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Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

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Abstract

Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

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Abbreviations

SSH:

Suppression subtractive hybridization

AFLP-PCR:

Amplified fragment length polymorphism PCR

DDRT-PCR or DD-PCR:

Differential display PCR

MAGE:

Microarray and gene expression

CTAB:

Cetyltrimethylammonium bromide

SDS:

Sodium dodecyl sulfate

NGS:

Next-generation sequencing

HGP:

Human genome project

References

  1. Ahmad, P., Ashraf, M., Younis, M., Hu, X., Kumar, A., Akram, N. A., & Al-Qurainy, F. (2012). Role of transgenic plants in agriculture and biopharming. Biotechnology Advances, 30, 524–540.

    Article  CAS  Google Scholar 

  2. Ashraf, M., & Akram, N. A. (2009). Improving salinity tolerance of plants through conventional breeding and genetic engineering: An analytical comparison. Biotechnology Advances, 27, 744–752.

    Article  CAS  Google Scholar 

  3. Sun, S. S. (2008). Application of agricultural biotechnology to improve food nutrition and healthcare products. Asia Pacific Journal of Clinical Nutrition, 17, 87–90.

    Google Scholar 

  4. Zimmermann, M. B., & Hurrell, R. F. (2002). Improving iron, zinc and vitamin A nutrition through plant biotechnology. Current Opinion in Biotechnology, 13, 142–145.

    Article  CAS  Google Scholar 

  5. Gasser, C. S., & Fraley, R. T. (1989). Genetically engineering plants for crop improvement. Science, 244, 1293–1299.

    Article  CAS  Google Scholar 

  6. Munis, M., Tu, L., Deng, F., Tan, J., Xu, L., Xu, S., et al. (2010). A thaumatin-like protein gene involved in cotton fiber secondary cell wall development enhances resistance against Verticillium dahliae and other stresses in transgenic tobacco. BBRC, 393, 38–44.

    CAS  Google Scholar 

  7. Ni, X., Tian, Z., Liu, J., Song, B., Li, J., Shi, X., & Xie, C. (2010). StPUB17, a novel potato UND/PUB/ARM repeat type gene, is associated with late blight resistance and NaCl stress. Plant Science, 178, 158–169.

    Article  CAS  Google Scholar 

  8. James, C. (2010). Global status of commercialized biotech/GM crops: 2010, International Service for the acquisition of agri-biotech applications (ISAAA) Ithaca, NY, USA.

  9. Rebrikov, D. V., Desai, S. M., Siebert, P. D., & Lukyanov, S. A. (2004). Suppression subtractive hybridization. Gene expression profiling (pp. 107–134). Berlin: Springer.

    Chapter  Google Scholar 

  10. Lukyanov, S. A., Rebrikov, D., & Buzdin, A. A. (2007). Suppression subtractive hybridization. Nucleic Acids Hybridization Modern Applications (pp. 53–84). Berlin: Springer.

    Chapter  Google Scholar 

  11. Adam, N. M., Sorooshian, S., Zhang, X., Tezara, C., Azizi, P., Sahebi, M., Bande, Y., Nurhaiza, S. & Kaiser, A. (2012). Engineering research methods, in comparison of supression subtractive hybridization with other methods used to identify differentially expressed genes in plants. In N. M. Adam and S. Sorooshian (Eds.), Lulu. com: Serdang, Malaysia, pp. 15–24.

  12. Sahebi, M., Hanafi, M. M., Abdullah, S. N. A., Rafii, M. Y., Azizi, P., Nejat, N., & Idris, A. S. (2014). Isolation and expression analysis of novel silicon absorption gene from roots of mangrove (Rhizophora apiculata) via suppression subtractive hybridization. BioMed Research International, 2014, 971985. doi:10.1155/2014/971985.

  13. Hutchison, C. A. (2007). DNA sequencing: Bench to bedside and beyond. NAR, 35, 6227–6237.

    Article  CAS  Google Scholar 

  14. Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74, 5463–5467.

    Article  CAS  Google Scholar 

  15. Venter, J. C., Levy, S., Stockwell, T., Remington, K., & Halpern, A. (2003). Massive parallelism, randomness and genomic advances. Nature Genetics, 33, 219–227.

    Article  CAS  Google Scholar 

  16. Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., Rosenbaum, A. M., et al. (2005). Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728–1732.

    Article  CAS  Google Scholar 

  17. Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376–380.

    CAS  Google Scholar 

  18. Novelli, G., Predazzi, I. M., Mango, R., Romeo, F., & Mehta, J. L. (2010). Role of genomics in cardiovascular medicine. World Journal of Cardiology, 2, 428.

    Article  Google Scholar 

  19. Fuller, C. W., Middendorf, L. R., Benner, S. A., Church, G. M., Harris, T., Huang, X., et al. (2009). The challenges of sequencing by synthesis. Nature Biotechnology, 27, 1013–1023.

    Article  CAS  Google Scholar 

  20. Schuster, S. C. (2007). Next-generation sequencing transforms today’s biology. Nature, 200, 16–18.

    Google Scholar 

  21. Shendure, J., & Ji, H. (2008). Next-generation DNA sequencing. Nature Biotechnology, 26, 1135–1145.

    Article  CAS  Google Scholar 

  22. Ng, P. C., Murray, S. S., Levy, S., & Venter, J. C. (2009). An agenda for personalized medicine. Nature, 461, 724–726.

    Article  CAS  Google Scholar 

  23. Metzker, M. L. (2009). Sequencing technologies—the next generation. Nature Reviews Genetics, 11, 31–46.

    Article  CAS  Google Scholar 

  24. Tucker, T., Marra, M., & Friedman, J. M. (2009). Massively parallel sequencing: The next big thing in genetic medicine. American Journal of Human Genetics, 85, 142–154.

    Article  CAS  Google Scholar 

  25. Wink, M. (2006). An introduction to molecular biotechnology: Molecular fundamentals methods and application in modem biotechnology. Weinheim, Germany: Wiley.

    Google Scholar 

  26. Doyle, K. (1996). The source of discovery: Protocols and applications guide. Madison, Wis, USA: Promega.

    Google Scholar 

  27. Buckingham, L. (2011). Molecular diagnostics: Fundamentals, methods and clinical applications. Philadelphia, PA, USA: FA Davis.

    Google Scholar 

  28. Cseke, L. J., Kirakosyan, A., Kaufman, P. B., & Westfall, M. V. (2011). Handbook of molecular and cellular methods in biology and medicine. USA: CRC Press.

    Google Scholar 

  29. Birtić, S., & Kranner, I. (2006). Isolation of high-quality RNA from polyphenol-, polysaccharide- and lipid-rich seeds. Phytochemical Analysis, 17, 144–148.

    Article  CAS  Google Scholar 

  30. Islas-Flores, I., Peraza-Echeverría, L., Canto-Canché, B., & Rodríguez-García, C. M. (2006). Extraction of high-quality, melanin-free RNA from Mycosphaerella fijiensis for cDNA preparation. Molecular Biotechnology, 34, 45–50.

    Article  CAS  Google Scholar 

  31. Portillo, M., Fenoll, C., & Escobar, C. (2006). Evaluation of different RNA extraction methods for small quantities of plant tissue: Combined effects of reagent type and homogenization procedure on RNA quality-integrity and yield. Physiologia Plantarum, 128, 1–7.

    Article  CAS  Google Scholar 

  32. Fleige, S., & Pfaffl, M. W. (2006). RNA integrity and the effect on the real-time qRT-PCR performance. Molecular Aspects of Medicine, 27, 126–139.

    Article  CAS  Google Scholar 

  33. Brooks, G. (1998). Biotechnology in Healthcare: An Introduction to Biopharmaceuticals. London, UK: Pharmaceutical Press.

    Google Scholar 

  34. Claros, M. G., & Cánovas, F. M. (1998). Rapid high quality RNA preparation from pine seedlings. Plant Molecular Biology Reporter, 16, 9–18.

    Article  CAS  Google Scholar 

  35. De Keukeleire, J., Roldán-Ruiz, I., Van Bockstaele, E., Heyerick, A., & De Keukeleire, D. (2006). Efficient extraction of high-quality total RNA from various hop tissues (Humulus lupulus L.). Preparative Biochemistry & Biotechnology, 36, 355–362.

    Article  CAS  Google Scholar 

  36. Li, J.-H., Tang, C.-H., Song, C.-Y., Chen, M.-J., Feng, Z.-Y., & Pan, Y.-J. (2006). A simple, rapid and effective method for total RNA extraction from Lentinula edodes. Biotechnology Letters, 28, 1193–1197.

    Article  CAS  Google Scholar 

  37. Manickavelu, A., Kambara, K., Mishina, K., & Koba, T. (2007). An efficient method for purifying high quality RNA from wheat pistils. Colloids and Surfaces B: Biointerfaces, 54, 254–258.

    Article  CAS  Google Scholar 

  38. John, M. E. (1992). An efficient method for isolation of RNA and DNA from plants containing polyphenolics. NAR, 20, 2381.

    Article  CAS  Google Scholar 

  39. Meisel, L., Fonseca, B., González, S., Baeza-Yates, R., Cambiazo, V., Campos, R., et al. (2005). A rapid and efficient method for purifying high quality total RNA from peaches (Prunus persica) for functional genomics analyses. Biological Research, 38, 83–88.

    Article  CAS  Google Scholar 

  40. Kim, S.-H., & Hamada, T. (2005). Rapid and reliable method of extracting DNA and RNA from sweetpotato, Ipomoea batatas (L.) Lam. Biotechnology Letters, 27, 1841–1845.

