Abdel-Ghany, S.E. and Pilon, M. (2008) MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. Journal of Biology Chemistry. 283, 15932–15945.
Acheampong, A.k., Zheng, C., Halaly, T., Giacomelli, L., Takebayashi, Y., Jikumaru, Y., Kamiya, Y., Lichter, A. and Or, E. (2017) Abnormal endogenous repression of GA signaling in a seedless table grape cultivar with high berry growth response to GA application. Frontiers in Plant Science 8.
Bai, B., Shi, B., Hou, N., Cao, Y., Meng, Y., Bian, H., Zhu, M. and Han, N. (2017) microRNAs participate in gene expression regulation and phytohormone cross-talk in barley embryo during seed development and germination. BMC Plant Biology 17, 150.
Bi, F., Meng, X., Ma, C. and Yi, G. (2015) Identification of miRNAs involved in fruit ripening in Cavendish bananas by deep sequencing. BMC Genomics 16, 776.
Callahan, A.M., Dardick, C. and Scorza, R. (2009) Characterization of ‘Stoneless’: A naturally occurring, partially stoneless plum cultivar. Journal of the American Society for Horticultural Science 134, 120–125.
Carra, A., Mica, E., Gambino, G., Pindo, M., Moser, C. and Schubert, A.P. (2009) Cloning andcharacterization of small non-coding RNAs from grape. The Plant Journal 59, 750–763.
Chen Yh, Cao Yy, Zou Mx. Involvement of AtGGS1 in GA and Glucose Signaling by Modulating GNL Expression J. Plant Biol. (2014) 57:186-197
Crisosto, C.H. and Day, K.R. (2012) Stone fruit. UK: Debbie Rees, Graham Farrell, John Orchard, 212.
Curaba, J., Spriggs, A., Taylor, J., Li, Z. and Helliwell, C. (2012) miRNA regulation in the early development of barley seed. BMC Plant Biology 12, 120.
Dardick, C.D., Callahan, A.M., Chiozzotto, R., Chiozzotto, R., Schaffer, R.J., Piagnani, M.C. and Scorza, R. (2010) Stone formation in peach fruit exhibits spatial coordination of the lignin and flavonoid pathways and similarity to Arabidopsis dehiscence. BMC Biology 8, 1–17.
Din, M. and Barozai, M.Y.K. (2014) Profiling and characterization of eggplant (Solanum melongena L.) microRNAs and their targets. Molecular Biology Reports 41, 889–894.
Gallusci, P., Hodgman, C., Teyssier, E. and Seymour, G.B. (2016) DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening. Frontiers in Plant Science 29.
Ge, A., Shangguan, L., Zhang, X., Dong, Q., Han, J., Liu, H., Wang, X. and Fang, J. (2013) Deep sequencing discovery of novel and conserved microRNAs in strawberry (Fragaria × ananassa). Physiologia Plantarum 148, 387–396.
Gonzalez-Ibeas, D., Blanca, J., Donaire, L., Saladié, M., Mascarell-Creus, A., Cano-Delgado, A.，Garcia-Mas, J., Llave, C. and Aranda, M.A. (2011) Analysis of the melon (Cucumismelo) small RNAome by high-throughput pyrosequencing. BMC Genomics 12, 393.
Han, J., Fang, J., Wang, C., Yin, Y., Sun, X., Leng, X. and Song, C. (2014) Grapevine microRNAs responsive to exogenous gibberellin. BMC Genomics 15, 111.
Henderson, I.R., Zhang, X., Lu, C., Johnson, L., Meyers, B.C., Green, P.J. and Jacobson, S.E. (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nature Genetics 38, 721–725.
Jagadeeswaran, G., Zheng, Y., Sumathipala, N., Jiang, H., Arrese, E.L., Soulages, J.L., Zhang, W. and Sunkar, R. (2010) Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 11, 52.
Joldersma D and Liu ZC, The making of virgin fruit: the molecular and genetic basis of parthenocarpy. Journal of Experimental Botany, 69(5): 955–962, 2018
Karlova, R., Haarst, J.C.V., Maliepaard, C., Geest, H.V.D., Bovy, A.G., Lammers, M., Angenent, G.C. and Maagd, R.A.D. (2013) Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. Journal of Experimental Botany 64, 1863–1878.
Kritzinger, I., Lӧtze, E. and Jooste, M. (2017) Stone hardening and broken stones in Japanese plums (Prunus salicina Lindl.) evaluated by means of computed tomography scans. Scientia Horticulturae 221:1–9.
Li, H., Yang, Y., Wang, Z., Guo, X., Liu, F., Jiang, J. and Liu, G. (2016) BpMADS12 gene role in lignin biosynthesis of Betulaplatyphylla Suk by transcriptome analysis. Journal of Forestry Research 27, 1111–1120.
