Apple Functional Genomics

  • Andrew C. Allan
  • Ross Crowhurst
  • Andrew Gleave
  • Richard Newcomb
  • Robert Schaffer
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 6)

Publicly available databases currently contain in excess of 250,000 Malus sequences (Park et al., 2006), the majority being derived from large-scale sequencing efforts of cDNA libraries from Washington University, United States and HortResearch, New Zealand (Korban et al., 2004, Newcomb et al., 2006). These Malus cDNA libraries have been sequenced to varying depths (Table 1), depending on library quality and novelty, to generate expressed sequence tags (ESTs). Malus cDNA libraries have been generated from material derived from numerous apple genotypes, many of which are cultivars of commercial significance including ‘Braeburn’, ‘Elstar’, ‘Fuji’, ‘Golden Delicious’, ‘Goldrush’, ‘Granny Smith’, ‘Holsteiner Cox’, ‘Red Delicious’, ‘Royal Gala’, ‘Pinkie’, ‘Sciros/Pacific Rose™’ and a number of dwarfing rootstocks. In addition to being derived from a range of genotypes, the Malus cDNA libraries originate from a wide variety of different tissues and developmental time points. For example, libraries have been generated from a staged series of developing and ripening ‘Royal Gala’ fruit, including flower, whole fruit, fruit cortex, skin, and seed samples (Newcomb et al., 2006). Such a series is a valuable resource of genes for experiments aimed at understanding important processes and transformations in fruit development, such as early cell proliferation, cell expansion, and ripening. This series is also of value in identification of genes encoding enzymes and transcription factors involved in the biosynthesis of health and flavor compounds from apple fruit. Other plant tissues sampled include buds, shoots, leaves, roots, phloem, and xylem. As many genes are only expressed in response to external effects, cDNA libraries have also been constructed from tissues, plants, and cell lines that were subjected to abiotic (e.g. fruit stored at high or low temperature and/or under altered atmospheric conditions), and biotic stresses, e.g. infection with the causal agents of some of the most significant bacterial and fungal diseases to affect apple cultivars including Erwinia amylovra (fire blight), Venturia inaequalis (apple scab or black spot) and Phytophthora sp. (root rot).