    Article  CAS  Google Scholar 

  41. Wang, S., Hunter, W., & Plant, A. (2000). Isolation and purification of functional total RNA from woody branches and needles of Sitka and white spruce. BioTechniques, 28, 292–296.

    CAS  Google Scholar 

  42. Salzman, R., Fujita, T., Zhu-Salzman, K., Hasegawa, P., & Bressan, R. (1999). An improved RNA isolation method for plant tissues containing high levels of phenolic compounds or carbohydrates. Plant Molecular Biology Reporter, 17, 11–17.

    Article  CAS  Google Scholar 

  43. Vareli, K., & Frangou-Lazaridis, M. (1996). Modification of the acid guanidinium thiocyanate-phenol-chloroform method for nuclear RNA isolation. BioTechniques, 21, 236.

    CAS  Google Scholar 

  44. Wan, C.-Y., & Wilkins, T. A. (1994). A Modified Hot Borate Method Significantly Enhances the Yield of High-Quality RNA from Cotton (Gossypium hirsutum L.). Analytical Biochemistry, 223, 7–12.

    Article  CAS  Google Scholar 

  45. Yao, Y., Zhao, L., Hao, Y., & Zhai, H. (2005). A modified hot borate method significantly enhances the yield of high-quality RNA from apple pulp. International Journal of Fruit Science, 22, 737–740.

    CAS  Google Scholar 

  46. Chang, S., Puryear, J., & Cairney, J. (1993). A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter, 11, 113–116.

    Article  CAS  Google Scholar 

  47. Hu, C. G., Honda, C., Kita, M., Zhang, Z., Tsuda, T., & Moriguchi, T. (2002). A simple protocol for RNA isolation from fruit trees containing high levels of polysaccharides and polyphenol compounds. Plant Molecular Biology Reporter, 20, 69a–69g.

    Article  Google Scholar 

  48. Jaakola, L., Pirttilä, A. M., Halonen, M., & Hohtola, A. (2001). Isolation of high quality RNA from bilberry (Vaccinium myrtillus L.) fruit. Molecular Biotechnology, 19, 201–203.

    Article  CAS  Google Scholar 

  49. Zeng, Y., & Yang, T. (2002). RNA isolation from highly viscous samples rich in polyphenols and polysaccharides. Plant Molecular Biology Reporter, 20, 417.

    Article  Google Scholar 

  50. Zhang, Y., Hao, X., Liang, Z., Ke, W., & Guo, H. (2013). Efficient isolation of high-quality RNA from lotus Nelumbo nucifera ssp nucifera tissues. Genetics and Molecular Research, 12, 223–229.

    Article  CAS  Google Scholar 

  51. Tong, Z., Qu, S., Zhang, J., Wang, F., Tao, J., Gao, Z., & Zhang, Z. (2012). A modified protocol for RNA extraction from different peach tissues suitable for gene isolation and real-time PCR analysis. Molecular Biotechnology, 50, 229–236.

    Article  CAS  Google Scholar 

  52. Sahebi, M., Hanafi, M. M., Abdullah, S. N. A., Nejat, N., Rafii, M. Y., & Azizi, P. (2013). Extraction of total RNA from mangrove plants to identify different genes involved in its adaptability to the variety of stresses. Pakistan Journal of Agricultural Science, 50, 1–9.

    Google Scholar 

  53. Ghawana, S., Paul, A., Kumar, H., Kumar, A., Singh, H., Bhardwaj, P. K., et al. (2011). An RNA isolation system for plant tissues rich in secondary metabolites. BMC Research Notes, 4, 85.

    Article  CAS  Google Scholar 

  54. Schneiderbauer, A., Sandermann, H., Jr, & Ernst, D. (1991). Isolation of functional RNA from plant tissues rich in phenolic compounds. Analytical Biochemistry, 197, 91–95.

    Article  CAS  Google Scholar 

  55. Smárason, S. V., & Smith, A. V. (2005). Method for desalting nucleic acids. United State patent US, 6(897), 027.

    Google Scholar 

  56. Green, M. R., & Sambrook, J. (2012). Molecular cloning: A laboratory manual. New York, NY, USA: Cold Spring Harbor Laboratory Press.

    Google Scholar 

  57. Chomczynski, P., & Sacchi, N. (2006). The single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction: Twenty-something years on. Nature Protocols, 1, 581–585.

    Article  CAS  Google Scholar 

  58. Johnson, M. T., Carpenter, E. J., Tian, Z., Bruskiewich, R., Burris, J. N., Carrigan, C. T., et al. (2012). Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS ONE, 7, e50226.

    Article  CAS  Google Scholar 

  59. Sambrook, J., & Russell, D. W. (2001). Molecular cloning: A laboratory manual. New York, NY, USA: Cold Spring Harbor Laboratory Press.

    Google Scholar 

  60. Martel, F., Grundemann, D., & Schomig, E. (2002). A simple method for elimination of false positive results in RT-PCR. Journal of Biochemistry and Molecular Biology, 35, 248–250.

    Article  CAS  Google Scholar 

  61. Oñate-Sánchez, L., & Vicente-Carbajosa, J. (2008). DNA-free RNA isolation protocols for Arabidopsis thaliana, including seeds and siliques. BMC Research Notes, 1, 93.

    Article  CAS  Google Scholar 

  62. Sambrook, J., & Russell, D. W. (2001). Molecular cloning: A laboratory manual (3-volume set). New York: Cold spring harbor laboratory press Cold Spring Harbor.

    Google Scholar 

  63. Lukyanov, S., Rebrikov, D., & Buzdin, A. (2007). Suppression subtractive hybridization. In A. A. Buzdin & S. A. Lukyanov (Eds.), Nucleic acids hybridization modern applications (pp. 53–84). Russian Academy of Sciences: Moscow.

    Chapter  Google Scholar 

  64. Gurskaya, N. G., Diatchenko, L., Chenchik, A., Siebert, P. D., Khaspekov, G. L., Lukyanov, K. A., et al. (1996). Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: Cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. Analytical Biochemistry, 240, 90–97.

    Article  CAS  Google Scholar 

  65. Diatchenko, L., Lau, Y. F., Campbell, A. P., Chenchik, A., Moqadam, F., Huang, B., et al. (1996). Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proceedings of the National Academy of Sciences, 93, 6025–6030.

    Article  CAS  Google Scholar 

  66. Rebrikov, D. V., Desai, S. M., Siebert, P. D., & Lukyanov, S. A. (2004). Suppression subtractive hybridization. Methods of Molecular Biology, 258, 107–134.

    CAS  Google Scholar 

  67. Zhang, W.-W., Jian, G.-L., Jiang, T.-F., Wang, S.-Z., Qi, F.-J., & Xu, S.-C. (2012). Cotton gene expression profiles in resistant Gossypium hirsutum cv. Zhongzhimian KV1 responding to Verticillium dahliae strain V991 infection. Molecular Biology Reports, 39, 9765–9774.

    Article  CAS  Google Scholar 

  68. Durrant, W. E., Rowland, O., Piedras, P., Hammond-Kosack, K. E., & Jones, J. D. G. (2000). cDNA-AFLP reveals a striking overlap in race-specific resistance and wound response gene expression profiles. Plant Cell, 12, 963–977.

    Article  CAS  Google Scholar 

  69. Qin, L., Overmars, H., Helder, J., Popeijus, H., van der Voort, J. R., Groenink, W., et al. (2000). An efficient cDNA-AFLP-based strategy for the identification of putative pathogenicity factors from the potato cyst nematode Globodera rostochiensis. Molecular Plant-Microbe Interactions, 13, 830–836.

    Article  CAS  Google Scholar 

  70. Sutcliffe, J. G., Foye, P. E., Erlander, M. G., Hilbush, B. S., Bodzin, L. J., Durham, J. T., & Hasel, K. W. (2000). TOGA: An automated parsing technology for analyzing expression of nearly all genes. Proceedings of the National Academy of Sciences, 97, 1976–1981.

    Article  CAS  Google Scholar 

  71. Kornmann, B., Preitner, N., Rifat, D., Fleury-Olela, F., & Schibler, U. (2001). Analysis of circadian liver gene expression by ADDER, a highly sensitive method for the display of differentially expressed mRNAs. Nucleic Acids Research, 29, 51.

    Article  Google Scholar 

  72. Breyne, P., Dreesen, R., Cannoot, B., Rombaut, D., Vandepoele, K., Rombauts, S., et al. (2003). Quantitative cDNA-AFLP analysis for genome-wide expression studies. Molecular Genetics and Genomics, 269, 173–179.

    CAS  Google Scholar 

  73. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van de Lee, T., Hornes, M., et al. (1995). AFLP: A new technique for DNA fingerprinting. NAR, 23, 4407–4414.

    Article  CAS  Google Scholar 

  74. Mueller, U. G., & Wolfenbarger, L. L. (1999). AFLP genotyping and fingerprinting. Trends in Ecology & Evolution, 14, 389–394.

    Article  Google Scholar 

  75. Meudt, H. M., & Clarke, A. C. (2007). Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends in Plant Science, 12, 106–117.

    Article  CAS  Google Scholar 

  76. Bin, W., & Manli, W. (1996). The principle and application of AFLP. Hybrid Rice, 05.

  77. Huber, W., Heydebreck, A. V., & Vingron, M. (2003). Analysis of microarray gene expression data. In Handbook of statistical genetics (2nd ed.). Wiley.