Liu, Q. and Chen, Y. (2009) Insights into the mechanism of plant development: Interactions of miRNAs pathway with phytohormone response. Biochemical and Biophysical Research Communications 384, 1–5.
Lu, S., Li, Q., Wei, H., Chang, M., Tunlaya-Anukit, S., Kim, H., Liu, J., Song, J., Sun, Y., Yuan, L., Yeh, T., Peszlen, I., Ralph, J., Sederoff, R. and Chiang, V. (2013) Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa. Proceedings of the National Academy of Sciences of the United States of America 110, 10848–10853.
Mica, E., Piccolo, V., Delledonne, M., Ferrarini, A., Pezzotti, M., Casati, C., Fabbro, C.D., Valle, G., Policriti, A., Morgante, M., Pesole, G., Enrico, P.M. and Horner, D.S. (2009) High-throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitisvinifera. BMC Genomics 11, 109.
Moxon, S., Jing, R., Szittya, G., Schwach, F., Rusholme Pilcher, R.L., Moulton, V. and Dalmay, T. (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Research 18, 1602–1609.
Moxon S, Schwach F, Dalmay T, MacLean D, Studholme D, Moulton V. A toolkit for analysing large-scale plant small RNA datasets. 2008, 24 (19): 2252–2253.
Nashima, K., Shimizu, T., Nishitani, C., Yamamoto, T., Takahashi, H., Nakazono, M., Itai, A., jiIsuzugawa, K., Hanada, T., Takashina, T., Matsumoto, S., Otagaki, S., Oikawa, A. and Shiratake, K. (2013) Microarray analysis of gene expression patterns during fruit development in European pear (Pyruscommunis). Scientia Horticulturae 164, 466–473.
Pantaleo, V., Szittya, G., Moxon, S., Miozzi, L., Moulton, V., Dalmay, T. and Burgyan, J. (2010) Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. The Plant Journal 62, 960–976.
Pilcher, R.L.R., Moxon, S., Pakseresht, N., Moulton, V., Manning, K., Seymour, G. and Dalmay, T. (2007) Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta 226, 709–717.
Ren, G., Wang, B., Zhu, X., Mu, Q., Wang, C., Tao, R. and Fang, J. (2014) Cloning, expression, and characterization of miR058 and its target PPO during the development of grapevine berry stone. Gene 548, 166–173.
Reuscher, S., Fukao, Y., Morimoto, R., Otagaki, S., Oikawa, A., Isuzugawa, K. and Shiratake, K. (2016) Quantitative Proteomics-Based Reconstruction and Identification of Metabolic Pathways and Membrane Transport Proteins Related to Sugar Accumulation in Developing Fruits of Pear (Pyrus communis). Plant and Cell Physiology 57, 505–518.
Ripoll, J.J., Bailey, L.J., Mai, Q.A., Wu, S.L., Hon. C.T., Chapman, E.J., Ditta, G.S., Estelle, M. and Yanofsky, M.F. (2015) MicroRNA regulation of fruit growth. Nature Plants 1, 15036.
Santos-Mendoza, M., Dubreucq, B., Baud, S., Parcy, F., Caboche, M. and Lepiniec, L. (2008) Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. The Plant Journal 54, 608–620.
Serrano, A., Espinoza, C., Armijo, G., Inostroza-Blancheteau, C., Problete, E., Meyer-Regueiro, C., Arce, A., Parada, F., Santibáñez, C. and Arce-Johnson, P. (2017) Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Response. Frontiers in Plant Science.;8.
Silva, E.M.D., Silva, G.F.F.E., Bidoia, D.B., Azevedo, M.D.S., Jesus, F.A.D., Pino, L.E., Peres, L.E.P., Carrera, E., López-Díaz, I. and Nogueira, F.T.S. (2017) MicroRNA159-targeted SlGAMYB transcription factors are required for fruit set in tomato. The Plant Journal 92, 95–109.
Song, C., Fang, J., Li, X., Liu, H. and Chao, T. (2009) Identification and characterization of 27 conserved microRNAs in citrus. Planta 230, 671–685.
Sun, X., Korir, N.K., Han, J., Shangguan, L., Kayesh, E., Leng, X. and Fang, J. (2012) Characterization of grapevine microR164 and its target genes. Molecular Biology Reports 39, 9463–9472.
Tang, W., Wang, J., Zhang, W., Cui, M., Zhu, X., Zhang, C. and Fang, J. (2018) The role of Lignin in Kernel degradation of fruit trees. Molecular plant breeding 16, 3752–3762.
Wang, C., Han, J., Liu, C., Kibet, K.N., Kayesh, E., Shangguan, L., Li, X. and Fang, J. (2012) Identification of microRNAs from Amur grape (VitisamurensisRupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. BMC Genomics 13, 122.