Codon Usage Apple Fruit Fire Blight Apple Scab Tentative Consensus Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1): 25–29.CrossRefPubMedGoogle Scholar
  2. Chen G, Hackett R, Walker D, Taylor A, Lin Z, Grierson D (2004) Identification of a specific isoform of tomato lipoxygenase (TomloxC) involved in the generation of fatty acid-derived flavour compounds. Plant Physiol 136: 2641–2651.CrossRefPubMedGoogle Scholar
  3. Chevreau E, Lespinasse Y, Gallet M (1985) Inheritance of pollen enzymes and polyploidy origin of apple Malus x domestiva Borkh. Theor Appl Genet 71: 268–277.Google Scholar
  4. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16(6):735–743.CrossRefPubMedGoogle Scholar
  5. Dong YH, Yao JL, Atkinson RG, Putterill JJ, Morris BA, Gardner RC (2000) MDH1: an apple homeobox gene belonging to the BEL1 family. Plant Mol Biol 42(4): 623–633.CrossRefPubMedGoogle Scholar
  6. Espley RV, Hellens RP, Putterill J, Stevenson DE, Kutty-Amma S, Allan AC (2007) Red Colouration in Apple Fruit is Due to the Activity of the MYB Transcription Factor, MdMYB10. Plant J 49(3): 414–427.CrossRefPubMedGoogle Scholar
  7. Fei ZJ, Tang X, Alba RM, White JA, Ronning CM, Martin GB, Tanksley SD, Giovannoni JJ (2004) Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. Plant J 40: 47–59.CrossRefPubMedGoogle Scholar
  8. Foster T, Kirk C, Jones W, Allan AC, Espley R, Karunairetnam S, Rakonjac J (2007) Characterisation of the DELLA subfamily in apple (Malus x domestica Borkh.). Tree Genet Genomes 3:187–197.CrossRefGoogle Scholar
  9. Gleave AP, Ampomah-Dwamena C, Berthold S, Dejnoprat S, Karunairetnam S, Nain N, Wang Y-Y, Crowhurst RN, MacDiarmid RM (2007) Identification and characterisation of primary microRNAs from apple (Malus domestica cv. ‘Royal Gala’) expressed sequence tags. Tree Genetics and Genomes (in press) doi 10.1007/s11295-007-0113-1.Google Scholar
  10. Goes da Silva F, Iandolino A, Al-Kayal F, Bohlmann MC, Cushman MA, Lim H, Ergul A, Figueroa R, Kabuloglu EK, Osborne C, et al. (2005) Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol 139: 574–597.CrossRefGoogle Scholar
  11. Hellens RP, Allan AC, Friel EN, Bolitho K, Grafton K, Templeton MD, Karunairetnam S, Laing WA (2005). Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants. Plant Methods 1: 13 (doi:10.1186/1746-4811-1-13).CrossRefPubMedGoogle Scholar
  12. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27–30.CrossRefPubMedGoogle Scholar
  13. Kitashiba H, Hao YJ, Honda C, Moriguchi T (2005) Two types of spermine synthase gene: MdACL5 and MdSPMS are differentially involved in apple fruit development and cell growth. Gene 361:101–111.CrossRefPubMedGoogle Scholar
  14. Korban SS, Vodkin LO, Liu L, Aldwinkle HS, Carrol N (2004) Towards apple functional genomics: the EST project (abstract no.39. In International Plant and Animal Genomes XII Conference, Genome Sequencing and ESTs section, January 10–14, San Diego.Google Scholar
  15. Lee Y-P, Yu G-H, Seo YS, Han SE, Choi Y-O, Kim D, Mok I-G, Kim WT, Sung S-K (2007) Microarray analysis of apple gene expression engaged in early fruit development. Plant Cell Rep 26(7): 917–926.CrossRefPubMedGoogle Scholar
  16. Mimida N, Kidou SI, Kotoda N (2007) Constitutive expression of two apple (Malus x domestica Borkh.) homolog genes of LIKE HETEROCHROMATIN PROTEIN1 affects flowering time and whole-plant growth in transgenic Arabidopsis. Mol Genet Genomics 2007 Jun 19; [Epub ahead of print].Google Scholar
  17. Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EHA, Allan AC, Beuning LL, Bowen JH, Gera E, Jamieson KR, Janssen BJ, Laing WA, McCartney S, Nain B, Ross GS, Snowden KC, Soulyere EJF, Walton EF, Yauk Y-K (2006) Analyses of expressed sequence tags from apple. Plant Physiol 141:147–166.CrossRefPubMedGoogle Scholar
  18. Park S, Sugimoto N, Larson MD, Beaudry R, van Nocker S (2006) Identification of genes with potential roles in apple fruit development and biochemistry through large-scale statistical analysis of expressed sequence tags. Plant Physiol 141 811–824.CrossRefPubMedGoogle Scholar
  19. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8: 517–527.CrossRefPubMedGoogle Scholar
  20. Souleyre EJF, Greenwood DR, Friel EN, Karunairetnam S, Newcomb RD (2005) An alcohol acyl transferase from apple (cv. Royal Gala), MpAAT1, produces esters involved in apple fruit flavour. FEBS J. 272: 3123–3144.CrossRefGoogle Scholar
  21. Smyth GK, Speed T (2003) Normalization of cDNA microarray data. Methods 31: 265–273.CrossRefPubMedGoogle Scholar
  22. Takos AM, Jaffe FW, Jacob SR, Bogs J, Robinson SP, Walker AR (2006) Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples. Plant Physiol 142(3): 1216–1232.CrossRefPubMedGoogle Scholar
  23. Tuskan G, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Bradshaw) Science 313: 1596–1604.CrossRefPubMedGoogle Scholar
  24. Wada M, Cao QF, Kotoda N, Soejima J, Masuda T (2002) Apple has two orthologues of FLORICAULA/LEAFY involved in flowering. Plant Mol Biol 49(6): 567–577.CrossRefPubMedGoogle Scholar
  25. Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46: 243–259.CrossRefPubMedGoogle Scholar
  26. Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterisation of new plant microRNAs using EST analysis. Cell Res 15: 336–360.CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Andrew C. Allan
    • 1
  • Ross Crowhurst
    • 1
  • Andrew Gleave
    • 1
  • Richard Newcomb
    • 1
  • Robert Schaffer
    • 1
  1. 1.Department of Natural Resources and Environmental SciencesUniversity of IllinoisUrbanaUSA 61801

Personalised recommendations