  78. Schena, M., Shalon, D., Davis, R. W., & Brown, P. O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467–470.

    Article  CAS  Google Scholar 

  79. Ball, C. A., Sherlock, G., Parkinson, H., Rocca-Sera, P., Brooksbank, C., Causton, H. C., et al. (2002). Standards for microarray data. Science (New York, NY), 298, 539.

    Article  CAS  Google Scholar 

  80. Frank, R. (2002). The SPOT-synthesis technique: Synthetic peptide arrays on membrane supports—principles and applications. Journal of Immunological Methods, 267, 13–26.

    Article  CAS  Google Scholar 

  81. Liang, P., & Pardee, A. (1993). Distribution and cloning of eukaryotic mRNAs by means of differential display: Refinements and optimization. Nucleic Acids Research, 21, 3269–3275.

    Article  CAS  Google Scholar 

  82. Sturtevant, J. (2000). Applications of differential-display reverse transcription-PCR to molecular pathogenesis and medical mycology. Clinical Microbiology Reviews, 13, 408–427.

    Article  CAS  Google Scholar 

  83. Hood, L. (2002). A personal view of molecular technology and how it has changed biology. Journal of Proteome Research, 1, 399–409.

    Article  CAS  Google Scholar 

  84. Thompson, O., Edgley, M., Strasbourger, P., Flibotte, S., Ewing, B., Adair, R., et al. (2013). The million mutation project: A new approach to genetics in Caenorhabditis elegans. Genome Research, 23, 1749–1762.

    Article  CAS  Google Scholar 

  85. Cole, M. F., & Gaucher, E. A. (2011). Exploiting models of molecular evolution to efficiently direct protein engineering. Journal of Molecular Evolution, 72, 193–203.

    Article  CAS  Google Scholar 

  86. Smith, L. M., Sanders, J. Z., Kaiser, R. J., Hughes, P., Dodd, C., Connell, C. R., et al. (1986). Fluorescence detection in automated DNA sequence analysis. Nature, 321, 674–679.

    Article  CAS  Google Scholar 

  87. Prober, J. M., Trainor, G. L., Dam, R. J., Hobbs, F. W., Robertson, C. W., Zagursky, R. J., et al. (1987). A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science, 238, 336–341.

    Article  CAS  Google Scholar 

  88. Ju, J., Li, Z., Tong, A., & Russo, J. J. (2003). Combinatorial fluorescence energy transfer tags and their applications for multiplex genetic analyses. (Google patents).

  89. Hall, N. (2007). Advanced sequencing technologies and their wider impact in microbiology. Journal of Experimental Biology, 210, 1518–1525.

    Article  CAS  Google Scholar 

  90. Tawfik, D. S., & Griffiths, A. D. (1998). Man-made cell-like compartments for molecular evolution. Nature Biotechnology, 16, 652–656.

    Article  CAS  Google Scholar 

  91. Griffiths, A., & Tawfik, D. (2002). In vitro sorting method. (Google patents).

  92. Ahmadian, A., Ehn, M., & Hober, S. (2006). Pyrosequencing: History, biochemistry and future. Clinica Chimica Acta, 363, 83–94.

    Article  CAS  Google Scholar 

  93. Cordero, P., Campion, J., Milagro, F. I., Goyenechea, E., Steemburgo, T., Javierre, B. M., & Martinez, J. A. (2011). Leptin and TNF-alpha promoter methylation levels measured by MSP could predict the response to a low-calorie diet. Journal of Physiology and Biochemistry, 67, 463–470.

    Article  CAS  Google Scholar 

  94. Bentley, D. R. (2006). Whole-genome re-sequencing. Current Opinion in Genetics & Development, 16, 545–552.

    Article  CAS  Google Scholar 

  95. Luo, C., Tsementzi, D., Kyrpides, N. C., & Konstantinidis, K. T. (2012). Individual genome assembly from complex community short-read metagenomic datasets. The ISME Journal, 6, 898–901.

    Article  CAS  Google Scholar 

  96. Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., et al. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505, 43–49.

    Article  CAS  Google Scholar 

  97. Paun, O., Fay, M. F., Soltis, D. E., & Chase, M. W. (2007). Genetic and epigenetic alterations after hybridization and genome doubling. Taxon, 56, 649.

    Article  Google Scholar 

  98. Huang, X., Li, Y., Niu, Q., & Zhang, K. (2007). Suppression Subtractive Hybridization (SSH) and its modifications in microbiological research. Applied Microbiology and Biotechnology, 76, 753–760.

    Article  CAS  Google Scholar 

  99. Pimentel, P., Salvatierra, A., Moya-León, M. A., & Herrera, R. (2010). Isolation of genes differentially expressed during development and ripening of Fragaria chiloensis fruit by suppression subtractive hybridization. Journal of Plant Physiology, 167, 1179–1187.

    Article  CAS  Google Scholar 

  100. Ma, G., Ning, G., Pang, R., Zhan, J., Li, X., Zhang, W., & Bao, M. (2011). Analysis of the Petunia hybrida double flower transcriptome using suppression subtractive hybridization. Scientia Horticulturae, 127, 398–404.

    Article  CAS  Google Scholar 

  101. Li, L., Wang, W.-Q., Wu, C.-X., Han, T.-F., & Hou, W.-S. (2012). Construction of two suppression subtractive hybridization libraries and identification of salt-induced genes in soybean. Journal of Integrative Agriculture, 11, 1075–1085.

    Article  CAS  Google Scholar 

  102. Bae, E.-K., Lee, H., Lee, J.-S., Noh, E.-W., Choi, Y.-I., Lee, B.-H., & Choi, D.-W. (2012). Microarray and suppression subtractive hybridization analyses of gene expression in hybrid poplar (Populus alba × Populus tremula var.glandulosa) cell suspension cultures after exposure to NaCl. Plant Physiology and Biochemistry, 58, 151–158.

    Article  CAS  Google Scholar 

  103. Perdiguero, P., Collada, C., Barbero, M. D. C., García Casado, G., Cervera, M. T., & Soto, Á. (2012). Identification of water stress genes in Pinus pinaster Ait. by controlled progressive stress and suppression-subtractive hybridization. Plant Physiology and Biochemistry, 50, 44–53.

    Article  CAS  Google Scholar 

  104. Liu, Y., Wang, G., Wang, Z., Yang, F., Wu, G., & Hong, N. (2012). Identification of differentially expressed genes in response to infection of a mild Citrus tristeza virus isolate in Citrus aurantifolia by suppression subtractive hybridization. Scientia Horticulturae, 134, 144–149.

    Article  CAS  Google Scholar 

  105. Qi, X., Xu, Q., Shen, L., Alfandi, M., Luo, J., & Chen, X. (2010). Identification of differentially expressed genes between powdery mildew resistant near-isogenic line and susceptible line of cucumber by suppression subtractive hybridization. Scientia Horticulturae, 126, 27–32.

    Article  CAS  Google Scholar 

  106. Shuai, Z., Jing, L., LI-min, L., Chun-yi, W., Jun-yu, L., & Jin-jie, C. (2014). Suppression Subtractive Hybridization Reveals Different Responses of Two Varieties of Gossypium arboreum L. under Apolygus lucorum stress. Journal of Integrative Agriculture, 13, 1250–1257.

    Article  CAS  Google Scholar 

  107. Swarupa, V., Ravishankar, K., & Rekha, A. (2013). Characterization of tolerance to Fusarium oxysporum F. sp., cubense infection in banana using suppression subtractive hybridization and gene expression analysis. Physiological and Molecular Plant Pathology, 83, 1–7.

    Article  CAS  Google Scholar 

  108. Backiyarani, S., Uma, S., Arunkumar, G., Saraswathi, M., & Sundararaju, P. (2014). Differentially expressed genes in incompatible interactions of Pratylenchus coffeae with Musa using suppression subtractive hybridization. Physiological and Molecular Plant Pathology, 86, 11–18.

    Article  CAS  Google Scholar 

  109. Sperotto, R. A., Ricachenevsky, F. K., Duarte, G. L., Boff, T., Lopes, K. L., Sperb, E. R., et al. (2009). Identification of up-regulated genes in flag leaves during rice grain filling and characterization of OsNAC5, a new ABA-dependent transcription factor. Planta, 230, 985–1002.

    Article  CAS  Google Scholar 

  110. Wang, L., Li, H., Wei, H., Wu, X., & Ke, L. (2014). Identification of cadmium-induced Agaricus blazei genes through suppression subtractive hybridization. Food and Chemical Toxicology, 63, 84–90.

    Article  CAS  Google Scholar 

  111. Aguilar-Hernández, H. S., Santos, L., León-Galván, F., Barrera-Pacheco, A., Espitia-Rangel, E., De León-Rodríguez, A., et al. (2011). Identification of calcium stress induced genes in amaranth leaves through suppression subtractive hybridization. Journal of Plant Physiology, 168, 2102–2109.

    Article  CAS  Google Scholar 

  112. Gao, F., Niu, Y.-D., Hao, J.-F., Bade, R., Zhang, L.-Q., & Hasi, A. (2013). Identification of differentially expressed genes during ethylene climacteric of melon fruit by suppression subtractive hybridization. Journal of Integrative Agriculture, 12, 1431–1440.

    Article  Google Scholar 

  113. Padmanabhan, P., & Sahi, S. V. (2011). Suppression subtractive hybridization reveals differential gene expression in sunflower grown in high P. Plant Physiology and Biochemistry, 49, 584–591.

