Proteomic and comparative genomic analysis of two Brassica napus lines differing in oil content

Journal of Proteome Research

Volumn 12, Issue 11, 2013, Pages 4965-4978

  Gan, Lu ^a,d   Zhang, Chun Yu ^b   Wang, Xiao Dong ^a   Wang, Hao ^c   Long, Yan ^b   Yin, Yong Tai ^a   Li, Dian Rong ^c   Tian, Jian Hua ^c   Li, Zai Yun ^b   Lin, Zhi Wei ^a   Yu, Long Jiang ^a   Li, Mao Teng ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^c Hybrid Rapeseed Research Center of Shaanxi Province   (China)

^d INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Brassica napus; comparative genomics; differentially expressed proteins; oil content; QTL mapping; transgenic analysis

Indexed keywords

COMPLEMENTARY DNA; FATTY ACID; GLUCOSINOLATE; PROTEIN; SEED STORAGE PROTEIN; VEGETABLE OIL;

ARTICLE; CELL SIZE; CELL WALL; COMPARATIVE STUDY; CONFOCAL LASER MICROSCOPY; GENETIC CORRELATION; GENOME ANALYSIS; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PHENOTYPE; PLANT SEED; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONTENT; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; PROTEOMICS; QUALITATIVE ANALYSIS; QUANTITATIVE TRAIT LOCUS MAPPING; RAPESEED; TANDEM MASS SPECTROMETRY; TRANSMISSION ELECTRON MICROSCOPY;

ARABIDOPSIS; BRASSICA NAPUS; CELL SIZE; DNA, COMPLEMENTARY; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FATTY ACIDS; GENOMICS; GLUCOSINOLATES; MICROSCOPY, CONFOCAL; MICROSCOPY, ELECTRON, TRANSMISSION; PLANT OILS; PLANT PROTEINS; PROTEOMICS; QUANTITATIVE TRAIT LOCI; SEEDS; SPECIES SPECIFICITY;

EID: 84887235186     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr4005635     Document Type: Article

References (72)

