Quantitative proteomics to study the response of potato to contrasting fertilisation regimes

Molecular Breeding

Volumn 31, Issue 2, 2013, Pages 363-378

  Rempelos, L ^a   Cooper, J ^a   Wilcockson, S ^a   Eyre, M ^a   Shotton, P ^a   Volakakis, N ^a,b   Orr, C H ^c   Leifert, C ^a   Gatehouse, A M R ^a   Tetard Jones C ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b Agricultural Science Consultants   (Greece)

^c NORTHUMBRIA UNIVERSITY   (United Kingdom)

Author keywords

Fertilisation regimes; Functional molecular markers; Nutrient use efficiency; Potato leaf proteome; Solanum tuberosum; Sustainability

Indexed keywords

COMPOSTING; CROP PROTECTION; CULTIVATION; EFFICIENCY; FERTILIZERS; MANURES; MINERALS; MOLECULAR BIOLOGY; NUTRIENTS; PLANTS (BOTANY); SUSTAINABLE DEVELOPMENT; TUBES (COMPONENTS);

CROP PROTECTION; FERTILISATION; FERTILIZATION REGIME; FUNCTIONAL MOLECULAR MARKER; MOLECULAR MARKER; NUTRIENT-USE EFFICIENCIES; ORGANIC FERTILIZERS; POTATO LEAF PROTEOME; SOLANUM TUBEROSUM; TUBER YIELD;

PROTEINS;

ANIMALIA; BOS; SOLANUM TUBEROSUM;

EID: 84873742578     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-012-9795-7     Document Type: Article

References (78)