    Article  CAS  Google Scholar 

  114. Kojima, H., Numata, T., Tadaki, R., & Omokawa, H. (2010). PCR-based suppression subtractive hybridization analyses of enantioselective gene expression in root tips of wheat treated with optically active urea compounds. Pesticide Biochemistry and Physiology, 98, 359–369.

    Article  CAS  Google Scholar 

  115. Linkies, A., Schuster-Sherpa, U., Tintelnot, S., Leubner-Metzger, G., & Müller, K. (2010). Peroxidases identified in a subtractive cDNA library approach show tissue-specific transcript abundance and enzyme activity during seed germination of Lepidium sativum. Journal of Experimental Botany, 61, 491–502.

    Article  CAS  Google Scholar 

  116. Agron, P. G., Walker, R. L., Kinde, H., Sawyer, S. J., Hayes, D. C., Wollard, J., & Andersen, G. L. (2001). Identification by subtractive hybridization of sequences specific for Salmonella enterica serovar Enteritidis. Applied and Environment Microbiology, 67, 4984–4991.

    Article  CAS  Google Scholar 

  117. Radnedge, L., Gamez-Chin, S., McCready, P. M., Worsham, P. L., & Andersen, G. L. (2001). Identification of nucleotide sequences for the specific and rapid detection of Yersinia pestis. Applied and Environment Microbiology, 67, 3759–3762.

    Article  CAS  Google Scholar 

  118. Dai, E., Tong, Z., Wang, X., Li, M., Cui, B., Dai, R., et al. (2005). Identification of different regions among strains of Yersinia pestis by suppression subtractive hybridization. Research in Microbiology, 156, 785–789.

    Article  CAS  Google Scholar 

  119. Fukumura, R., Takahashi, H., Saito, T., Tsutsumi, Y., Fujimori, A., Sato, S., et al. (2003). A sensitive transcriptome analysis method that can detect unknown transcripts. NAR, 31, e94.

    Article  CAS  Google Scholar 

  120. Yang, L., Zheng, B., Mao, C., Qi, X., Liu, F., & Wu, P. (2004). Analysis of transcripts that are differentially expressed in three sectors of the rice root system under water deficit. Molecular Genetics and Genomics, 272, 433–442.

    Article  CAS  Google Scholar 

  121. Rodríguez, M., Canales, E., Borroto, C. J., Carmona, E., Lopez, J., Pujol, M., & Borrás-Hidalgo, O. (2006). Identification of genes induced upon water-deficit stress in a drought-tolerant rice cultivar. Journal of Plant Physiology, 163, 577–584.

    Article  CAS  Google Scholar 

  122. Dubos, C., & Plomion, C. (2003). Identification of water-deficit responsive genes in maritime pine (Pinus pinaster Ait.) roots. Plant Molecular Biology, 51, 249–262.

    Article  CAS  Google Scholar 

  123. Jonavičienė, K., Studer, B., Asp, T., Jensen, L. B., Paplauskienė, V., Lazauskas, S., & Brazauskas, G. (2012). Identification of genes involved in a water stress response in timothy and mapping of orthologous loci in perennial ryegrass. Biologia Plantarum, 56, 473–483.

    Article  CAS  Google Scholar 

  124. Campalans, A., Pagès, M., & Messeguer, R. (2001). Identification of differentially expressed genes by the cDNA-AFLP technique during dehydration of almond (Prunus amygdalus). Tree Physiology, 21, 633–643.

    Article  CAS  Google Scholar 

  125. Geuna, F., Banfi, R., & Bassi, D. (2005). Identification and characterization of transcripts differentially expressed during development of apricot (Prunus armeniaca L.) fruit. Tree Genetics and Genomes, 1, 69–78.

    Article  Google Scholar 

  126. Lee, Y.-P., Yu, G.-H., Seo, Y. S., Han, S. E., Choi, Y.-O., Kim, D., et al. (2007). Microarray analysis of apple gene expression engaged in early fruit development. Plant Cell Reports, 26, 917–926.

    Article  CAS  Google Scholar 

  127. Schaffer, R. J., Friel, E. N., Souleyre, E. J., Bolitho, K., Thodey, K., Ledger, S., et al. (2007). A genomics approach reveals that aroma production in apple is controlled by ethylene predominantly at the final step in each biosynthetic pathway. Plant Physiology, 144, 1899–1912.

    Article  CAS  Google Scholar 

  128. Janssen, B. J., Thodey, K., Schaffer, R. J., Alba, R., Balakrishnan, L., Bishop, R., et al. (2008). Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biology, 8, 16.

    Article  CAS  Google Scholar 

  129. Deluc, L., Grimplet, J., Wheatley, M., Tillett, R., Quilici, D., Osborne, C., et al. (2007). Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development. BMC Genomics, 8, 429.

    Article  Google Scholar 

  130. Grimplet, J., Deluc, L. G., Tillett, R. L., Wheatley, M. D., Schlauch, K. A., Cramer, G. R., & Cushman, J. C. (2007). Tissue-specific mRNA expression profiling in grape berry tissues. BMC Genomics, 8, 187.

    Article  CAS  Google Scholar 

  131. Crowhurst, R. N., Gleave, A. P., MacRae, E. A., Ampomah-Dwamena, C., Atkinson, R. G., Beuning, L. L., et al. (2008). Analysis of expressed sequence tags from Actinidia: Applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics, 9, 351.

    Article  CAS  Google Scholar 

  132. Aharoni, A., Keizer, L. C., Van Den Broeck, H. C., Blanco-Portales, R., Muñoz-Blanco, J., Bois, G., et al. (2002). Novel insight into vascular, stress, and auxin-dependent and-independent gene expression programs in strawberry, a non-climacteric fruit. Plant Physiology, 129, 1019–1031.

    Article  CAS  Google Scholar 

  133. Liang, P. (2002). A decade of differential display. BioTechniques, 33, 338–347.

    CAS  Google Scholar 

  134. Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., et al. (2008). The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872–876.

    Article  CAS  Google Scholar 

  135. Moorthie, S., Mattocks, C. J., & Wright, C. F. (2011). Review of massively parallel DNA sequencing technologies. The HUGO Journal, 5, 1–12.

    Article  Google Scholar 

  136. Van Tassell, C. P., Smith, T. P., Matukumalli, L. K., Taylor, J. F., Schnabel, R. D., Lawley, C. T., et al. (2008). SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods, 5, 247–252.

    Article  CAS  Google Scholar 

  137. Zeggini, E. (2011). Next-generation association studies for complex traits. Nature Genetics, 43, 287–288.

    Article  CAS  Google Scholar 

  138. Gudbjartsson, D. F., Helgason, H., Gudjonsson, S. A., Zink, F., Oddson, A., Gylfason, A., et al. (2015). Large-scale whole-genome sequencing of the Icelandic population. Nature Genetics, 47, 435–444.

    Article  CAS  Google Scholar 

  139. Fredriksson, S., Baner, J., Dahl, F., Chu, A., Ji, H., Welch, K., & Davis, R. W. (2007). Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. Nucleic Acids Research, 35, e47.

    Article  CAS  Google Scholar 

  140. Chen, W., Kalscheuer, V., Tzschach, A., Menzel, C., Ullmann, R., Schulz, M. H., et al. (2008). Mapping translocation breakpoints by next-generation sequencing. Genome Research, 18, 1143–1149.

    Article  CAS  Google Scholar 

  141. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., et al. (2010). The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297–1303.

    Article  CAS  Google Scholar 

  142. Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., et al. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder. Science, 318, 283–287.

    Article  CAS  Google Scholar 

  143. Brown, M. J., & Paxton, R. J. (2009). The conservation of bees: A global perspective. Apidologie, 40, 410–416.

    Article  Google Scholar 

  144. Chen, P.-Y., Cokus, S. J., & Pellegrini, M. (2010). BS seeker: Precise mapping for bisulfite sequencing. BMC Bioinformatics, 11, 203.

    Article  CAS  Google Scholar 

  145. Horan, M. P. (2009). Application of serial analysis of gene expression to the study of human genetic disease. Human Genetics, 126, 605–614.

    Article  CAS  Google Scholar 

  146. Christodoulou, D. C., Gorham, J. M., Herman, D. S. & Seidman, J. (2011). Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Current Protocols in Molecular Biology 4.12. 11–14.12. 11.

  147. Sugarbaker, D. J., Richards, W. G., Gordon, G. J., Dong, L., De Rienzo, A., Maulik, G., et al. (2008). Transcriptome sequencing of malignant pleural mesothelioma tumors. Proceedings of the National Academy of Sciences, 105, 3521–3526.

    Article  CAS  Google Scholar 

  148. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5, 621–628.

    Article  CAS  Google Scholar 

  149. Lister, R., O’Malley, R. C., Tonti-Filippini, J., Gregory, B. D., Berry, C. C., Millar, A. H., & Ecker, J. R. (2008). Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523–536.

    Article  CAS  Google Scholar 

  150. Kim, J. B., Porreca, G. J., Song, L., Greenway, S. C., Gorham, J. M., Church, G. M., et al. (2007). Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science, 316, 1481–1484.

    Article  CAS  Google Scholar 

  151. Cloonan, N., Forrest, A. R., Kolle, G., Gardiner, B. B., Faulkner, G. J., Brown, M. K., et al. (2008). Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods, 5, 613–619.

    Article  CAS  Google Scholar 

  152. Marguerat, S., & Bähler, J. (2010). RNA-seq: From technology to biology. Cellular and Molecular Life Sciences, 67, 569–579.

