Exploring the Potential of Genetic Diversity via Proteomics: Past, Present, and Future Perspectives for Banana

  • S. CarpentierEmail author
Part of the Sustainable Development and Biodiversity book series (SDEB, volume 7)


KU Leuven is hosting the Global Collection of banana (Musa spp.) managed by Bioversity International for safe storage and distribution. Our mandate is to secure the crop’s gene pool and encourage its use. The latter, however, requires an in-depth knowledge of the variability among the varieties and their potential. Most edible varieties are sterile and triploid involving the parental A genome of Musa acuminata and/or the parental B genome of Musa balbisiana, with hybrid genomes (AAA, AAB or ABB). A very efficient way of characterising the genetic diversity in search of interesting traits is analysing the different genomes via next generation sequencing (NGS) techniques. However, population-based associations to the genome are challenging in banana and need to fall back on crossing fertile inedible diploids. Moreover, proteins and metabolites are the main determinants of a trait/phenotype and finding correlations between the genome or transcriptome and a phenotype can be quite challenging. Therefore, proteomics is quite complementary to characterize the biodiversity and find correlations between a phenotype and the genotype. To characterize and evaluate Musa varieties belonging to different genomic groups and exploring their potential, we have been optimizing proteomics techniques over the years. This chapter gives a brief overview of what proteomics is, its challenges and recent improvements, and applications of proteomics approaches used in banana research.


Genetic diversity Proteomics Hybrid genomes Musa balbisiana Musa acuminate A genome B genome 



Financial support from ‘CIALCA’ and the Bioversity International project ‘ITC characterization’ (research projects financed by the Belgian Directorate-General for Development Cooperation (DGDC)) is gratefully acknowledged.


