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Correlation analysis of the transcriptome and metabolome reveals the regulatory network for lipid synthesis in developing Brassica napus embryos

  • Helin Tan
  • Jiahuan Zhang
  • Xiao Qi
  • Xiaoli Shi
  • Jianguo Zhou
  • Xingchun Wang
  • Xiaoe Xiang
Article

Abstract

Key message

In this manuscript, we explored the key molecular networks for oil biosynthesis with the transcriptome and metabolome of B. napus embryo at different developmental stages.

Abstract

Brassica napus (B. napus) is an important oil crop worldwide, yet the molecular pathways involved in oil biosynthesis in seeds are not fully understood. In this study, we performed a combined investigation of the gene expression profiles and metabolite content in B. napus seeds at 21, 28 and 35 days after flowering (DAF), when seed oil biosynthesis takes place. The total triacylglycerol (TAG) content in seed embryos increased over the course of seed maturation, and was accompanied by changes in the fatty acid profile, an increase in lipid droplets, and a reduction in starch grains. Metabolome analysis showed that the total amino acid, free fatty acid and organic acid contents in seed embryos decreased during seed maturation. In total, the abundance of 76 metabolites was significantly different between 21 and 28 DAF, and 68 metabolites changed in abundance between 28 and 35 DAF. Transcriptome analysis showed that the set of genes differentially expressed between stages was significantly enriched in those related to lipid metabolism, transport, protein and RNA metabolism, development and signaling, covering most steps of plant lipid biosynthesis and metabolism. Importantly, the metabolite and gene expression profiles were closely correlated during seed development, especially those associated with TAG and fatty acid biosynthesis. Further, the expression of major carbohydrate metabolism-regulating genes was closely correlated with carbohydrate content during seed maturation. Our results provide novel insights into the regulation of oil biosynthesis in B. napus seeds and highlights the coordination of gene expression and metabolism in this process.

Keywords

Brassica napus Oil accumulation Seed Transcriptome Metabolome 

Notes

Acknowledgements

This work was supported by the NSFC Project (31671730), the National Key R&D Program of China (2016YFD0100506) and the Fundamental Research Funds for the Central Universities (KYZ201301 and KJSY201510).

Author contributions

TH, XX, QX, SX, WX, LX, SX and ZJ carried out the experiments. TH drafted the manuscript. TH and XX conceived and designed the study and finalized the manuscript. All the authors have read and approved the final manuscript.

Supplementary material

11103_2018_800_MOESM1_ESM.xlsx (57 kb)
Supplementary material 1 (XLSX 57 KB)
11103_2018_800_MOESM2_ESM.xlsx (269 kb)
Supplementary material 2 (XLSX 269 KB)