1. Burns, M.; Barnes, S.; Bowman, J.; Clarke, M.; Werner, C.; Kearsey, M. QTL analysis of an intervarietal set of substitution lines in Brassica napus (i) Seed oil content and fatty acid composition Heredity 2003, 90, 39-48
2. Vigeolas, H.; Waldeck, P.; Zank, T.; Geigenberger, P. Increasing seed oil content in oil-seed rape (Brassica napus L.) by over-expression of a yeast glycerol-3-phosphate dehydrogenase under the control of a seed-specific promoter Plant Biotechnol. J. 2007, 5, 431-441
3. Wang, H. Z. Review and future development of rapeseed industry in China Chin. J. Oil Crop Sci. 2010, 32 (2) 300-302
4. Thelen, J. J.; Ohlrogge, J. B. Metabolic Engineering of Fatty Acid Biosynthesis in Plants Metab. Eng. 2002, 4, 12-21
5. Qiu, D.; Morgan, C.; Shi, J.; Long, Y.; Liu, J.; Li, R.; Zhuang, X.; Wang, Y.; Tan, X.; Dietrich, E.; Weihmann, T.; Everett, C.; Vanstraelen, S.; Beckett, P.; Fraser, F.; Trick, M.; Barnes, S.; Wilmer, J.; Schmidt, R.; Li, J.; Li, D.; Meng, J.; Bancroft, I. A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content Theor. Appl. Genet. 2006, 114, 67-80
6. Zhao, J.; Becker, H. C.; Zhang, D.; Zhang, Y.; Ecke, W. Oil Content in a European×Chinese Rapeseed Population: QTL with Additive and Epistatic Effects and Their Genotype-Environment Interactions Crop Sci. 2005, 45, 51-59
7. Fu, S.; Cheng, H.; Qi, C. Microarray analysis of gene expression in seeds of Brassica napus planted in Nanjing (altitude: 8.9 m), Xining (altitude: 2261.2 m) and Lhasa (altitude: 3658 m) with different oil content Mol. Biol. Rep. 2009, 36 (8) 2375-2386
8. Sarmiento, C.; Rossl, J. H. E.; Herman, E.; Murphyl, D. J. Expression and subcellular targeting of a soybean oleosin in transgenic rapeseed. Implications for the mechanism of oil-body formation in seeds Plant J. 1997, 11 (4) 783-796
9. Tzen, J. T. C.; Peng, C.; Cheng, D.; Chen, E. C. F.; Chiu, J. M. H. A new method for seed oil body purification and examination of oil body integrity following germination J. Biochem. 1997, 121, 762-768
10. Katavic, V.; Agrawal, G. K.; Hajduch, M.; Harris, S. L.; Thelen, J. J. Protein and lipid composition analysis of oil bodies from two Brassica napus cultivars Proteomics 2006, 6, 4586-4598
11. Leprince, O.; van Aelst, A. C.; Pritchard, H. W.; Murphy, D. J. Oleosins prevent oil-body coalescence during seed imbibition as suggested by a low-temperature scanning electron microscope study of desiccation-tolerant and -sensitive oilseeds Planta 1998, 204, 109-119
12. Jolivet, P.; Boulard, C. L.; Bellamy, A.; Larre, C.; Barre, M.; le Ne Rogniaux, H.; A, S. D. A.; Chardot, T.; Nesi, N. Protein composition of oil bodies from mature Brassica napus seeds Proteomics 2009, 9, 3268-3284
13. Hu, Z.; Wang, X.; Zhan, G.; Liu, G.; Hua, W.; Wang, H. Unusually large oilbodies are highly correlated with lower oil content in Brassica napus Plant Cell Rep. 2009, 28, 541-549
14. Hu, Z.; Hua, W.; Zhang, L.; Deng, L.; Wang, X.; Liu, G.; Hao, W.; Wang, H. Seed Structure Characteristics to Form Ultrahigh Oil Content in Rapeseed PLoS One 2013, 8 (4) e62099
15. Jolivet, P.; Deruyffelaere, C.; Boulard, C.; Quinsac, A.; Savoire, R.; Nesi, N.; Chardot, T. Deciphering the structural organization of the oil bodies in the Brassica napus seed as a mean to improve the oil extraction yield Ind. Crops Prod. 2013, 44, 549-557
16. Consoli, L.; Evre, A. L.; Zivy, M.; de Vienne, D.; Damerval, C. QTL analysis of proteome and transcriptome variations for dissecting the genetic architecture of complex traits in maize Plant Mol. Biol. 2002, 48, 575-581
17. Dzau, V. J.; Glueck, S. Physiological Genomics: Who we are and where we are going Physiol Genomics 2001, 7, 65-67
18. Meza-Basso, L.; Alberdi, M.; Raynal, M.; Ferrero-Cadinanos, M. L.; Delseny, M. Changes in Protein Synthesis in Rapeseed (Brassica napus) Seedlings during a Low Temperature Treatment Plant Physiol. 1986, 82, 733-738
