Transcription analysis of apple fruit development using cDNA microarrays

Tree Genetics and Genomes

Volumn 5, Issue 4, 2009, Pages 685-698

  Soglio, V ^a   Costa, F ^b,c   Molthoff, J W ^d   Weemen Hendriks, W M J ^d   Schouten, H J ^d   Gianfranceschi, L ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

^c RESEARCH AND INNOVATION CENTRE   (Italy)

^d WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

CDNA microarray; Fruit development; Malus x domestica Borkh

Indexed keywords

MALUS X DOMESTICA;

EID: 70349502120     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-009-0219-8     Document Type: Article

References (46)

1. Adams-Phillips L, Barry C, Giovannoni J (2004) Signal transduction systems regulating fruit ripening. Trends Plant Sci 9:331-338
2. Alba R, Fei Z, Payton P, Liu Y, Moore SL, Debbie P, Cohn J, D'Ascenzo M, Gordon JS, Rose JKC, Martin G, Tanksley SD, Bouzayen M, Jahn MM, Giovannoni J (2004) ESTs cDNA microarrays and gene expression profiling: tools for dissecting plant physiology and development. Plant J 39:697-714
3. Alba R, Payton P, Fei Z, McQuinn R, Debbie P, Martin GB, Tanksley SD, Giovannoni JJ (2005) Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. Plant Cell 17:2954-2965
4. Alexander L, Grierson D (2002) Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening. J Exp Bot 53:2039-2055
5. Beekwilder J, Alvarez-Huerta M, Neef E, Verstappen FWA, Bouwmeester HJ, Aharoni A (2004) Functional characterization of enzymes forming volatile esters from strawberry and banana. Plant Physiol 135:1865-1878
6. Berüter J (2004) Carbohydrate metabolism in two apple genotypes that differ in malate accumulation. J Plant Physiol 161:1011-1029
7. Calenge F, Drouet D, Denancé C, van de Weg WE, Brisset M, Paulin J, Durel C (2005) Identification of a major QTL together with several minor additive or epistatic QTLs for resistance to fire blight in apple in two related progenies. Theor Appl Genet 111:128-135
8. Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55:1671-1685
9. Cercós M, Soler G, Iglesias DJ, Gadea J, Forment J, Talón M (2006) Global analysis of gene expression during development and ripening of citrus fruit flesh. A proposed mechanism for citric acid utilization. Plant Mol Biol 62:513-527
10. Chang C, Shockey JA (1999) The ethylene-response pathway: signal perception to gene regulation. Curr Opin Plant Biol 2:352-358
11. Clarke JD, Zhu T (2006) Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives. Plant J 45:630-650
12. Davey MW, Kenis K, Keulemans J (2006) Genetic control of fruit vitamin C contents. Plant Physiol 142:343-351
13. Davies KM, Seelye JF, Irving DE, Borst WM, Hurst PL, King GA (1996) Sugar regulation of harvest-related genes in asparagus. Plant Physiol 111:877-883
14. 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 49:414-427
15. Fonseca S, Hackler L, Zvara Á, Ferreira S, Baldé A, Dudits D, Pais MS, Puskás LG (2004) Monitoring gene expression along pear fruit development ripening and senescence using cDNA microarrays. Plant Sci 167:457-469
16. Gao ZS, van de Weg WE, Schaart JG, van Arkel G, Breiteneder H, Hoffmann-Sommergruber K, Gilissen LJWJ (2005) Genomic characterization and linkage mapping of the apple allergen genes Mal d 2 (thaumatin-like protein) and Mal d 4 (profilin). Theor Appl Genet 111:1087-1097
17. Gianfranceschi L, Soglio V (2004) The European project HiDRAS: innovative multidisciplinary approaches to breeding high quality disease resistant apples. Acta Hort 663:327-330
18. Gillaspy G, Ben-David H, Gruissem W (1993) Fruits: a developmental perspective. Plant Cell 5:1439-1451
19. Giovannoni J (2001) Molecular biology of fruit maturation and ripening. Annu Rev Plant Physiol Plant Mol Biol 52:725-749
20. Grimplet J, Romieu C, Audergon J, Marty I, Albagnac G, Lambert P, Bouchet J, Terrier N (2005) Transcriptomic study of apricot fruit (Prunus armeniaca) ripening among 13006 expressed sequence tags. Physiol Plant 125:281-292
21. Guo H, Ecker JR (2003) Plant responses to ethylene gas are mediated by SCF(EBF1/EBF2)-dependent proteolysis of EIN3 transcription factor. Cell 115:667-677
22. Han S, Seo Y, Kim D, Sung S, Kim W (2007) Expression of MdCAS1 and MdCAS2, encoding apple b-cyanoalanine synthase homologs, is concomitantly induced during ripening and implicates MdCASs in the possible role of the cyanide detoxification in Fuji apple (Malus domestica Borkh.) fruit. Plant Cell Rep 26:1321-1331
