Plant Growth Regulation

, Volume 84, Issue 2, pp 359–371 | Cite as

Differential proteomic analysis of rice seedlings reveals the advantage of dry-raising nursery practices

  • Zhixing Zhang
  • Fenglian Huang
  • CaiHong Shao
  • Hongfei Chen
  • Wenxiong Lin
Original paper


Dry-raising rice seedlings in nurseries is a key technique in high-yield rice cultivation. The present study of morphological and physiological indexes showed dry-raised seedlings (DRS) had a shorter stature, more developed root systems, and significantly higher soluble sugar, starch, and N content than moist-raised seedlings (MRS), resulting in significantly increased grain yield. Compared to the MRS techniques, the dry-raised measures induced higher levels of abscisic acid (ABA), gibberellins (GA3), and indole-3-acetic acid (IAA) in leaves and roots of seedlings. We then utilized tandem mass tags (TMT) quantitative proteomics technology to analyze the mechanism by which rice exposed to the appropriate drought stress (dry-raised measures) during the seedling stage develop differently. Through mass spectrometry, we identified 281 significantly expressed proteins in roots and 268 in leaves. The differentially expressed proteins were then divided into 23 categories based on MapMan ontology. In addition, the hormonal-related protein expression patterns of DRS were confirmed with RT-PCR at the transcript level. On the basis of these findings, we proposed that appropriate drought stress during the rice seedling stage can change the expression of key proteins involved in nitrogen uptake and translocation, hormone synthesis, photosynthesis, and CHO metabolic processes, thus regulating rice seedling growth. In this process, the differentially expressed key proteins, such as the 14-3-3 protein, GTP-binding protein, and calcium, play important roles in transduction of signals regarding soil drought, and the upregulated heat shock protein, glutathione S-transferases, and peroxidases function in enhancing the stress tolerance of the seedlings under dry-raising nursery conditions. This study established the high yielding mechanism of dry-raised cultivates methods during seedling stage at the protein expression level.


Rice Seedling Dry-raising nursery Quantitative proteomics 



Tandem mass tags


High-performance liquid chromatography


Dry-raising seedlings


Moist-raising seedlings


Tricarboxylic acid cycle


Nitrate reductase 1


Nitrite reductase


Glutamine synthetase


Glutamine synthetase root isozyme 2


Abscisic acid




Indole-3-acetic acid




Heat shock proteins


Glutathione S transferases


Triethylammonium bicarbonate


Room temperature


Mass spectrometer


Rice Genome Annotation Project database


Glutamate synthase


Abscisic aldehyde oxidase


Carotenoid cleavage dioxygenase 1


IAA-Amino acid hydrolase ILR1


Gibberellin 20 oxidase 2


Lipoxygenase 2.3


Allene oxide cyclase 4


1-Aminocyclopropane-1-carboxylate oxidase


12-Oxophytodienoate reductase 2



This work was sponsored by the National Natural Science Foundation of China (No. 31401306), the Fujian-Taiwan Joint Innovative Centre for Germplasm Resources and cultivation of crop (Fujian 2011 Program, No. 2015-75), the National Key Research and Development Program of China (2016YFD0300508) and the Natural Foundation of Fujian Higher Education Institutions for Young Scientists (Key Project) (JZ160435).

Supplementary material

10725_2017_347_MOESM1_ESM.docx (13 kb)
Table S1: The RT-PCR primer of hormonal-related genes. (DOCX 19 KB)
10725_2017_347_MOESM2_ESM.docx (14 kb)
Table S2: Effects of different seedling-raising ways on rice grain yield and its components. (DOCX 14 KB)
10725_2017_347_MOESM3_ESM.xlsx (303 kb)
The detailed information of the 2918 root proteins from the Rice Genome Annotation Project database (RAP-DB). (XLSX 302 KB)
10725_2017_347_MOESM4_ESM.xlsx (308 kb)
The detailed information of the 2674 leaf proteins from the Rice Genome Annotation Project database (RAP-DB). (XLSX 308 KB)
10725_2017_347_MOESM5_ESM.xls (93 kb)
Functional categories of the 281 root proteins according to MapMan ontology (XLS 93 KB)
10725_2017_347_MOESM6_ESM.xlsx (29 kb)
Functional categories of the 268 leaf proteins according to MapMan ontology (XLSX 29 KB)
10725_2017_347_MOESM7_ESM.docx (1.5 mb)
Figure S1: MapMan overview of leaf photosynthesis proteins with significant differences in abundance in dry-raised seedlings. (DOCX 1502 KB)