1. Aghaei K, Ehsanpour AA, Komatsu S (2008) Proteome analysis of potato under salt stress. J Proteome Res 7: 4858-4868.
2. Ahsan N, Renaut J, Komatsu S (2009) Recent developments in the application of proteomics to the analysis of plant responses to heavy metals. Proteomics 9: 2602-2621.
3. Bahrman N, Le Gouis J, Negroni L, Amilhat L, Leroy P, Lainé A-L, Jaminon O (2004) Differential protein expression assessed by two-dimensional gel electrophoresis for two wheat varieties grown at four nitrogen levels. Proteomics 4: 709-719.
4. Beffa R, Meins FJ (1996) Pathogenesis-related functions of plant beta-1, 3-glucanases investigated by antisense transformation-a review. Gene 179(7): 97-103.
5. Chen Z, Gallie DR (2008) Dehydroascorbate reductase affects non-photochemical quenching and photosynthetic performance. J Biol Chem 283(31): 21347-21361. doi: 10. 1074/jbc. M802601200.
6. Cheruth AJ, Ksouri R, Ragupathi G, Paramasivam M, Jallali IS, Hameed JA-J, Zhao C-X, Shao H-B, Rajaram P (2009) Antioxidant defense responses: physiological plasticity in higher plants under abiotic constraints. Acta Physiol Plant 31: 427-436.
7. Chung H-J, Ferl RJ (1999) Arabidopsis alcohol dehydrogenase expression in both shoots and roots is conditioned by root growth environment. Plant Physiol 121: 429-436.
8. Communities TcotE (1991) Council Directive 91/676/EEC of 12 December 1991 concerning the protection of waters against pollution caused by nitrates from agricultural sources, vol 91/676/EEC 375 edn. Official Journal of the European Union L 375.
9. Cooper J, Sanderson R, Cakmak I, Ozturk L, Shotton P, Caramichael A, Sadrabadi R, Tetard Jones C, Volakakis N, Eyre MD, Leifert C (2011) Effect of organic and conventional crop rotation, fertilization and crop protection on metal contents in wheat. J Agric Food Chem 59: 4715-4724.
10. Cordell D, Dangert J-O, White S (2009) The story of phosphorus: global food security and food for thought. Glob Environ Change 19: 292-305.
11. Dawson JC, Huggins DR, Jones SS (2008) Characterizing nitrogen use efficiency in natural and agricultural ecosystems to improve the performance of cereal crops in low-input and organic agricultural systems. Field Crop Res 107(2): 89-101.
12. ®ed ribulose-1, 5-bisphosphate carboxylase/oxygenase by chloroplastic proteases requires ATP-hydrolysis. Planta 205: 459-466.
13. Deuce R, Neuburger M (1999) Biochemical dissection of photorespiration. Curr Opin Plant Biol 2: 214-222.
14. Didierjean L, Frendo P, Burkard G (1992) Stress responses in maize: sequence analysis of cDNA encoding glycine-rich proteins. Plant Mol Biol 18: 847-849.
15. Dolferus R, De Bruxelles G, Dennis ES, Peacock WJ (1994) Regulation of the Arabidopsis Adh gene by anaerobic and other environmental stresses. Ann Bot 74: 301-308.
16. Drescher A, Ruf S, Calsa TJ, Carrer H, Bock R (2000) The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J 22(2): 97-104.
17. Eyre MD, Sanderson RA, Shotton PN, Leifert C (2009) Investigating the effects of crop type, fertility management and crop protection on the activity of beneficial invertebrates in an extensive farm management comparison trial. Ann Appl Biol 155: 267-276.
18. Fantel RJ, Peterson GR, Stowasser WF (1985) The worldwide availability of phosphate rock. Nat Resour Forum 9: 5-24.
19. Finckh MR, Schulte-Geldermann E, Bruns C (2006) Challenges to organic potato farming: disease and nutrient management. Potato Res 49: 27-42.
20. Fliessbach A, Oberholzer HR, Gunst L, Mäder P (2007) Soil organic matter and biological soil quality indicators after 21 years of organic and conventional farming. Agric Ecosyst Environ 118: 273-284.
21. Flynn HC, Smith P (2010) Greenhouse gas budgets of crop production-current and likely future trends. International Fertiliser Industry Association, Paris.
22. Gaude N, Brehelin C, Tischendorf G, Kessler F, Domann P (2007) Nitrogen deficiency in Arabidopsis affects galactolipid composition and gene expression and results in accumulation of fatty acid phytyl esters. Plant J 49: 729-739.
23. Ghorani R, Wilcockson S, Koiocheki A, Leifert C (2008) Soil management for sustainable crop disease control: a review. Environ Chem Lett 6: 149-162.
24. Gill SS, Tuteja N (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem 48: 909-930.
25. Giotis C, Markelou E, Theodoropoulou A, Toufexi E, Hodson R, Shotton P, Shiel R, Cooper J, Leifert C (2009) Effect of soil amendments and biological control agents on soil borne root diseases caused by Pyrenochaeta lycopersici and Verticillium albo-atrum in organic greenhouse tomato production systems. Eur J Plant Pathol 123: 387-400.