    Article  CAS  Google Scholar 

  153. Morin, R. D., O’Connor, M. D., Griffith, M., Kuchenbauer, F., Delaney, A., Prabhu, A.-L., et al. (2008). Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Research, 18, 610–621.

    Article  CAS  Google Scholar 

  154. Williams, Z., Ben-Dov, I. Z., Elias, R., Mihailovic, A., Brown, M., Rosenwaks, Z., & Tuschl, T. (2013). Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. Proceedings of the National Academy of Sciences, 110, 4255–4260.

    Article  CAS  Google Scholar 

  155. Wold, B., & Myers, R. M. (2008). Sequence census methods for functional genomics. Nature Methods, 5, 19.

    Article  CAS  Google Scholar 

  156. Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., et al. (2007). Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods, 4, 651–657.

    Article  CAS  Google Scholar 

  157. Schones, D. E., Cui, K., Cuddapah, S., Roh, T.-Y., Barski, A., Wang, Z., et al. (2008). Dynamic regulation of nucleosome positioning in the human genome. Cell, 132, 887–898.

    Article  CAS  Google Scholar 

  158. Meyer, M., Stenzel, U., & Hofreiter, M. (2008). Parallel tagged sequencing on the 454 platform. Nature Protocals, 3, 267–278.

    Article  CAS  Google Scholar 

  159. Kozarewa, I., & Turner, D. J. (2011). 96-plex molecular barcoding for the illumina genome analyzer. high-throughput next generation sequencing (pp. 279–298). Berlin: Springer.

    Chapter  Google Scholar 

  160. Vargas-Hernández, M., Munguía-Fragozo, P. V., Cruz-Hernández, A., Guerrero, B. Z., Gonzalez-Chavira, M. M., Feregrino-Pérez, A. A., et al. (2014). Bioactivity and gene expression studies of an arbustive Mexican specie Acaciella angustissima (Timbe). Industrial Crops and Products, 52, 649–655.

    Article  CAS  Google Scholar 

  161. Asif, M. H., Dhawan, P., & Nath, P. (2000). A simple procedure for the isolation of high quality RNA from ripening banana fruit. Plant Molecular Biology Reporter, 18, 109–115.

    Article  CAS  Google Scholar 

  162. Li, J., Li, M., Liang, D., Ma, F., & Lei, Y. (2014). Comparison of expression pattern, genomic structure, and promoter analysis of the gene encoding GDP-l-galactose phosphorylase from two Actinidia species. Scientia Horticulturae, 169, 206–213.

    Article  CAS  Google Scholar 

  163. Hoshino, Y., Igarashi, T., Ohshima, M., Shinoda, K., Murata, N., Kanno, A., & Nakano, M. (2014). Characterization of CYCLOIDEA-like genes in controlling floral zygomorphy in the monocotyledon Alstroemeria. Scientia Horticulturae, 169, 6–13.

    Article  CAS  Google Scholar 

  164. Maldonado-Cervantes, E., Huerta-Ocampo, J. A., Montero-Morán, G. M., Barrera-Pacheco, A., Espitia-Rangel, E., & Barba de la Rosa, A. P. (2014). Characterization of Amaranthus cruentus L. seed proteins by 2-DE and LC/MS–MS: Identification and cloning of a novel late embryogenesis-abundant protein. Journal of Cereal Science, 60, 172–178.

    Article  CAS  Google Scholar 

  165. Jiang, Q., Wang, F., Li, M.-Y., Tan, H.-W., Ma, J., & Xiong, A.-S. (2014). High-throughput analysis of small RNAs and characterization of novel microRNAs affected by abiotic stress in a local celery cultivar. Scientia Horticulturae, 169, 36–43.

    Article  CAS  Google Scholar 

  166. Min, J.-H., Ju, H.-W., Yang, K.-Y., Chung, J.-S., Cho, B.-H., & Kim, C. S. (2014). Heterologous expression of the gourd E3 ubiquitin ligase gene LsRZF1 compromises the drought stress tolerance in Arabidopsis thaliana. Plant Physiology and Biochemistry, 77, 7–14.

    Article  CAS  Google Scholar 

  167. Yadav, R. K., Sangwan, R. S., Sabir, F., Srivastava, A. K., & Sangwan, N. S. (2014). Effect of prolonged water stress on specialized secondary metabolites, peltate glandular trichomes, and pathway gene expression in Artemisia annua L. Plant Physiology and Biochemistry, 74, 70–83.

    Article  CAS  Google Scholar 

  168. Li, T., Li, X., Tan, D., Jiang, Z., Wei, Y., Li, J., et al. (2014). Distinct expression profiles of ripening related genes in the ‘Nanguo’pear (Pyrus ussuriensis) fruits. Scientia Horticulturae, 171, 78–82.

    Article  CAS  Google Scholar 

  169. Bayramov, S., & Guliyev, N. (2014). Changes in Rubisco activase gene expression and polypeptide content in Brachypodium distachyon. Plant Physiology and Biochemistry, 81, 61–66.

    Article  CAS  Google Scholar 

  170. Vuorinen, A. L., Kalpio, M., Linderborg, K. M., Kortesniemi, M., Lehto, K., Niemi, J., et al. (2014). Coordinate changes in gene expression and triacylglycerol composition in the developing seeds of oilseed rape (Brassica napus) and turnip rape (Brassica rapa). Food Chemistry, 145, 664–673.

    Article  CAS  Google Scholar 

  171. Yang, H., Liu, J., Huang, S., Guo, T., Deng, L., & Hua, W. (2014). Selection and evaluation of novel reference genes for quantitative reverse transcription PCR (qRT-PCR) based on genome and transcriptome data in Brassica napus L. Gene, 538, 113–122.

    Article  CAS  Google Scholar 

  172. Eason, J. R., West, P. J., Brummell, D. A., Watson, L. M., Somerfield, S. D., & McLachlan, A. R. (2014). Overexpression of the protease inhibitor BoCPI-1 in broccoli delays chlorophyll loss after harvest and causes down-regulation of cysteine protease gene expression. Postharvest Biology and Technology, 97, 23–31.

    Article  CAS  Google Scholar 

  173. Jiang, C., Wen, Q., Chen, Y., Xu, L.-A., & Huang, M.-R. (2013). Efficient extraction of RNA from various Camellia species rich in secondary metabolites for deep transcriptome sequencing and gene expression analysis. African Journal of Biotechnology, 10, 16763–16768.

    Google Scholar 

  174. Wang, L., Wang, X., Yue, C., Cao, H., Zhou, Y., & Yang, Y. (2014). Development of a 44 K custom oligo microarray using 454 pyrosequencing data for large-scale gene expression analysis of Camellia sinensis. Scientia Horticulturae, 174, 133–141.

    Article  CAS  Google Scholar 

  175. Tian, S.-L., Lu, B.-Y., Gong, Z.-H., & Shah, S. N. M. (2014). Effects of drought stress on capsanthin during fruit development and ripening in pepper (Capsicum annuum L.). Agricultural Water Management, 137, 46–51.

    Article  Google Scholar 

  176. Santamaría, M., Toorop, P. E., Rodríguez, R., & Cañal, M. (2010). Dormant and non-dormant Castanea sativa Mill. buds require different polyvinylpyrrolidone concentrations for optimal RNA isolation. Plant Science, 178, 55–60.

    Article  CAS  Google Scholar 

  177. Zhang, M., Huang, H., & Dai, S. (2014). Isolation and expression analysis of proline metabolism-related genes in Chrysanthemum lavandulifolium. Gene, 537, 203–213.

    Article  CAS  Google Scholar 

  178. Kazemi-Shahandashti, S.-S., Maali-Amiri, R., Zeinali, H., Khazaei, M., Talei, A., & Ramezanpour, S.-S. (2014). Effect of short-term cold stress on oxidative damage and transcript accumulation of defense-related genes in chickpea seedlings. Journal of Plant Physiology, 171, 1106–1116.

    Article  CAS  Google Scholar 

  179. Hajeri, S., Killiny, N., El-Mohtar, C., Dawson, W. O., & Gowda, S. (2014). Citrus tristeza virus based RNAi in citrus plants induces gene silencing in Diaphorina citri, a phloem-sap sucking insect vector of citrus greening disease (Huanglongbing). Journal of Biotechnology, 176, 42–49.

    Article  CAS  Google Scholar 

  180. Zhang, G., Zhang, Y., Xu, J., Niu, X., Qi, J., Tao, A., et al. (2014). The CCoAOMT1 gene from jute (Corchorus capsularis L.) is involved in lignin biosynthesis in Arabidopsis thaliana. Gene, 546, 398–402.

    Article  CAS  Google Scholar 

  181. Zhang, C., Jin, Y., Liu, J., Tang, Y., Cao, S., & Qi, H. (2014). The phylogeny and expression profiles of the lipoxygenase (LOX) family genes in the melon (Cucumis melo L.) genome. Scientia Horticulturae, 170, 94–102.

    Article  CAS  Google Scholar 

  182. Kumar, A., Kaachra, A., Bhardwaj, S., & Kumar, S. (2014). Copper, zinc superoxide dismutase of Curcuma aromatica is a kinetically stable protein. Process Biochemistry, 49, 1288–1296.

    Article  CAS  Google Scholar 

  183. Yan, Y.-S., Chen, X.-Y., Yang, K., Sun, Z.-X., Fu, Y.-P., Zhang, Y.-M., & Fang, R.-X. (2010). Overexpression of an F-box protein gene reduces abiotic stress tolerance and promotes root growth in rice. Molecular Plant, 4, 1–8.