  1. Burger JC, Chapman MA, Burke JM (2008) Molecular insights into the evolution of crop plants. Am J Bot 95(2):113–122CrossRefPubMedGoogle Scholar
  2. Campo S, Peris-Peris C, Montesinos L, Peñas G, Messeguer J, San Segundo B (2012) Expression of the maize ZmGF14-6 gene in rice confers tolerance to drought stress while enhancing susceptibility to pathogen infection. J Exp Bot 63(2):983–999CrossRefPubMedGoogle Scholar
  3. Chauvin A, Caldelari D, Wolfender JL, Farmer EE (2013) Four 13-lipoxygenases contribute to rapid jasmonate synthesis in wounded Arabidopsis thaliana leaves: a role for lipoxygenase 6 in responses to long-distance wound signals. New Phytol 197(2):566–575CrossRefPubMedGoogle Scholar
  4. Chen YP, Yang WY (2005) Determination of GA3, IAA, ABA and ZT in dormant buds of Allium ovalifolium by HPLC. J Sichuan Agric Univ 23:498–500Google Scholar
  5. Chen F, Li Q, Sun L, He Z (2006) The rice 14-3-3 gene family and its involvement in responses to biotic and abiotic stress. DNA Res 13(16766513):53–63CrossRefPubMedGoogle Scholar
  6. Chen H, Liang Y, Lin W, Zheng L, Liang K (2007) Quality and physiobiochemical characteristics of the first rice crop seedlings under different raising seedling patterns for early rice and its ratoonal crop (I)—studies on super high-yield ecophysiology and its regulation technology in hybridize rice. Chin Agric Sci Bull 23(2):247–250Google Scholar
  7. Comparot S, Lingiah G, Martin T (2003) Function and specificity of 14-3-3 proteins in the regulation of carbohydrate and nitrogen metabolism. J Exp Bot 54(382):595–604CrossRefPubMedGoogle Scholar
  8. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372CrossRefPubMedGoogle Scholar
  9. Creelman RA, Mullet JE (1995) Jasmonic acid distribution and action in plants: regulation during development and response to biotic and abiotic stress. Proc Natl Acad Sci USA 92(10):4114–4119CrossRefPubMedPubMedCentralGoogle Scholar
  10. Del Viso F, Casaretto JA, Quatrano RS (2007) 14-3-3 Proteins are components of the transcription complex of the ATEM1 promoter in Arabidopsis. Planta 227(1):167–175CrossRefPubMedGoogle Scholar
  11. Deryng D, Conway D, Ramankutty N, Price J, Warren R (2014) Global crop yield response to extreme heat stress under multiple climate change futures. Environ Res Lett 9(3):034011CrossRefGoogle Scholar
  12. Ding Y, Wang Q, Wang S, Huang P (2001) Comparison studies of roots physiology activity between rice dry seedbed seedlings and wet seedbed seedlings. J Nangjing Agric Univ 24(3):1–5Google Scholar
  13. Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127(7):1309–1321CrossRefPubMedGoogle Scholar
  14. Dong JG, Fernandez-Maculet JC, Yang SF (1992) Purification and characterization of 1-aminocyclopropane-1-carboxylate oxidase from apple fruit. Proc Natl Acad Sci USA 89(20):9789–9793CrossRefPubMedPubMedCentralGoogle Scholar
  15. El-Sharkawy I, Mila I, Bouzayen M, Jayasankar S (2010) Regulation of two germinlike protein genes during plum fruit development. J Exp Bot 61(6):1761–1770CrossRefPubMedPubMedCentralGoogle Scholar
  16. He Y, Wu J, Lv B, Li J, Gao Z, Xu W, Baluska F, Shi W, Shaw PC, Zhang J (2015) Involvement of 14-3-3 protein GRF9 in root growth and response under polyethylene glycol-induced water stress. J Exp Bot 66(8):2271–2281CrossRefPubMedPubMedCentralGoogle Scholar
  17. Islam E, Yang X, Li T, Liu D, Jin X, Meng F (2007) Effect of Pb toxicity on root morphology, physiology and ultrastructure in the two ecotypes of Elsholtzia argyi. J Hazard Mater 147(3):806–816CrossRefPubMedGoogle Scholar
  18. Ji W, Zhu Y, Li Y, Yang L, Zhao X, Cai H, Bai X (2010) Over-expression of a glutathione S-transferase gene, GsGST, from wild soybean (Glycine soja) enhances drought and salt tolerance in transgenic tobacco. Biotechnol Lett 32(8):1173–1179CrossRefPubMedGoogle Scholar
  19. Koda Y (1992) The role of jasmonic acid and related compounds in the regulation of plant development. Int Rev Cytol 135:155–199CrossRefPubMedGoogle Scholar
  20. LeClere S, Tellez R, Rampey RA, Matsuda SP, Bartel B (2002) Characterization of a family of IAA-amino acid conjugate hydrolases from Arabidopsis. J Biol Chem 277(23):20446–20452CrossRefPubMedGoogle Scholar