References

  1. Arondel V, Lemieux B, Hwang I, Gibson S, Goodman HM, Somerville CR (1992) Map-based cloning of a gene controlling omega-3 fatty acid desaturation in arabidopsis. Science 258:1353–1355CrossRefGoogle Scholar
  2. Baud S, Mendoza MS, To A, Harscoët E, Lepiniec L, Dubreucq B (2010) WRINKLED1 specifies the regulatory action of LEAFY COTYLEDON2 towards fatty acid metabolism during seed maturation in Arabidopsis. Plant J 50:825–838CrossRefGoogle Scholar
  3. Beaudoin F, Lacey DJ, Napier JA (1999) The biogenesis of the plant seed oil body: Oleosin protein is synthesised by ER-bound ribosomes. Plant Physiol Biochem 37:481–490CrossRefGoogle Scholar
  4. Beisson F, Koo AJK, Ruuska S, Schwender J, Pollard M, Thelen JJ, Paddock T, Salas JJ, Savage L, Milcamps A (2003) Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database. Plant Physiol 132:681–697CrossRefGoogle Scholar
  5. Bocianowski J, Mikoإéajczyk K, Bartkowiak-Broda I (2012) Determination of fatty acid composition in seed oil of rapeseed (Brassica napus L.) by mutated alleles of the FAD3 desaturase genes. J Appl Genet 53:27–30CrossRefGoogle Scholar
  6. Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Correa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VH, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CH, Wang X, Canaguier A, Chauveau A, Berard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P (2014) Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345:950–953CrossRefGoogle Scholar
  7. Chen W, Chi Y, Taylor NL, Lambers H, Finnegan PM (2010) Disruption of ptLPD1 or ptLPD2, genes that encode isoforms of the plastidial lipoamide dehydrogenase, confers arsenate hypersensitivity in Arabidopsis. Plant Physiol 153:1385–1397CrossRefGoogle Scholar
  8. Dawidowicz-Grzegorzewska A, Podstolski A (1992) Age-related changes in the ultrastructure and membrane properties of Brassica napus L. seeds. AoB Plants 69:39–46Google Scholar
  9. Ekman Å, Hayden DM, Dehesh K, Bülow L, Stymne S (2008) Carbon partitioning between oil and carbohydrates in developing oat (Avena sativa L.) seeds. J Exp Bot 59:4247–4257CrossRefGoogle Scholar
  10. Flakelar CL, Prenzler PD, Luckett DJ, Howitt JA (2017) A rapid method for the simultaneous quantification of the major tocopherols, carotenoids, free and esterified sterols in canola (Brassica napus) oil using normal phase liquid chromatography. Food Chem 214:147–155CrossRefGoogle Scholar
  11. Flores T, Karpova O, Su X, Zeng P, Bilyeu K, Sleper DA, Nguyen HT, Zhang ZJ (2008) Silencing of GmFAD3 gene by siRNA leads to low alpha-linolenic acids (18:3) of fad3-mutant phenotype in soybean [Glycine max (Merr.)]. Transgenic Res 17:839–850CrossRefGoogle Scholar
  12. Hannoufa A, Pillai BVS, Chellamma S (2014) Genetic enhancement of Brassica napus seed quality. Transgenic Res 23:39CrossRefGoogle Scholar
  13. Harper AL, Trick M, Higgins J, Fraser F, Clissold L, Wells R, Hattori C, Werner P, Bancroft I (2012) Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol 30:798–802CrossRefGoogle Scholar
  14. Hu Y, Wu G, Cao Y, Wu Y, Xiao L, Li X, Lu C (2009) Breeding response of transcript profiling in developing seeds of Brassica napus. BMC Mol Biol 10:49CrossRefGoogle Scholar
  15. Hua W, Li RJ, Zhan GM, Liu J, Li J, Wang XF, Liu GH, Wang HZ (2012) Maternal control of seed oil content in Brassica napus: the role of silique wall photosynthesis. Plant J 69:432CrossRefGoogle Scholar
  16. Hua S, Chen ZH, Zhang Y, Yu H, Lin B, Zhang D (2014) Chlorophyll and carbohydrate metabolism in developing silique and seed are prerequisite to seed oil content of Brassica napus L. Bot Stud 55:34CrossRefGoogle Scholar
  17. Jako C, Kumar A, Wei Y, Zou J, Barton DL, Giblin EM, Covello PS, Taylor DC (2001) Seed-specific over-expression of an Arabidopsis cDNA encoding a diacylglycerol acyltransferase enhances seed oil content and seed weight. Plant Physiol 126:861CrossRefGoogle Scholar
  18. Li Z, Cheng Y, Cui J, Zhang P, Zhao H, Hu S (2015) Comparative transcriptome analysis reveals carbohydrate and lipid metabolism blocks in Brassica napus L. male sterility induced by the chemical hybridization agent monosulfuron ester sodium. BMC Genom 16:206CrossRefGoogle Scholar
  19. Li Z, Hua S, Zhang D, Yu H, Zhang Y, Lin B, Jiang L (2016) Comparison on the carbohydrate metabolic enzyme activities and their gene expression patterns in canola differing seed oil content. Plant Growth Regul 78:357–369CrossRefGoogle Scholar
  20. Malik MR, Wang F, Dirpaul JM, Zhou N, Polowick PL, Ferrie AMR, Krochko JE (2007) Transcript profiling and identification of molecular markers for early microspore embryogenesis in Brassica napus. Plant Physiol 144:134–154CrossRefGoogle Scholar