19. Pi, P.; Hill, R. D.; Scarth, R. Comparative analysis of stamen polypeptides of a rapeseed cultivar, Regent, a CMS polima line, and temperature-restored male-fertile polima line Sex. Plant Reprod. 1988, 1, 114-118
20. Mihr, C.; Baumgärtner, M.; Dieterich, J.; Schmitz, U. K.; Braun, H. Proteomic approach for investigation of cytoplasmic male sterility (CMS) in Brassica J. Plant Physiol. 2001, 158, 787-794
21. Albertin, W.; Langella, O.; Joets, J.; Négroni, L.; Zivy, M.; Damerval, C.; Thiellement, H. Comparative proteomics of leaf, stem, and root tissues of synthetic Brassica napus Proteomics 2009, 9, 793-799
22. Sheoran, I. S.; Pedersen, E. J.; Ross, A. R. S.; Sawhney, V. K. Dynamics of protein expression during pollen germination in canola (Brassica napus) Planta 2009, 230, 779-793
23. Li, R.; Wang, H.; Mao, H.; Lu, Y.; Hua, W. Identification of differentially expressed genes in seeds of two near-isogenic Brassica napus lines with different oil content Planta 2006, 224, 952-962
24. Agrawal, G. K.; Hajduch, M.; Graham, K.; Thelen, J. J. In-Depth Investigation of the Soybean Seed-Filling Proteome and Comparison with a Parallel Study of Rapeseed Plant Physiol. 2008, 148, 504-518
25. Hajduch, M.; Casteel, J. E.; Hurrelmeyer, K. E.; Song, Z.; Agrawal, G. K.; Thelen, J. J. Proteomic Analysis of Seed Filling in Brassica napus. Developmental Characterization of Metabolic Isozymes Using High-Resolution Two-Dimensional Gel Electrophoresis Plant Physiol. 2006, 141, 32-46
26. Hajduch, M.; Casteel, J. E.; Tang, S.; Hearne, L. B.; Knapp, S.; Thelen, J. J. Proteomic Analysis of Near-Isogenic Sunflower Varieties Differing in Seed Oil Traits J. Proteome Res. 2007, 6 (8) 3232-3241
27. Kottapalli, K. R.; Payton, P.; Rakwal, R.; Agrawal, G. K.; Shibato, J.; Burow, M.; Puppala, N. Proteomics analysis of mature seed of four peanut cultivars using two-dimensional gel electrophoresis reveals distinct differential expression of storage, anti-nutritional, and allergenic proteins Plant Sci. 2008, 175, 321-329
28. Houston, N. L.; Hajduch, M.; Thelen, J. J. Quantitative Proteomics of Seed Filling in Castor: Comparison with Soybean and Rapeseed Reveals Differences between Photosynthetic and Nonphotosynthetic Seed Metabolism Plant Physiol. 2009, 151, 857-868
29. Yang, Y. W.; Lai, K. N.; Tai, P. Y.; Li, W. H. Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages J. Mol. Evol. 1999, 48 (5) 597-604
30. Lan, T. H.; DelMonte, T. A.; Reischmann, K. P.; Hyman, J.; Kowalski, S. P.; McFerson, J.; Kresovich, S.; Paterson, A. H. An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana Genome Res. 2000, 10 (6) 776-788
31. Parkin I, A. P.; Gulden, S. M.; Sharpe, A. G.; Lukens, L.; Trick, M.; Osborn, T. C.; Lydiate, D. J. Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana Genetics 2005, 171, 765-781
32. Long, Y.; Shi, J.; Qiu, D.; Li, R.; Zhang, C.; Wang, J.; Hou, J.; Zhao, J.; Shi, L.; Park, B. S.; Choi, S. R.; Lim, Y. P.; Meng, J. Flowering time quantitative trait loci analysis of oilseed Brassica in multiple environments and genomewide alignment with Arabidopsis Genetics 2007, 177 (4) 2433-2444
33. Hou, J. N.; Long, Y.; Raman, H.; Zou, X. X.; Wang, J.; Dai, S. T.; Xiao, Q. Q.; Li, C.; Fan, L. J.; Liu, B.; Meng, J. L. A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 Gene is associated with vernalization requirement in rapeseed (Brassica napus L.) BMC Plant Biol. 2012, 12, 238
34. Rücker, B.; Röbbelen, G. Impact of low linolenic acid content on seed yield of winter oilseed rape (Brassica napus L.) Plant Breed. 1996, 115 (4) 226-230
35. Robertson, J. A.; Morrison, W. H. Analysis of Oil Content of Sunflower Seed by Wide-Line NMR J. Am. Oil Chem. Soc 1979, 56, 961-964