  21. Lima L, Seabra A, Melo P, Cullimore J, Carvalho H (2006) Post-translational regulation of cytosolic glutamine synthetase of Medicago truncatula. J Exp Bot 57(11):2751–2761CrossRefPubMedGoogle Scholar
  22. Lin W, Wang S, Liang Y, Guo Y, He S, Hong L, Zheng L, Weng D, Pang Z (1997) Physioecological study on highyielding cultivation of rice by dryraising seedling and thinspacing transplanting techniques I. Quality and ecophysiological characteristics of rice seedlings grown on dryfertile nursery. Chin J Appl Ecol 8(6):566–570Google Scholar
  23. Lin W, Wang S, Liang Y, Guo Y, He S, Zheng F, Weng D, Hong L, Pan Z (1998) Physio-ecological study on high yielding cultivation of rice by dry raising seedling and thin spacing transplanting techniques II. High yielding formation and its physiobiochemical properties of early rice. Chin J Appl Ecol 9(4):395–399Google Scholar
  24. Lo S-F, Yang SY, Chen KT, Hsing YI, Zeevaart JA, Chen LJ, Yu SM (2008) A novel class of gibberellin 2-oxidases control semidwarfism, tillering, and root development in rice. Plant Cell 20(10):2603–2618CrossRefPubMedPubMedCentralGoogle Scholar
  25. Lu X, Peng L, Tang X, Liu X, Luo Z (1995) Studies on physiological reason for cold resistance of early rice seedlings raised in dry nursery. J Hunan Agric Univ 22(3):225–230Google Scholar
  26. Lu X, Tang X, Peng L, Liu X, Zheng X, Luo Z (1996) The characteristics of morphology, physiology and biochemistry of late rice plants cultivated by raising seedlings with dry nursery management. J Hunan Agric Univ 23(4):307–315Google Scholar
  27. Lu X, Peng L, Tang X, Liu X, Luo Z (1997) Studies on the morphology, tissue structure and physiological characteristics of early rice (Oryza sativa L.) seedlings raised in dry nursery. Acta Agron Sin 23(3):360–369Google Scholar
  28. Marrs KA (1996) The functions and regulation of glutathione S-transferases in plants. Annu Rev Plant Biol 47:127–158CrossRefGoogle Scholar
  29. Mishra A, Salokhe V (2008) Seedling characteristics and the early growth of transplanted rice under different water regimes. Exp Agric 44(03):365–383CrossRefGoogle Scholar
  30. Netto AT, Campostrini E, de Oliveira JG, Bressan-Smith RE (2005) Photosynthetic pigments, nitrogen, chlorophyll a fluorescence and SPAD-502 readings in coffee leaves. Sci Hortic 104(2):199–209CrossRefGoogle Scholar
  31. Pitts RJ, Cernac A, Estelle M (1998) Auxin and ethylene promote root hair elongation in Arabidopsis. Plant J 16(5):553–560CrossRefPubMedGoogle Scholar
  32. Ramachandra RA, Chaitanya KV, Vivekanandan M (2004) Drought-induced responses of photosynthesis and antioxidant metabolism in higher plants. J Plant Physiol 161(11):1189–1202CrossRefGoogle Scholar
  33. Redona E, Mackill D (1996) Genetic variation for seedling vigor traits in rice. Crop Sci 36(2):285–290CrossRefGoogle Scholar
  34. Schaller F, Biesgen C, Mussig C, Altmann T, Weiler EW (2000) 12-Oxophytodienoate reductase 3 (OPR3) is the isoenzyme involved in jasmonate biosynthesis. Planta 210(6):979–984CrossRefPubMedGoogle Scholar
  35. Schwartz SH, Tan BC, McCarty DR, Welch W, Zeevaart JA (2003) Substrate specificity and kinetics for VP14, a carotenoid cleavage dioxygenase in the ABA biosynthetic pathway. BBA-Biomembr 1619(1):9–14Google Scholar
  36. Sehnke PC, Chung HJ, Wu K, Ferl RJ (2001) Regulation of starch accumulation by granule-associated plant 14-3-3 proteins. Proc Natl Acad Sci USA 98(2):765–770CrossRefPubMedPubMedCentralGoogle Scholar
  37. Seo M, Peeters AJ, Koiwai H, Oritani T, Marion-Poll A, Zeevaart JA, Koornneef M, Kamiya Y, Koshiba T (2000) The Arabidopsis aldehyde oxidase 3 (AAO3) gene product catalyzes the final step in abscisic acid biosynthesis in leaves. Proc Natl Acad Sci USA 97(23):12908–12913CrossRefPubMedPubMedCentralGoogle Scholar
  38. Sharp RE, LeNoble ME (2002) ABA, ethylene and the control of shoot and root growth under water stress. J Exp Bot 53(366):33–37CrossRefPubMedGoogle Scholar
  39. Sinclair T, Horie T (1989) Leaf nitrogen, photosynthesis, and crop radiation use efficiency: a review. Crop sci 29(1):90–98CrossRefGoogle Scholar
