientific Reports 7:12620

doi: 10.1038/s41598-017-13093-w
[36]

Xie Z, Zhang ZL, Hanzlik S, Cook E, Shen QJ. 2007. Salicylic acid inhibits gibberellin-induced alpha-amylase expression and seed germination via a pathway involving an abscisic-acid-inducible WRKY gene. Plant Molecular Biology 64:293−303

doi: 10.1007/s11103-007-9152-0
[37]

Nonogaki H. 2006. Seed germination − the biochemical and molecular mechanisms. Breeding Science 56:93−105

doi: 10.1270/jsbbs.56.93
[38]

Li X, Qi L, Zang N, Zhao L, Sun Y, et al. 2022. Integrated metabolome and transcriptome analysis of the regulatory network of volatile ester formation during fruit ripening in pear. Plant Physiology and Biochemistry 185:80−90

doi: 10.1016/j.plaphy.2022.04.030
[39]

Li H, Quan J, Rana S, Yao S, Wang Y, et al. 2023. Comprehensive metabolomic and transcriptomic analysis of the regulatory network of volatile terpenoid formation during the growth and development of pears (Pyrus spp. 'Panguxiang'). Horticulturae 9:483

doi: 10.3390/horticulturae9040483
[40]

Jiang CC, Lyu KL, Zeng SM, Wang XA. 2025. Integrated metabonomics and transcriptomics analysis of fruit sugar biosynthesis in two pear cultivars with different sugar contents. Scientia Horticulturae 345:114135

doi: 10.1016/j.scienta.2025.114135
[41]

Gong X, Qi K, Chen J, Zhao L, Xie Z, et al. 2023. Multi-omics analyses reveal stone cell distribution pattern in pear fruit. The Plant Journal 113:626−642

doi: 10.1111/tpj.16073
[42]

Xu R, Zhou J, Deng L, Zhang S, Golding JB, et al. 2025. Transcriptomics integrated with metabolomics analysis of cold-induced lenticel disorder via the lignin pathway upon postharvest 'Xinli No. 7' pear fruit. Postharvest Biology and Technology 220:113315

doi: 10.1016/j.postharvbio.2024.113315
[43]

Jiang C, Lyu K, Zeng S, Wang XA, Chen X. 2024. A combined metabolome and transcriptome reveals the lignin metabolic pathway during the developmental stages of peel coloration in the 'Xinyu' pear. International Journal of Molecular Sciences 25:7481

doi: 10.3390/ijms25137481
[44]

Zhang Z, Tian C, Zhang Y, Li C, Li X, et al. 2020. Transcriptomic and metabolomic analysis provides insights into anthocyanin and procyanidin accumulation in pear. BMC Plant Biology 20:129

doi: 10.1186/s12870-020-02344-0
[45]

Shi CH, Wang XQ, Xu JF, Zhang YX, Qi B, et al. 2021. Dissecting the molecular mechanism of russeting in sand pear (Pyrus pyrifolia Nakai) by metabolomics, transcriptomics, and proteomics. The Plant Journal 108:1644−1661

doi: 10.1111/tpj.15532
[46]

Wang Q, Wu X, Liu L, Yao D, Li J, et al. 2021. Transcriptome and metabolomic analysis to reveal the browning spot formation of 'Huangguan' pear. BMC Plant Biology 21:321

doi: 10.1186/s12870-021-03049-8
[47]

Wang R, Shu P, Zhang C, Zhang J, Chen Y, et al. 2022. Integrative analyses of metabolome and genome-wide transcriptome reveal the regulatory network governing flavor formation in kiwifruit (Actinidia chinensis). New Phytologist 233:373−389

doi: 10.1111/nph.17618
[48]

Wu X, Shi X, Bai M, Chen Y, Li X, et al. 2019. Transcriptomic and gas chromatography–mass spectrometry metabolomic profiling analysis of the epidermis provides insights into cuticular wax regulation in developing 'Yuluxiang' pear fruit. Journal of Agricultural and Food Chemistry 67:8319−8331

doi: 10.1021/acs.jafc.9b01899
[49]

Yan S, Zhao L, Zhao D, Xu G, Wang Y, et al. 2025. Transcriptomic and metabolomic analyses reveal phenolic metabolism regulated by melatonin in pear peel. Chemical and Biological Technologies in Agriculture 12:45

doi: 10.1186/s40538-025-00763-5
[50]

Zheng P, Zhang M, Fang X, Tang L, Wang Z, et al. 2022. Analysis of the fruit quality of pear (Pyrus spp.) using widely targeted metabolomics. Foods 11:1440

doi: 10.3390/foods11101440
[51]

Jiang F, Wang Y, Li J, Yu Q, Li Q, et al. 2025. Transcriptome and metabolome analyses of 'Bartlett' and 'Xiang Shuomi' pears (Pyrus communis L.) unveil the candidate pathways and genes regulating leaf and fruit size. Horticulturae 11:215

doi: 10.3390/horticulturae11020215
[52]

Klupczyńska EA, Pawłowski TA. 2021. Regulation of seed dormancy and germination mechanisms in a changing environment. International Journal of Molecular Sciences 22:1357

doi: 10.3390/ijms22031357
[53]

Miao C, Wang Z, Zhang L, Yao J, Hua K, et al. 2019. The grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice. Nature Communications 10:3822

doi: 10.1038/s41467-019-11830-5
[54]

Chung PJ, Park BS, Wang H, Liu J, Jang IC, et al. 2016. Light-inducible MiR163 targets PXMT1 transcripts to promote seed germination and primary root elongation in Arabidopsis. Plant Physiology 170:1772−1782

doi: 10.1104/pp.15.01188
[55]

Ortega-Galisteo AP, Morales-Ruiz T, Ariza RR, Roldán-Arjona T. 2008. Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Molecular Biology 67:671−681

doi: 10.1007/s11103-008-9346-0
[56]

Liu PP, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, et al. 2007. Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. The Plant Journal 52:133−146

doi: 10.1111/j.1365-313X.2007.03218.x
[57]

Achard P, Herr A, Baulcombe DC, Harberd NP. 2004. Modulation of floral development by a gibberellin-regulated microRNA. Development 131:3357−3365

doi: 10.1242/dev.01206
[58]

Martin RC, Liu PP, Goloviznina NA, Nonogaki H. 2010. microRNA, seeds, and Darwin?: diverse function of miRNA in seed biology and plant responses to stress. Journal of Experimental Botany 61:2229−2234

doi: 10.1093/jxb/erq063
[59]

Yuan H, Liu S, Yan R, Liu Z, Xu K, et al. 2025. AtR8 lncRNA integrates WRKY46 into ABA signaling to regulate seed and seeding growth in Arabidopsis. Plant Physiology and Biochemistry 223:109732

doi: 10.1016/j.plaphy.2025.109732
[60]

Wu J, Liu C, Liu Z, Li S, Li D, et al. 2019. Pol III-dependent cabbage BoNR8 long ncRNA affects seed germination and growth in Arabidopsis. Plant and Cell Physiology 60:421−435

doi: 10.1093/pcp/pcy220