36. Agerbirk, N.; Olsen, C. E.; Nielsen, J. K. Seasonal variation in leaf glucosinolates and insect resistance in two types of Barbarea vulgaris ssp. arcuata Phytochemistry 2001, 58, 91-100
37. Siloto, R. M. P.; Findlay, K.; Arturo, L. V.; Yeung, E. C.; Nykiforuk, C. L.; Moloney, M. M. The Accumulation of Oleosins Determines the Size of Seed Oilbodies in Arabidopsis Plant Cell 2006, 18, 1961-1974
38. Gan, L.; Li, D.; Zang, X.; Fu, C.; Yu, L.; Li, M. Construction of Two-Dimensional Polyacrylamide Gel Electrophoresis System for Proteins in Brassica napus Acta Agron. Sin. 2010, 36 (4) 612-619
39. Candiano, G.; Bruschi, M.; Musante, L.; Santucci, L.; Ghiggeri, G. M.; Carnemolla, B.; Orecchia, P.; Zardi, L.; Righetti, P. G. Blue silver A very sensitive colloidal Coomassie G-250 staining for proteome analysis Electrophoresis 2004, 25, 1327-1333
40. Shu, L. B.; Lou, Q. J.; Ma, C. F.; Ding, W.; Zhou, J.; Wu, J. H.; Feng, F. J.; Lu, X.; Luo, L. J.; Xu, G. W.; Mei, H. W. Genetic, proteomic and metabolic analysis of the regulation of energy storage in rice seedlings in response to drought Proteomics 2011, 11, 4122-4138
41. Salavati, A.; Khatoona, A.; Nanjoa, Y.; Komatsua, S. Analysis of proteomic changes in roots of soybean seedlings during recovery after flooding J. Proteomics 2012, 75, 878-893
42. Caraux, G.; Pinloche, S. PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order Bioinformatics 2005, 21 (7) 1280-1281
43. Qiu, D.; Morgan, C.; Shi, J.; Long, J Y.; Liu, J.; Li, R.; Zhuang, X.; Wang, Y.; Tan, X.; Dietrich, E.; Weihmann, T.; Everett, C.; Vanstraelen, S.; Beckett, P.; Fraser, F.; Trick, M.; Barnes, S.; Wilmer, J.; Schmidt, R.; Li, J.; Li, D.; Meng, J.; Bancroft, I. A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content Theor. Appl. Genet. 2006, 114, 67-80
44. Jiang, C. C.; Ramchiary, N.; Ma, Y. B.; Jin, M. N.; Feng, J.; Li, R. Y.; Wang, H.; Long, Y.; Choi, S. Y.; Zhang, C. Y.; Cowling, W. A.; Park, B. S.; Lim, Y. P.; Meng, J. L. Structural and functional comparative mapping between the Brassica A genomes in allotetraploid Brassica napus and diploid Brassica rapa Theor. Appl. Genet. 2011, 123, 927-941
45. Zeng, Z. B. Precision mapping of quantitative trait loci Genetics 1994, 136, 1457-1468
46. Long, Y.; Shi, J.; Qiu, D.; Li, R.; Zhang, C.; Wang, J.; Hou, J.; Zhao, J.; Shi, L.; Park, B. S.; Choi, S. R.; Lim, Y. P.; Meng, J. Flowering time quantitative trait loci analysis of oilseed Brassica in multiple environments and genomewide alignment with Arabidopsis Genetics 2007, 177, 2433-2444
47. Schranz, M. E.; Lysak, M. A.; Mitchell-Olds, T. The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes Trends Plant Sci 2006, 11, 535-542
48. Ichikawa, T.; Nakazawa, M.; Kawashima, M.; Iizumi, H.; Kuroda, H.; Kondou, Y.; Tsuhara, Y.; Suzuki, K.; Ishikawa, A.; Seki, M.; Fujita, M.; Motohashi, R.; Nagata, N.; Takagi, T.; Shinozaki, K.; Matsui, M. The FOX hunting system: an alternative gain-of-function gene hunting technique Plant J. 2006, 48, 974-985
49. Koo, J. C.; Asurmendi, S.; Bick, J.; Woodford-Thomas, T.; Beachy, R. N. Ecdysone agonist-inducible expression of a coat protein gene from tobacco mosaic virus confers viral resistance in transgenic Arabidopsis Plant J. 2004, 37, 439-448
50. Devouge, V.; le Ne Rogniaux, H.; Si, N. N.; Tessier, D.; Guen, J. G.; Larre, C. Differential Proteomic Analysis of Four Near-Isogenic Brassica napus Varieties Bred for their Erucic Acid and Glucosinolate Contents J. Proteome Res. 2007, 6, 1342-1353
51. Gül, M.; Becker, H. C.; Ecke, W. QTL mapping and analysis of QTL× nitrogen interactions for protein and oil contents in Brassica napus L Proceedings of the 11th International Rapeseed Congress, Copenhagen, Denmark 2003, 91-93
52. Zhao, J.; Becker, H. C.; Zhang, D.; Zhang, Y.; Ecke, W. Conditional QTL mapping of oil content in rapeseed with respect to protein content and traits related to plant development and grain yield Theor. Appl. Genet. 2006, 113 (1) 33-8