26. Good AG, Shrawat AK, Muench DG (2004) Can less yield more? Is reducing nutrient input into the environment compatible with maintaining crop production? Trends Plant Sci Rev 9(12): 597-604.
27. Guan LM, Scandalios JG (2002) Catalase gene expression in response to auxin-mediated developmental signals. Physiol Plant 114: 288-295.
28. Hack (2001) Potato (Solanum tuberosum L.) Phenological growth stages. In: Meier U (ed) Growth stages of mono-and dicotyledonous plants. Federal Biological Research Centre for Agriculture and Forestry.
29. Hahn K, Strittmatter G (1994) Pathogen-defence gene prpl-1 from potato encodes an auxin-responsive glutathione S-transferase. Eur J Biochem 226: 619-626.
30. Hartel H, Dormann P, Benning C (2000) DGD1-independent biosynthesis of extraplastidic galactolipids following phosphate deprivation in Arabidopsis. Proc Natl Acad Sci USA 97: 10649-10654.
31. Hepperly P, Lotter D, Ziegler C, Seidel R, Reider C (2009) Compost, manure and synthetic fertilizer influences crop yields, soil properties, nitrate leaching and crop nutrient content. Compos Sci Util 17: 117-126.
32. Herencia JF, Ruiz-Porras JC, Melero S, Garcia-Galavis PA, Morillo E, Maqueda C (2007) Comparison between organic and mineral fertilization for soil fertility levels, crop macronutrient concentrations, and yield. Agron J 99: 973-983.
33. Hsu YT, Kao CH (2004) Cadmium toxicity is reduced by nitric oxide in rice leaves. Plant Growth Regul 42: 227-238.
34. Kaldenhoff R, Richter G (1989) Sequence of cDNA for a novel light-induced glycine-rich protein. Nucleic Acids Res 17(7): 2853.
35. Kelly A, Dormann P (2002) DGD2, an Arabidopsis gene encoding a UDPgalactose-dependent digalactosyldiacylglycerol synthase is expressed during growth under phosphate-limiting conditions. J Biol Chem 277: 1166-1173.
36. Kelly AA, Froehlich JE, Dormann P (2003) Disruption of the two digalactosyldiacylglycerol synthase genes DGD1 and DGD2 in Arabidopsis reveals the existence of an additional enzyme of galactolipid synthesis. Plant Cell 15: 2694-2706.
37. Khan NA, Singh S, Nazar R (2007) Activities of antioxidative enzymes, sulphur assimilation, photosynthetic activity and growth of wheat (Triticum aestivum) cultivars differing in yield potential under cadmium stress. J AgroCrop Sci 193: 435-444.
38. Kopriva S, Bauwe H (1995) Serine hydroxymethyltransferase from Solanum tuberosum. Plant Physiol 107: 271-272.
39. Kosová K, Vítámvás P, Prášil T, Renaut J (2011) Plant proteome changes under abiotic stress-contribution of proteomics studies to understanding plant stress response. J Proteomics 74: 1301-1322. doi: 10. 1016/j. jprot. 2011. 1002. 1006.
40. Lammerts van Bueren ET, Jones SS, Tamm L, Murphy KM, Myers JR, Leifert C, Messmer MM (2010) The need to breed crop varieties suitable for organic farming, using wheat, tomato and broccoli as examples: a review. NJAS-Wageningen J Life Sci 58: 193-205. doi: 10. 1016/j. njas. 2010. 04. 001.
41. Lehesranta SJ, Koistinen KM, Massat N, Davies HV, Shepherd LVT, McNicol JW, Cakmak I, Cooper J, Lück L, Kärenlampi SO, Leifert C (2007) Effects of agricultural production systems and their components on protein profiles of potato tubers. Proteomics 7: 597-604.
42. Liu Z, Halterman D (2009) Analysis of proteins differentially accumulated during potato late blight resistance mediated by the RB resistance gene. Physiol Mol Plant Pathol 74: 151-160.
43. Liu J, Hal WuY, Jie Yang J, Liu YD, Shen FF (2008) Protein degradation and nitrogen remobilization during leaf senescence. J Plant Biol 51(1): 1-19.
44. Mäder P, Fliessbach A, Dubois D, Gunst L, Fried P, Niggli U (2002) Soil fertility and biodiversity in organic farming. Science 296(5573): 1694-1697.
45. Maggio A, Carillo P, Bulmetti GS, Fuggi A, Barbieri G, De Pascale S (2008) Potato yield and metabolic profiling under conventional and organic farming. Eur J Agron 28: 343-350.
46. Marrs KA (1996) The functions and regulation of glutathione S-transferases in plants. Annu Rev Plant Physiol 47: 127-158.
47. McArthur DAJ, Knowles NR (1992) Resistance responses of potato to vesicular-arbuscular mycorrhizal fungi under varying abiotic phosphorus levels. Plant Physiol 100(1): 341-351.
48. Mobin M, Khan NA (2007) Photosynthetic activity, pigment composition and antioxidative response of two mustard (Brassica juncea) cultivars differing in photosynthetic capacity subjected to cadmium stress. J Plant Physiol 164: 601-610.
49. Mousavi A, Hotta Y (2005) Glycine-rich proteins: a class of novel proteins. Appl Biochem Biotechnol 120: 169-174.
50. Munoza F, Mylavarapu RS, Hutchinson CM (2005) Environmentally responsible potato production systems: a review. J Plant Nutr 28: 1287-1309.