  40. Solaiman M, Hirata H (1997) Effect of arbuscular mycorrhizal fungi inoculation of rice seedlings at the nursery stage upon performance in the paddy field and greenhouse. Plant Soil 191(1):1–12CrossRefGoogle Scholar
  41. Stenzel I, Hause B, Miersch O, Kurz T, Maucher H, Weichert H, Ziegler J, Feussner I, Wasternack C (2003) Jasmonate biosynthesis and the allene oxide cyclase family of Arabidopsis thaliana. Plant Mol Biol 51(6):895–911CrossRefPubMedGoogle Scholar
  42. Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M (2004) mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37(6):914–939CrossRefPubMedGoogle Scholar
  43. Van de Poel B, Smet D, Van Der Straeten D (2015) Ethylene and hormonal cross talk in vegetative growth and development. Plant Physiol 169(1):61–72CrossRefPubMedPubMedCentralGoogle Scholar
  44. Voss I, Sunil B, Scheibe R, Raghavendra A (2013) Emerging concept for the role of photorespiration as an important part of abiotic stress response. Plant Biol 15(4):713–722CrossRefPubMedGoogle Scholar
  45. Walker BJ, VanLoocke A, Bernacchi CJ, Ort DR (2016) The costs of photorespiration to food production now and in the future. Annu Rev Plant Biol 67:107–129CrossRefPubMedGoogle Scholar
  46. Wang S, Lin W (1999) The mechanism of high-yielding in rice under dry-raising and thin-planting and its regulating technique I. Advances in the mechanism of high-yielding in rice under dry-raising and thin-planting and its prospects. J Fujian Agric Univ 28(1):12–17Google Scholar
  47. Wang Q, Ding Y, Wang S, Huang P, Miao B (2003) Physiological effects of sustainable water saturation in seedbed on rice dry nursery seedlings. Acta Agron Sin 30(3):210–214Google Scholar
  48. Wen H, Zhao J, Zhao W, Mao G (2000) Rooting advantage of rice seedlings nursed by dry-nursing and its impact on characteristics of growth and development of aerial part. J Zhejiang Agric Sci 1:1–5CrossRefGoogle Scholar
  49. Yang D, Duang Z, Hang J, Liu C, Wu S (2000) Study on the growth and development characters of dry nursery seedlings and their regularities of yield formation in hybrid early rice III. Characteristics of tillering and earing of dry nursery seedlings. Hubei Agric Sci 6:13–14Google Scholar
  50. Yao Y, Du Y, Jiang L, Liu JY (2007) I Interaction between ACC synthase 1 and 14–3-3 proteins in rice: a new insight. Biochemistry 72(9):1003–1007PubMedGoogle Scholar
  51. Zhang Z, Qu W (2003) Guidance of plant physiology experiments, 3rd edn. Higher Education Press, Beijing. pp 127–132Google Scholar
  52. Zhang Y, Wu H, Wang Z, Xiong F, Xie Y, Li A (1999) Effect of rice seedling raising conditions on rice seedling growth. Chinese J Rice Sci 13(2):86–90Google Scholar
  53. Zhang J, Jia W, Yang J, Ismail AM (2006) Role of ABA in integrating plant responses to drought and salt stresses. Field Crop Res 97(1):111–119CrossRefGoogle Scholar
  54. Zhang Z, Zhang Y, Liu X, Li Z, Lin W (2017) The use of comparative quantitative proteomics analysis in rice grain-filling in determining response to moderate soil drying stress. Plant Growth Regul 82(2):219–232CrossRefGoogle Scholar
  55. Zhao Y, Ding Y, Chen L, Huang P (2001) Physiological characteristics of drought resistance of rice dry nursery seedlings. Sci Agric Sin 34(3):289–291Google Scholar
  56. Zhou Q, Chen G, Chen L, Wang J, Zhang C, Lu C (2004) Study on antioxidation system in high yield hybrid rice Langyoupeijiu seedlings under dry raising conditions. Bull Bot Res 25(1):80–88Google Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2017

Authors and Affiliations

  • Zhixing Zhang
    • 1
    • 2
  • Fenglian Huang
    • 1
    • 2
  • CaiHong Shao
    • 3
  • Hongfei Chen
    • 1
    • 2
  • Wenxiong Lin
    • 1
    • 2
  1. 1.Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouPeople’s Republic of China
  2. 2.Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University)Fujian Province UniversityFuzhouPeople’s Republic of China
  3. 3.Soil and Fertilizer & Resources and Environment InstituteJiangxi Academy of Agricultural SciencesNanchangPeople’s Republic of China

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