  1. Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I (2003) A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3(1):36–44CrossRefPubMedGoogle Scholar
  2. Buts K, Michielssens S, Hertog ML, Hayakawa E, Cordewener J, America AH, Nicolai BM, Carpentier SC (2014) Improving the identification rate of data independent label-free quantitative proteomics experiments on non-model crops: a case study on apple fruit. J Proteomics 105:31–45CrossRefPubMedGoogle Scholar
  3. Carpentier SC, America T (2014) Proteome analysis of orphan plant species, fact or fiction? Methods Mol Biol 1072:333–346CrossRefPubMedGoogle Scholar
  4. Carpentier SC, Witters E, Laukens K, Deckers P, Swennen R, Panis B (2005) Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis. Proteomics 5(10):2497–2507CrossRefPubMedGoogle Scholar
  5. Carpentier SC, Dens K, Van den houwe I, Van den houwe R, B B (2007) Lyophilization, a practical way to store and transport tissues prior to protein extraction for 2DE analysis? Proteomics 7(S1):64–69CrossRefPubMedGoogle Scholar
  6. Carpentier SC, Coemans B, Podevin N, Laukens K, Witters E, Matsumura H, Terauchi R, Swennen R, Panis B (2008a) Functional genomics in a non-model crop: transcriptomics or proteomics? Physiol Plant 133(2):117–130CrossRefPubMedGoogle Scholar
  7. Carpentier SC, Panis B, Vertommen A, Swennen R, Sergeant K, Renaut J, Laukens K, Witters E, Samyn B, Devreese B (2008b) Proteome analysis of non-model plants: a challenging but powerful approach. Mass Spectrom Rev 27(4):354–377CrossRefPubMedGoogle Scholar
  8. Carpentier SC, Swennen R, Panis B (2009) Plant protein sample preparation for 2DE. In: Walker JM (ed) The protein protocols handbook. Humana Press, Totowa, pp 107–117Google Scholar
  9. Carpentier SC, Panis B, Renaut J, Samyn B, Vertommen A, Vanhove A, Swennen R, Sergeant K (2011a) The use of 2D-electrophoresis and de novo sequencing to characterize inter- and intra-cultivar protein polymorphisms in an allopolyploid crop. Phytochemistry 72(10):1243–1250CrossRefPubMedGoogle Scholar
  10. Carpentier SC, Panis B, Renaut J, Samyn B, Vertommen A, Vanhove AC, Swennen R, Sergeant K (2011b) The use of 2D-electrophoresis and de novo sequencing to characterize inter- and intra-cultivar protein polymorphisms in an allopolyploid crop. Phytochemistry 72(10):1243–1250CrossRefPubMedGoogle Scholar
  11. Chelius D, Bondarenko PV (2002) Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res 1(4):317–323CrossRefPubMedGoogle Scholar
  12. Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J (2013) A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids. BMC Genom 14:683CrossRefGoogle Scholar
  13. De Langhe E, Hřibová E, Carpentier S, Doležel J, Swennen R (2010) Did backcrossing contribute to the origin of hybrid edible bananas? Ann BotGoogle Scholar
  14. D’Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengelle J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, McKain MR, Leebens-Mack J, Burgess D, Freeling M, Mbeguie AMD, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quetier F, Yahiaoui N, Wincker P (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217CrossRefPubMedGoogle Scholar
  15. Domon B, Aebersold R (2006) Mass spectrometry and protein analysis. Science 312(5771):212–217CrossRefPubMedGoogle Scholar
  16. Ducret A, Van Oostveen I, Eng JK, Yates JR, Aebersold R (1998) High throughput protein characterization by automated reverse-phase chromatography electrospray tandem mass spectrometry. Protein Sci 7(3):706–719CrossRefPubMedPubMedCentralGoogle Scholar
  17. Ekanayake IJ, Ortiz R, Vuylsteke DR (1994) Influence of leaf age, soil moisture, VPD and time of day on leaf conductance of various Musa Genotypes in a humid forest-moist savanna transition site. Ann Bot 74(2):173–178CrossRefGoogle Scholar
  18. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for mass-spectrometry of large biomolecules. Science 246(4926):64–71CrossRefPubMedGoogle Scholar
  19. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100(12):6940–6945CrossRefPubMedPubMedCentralGoogle Scholar
  20. Gooding PS, Bird C, Robinson SP (2001) Molecular cloning and characterisation of banana fruit polyphenol oxidase. Planta 213(5):748–757CrossRefPubMedGoogle Scholar
  21. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17(10):994–999CrossRefPubMedGoogle Scholar
  22. Henry IM, Carpentier SC, Pampurova S, Van Hoylandt A, Panis B, Swennen R, Remy S (2011) Structure and regulation of the Asr gene family in banana. Planta 234(4):785–798CrossRefPubMedPubMedCentralGoogle Scholar
  23. Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci USA 90(11):5011–5015CrossRefPubMedPubMedCentralGoogle Scholar
  24. Heslop-Harrison JS, Schwarzacher T (2007) Domestication, genomics and the future for banana. Ann Bot 100(5):1073–1084CrossRefPubMedPubMedCentralGoogle Scholar
  25. Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 Daltons. Anal Chem 60(20):2299–2301CrossRefPubMedGoogle Scholar
  26. Kelstrup CD, Young C, Lavallee R, Nielsen ML, Olsen JV (2012) Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer. J Proteome Res 11(6):3487–3497CrossRefPubMedGoogle Scholar
  27. Klose J (1975) Protein mapping by combined isoelectric focusing and electrophoresis in mouse tissues: a novel approach to test for induced point mutations in mammals. Humangenetik 26:231–243PubMedGoogle Scholar
  28. Lebedev AT, Damoc E, Makarov AA, Samgina TY (2014) Discrimination of leucine and isoleucine in peptides sequencing with Orbitrap Fusion mass spectrometer. Anal Chem 86(14):7017–7022CrossRefPubMedGoogle Scholar
  29. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR (1999) Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17(7):676–682CrossRefPubMedGoogle Scholar