53. Shoemaker, R. C.; Polzin, K.; Labate, J.; Specht, J.; Brummer, E. C.; Olson, T.; Young, N.; Concibido, V.; Wilcox, J.; Tamulonis, J. P.; Kochert, G.; Boerma, H. R. Genome duplication in soybean (Glycine subgenus soja) Genetics 1996, 144 (1) 329-338
54. Mahmood, T.; Rahman, M. H.; Stringam, G. R.; Yeh, F.; Good, A. G. Identification of quantitative trait loci (QTL) for oil and protein contents and their relationships with other seed quality traits in Brassica juncea Theor. Appl. Genet. 2006, 113 (7) 1211-20
55. Jain, R.; Katavic, V.; Agrawal, G. K.; Guzov, V. M.; Thelen, J. J. Purification and proteomic characterization of plastids from Brassica napus developing embryos Proteomics 2008, 8, 3397-3405
56. Miziorko, H. M.; Lorimer, G. H. Ribulose-1,5-Bisphosphate carboexlase-Oxygenase Annu. Rev. Biochem. 1983, 52, 507-35
57. Wagnera, D.; Salnikow, J.; Ottob, A.; Thiedeb, B.; Vatera, J. A protein chemical analysis of the heterogeneity of the small subunit of ribulose-1,5-bisphosphate carboxylase oxygenase from Zea mays Plant Sci. 1996, 113, 13-20
58. Hua, W.; Li, R.; Zhan, G.; Liu, J.; Li, J.; Wang, X.; Liu, G.; Wang, H. Maternal control of seed oil content in Brassica napus: the role of silique wall photosynthesis Plant J. 2012, 69 (3) 432-444
59. Schwender, J.; Goffman, F.; Ohlrogge, J. B.; Shachar-Hill, Y. Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds Nature 2004, 432 (7018) 779-82
60. Munoz-Bertomeu, J. S.; Cascales-Minana, B.; Irles-Segura, A.; Mateu, I.; Nunes-Nesi, A.; Fernie, A. R.; Segura, J.; Ros, R. The Plastidial Glyceraldehyde-3-Phosphate Dehydrogenase Is Critical for Viable Pollen Development in Arabidopsis Plant Physiol. 2010, 152, 1830-1841
61. Konishi, H.; Yamane, H.; Maeshima, M.; Komatsu, S. Characterization of fructose-bisphosphate aldolase regulated by gibberellin in roots of rice seedling Plant Mol. Biol. 2004, 56, 839-848
62. 3 Plant, Rice Plant Physiol. 2001, 127, 1136-1146
63. Petrash, J. M. All in the family: aldose reductase and closely related aldoketo reductases Cell. Mol. Life Sci. 2004, 61, 737-749
64. Cox, M.; Lehninger, A. L.; Nelson, D. R. Lehninger Principles of Biochemistry; Worth Publishers: New York, 2000; pp 306-308.
65. Troncoso-Ponce, M. A.; Kilaru, A.; Cao, X.; Durrett, T. P.; Fan, J.; Jensen, J. K.; Thrower, N. A.; Pauly, M.; Wilkerson, C.; Ohlrogge, J. B. Comparative deep transcriptional profiling of four developing oilseeds Plant J. 2011, 68 (6) 1014-27
66. Bourgis, F.; Kilaru, A.; Cao, X.; Ngando-Ebongue, G. F.; Drira, N.; Ohlrogge, J. B.; Arondel, V. Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning Proc. Natl. Acad. Sci. U.S.A. 2011, 108 (30) 12527-12532
67. Falk, A.; Taipalensuu, J.; Ek, B.; Lenman, M.; Rask, L. Characterization of rapeseed myrosinase-binding protein Planta 1995, 195, 387-395
68. Asson, E. A.; Jørgensen, L. B.; Glund, A. H.; Rask, L.; Meijer, J. Different Myrosinase and Idioblast Distribution in Arabidopsis and Brassica napus Plant Physiol. 2001, 127, 1750-1763
69. Dong, J.; Keller, W. A.; Yan, W.; Georges, F. Gene expression at early stages of Brassica napus seed development as revealed by transcript profiling of seed-abundant cDNAs Planta 2004, 218, 483-491
70. Tunnacliffe, A.; Wise, M. J. The continuing conundrum of the LEA proteins Naturwissenschaften 2007, 94, 791-812
71. Fowler, S.; Thomashow, M. F. Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway Plant Cell 2002, 14, 1675-1690
72. Mulako, I.; Farrant, J. M.; Collett, H.; Illing, N. Expression of Xhdsi-1VOC, a novel member of the vicinal oxygen chelate (VOC) metalloenzyme superfamily, is up-regulated in leaves and roots during desiccation in the resurrection plant Xerophyta humilis (Bak) Dur and Schinz J. Exp. Bot. 2008, 3885-3901