    Google Scholar 

  184. Xia, W., Mason, A. S., Xiao, Y., Liu, Z., Yang, Y., Lei, X., et al. (2014). Analysis of multiple transcriptomes of the African oil palm (Elaeis guineensis) to identify reference genes for RT-qPCR. Journal of Biotechnology, 184, 63–73.

    Article  CAS  Google Scholar 

  185. Reid, K. E., Olsson, N., Schlosser, J., Peng, F., & Lund, S. T. (2006). An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biology, 6, 27.

    Article  CAS  Google Scholar 

  186. Morante-Carriel, J., Sellés-Marchart, S., Martínez-Márquez, A., Martínez-Esteso, M. J., Luque, I., & Bru-Martínez, R. (2014). RNA isolation from loquat and other recalcitrant woody plants with high quality and yield. Analytical Biochemistry, 452, 46–53.

    Article  CAS  Google Scholar 

  187. Munkert, J., Ernst, M., Müller-Uri, F., & Kreis, W. (2014). Identification and stress-induced expression of three 3β-hydroxysteroid dehydrogenases from Erysimum crepidifolium Rchb. and their putative role in cardenolide biosynthesis. Phytochemistry, 100, 26–33.

    Article  CAS  Google Scholar 

  188. Zhao, W., Xia, W., Li, J., Sheng, S., Lei, L., & Zhao, S. (2014). Transcriptome profiling and digital gene expression analysis of Fallopia multiflora to discover putative genes involved in the biosynthesis of 2, 3, 5, 4′-tetrahydroxy stilbene-2-O-β-d-glucoside. Gene, 547, 126–135.

    Article  CAS  Google Scholar 

  189. Mortaji, Z., & Samadi, B. Y. (2008). RNA isolation and expression from different dormant and after-ripened wheat. Asian Journal of Plant Science, 7, 201–206.

    Article  CAS  Google Scholar 

  190. Christou, A., Georgiadou, E. C., Filippou, P., Manganaris, G. A., & Fotopoulos, V. (2014). Establishment of a rapid, inexpensive protocol for extraction of high quality RNA from small amounts of strawberry plant tissues and other recalcitrant fruit crops. Gene, 537, 169–173.

    Article  CAS  Google Scholar 

  191. Lopez-Gomez, R., & Gomez-Lim, M. (1992). A method for extracting intact RNA from fruits rich in polysaccharides using ripe mango mesocarp. HortScience, 27, 440–442.

    CAS  Google Scholar 

  192. Kamdee, C., Imsabai, W., Kirk, R., Allan, A. C., Ferguson, I. B., & Ketsa, S. (2014). Regulation of lignin biosynthesis in fruit pericarp hardening of mangosteen (Garcinia mangostana L.) after impact. Postharvest Biology and Technology, 97, 68–76.

    Article  CAS  Google Scholar 

  193. Yin, G., Xu, H., Liu, J., Gao, C., Sun, J., Yan, Y., & Hu, Y. (2014). Screening and identification of soybean seed-specific genes by using integrated bioinformatics of digital differential display, microarray, and RNA-seq data. Gene, 546, 177–186.

    Article  CAS  Google Scholar 

  194. Yang, L., Wu, K., Gao, P., Liu, X., Li, G., & Wu, Z. (2014). GsLRPK, a novel cold-activated leucine-rich repeat receptor-like protein kinase from Glycine soja, is a positive regulator to cold stress tolerance. Plant Science, 215, 19–28.

    Article  CAS  Google Scholar 

  195. Nasrollahi, V., Mirzaie-asl, A., Piri, K., Nazeri, S., & Mehrabi, R. (2014). The effect of drought stress on the expression of key genes involved in the biosynthesis of triterpenoid saponins in liquorice (Glycyrrhiza glabra). Phytochemistry, 103, 32–37.

    Article  CAS  Google Scholar 

  196. Jiang, J., & Zhang, T. (2003). Extraction of total RNA in cotton tissues with CTAB-acidic phenolic method. Journal of Cotton Science, 15, 166–167.

    Google Scholar 

  197. Ding, M., Jiang, Y., Cao, Y., Lin, L., He, S., Zhou, W., & Rong, J. (2014). Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development. Gene, 535, 273–285.

    Article  CAS  Google Scholar 

  198. Cai, C., Niu, E., Du, H., Zhao, L., Feng, Y., & Guo, W. (2014). Genome-wide analysis of the WRKY transcription factor gene family in Gossypium raimondii and the expression of orthologs in cultivated tetraploid cotton. The Crop Journal, 2, 87–101.

    Article  Google Scholar 

  199. Bekesiova, I., Nap, J.-P., & Mlynarova, L. (1999). Isolation of high quality DNA and RNA from leaves of the carnivorous plant Drosera rotundifolia. Plant Molecular Biology Reporter, 17, 269–277.

    Article  CAS  Google Scholar 

  200. Aguado, A., Capote, N., Romero, F., Dodd, I. C., & Colmenero-Flores, J. M. (2014). Physiological and gene expression responses of sunflower (Helianthus annuus L.) plants differ according to irrigation placement. Plant Science, 227, 37–44.

    Article  CAS  Google Scholar 

  201. Tang, C., Qi, J., Li, H., Zhang, C., & Wang, Y. (2007). A convenient and efficient protocol for isolating high-quality RNA from latex of Hevea brasiliensis (para rubber tree). JBBM, 70, 749–754.

    CAS  Google Scholar 

  202. Qin, Y., Huang, Y., Fang, Y., Qi, J., & Tang, C. (2014). Molecular characterization and expression analysis of the small GTPase ROP members expressed in laticifers of the rubber tree (Hevea brasiliensis). Plant Physiology and Biochemistry, 74, 193–204.

    Article  CAS  Google Scholar 

  203. Aoki, Y., Takahashi, S., Takayama, D., Ogata, Y., Sakurai, N., Suzuki, H., et al. (2014). Identification of laticifer-specific genes and their promoter regions from a natural rubber producing plant Hevea brasiliensis. Sci: Plant.

    Google Scholar 

  204. Lertpanyasampatha, M., Viboonjun, U., Kongsawadworakul, P., Chrestin, H., & Narangajavana, J. (2014). Differential expression of microRNAs and their targets reveals a possible dual role in physiological bark disorder in rubber tree. Journal of Plant Physiology, 171, 1117–1126.

    Article  CAS  Google Scholar 

  205. Hu, G., Burton, C., Hong, Z., & Jackson, E. (2014). A mutation of the cellulose-synthase-like (CslF6) gene in barley (Hordeum vulgare L.) partially affects the β-glucan content in grains. Journal of Cereal Science, 59, 189–195.

    Article  CAS  Google Scholar 

  206. Gu, C.-S., Liu, L.-Q., Deng, Y.-M., Zhu, X.-D., Lu, X.-Q., & Huang, S.-Z. (2014). Validation of reference genes for RT-qPCR normalization in Iris. lactea var. chinensis leaves under different experimental conditions. Scientia Horticulturae, 175, 144–149.

    Article  CAS  Google Scholar 

  207. Battelli, R., Lombardi, L., Picciarelli, P., Lorenzi, R., Frigerio, L., & Rogers, H. J. (2014). Expression and localisation of a senescence-associated KDEL-cysteine protease from Lilium longiflorum tepals. Plant Science, 214, 38–46.

    Article  CAS  Google Scholar 

  208. Yang, Y., Xu, M., Luo, Q., Wang, J., & Li, H. (2014). De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing. Gene, 534, 155–162.

    Article  CAS  Google Scholar 

  209. Yuan, Y., Wang, Z., Jiang, C., Wang, X., & Huang, L. (2014). Exploiting genes and functional diversity of chlorogenic acid and luteolin biosyntheses in Lonicera japonica and their substitutes. Gene, 534, 408–416.

    Article  CAS  Google Scholar 

  210. Wu, H.-X., Jia, H.-M., Ma, X.-W., Wang, S.-B., Yao, Q.-S., Xu, W.-T., et al. (2014). Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits. Journal of Proteomics, 105, 19–30.

    Article  CAS  Google Scholar 

  211. Shan, L. L., Li, X., Wang, P., Cai, C., Zhang, B., De Sun, C., et al. (2008). Characterization of cDNAs associated with lignification and their expression profiles in loquat fruit with different lignin accumulation. Planta, 227, 1243–1254.

    Article  CAS  Google Scholar 

  212. Jorgensen, S. A., & Preston, J. C. (2014). Differential SPL gene expression patterns reveal candidate genes underlying flowering time and architectural differences in Mimulus and Arabidopsis. Molecular Phylogenetics and Evolution, 73, 129–139.

    Article  CAS  Google Scholar 

  213. Liu, F., Tan, G., Li, X., Chen, H., Li, R., & Li, F. (2014). Simultaneous detection of four causal agents of tobacco bushy top disease by a multiplex one-step RT-PCR. Journal of Virological Methods, 205, 99–103.

    Article  CAS  Google Scholar 

  214. Li, R., Mock, R., Huang, Q., Abad, J., Hartung, J., & Kinard, G. (2008). A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. Journal of Virological Methods, 154, 48–55.

    Article  CAS  Google Scholar 

  215. Li, F.-P., Yoon, M.-Y., Li, G., Ra, W.-H., Park, J.-W., Kwon, S.-J., et al. (2014). Transcriptome analysis of grain-filling caryopses reveals the potential formation mechanism of the rice sugary mutant. Gene, 546, 318–326.