  21. Mandal S, Yadav S, Singh R, Begum G, Suneja P, Singh M (2002) Correlation studies on oil content and fatty acid profile of some Cruciferous species. Genet Resour Crop Evol 49:551–556CrossRefGoogle Scholar
  22. Niu Y, Wu G-Z, Ye R, Lin W-H, Shi Q-M, Xue L-J, Xu X-D, Li Y, Du Y-G, Xue H-W (2009) Global analysis of gene expression profiles in Brassica napus developing seeds reveals a conserved lipid metabolism regulation with Arabidopsis thaliana. Mol Plant 2:1107–1122CrossRefGoogle Scholar
  23. Ohlrogge J, Browse J (1995) Lipid biosynthesis. Plant Cell 7:957–970CrossRefGoogle Scholar
  24. Pouvreau B, Baud S, Vernoud V, Morin V, Py C, Gendrot G, Pichon JP, Rouster J, Paul W, Rogowsky PM (2011) Duplicate maize Wrinkled1 transcription factors activate target genes involved in seed oil biosynthesis. Plant Physiol 156:674–686CrossRefGoogle Scholar
  25. Rakopoulos DC, Rakopoulos CD, Giakoumis EG (2015) Impact of properties of vegetable oil, bio-diesel, ethanol and n-butanol on the combustion and emissions of turbocharged HDDI diesel engine operating under steady and transient conditions. Fuel 156:1–19CrossRefGoogle Scholar
  26. Rathke GW, Behrens T, Diepenbrock W (2006) Integrated nitrogen management strategies to improve seed yield, oil content and nitrogen efficiency of winter oilseed rape (Brassica napus L.): a review. Agric Ecosyst Environ 117:80–108CrossRefGoogle Scholar
  27. Roesler K, Shintani D, Savage L, Boddupalli S, Ohlrogge J (1997) Targeting of the Arabidopsis homomeric acetyl-coenzyme A carboxylase to plastids of rapeseeds. Plant Physiol 113:75CrossRefGoogle Scholar
  28. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34:374–378CrossRefGoogle Scholar
  29. Schwender J, Ohlrogge JB (2002) Probing in vivo metabolism by stable isotope labeling of storage lipids and proteins in developing Brassica napus embryos. Plant Physiol 130:347CrossRefGoogle Scholar
  30. Semenkovich CF (1997) Regulation of fatty acid synthase (FAS). Prog Lipid Res 36:43–53CrossRefGoogle Scholar
  31. Slocombe SP, Piffanelli P, Fairbairn D, Bowra S, Hatzopoulos P, Tsiantis M, Murphy DJ (1994) Temporal and tissue-specific regulation of a Brassica napus stearoyl-acyl carrier protein desaturase gene. Plant Physiol 104:1167–1176CrossRefGoogle Scholar
  32. Tan H, Yang X, Zhang F, Zheng X, Qu C, Mu J, Fu F, Li J, Guan R, Zhang H (2011) Enhanced seed oil production in canola by conditional expression of Brassica napus LEAFY COTYLEDON1 and LEC1-LIKE in developing seeds. Plant Physiol 156:1577–1588CrossRefGoogle Scholar
  33. Tan H, Xie Q, Xiang X, Li J, Zheng S, Xu X, Guo H, Ye W (2015) Dynamic metabolic profiles and tissue-specific source effects on the metabolome of developing seeds of Brassica napus. PLoS ONE 10:e0124794CrossRefGoogle Scholar
  34. Tan H, Xiang X, Tang J, Wang X (2016) Nutritional functions of the funiculus in Brassica napus seed maturation revealed by transcriptome and dynamic metabolite profile analyses. Plant Mol Biol 92:539–553CrossRefGoogle Scholar
  35. Turnham E, Northcote DH (1983) Changes in the activity of acetyl-CoA carboxylase during rape-seed formation. Biochem J 212:223–229CrossRefGoogle Scholar
  36. Voelker T, Kinney AJ (2001) Variations in the biosynthesis of seed-storage lipids. Annu Rev Plant Physiol Plant Mol Biol 52:335CrossRefGoogle Scholar
  37. Wang C, Hai J, Yang J, Tian J, Chen W, Chen T, Luo H, Wang H (2016) Influence of leaf and silique photosynthesis on seeds yield and seeds oil quality of oilseed rape (Brassica napus L.). Eur J Agron 74:112–118CrossRefGoogle Scholar
  38. Woodfield HK, Sturtevant D, Borisjuk L, Munz E, Guschina IA, Chapman K, Harwood JL (2017) Spatial and temporal mapping of key lipid species in Brassica napus seeds. Plant Physiol 173:1998–2009CrossRefGoogle Scholar
  39. Woodfield HK, Cazenave-Gassiot A, Haslam RP, Guschina IA, Wenk MR, Harwood JL (2018) Using lipidomics to reveal details of lipid accumulation in developing seeds from oilseed rape (Brassica napus L.). Biochim Biophys Acta Mol Cell Biol Lipids 1863:339–348CrossRefGoogle Scholar
  40. Zou J, Katavic V, Giblin EM, Barton DL, Mackenzie SL, Keller WA, Hu X, Taylor DC (1997) Modification of seed oil content and acyl composition in the brassicaceae by expression of a yeast sn-2 acyltransferase (SLC1-1) gene. Plant Cell 9:909CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
  2. 2.Plant Sciences Division, School of BiosciencesUniversity of NottinghamLoughboroughUK
  3. 3.College of Life SciencesShanxi Agricultural UniversityTaiguChina
  4. 4.Animal Sciences National Teaching Demonstration CenterNanjing Agricultural UniversityNanjingChina

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