Wang, C., Han, J., Nicholas, K.K., Wang, X., Liu, H., Li, X., Leng, X. and Fang, J. (2013) The characterization of target mRNAs for table grapevines miRNAs with an integrated strategy of modified RLM RACE, PPM RACE and qRT-PCRs of cleavage products. Journal of Plant Physiology 170, 943–957.
Wang, C., Jogaiah, S., Zhang, W., Abdelrahman, M. and Fang, J. (2018) Spatio-temporal expression of miRNA159 family members and their GAMYB target gene during the modulation of gibberellin-induced grapevine parthenocarpy. Journal of Experimental Botany 69, 3639–3650.
Wang, C., Leng, X., Zhang, Y., Kayesh, E., Zhang, Y., Sun, X. and Fang, J. (2014) Transcriptome-wide analysis of dynamic variations in regulation modes of grapevine microRNAs on their target genes during grapevine development. Plant Molecular Biology 84, 269–285.
Wang, C., Shangguan, L., Kibet, K.N., Wang, X., Han, J., Song, C. and Fang, J. (2011a) Characterization of microRNAs identified in a table grapevine cultivar with validation of computationally predicted grapevine miRNAs by miR-RACE. PLOS ONE 6, e21259.
Wang, C., Wang, X., Kibet, N.K., Song, C., Zhang, C., Li, X., Han, J. and Fang, J. (2011b). Deep sequencing of grapevine flower and berry short RNA library for discovery of novel microRNAs and validation of precise sequences of grapevine microRNAs deposited in miRBase. Physiologia Plantarum 143, 64–81.
Wang, M., Sun, X., Wang, C., Cui, L., Chen, L., Zhang, C., Shangguan, L. and Fang, J. (2017) Characterization of miR061 and its target genes in grapevine responding to exogenous gibberellic acid. Functional & Integrative Genomics 17, 537–549.
Wang, W., Wang, C., Xie, Z., Jia, H., Tang, W., Cui, M. and Fang, J. (2018) Function analysis of VvmiR397a and its target genes VvLACs in grape berry development. Acta Horticulturae Sinica 45, 1441–1455.
Wu, J., Wang, D., Liu, Y., Wang, L., Qiao, X. and Zhang, S. (2014) Identification of miRNAs involved in pear fruit development and quality. BMC Genomics 15, 953.
Wu, M., Tian, Q. and Reed, J.W. (2006) Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133, 4211–4218.
Xia, R., Zhu, H., An, Y., Beers, E.P. and Liu, Z. (2012) Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biology 13, R47.
Xu, J., Xu, H., Xu, Q. and Deng, X. (2015) Characterization of DNA methylation variations during fruit development and ripening of sweet orange. Plant Molecular Biology Reporter 33, 1–11.
Xu, Q., Liu, Y., Zhu, A., Wu, X., Ye, J., Yu, K., Guo, W. and Deng, X. (2010) Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type. BMC Genomics 11, 246.
Xu, X., Yin, L., Ying, Q., Song, H., Xue, D., Lai, T., Xu, M., Shen, B. and Wang, H. (2013) High-throughput sequencing and degradome analysis identify miRNAs and their targets involved in fruit senescence of Fragariaananassa. PLOS ONE 8, e70959.
Xue, C., Yao, J., Qin, M., Zhang, M., Allan, A.C., Wang, D. and Wu, J. (2018) PbrmiR397a regulates lignification during stone cell development in pear fruit. Plant Biotechnology Journa l17, 103–117.
Xue, H., Cao, S., Li, H., Zhang, J., Niu, J., Chen, L., Zhang, F. and Zhao, D. (2017) De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punicagranatum L.). PLOS ONE 12, e0178809.
Yamasaki, H., Hayashi, M., Fukazawa, M., Kobayashi, Y. and Shikanai, T. (2009) SQUAMOSA promoter binding protein-Like7 is a central regulator for copper homeostasis in Arabidopsis. The Plant Cell 21, 347–361.
Zeng, S., Liu, Y., Pan, L., Hayward, A. and Wang, Y. (2015) Identification and characterization of miRNAs in ripening fruit of Lyciumbarbarum L. using high-throughput sequencing. Frontiers in Plant Science 6.
Zhang, H.，Jin, J.，Tang, L.，Zhao, Y.，Gu, X.，Gao, G. and Luo, J. (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Research 39, 1114–1117.
Zhang, W., Abdelrahman, M., Jiu, S., Guan, L., Han, J., Zheng, T., Jia, H., Song, C., Fang, J. and Wang, C. (2019) VvmiR160s/VvARFs interaction and their spatio-temporal expression/cleavage products during GA-induced grape parthenocarpy. BMC Plant Biology. 19:111.