    Article  CAS  Google Scholar 

  216. Zhang, C., Wang, W., Wang, Y., Gao, S., Du, D., Fu, J., & Dong, L. (2014). Anthocyanin biosynthesis and accumulation in developing flowers of tree peony (Paeonia suffruticosa)‘Luoyang Hong’. Postharvest Biology and Technology, 97, 11–22.

    Article  CAS  Google Scholar 

  217. Niu, Y., Luo, H., Sun, C., Yang, T.-J., Dong, L., Huang, L., & Chen, S. (2014). Expression profiling of the triterpene saponin biosynthesis genes FPS, SS, SE, and DS in the medicinal plant Panax notoginseng. Gene, 533, 295–303.

    Article  CAS  Google Scholar 

  218. Aimar, D., Calafat, M., Andrade, A., Carassay, L., Bouteau, F., Abdala, G., & Molas, M. (2014). Drought effects on the early development stages of Panicum virgatum L.: Cultivar differences. Biomass and Bioenergy, 66, 49–59.

    Article  CAS  Google Scholar 

  219. Djami-Tchatchou, A., & Straker, C. (2012). The isolation of high quality RNA from the fruit of avocado (Persea americana Mill.). South + A1443 African Journal of Botany, 78, 44–46.

    Article  CAS  Google Scholar 

  220. Smart, M., & Roden, L. (2010). A small-scale RNA isolation protocol useful for high-throughput extractions from recalcitrant plants. South + A1443 African Journal of Botany, 76, 375–379.

    Article  CAS  Google Scholar 

  221. Wang, G., Wang, G., Zhang, X., Wang, F., & Song, R. (2012). Isolation of high quality RNA from cereal seeds containing high levels of starch. Phytochemical Analysis, 23, 159–163.

    Article  CAS  Google Scholar 

  222. Lahuta, L. B., Pluskota, W. E., Stelmaszewska, J., & Szablińska, J. (2014). Dehydration induces expression of GALACTINOL SYNTHASE and RAFFINOSE SYNTHASE in seedlings of pea (Pisum sativum L.). Journal of Plant Physiology, 171, 1306–1314.

    Article  CAS  Google Scholar 

  223. Shangguan, L., Song, C., Han, J., Leng, X., Kibet, K. N., Mu, Q., et al. (2014). Characterization of regulatory mechanism of Poncirus trifoliata microRNAs on their target genes with an integrated strategy of newly developed PPM-RACE and RLM-RACE. Gene, 535, 42–52.

    Article  CAS  Google Scholar 

  224. Wang, L., Su, H., Han, L., Wang, C., Sun, Y., & Liu, F. (2014). Differential expression profiles of poplar MAP kinase kinases in response to abiotic stresses and plant hormones, and overexpression of PtMKK4 improves the drought tolerance of poplar. Gene, 545, 141–148.

    Article  CAS  Google Scholar 

  225. Yang, C., Xu, M., Xuan, L., Jiang, X., & Huang, M. (2014). Identification and expression analysis of twenty ARF genes in Populus. Gene, 544, 134–144.

    Article  CAS  Google Scholar 

  226. Zhang, Y., Han, J., Yu, M., Ma, R., Pervaiz, T., & Fang, J. (2014). Characterization of target mRNAs for Prunus persica microRNAs using an integrated strategy of PLM-RACE, PPM-RACE and qRT-PCR. Sci. Hort., 170, 8–16.

    Article  CAS  Google Scholar 

  227. Wang, C.-S., & Vodkin, L. O. (1994). Extraction of RNA from tissues containing high levels of procyanidins that bind RNA. Plant. Mol. Bio. Rep., 12, 132–145.

    Article  CAS  Google Scholar 

  228. Tosetti, R., Tardelli, F., Tadiello, A., Zaffalon, V., Giorgi, F. M., Guidi, L., et al. (2014). Molecular and biochemical responses to wounding in mesocarp of ripe peach (Prunus persica L. Batsch) fruit. Postharvest Biology and Technology, 90, 40–51.

    Article  CAS  Google Scholar 

  229. Dong, S., Liu, Y., Niu, J., Ning, Y., Lin, S., & Zhang, Z. (2014). De novo transcriptome analysis of the Siberian apricot (Prunus sibirica L.) and search for potential SSR markers by 454 pyrosequencing. Gene, 544, 220–227.

    Article  CAS  Google Scholar 

  230. Gasic, K., Hernandez, A., & Korban, S. S. (2004). RNA extraction from different apple tissues rich in polyphenols and polysaccharides for cDNA library construction. Plant Molecular Biology Reporter, 22, 437–438.

    Article  CAS  Google Scholar 

  231. Li, G., Jia, H., Li, J., Wang, Q., Zhang, M., & Teng, Y. (2014). Emission of volatile esters and transcription of ethylene-and aroma-related genes during ripening of ‘Pingxiangli’pear fruit (Pyrus ussuriensis Maxim). Scientia Horticulturae, 170, 17–23.

    Article  CAS  Google Scholar 

  232. Zhang, D., Yu, B., Bai, J., Qian, M., Shu, Q., Su, J., & Teng, Y. (2012). Effects of high temperatures on UV-B/visible irradiation induced postharvest anthocyanin accumulation in ‘Yunhongli No. 1′(Pyrus pyrifoliaNakai) pears. Scientia Horticulturae, 134, 53–59.

    Article  CAS  Google Scholar 

  233. Wang, L., Wang, Y., Wang, X., Li, Y., Peng, F., & Wang, L. (2014). Regulation of POD activity by pelargonidin during vegetative growth in radish (Raphanus sativus L.). Scientia Horticulturae, 174, 105–111.

    Article  CAS  Google Scholar 

  234. Yan, H., Zhang, H., Chen, M., Jian, H., Baudino, S., Caissard, J.-C., et al. (2014). Transcriptome and gene expression analysis during flower blooming in Rosa chinensis‘Pallida’. Gene, 540, 96–103.

    Article  CAS  Google Scholar 

  235. Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical Biochemistry, 162, 156–159.

    Article  CAS  Google Scholar 

  236. Khan, M. S., Khraiwesh, B., Pugalenthi, G., Gupta, R. S., Singh, J., Duttamajumder, S. K., & Kapur, R. (2014). Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.). FEBS Open Bio, 4, 533–541.

    Article  CAS  Google Scholar 

  237. El-Moneim, D. A., Contreras, R., Silva-Navas, J., Gallego, F. J., Figueiras, A. M., & Benito, C. (2014). Pectin methylesterase gene and aluminum tolerance in Secale cereale. Environmental and Experimental Botany, 107, 125–133.

    Article  CAS  Google Scholar 

  238. Han, J., Xie, H., Sun, Q., Wang, J., Lu, M., Wang, W., et al. (2014). Bioinformatic identification and experimental validation of miRNAs from foxtail millet (Setaria italica). Gene, 546, 367–377.

    Article  CAS  Google Scholar 

  239. Djanaguiraman, M., Vara Prasad, P., Murugan, M., Perumal, R., & Reddy, U. K. (2014). Physiological differences among sorghum (Sorghum bicolor L. Moench) genotypes under high temperature stress. Environmental and Experimental Botany, 100, 43–54.

    Article  CAS  Google Scholar 

  240. Li, F., Wu, B., Qin, X., Yan, L., Hao, C., Tan, L., & Lai, J. (2014). Molecular cloning and expression analysis of the sucrose transporter gene family from Theobroma cacao L. Gene, 546, 336–341.

    Article  CAS  Google Scholar 

  241. Mendes, M. D., Barroso, J. G., Oliveira, M. M., & Trindade, H. (2014). Identification and characterization of a second isogene encoding γ-terpinene synthase in Thymus caespititius. Journal of Plant Physiology, 171, 1017–1027.

    Article  CAS  Google Scholar 

  242. Vaseva, I. I., Anders, I., & Feller, U. (2014). Identification and expression of different dehydrin subclasses involved in the drought response of Trifolium repens. Journal of Plant Physiology, 171, 213–224.

    Article  CAS  Google Scholar 

  243. Wang, B., Sun, Y.-F., Song, N., Wei, J.-P., Wang, X.-J., Feng, H., et al. (2014). MicroRNAs involving in cold, wounding and salt stresses in Triticum aestivum L. Plant Physiology and Biochemistry, 80, 90–96.

    Article  CAS  Google Scholar 

  244. Shoeva, O. Y., Khlestkina, E. K., Berges, H., & Salina, E. A. (2014). The homoeologous genes encoding chalcone–flavanone isomerase in Triticum aestivum L.: Structural characterization and expression in different parts of wheat plant. Gene, 538, 334–341.

    Article  CAS  Google Scholar 

  245. Die, J. V., & Rowland, L. J. (2014). Elucidating cold acclimation pathway in blueberry by transcriptome profiling. Environmental and Experimental Botany, 106, 87–98.

    Article  CAS  Google Scholar 

  246. Fock-Bastide, I., Palama, T. L., Bory, S., Lécolier, A., Noirot, M., & Joët, T. (2014). Expression profiles of key phenylpropanoid genes during Vanilla planifolia pod development reveal a positive correlation between PAL gene expression and vanillin biosynthesis. Plant Physiology and Biochemistry, 74, 304–314.

    Article  CAS  Google Scholar 

  247. Katoch, R., Singh, S. K., Thakur, N., Dutt, S., Yadav, S. K., & Shukle, R. (2014). Cloning, characterization, expression analysis and inhibition studies of a novel gene encoding Bowman-Birk type protease inhibitor from rice bean. Gene, 546, 342–351.