51. Nawrocki A, Thorup-Kristensen K, Jensen ON (2011) Quantitative proteomics by 2DE and MALDI MS/MS uncover the effects of organic and conventional cropping methods on vegetable products. J Proteomics 74(12): 2810-2825.
52. Orr CH, James A, Leifert C, Cooper JM, Cummings SP (2011) Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils. Appl Environ Microbiol 77(3): 911-919.
53. Osaki M, Shinano T, Tadano T (1993) Effect of nitrogen, phosphorus, or potassium deficiency on the accumulation of ribulose-1, 5-bisphosphate carboxylase/oxygenase and chlorophyll in several field crops. Soil Sci Plant Nutr 39: 417-425.
54. Peters J, Frenkel C (2004) Relationship between alcohol dehydrogenase activity and low-temperature in two maize genotypes, Silverado F1 and Adh1-Adh2- doubly null. Plant Physiol Biochem 42: 841-846.
55. Pinheiro J, Bates D (2000) Mixed-effects models in s and s-plus. Springer, New York.
56. Portis AR (2003) Rubisco activase-Rubisco's catalytic chaperone. Photosynth Res 75: 11-27.
57. QLIF (2009) www. qlif. org.
58. RDC Team (2009) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna.
59. Robertson GP, Vitousek PM (2009) Nitrogen in agriculture: balancing the cost of an essential resource. Annu Rev Environ Resour 34: 97-125.
60. Rossi F, Godani F, Bertuzzi T, Trevisan M, Ferrari F, Gatti S (2008) Health promoting substances and heavy metal content in tomatoes grown with different farming techniques. Eur J Nutr 47: 266-272.
61. Sakurai I, Mizusawa N, Wada H, Sato N (2007) Digalactosyldiacylglycerol is required for stabilization of the oxygen-evolving complex in photosystem II. Plant Physiol 145: 1361-1370.
62. Scandalios J (1994) Regulation and properties of plant catalases. In: Foyer C, Mullineaux P (eds) Causes of photooxidative stress and amelioration of defense systems in plants. CRC Press, Boca Raton, pp 275-315.
63. Shah S, Lee Y-J, Hannapel DJ, Rao AG (2011) Protein profiling of the potato petiole under short day and long day photoperiod. J Proteomics 74: 212-230.
64. Singh S, Khan NA, Nazar R, Anjum NA (2008) Photosynthetic traits and activities of antioxidant enzymes in blackgram (Vigna mungo L. Hepper) under cadmium stress. Am J Plant Physiol 3: 25-32.
65. Singh RK, Vidhu AS, Aparna M, Sharique AA, Pravendra N (2010) Differential expression of the mango alcohol dehydrogenase gene family during ripening. Phytochemistry 71: 1485-1494.
66. Ter Braak CJF, Šmilauer P (1998) CANOCO reference manual and user's guide to Canoco for windows: software for canonical community ordination, version 4 edn. Centre for Biometry, Wageningen.
67. Tilman D, Cassman KG, Matson PA, Naylor R, Polasky S (2002) Agricultural sustainability and intensive production practices. Nature 418: 671-677.
68. Trehan SP, Sharma RC (2005) Differences in phosphorus use efficiency in potato genotypes. Adv Hortic Sci 19: 13-20.
69. van Dijk JP, Cankar K, Hendriksen PJM, Beenen HG, Zhu M, Scheffer S, Shepherd LVT, Stewart D, Davies HV, Leifert C, Wilkockson SJ, Gruden K, Kok EJ (2012) The identification and interpretation of differences in the transcriptomes of organically and conventionally grown potato tubers. J Agric Food Chem 60: 2090-2101.
70. Vranova E, Inze D, van Breusegem F (2002) Signal transduction during oxidative stress. J Exp Bot 53: 1227-1236.
71. Wang Q, Sullivan R, Kight A, Henry R, Huang J, Jones A, Korth K (2004) Deletion of the chloroplast-localized thylakoid formation1 gene product in Arabidopsis leads to deficient thylakoid formation and variegated leaves. Plant Physiol 136: 3594-3604.
72. Warman PR, Burnham JC, Eaton LJ (2009) Effects of repeated applications of municipal solid waste compost and fertilizers to three lowbush blueberry fields. Sci Hortic 122: 393-398.
73. Warren CR, Adams MA (2002) Phosphorus affects growth and partitioning of nitrogen to Rubisco in Pinus pinaster. Tree Physiol 22(1): 11-19.
74. Westermann DT (2006) Nutritional requirements of potatoes. Am J Potato Res 82: 301-307.
75. White P, Wheatley RE, Hammond JP, Zhang K (2008) Minerals, soils and roots. In: Vreugdenhil D (ed) Potato biology and biotechnology, advances and perspectives. Elsevier, Amsterdam.
76. Xingming L, Shiping W, Jianwei Z, Qi F, Lida Z, Danlin F, Xianghua L, Dejun Y, Bin H, Qifa Z (2006) Expression profiles of 10, 422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray. Plant Mol Biol 60(5): 617-631.
77. Yin L, Wang S, Eltayeb AE, Imtiaz Uddin Md, Yamamoto Y, Tsuji W, Takeuchi Y, Tanaka K (2010) Overexpression of dehydroascorbate reductase, but not monodehydroascorbate reductase, confers tolerance to aluminium stress in transgenic tobacco. Planta 231: 609-621.
78. Zebarth BJ, Tai G, Tarn R, de Jong H, Milburn PH (2004) Nitrogen use efficiency characteristics of commercial potato cultivars. Can J Plant Sci 84: 589-598.