  30. Liska AJ, Shevchenko A (2003) Expanding the organismal scope of proteomics: cross-species protein identification by mass spectrometry and its implications. Proteomics 3(1):19–28CrossRefPubMedGoogle Scholar
  31. Liu J, Bell AW, Bergeron JJ, Yanofsky CM, Carrillo B, Beaudrie CE, Kearney RE (2007) Methods for peptide identification by spectral comparison. Proteome Sci 5:3CrossRefPubMedPubMedCentralGoogle Scholar
  32. Makarov A, Denisov E, Kholomeev A, Balschun W, Lange O, Strupat K, Horning S (2006) Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal Chem 78(7):2113–2120CrossRefPubMedGoogle Scholar
  33. Mann M, Kelleher NL (2008) Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci U S A 105(47):18132–18138CrossRefPubMedPubMedCentralGoogle Scholar
  34. McCormack AL, Schieltz DM, Goode B, Yang S, Barnes G, Drubin D, Yates JR (1997) Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal Chem 69(4):767–776CrossRefPubMedGoogle Scholar
  35. Michalski A, Damoc E, Hauschild JP, Lange O, Wieghaus A, Makarov A, Nagaraj N, Cox J, Mann M, Horning S (2011) Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics 10(9):M111 011015Google Scholar
  36. Nesvizhskii AI, Aebersold R (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics 4(10):1419–1440CrossRefPubMedGoogle Scholar
  37. O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250(10):4007–4021PubMedPubMedCentralGoogle Scholar
  38. Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M (2007) Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods 4(9):709–712CrossRefPubMedGoogle Scholar
  39. Olsen JV, Schwartz JC, Griep-Raming J, Nielsen ML, Damoc E, Denisov E, Lange O, Remes P, Taylor D, Splendore M, Wouters ER, Senko M, Makarov A, Mann M, Horning S (2009) A dual pressure linear ion trap orbitrap instrument with very high sequencing speed. Mol Cell Proteomics 8(12):2759–2769CrossRefPubMedPubMedCentralGoogle Scholar
  40. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376–386CrossRefPubMedGoogle Scholar
  41. Panis B, Totte N, Van Nimmen K, Withers LA, Swennen R (1996) Cryopreservation of banana (Musa spp.) meristems cultures after preculture on sucrose. Plant Sci 21:95–106CrossRefGoogle Scholar
  42. Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ (2012) Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteomics 11(11):1475–1488CrossRefPubMedPubMedCentralGoogle Scholar
  43. Plumb RS, Johnson KA, Rainville P, Smith BW, Wilson ID, Castro-Perez JM, Nicholson JK (2006) UPLC/MS (E); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun Mass Spectrom 20(13):1989–1994CrossRefPubMedGoogle Scholar
  44. Samyn B, Sergeant K, Carpentier S, Debyser G, Panis B, Swennen R, Van Beeumen J (2007) Functional proteome analysis of the banana plant (Musa spp.) using de novo sequence analysis of derivatized peptides. J Proteome Res 6(1):70–80CrossRefPubMedGoogle Scholar
  45. Schatz MC, Witkowski J, McCombie WR (2012) Current challenges in de novo plant genome sequencing and assembly. Genome Biol 13(4):243CrossRefPubMedPubMedCentralGoogle Scholar
  46. Scheele GA (1975) Two-dimensional gel analysis of soluble proteins: charaterization of guinea pig exocrine pancreatic proteins. J Biol Chem 250(14):5375–5385PubMedGoogle Scholar
  47. Simmonds NW, Sheppard K (1955) The taxonomy and origins of cultivated bananas. Bot J Linn Soc 55:302–312CrossRefGoogle Scholar
  48. Thomas DS, Turner D, Eamus D (1998) Independent effects of the environment on the leaf gas exchange of three banana (Musa spp.) cultivars of different genomic constitution. Sci Hortic 75(1–2):41–57CrossRefGoogle Scholar
  49. Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75(8):1895–1904CrossRefPubMedGoogle Scholar
  50. Tiselius A (1937) Trans Faraday Soc 33:524–531CrossRefGoogle Scholar
  51. Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18(11):2071–2077CrossRefPubMedGoogle Scholar
  52. Van den houwe I, De Smet K, Tezenas du Montcel H, Swennen R (1995) Variability in storage potential of banana shoot cultures under medium term storage conditions. Plant Cell, Tissue Organ Cult 42:269–274CrossRefGoogle Scholar
  53. Vanhove A, Garcia S, Swennen R, Panis B, Carpentier SC (2012) Understanding Musa drought stress physiology using an autotrophic growth system. Commun Agric Appl Biol Sci 77(1):89–93PubMedGoogle Scholar
  54. Vanhove A, Vermaelen, W, Swennen R, Carpentier S (2015) A look behind the screens: characterization of the HSP70 family during osmotic stress in a non-model crop. J Proteomics, 119:10–20Google Scholar
  55. Vertommen A, Panis B, Swennen R, Carpentier SC (2010) Evaluation of chloroform/methanol extraction to facilitate the study of membrane proteins of non-model plants. Planta 231(5):1113–1125CrossRefPubMedPubMedCentralGoogle Scholar
  56. Vertommen A, Møller ALB, Cordewener JHG, Swennen R, Panis B, Finnie C, America AHP, Carpentier SC (2011a) A workflow for peptide-based proteomics in a poorly sequenced plant: a case study on the plasma membrane proteome of banana. J Proteomics 74(8):1218–1229CrossRefPubMedGoogle Scholar
  57. Vertommen A, Panis B, Swennen R, Carpentier SC (2011b) Challenges and solutions for the identification of membrane proteins in non-model plants. J Proteomics 74(8):1165–1181CrossRefPubMedGoogle Scholar
  58. Washburn MP, Wolters D, Yates JR (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19(3):242–247CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Department of Biosystems, Division of Crop BiotechnicsKU LeuvenLouvainBelgium
  2. 2.SYBIOMA: Facility for Systems Biology Based Mass SpectrometryKU LeuvenLouvainBelgium

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