    Article  CAS  Google Scholar 

  248. Vasanthaiah, H. K., Katam, R., & Sheikh, M. B. (2008). Efficient protocol for isolation of functional RNA from different grape tissue rich in polyphenols and polysaccharides for gene expression studies. Electronic Journal of Biotechnology, 11, 42–51.

    Article  CAS  Google Scholar 

  249. Nopo-Olazabal, C., Condori, J., Nopo-Olazabal, L., & Medina-Bolivar, F. (2014). Differential induction of antioxidant stilbenoids in hairy roots of Vitis rotundifolia treated with methyl jasmonate and hydrogen peroxide. Plant Physiology and Biochemistry, 74, 50–69.

    Article  CAS  Google Scholar 

  250. Zhang, J., Wang, Y., Wang, X., Yang, K., & Yang, J. (2003). An improved method for rapidly extracting total RNA from Vitis. Journal of Fruit Science, 20, 178–181.

    CAS  Google Scholar 

  251. Shi, J., He, M., Cao, J., Wang, H., Ding, J., Jiao, Y., et al. (2014). The comparative analysis of the potential relationship between resveratrol and stilbene synthase gene family in the development stages of grapes (Vitis quinquangularis and Vitis vinifera). Plant Physiology and Biochemistry, 74, 24–32.

    Article  CAS  Google Scholar 

  252. Blondel, C., Melesan, M., Miguel, A. S., Veyrenc, S., Meresse, P., Pezet, M., et al. (2014). Cell cycle disruption and apoptosis as mechanisms of toxicity of organochlorines in Zea mays roots. Journal of Hazardous Materials, 276, 312–322.

    Article  CAS  Google Scholar 

  253. Ma, C.-L., Chen, L., Wang, X.-C., Jin, J.-Q., Ma, J.-Q., Yao, M.-Z., & Wang, Z.-L. (2012). Differential expression analysis of different albescent stages of ‘Anji Baicha’(Camellia sinensis (L.) O. Kuntze) using cDNA microarray. Scientia Horticulturae, 148, 246–254.

    Article  CAS  Google Scholar 

  254. Wei, K., Wang, L., Cheng, H., Zhang, C., Ma, C., Zhang, L., & Gong, W. (2013). Identification of genes involved in indole-3-butyric acid-induced adventitious root formation in nodal cuttings of Camellia sinensis (L.) by suppression subtractive hybridization. Gene, 514, 91–98.

    Article  CAS  Google Scholar 

  255. Li, Y., Wang, Z., Chang, H., Wang, Y., & Guo, M. (2010). Expression of CT-wpr, screened by cDNA-AFLP approach, associated with hydroxysafflor yellow A in Carthamus tinctorius L. Biochemical Systematics and Ecology, 38, 1148–1155.

    Article  CAS  Google Scholar 

  256. Feng, N., Li, Y., Tang, J., Wang, Y., & Guo, M. (2010). cDNA-AFLP analysis on transcripts associated with hydroxysafflor yellow A (HSYA) biosynthetic pathway in Carthamus tinctorius. Biochemical Systematics and Ecology, 38, 971–980.

    Article  CAS  Google Scholar 

  257. Tang, J., Lou, Z., Wang, Y., & Guo, M. (2010). Expression of a small heat shock protein (CTL-hsyapr) screened by cDNA-AFLP approach is correlated with hydroxysafflor yellow A in safflower (Carthamus tinctorius L.). Biochemical Systematics and Ecology, 38, 722–730.

    Article  CAS  Google Scholar 

  258. Li, Y., Chen, W., Ma, D., & Wu, Y. (2013). cDNA-AFLP analysis revealed genes potentially implicated in Catharanthus roseus flowers during wheat blue dwarf phytoplasma infection. Physiological and Molecular Plant Pathology, 84, 1–9.

    Article  CAS  Google Scholar 

  259. He, H., Yajing, N., Huawen, C., Xingjiao, T., Xinli, X., Weilun, Y., & Silan, D. (2012). cDNA-AFLP analysis of salt-inducible genes expression in Chrysanthemum lavandulifolium under salt treatment. Journal of Plant Physiology, 169, 410–420.

    Article  CAS  Google Scholar 

  260. Zeng, J., Gao, C., Deng, G., Jiang, B., Yi, G., Peng, X., et al. (2012). Transcriptome analysis of fruit development of a citrus late-ripening mutant by microarray. Scientia Horticulturae, 134, 32–39.

    Article  CAS  Google Scholar 

  261. Kawabata, S., Li, Y., & Miyamoto, K. (2012). EST sequencing and microarray analysis of the floral transcriptome of Eustoma grandiflorum. Scientia Horticulturae, 144, 230–235.

    Article  CAS  Google Scholar 

  262. Dinkins, R. D., Barnes, A., & Waters, W. (2010). Microarray analysis of endophyte-infected and endophyte-free tall fescue. Journal of Plant Physiology, 167, 1197–1203.

    Article  CAS  Google Scholar 

  263. Zhang, W.-W., Wang, S.-Z., Liu, K., Si, N., Qi, F.-J., & Jian, G.-L. (2012). Comparative expression analysis in susceptible and resistant Gossypium hirsutum responding to Verticillium dahliae infection by cDNA-AFLP. Physiological and Molecular Plant Pathology, 80, 50–57.

    Article  CAS  Google Scholar 

  264. Rodriguez-Uribe, L., Higbie, S. M., Stewart, J. M., Wilkins, T., Lindemann, W., Sengupta-Gopalan, C., & Zhang, J. (2011). Identification of salt responsive genes using comparative microarray analysis in Upland cotton (Gossypium hirsutum L.). Plant Science, 180, 461–469.

    Article  CAS  Google Scholar 

  265. Rong-Ping, C., Lie, L., Xiu-Qing, W., En-Jian, Q., Chun-Jun, W., Bao-Gang, S., et al. (2012). cDNA-AFLP analysis of differentially expressed genes in tobacco infected by tobacco mosaic virus. Acta Agronomica Sinica, 38, 62–70.

    Article  Google Scholar 

  266. Qu, X., Jiang, J., Shang, X., Cheng, C., Feng, L., & Liu, Q. (2014). Construction and analysis of gonad suppression subtractive hybridization libraries for the rice field eel, Monopterus albus. Gene, 540, 20–25.

    Article  CAS  Google Scholar 

  267. Bae, E.-K., Lee, H., Lee, J.-S., & Noh, E.-W. (2010). Isolation and characterization of osmotic stress-induced genes in poplar cells by suppression subtractive hybridization and cDNA microarray analysis. Plant Physiology and Biochemistry, 48, 136–141.

    Article  CAS  Google Scholar 

  268. Li, X., Korir, N. K., Liu, L., Shangguan, L., Wang, Y., Han, J., et al. (2012). Microarray analysis of differentially expressed genes engaged in fruit development between Prunus mume and Prunus armeniaca. Journal of Plant Physiology, 169, 1776–1788.

    Article  CAS  Google Scholar 

  269. Alimohammadi, A., Shiran, B., Martínez-Gómez, P., & Ebrahimie, E. (2013). Identification of water-deficit resistance genes in wild almond Prunus scoparia using cDNA-AFLP. Scientia Horticulturae, 159, 19–28.

    Article  CAS  Google Scholar 

  270. Nashima, K., Shimizu, T., Nishitani, C., Yamamoto, T., Takahashi, H., Nakazono, M., et al. (2013). Microarray analysis of gene expression patterns during fruit development in European pear (Pyrus communis). Scientia Horticulturae, 164, 466–473.

    Article  CAS  Google Scholar 

  271. Chao, Y.-E., Zhang, M., Feng, Y., Yang, X.-E., & Islam, E. (2010). cDNA-AFLP analysis of inducible gene expression in zinc hyperaccumulator Sedum alfredii Hance under zinc induction. Environmental and Experimental Botany, 68, 107–112.

    Article  CAS  Google Scholar 

  272. Wang, L., Zhou, B., Wu, L., Guo, B., & Jiang, T. (2011). Differentially expressed genes in Populus simonii × Populus nigra in response to NaCl stress using cDNA-AFLP. Plant Science, 180, 796–801.

    Article  CAS  Google Scholar 

  273. Nazeem, P., Jose, S., Sheeba, N., Madhavan, S., Baby, A., Sadhan Kumar, P., & Devi, N. (2011). Differential gene expression for bacterial wilt incidence in tomato (Solanum lycopersicum L.) revealed by cDNA-AFLP analysis. Physiological and Molecular Plant Pathology, 76, 197–203.

    Article  CAS  Google Scholar 

  274. Pasini, L., Bergonti, M., Fracasso, A., Marocco, A., & Amaducci, S. (2014). Microarray analysis of differentially expressed mRNAs and miRNAs in young leaves of sorghum under dry-down conditions. Journal of Plant Physiology, 171, 537–548.

    Article  CAS  Google Scholar 

  275. Mattiello, L., da Silva, F. R., & Menossi, M. (2012). Linking microarray data to QTLs highlights new genes related to Al tolerance in maize. Plant Science, 191, 8–15.

    Article  CAS  Google Scholar 

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Correspondence to Mahbod Sahebi or Mohamed M. Hanafi.

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Sahebi, M., Hanafi, M.M., Azizi, P. et al. Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives. Mol Biotechnol 57, 880–903 (2015). https://doi.org/10.1007/s12033-015-9884-z

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