23. Horn R, Lecouls A, Callahan A, Dandekar A, Garay L, McCord P, Howad W, Chan H, Verde I, Main D, Jung S, Georgi L, Forrest S, Mook J, Zhebentyayeva T, Yu Y, Kim HR, Jesudurai C, Sosinski B, Arús P, Baird V, Parfitt D, Reighard G, Scorza R, Tomkins J, Wing R, Abbott AG (2005) Candidate gene database and transcript map for peach a model species for fruit trees. Theor Appl Genet 110:1419-1428
24. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868-877
25. Janssen BJ, Thodey K, Schaffer RJ, Alba R, Balakrishnan L, Bishop R, Bowen JH, Crowhurst RN, Gleave AP, Ledger S, McArtney S, Pichler FB, Snowden KC, Ward S (2008) Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biol 8:16
26. King GJ, Maliepaard C, Lynn JR, Alston FH, Durel CE, Evans KM, Griffon B, Laurens F, Manganaris AG, Schrevens E, Tartarini S, Verhaegh J (2000) Quantitative genetic analysis and comparison of physical and sensory descriptors relating to fruit flesh firmness in apple (Malus pumila Mill). Theor Appl Genet 100:1074-1084
27. King GJ, Lynn JR, Dover CJ, Evans KM, Seymour GB (2001) Resolution of quantitative trait loci for mechanical measures accounting for genetic variation in fruit texture of apple (Malus pumila Mill.). Theor Appl Genet 102:1227-1235
28. Lee Y, Yu G, Seo YS, Han SE, Choi Y, Kim D, Mok I, Kim WT, Sung S (2007) Microarray analysis of apple gene expression engaged in early fruit development. Plant Cell Rep 26:917-926
29. Liebhard R, Kellerhals M, Pfammatter W, Jertmini M, Gessler C (2003) Mapping quantitative physiological traits in apple (Malus x domestica Borkh.). Plant Mol Biol 52:511-526
30. Maruyama A, Saito K, Ishizawa K (2001) Beta-cyanoalanine synthase and cysteine synthase from potato: molecular cloning biochemical characterization and spatial and hormonal regulation. Plant Mol Biol 46:749-760
31. McClellan CA, Chang C (2008) The role of protein turnover in ethylene biosynthesis and response. Plant Sci 175:24-31
32. Mehrtens F, Kranz H, Bednarek P, Weisshaar B (2005) The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiol 138:1083-1096
33. Moore S, Vrebalov J, Payton P, Giovannoni J (2002) Use of genomics tools to isolate key ripening genes and analyse fruit maturation in tomato. J Exp Bot 53:2023-2030
34. Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EHA, Allan AC, Beuning LL, Bowen JH, Gera E, Jamieson KR, Janssen BJ, Laing WA, McArtney S, Nain B, Ross GS, Snowden KC, Souleyre EJF, Walton EF, Yauk Y (2006) Analyses of expressed sequence tags from apple. Plant Physiol 141:147-166
35. 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
36. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45
37. Pflieger S, Lefebvre V, Causse M (2001) The candidate gene approach in plant genetics: a review. Mol Breed 7:275-291
38. Prior RL (2003) Fruits and vegetables in the prevention of cellular oxidative damage. Am J Clin Nutr 78:570S-578S
39. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana, Totowa, NJ, pp 365-386
40. Schaffer RJ, Friel EN, Souleyre EJF, Bolitho K, Thodey K, Ledger S, Bowen JH, Ma J, Nain B, Cohen D, Gleave AP, Crowhurst RN, Janssen BJ, Yao J, Newcomb RD (2007) A genomics approach reveals that aroma production in apple is controlled by ethylene predominantly at the final step in each biosynthetic pathway. Plant Physiol 144:1899-1912
41. Temussi P (2006) Natural sweet macromolecules: how sweet proteins work. Cel Mol Life Sci 63:1876-1888
42. Trainotti L, Bonghi C, Ziliotto F, Zanin D, Rasori A, Casadoro G, Ramina A, Tonutti P (2006) The use of microarray [μ]PEACH10 to investigate transcriptome changes during transition from pre-climacteric to climacteric phase in peach fruit. Plant Sci 170:606-613
43. Yao Y, Li M, Liu Z, Hao Y, Zhai H (2007) A novel gene screened by cDNA-AFLP approach contributes to lowering the acidity of fruit in apple. Plant Physiol 45:139-145
44. Yokotani N, Tamura S, Nakano R, Inaba A, Kubo Y (2003) Characterization of a novel tomato EIN3-like gene (LeEIL4). J Exp Bot 54:2775-2776
45. Zeng Y, Yang T (2002) RNA isolation from highly viscous samples rich in polyphenols and polysaccharides. Plant Mol Biol Report 20:417-417
46. Zini E, Biasioli F, Gasperi F, Mott D, Aprea E, Märk T, Patocchi A, Gessler C, Komjanc M (2005) QTL mapping of volatile compounds in ripe apples detected by proton transfer reaction-mass spectrometry. Euphytica 145:269-279