Microarray analysis of differentially expressed genes engaged in fruit development between Prunus mume and Prunus armeniaca

Journal of Plant Physiology

Volumn 169, Issue 17, 2012, Pages 1776-1788

  Li, Xiaoying ^a   Korir, Nicholas Kibet ^a   Liu, Lili ^c   Shangguan, Lingfei ^a   Wang, Yuzhu ^b   Han, Jian ^a   Chen, Ming ^c   Fang, Jinggui ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT AND ENVIRONMENT PROTECTION   (China)

^c ZHEJIANG UNIVERSITY   (China)

Author keywords

Differentially expressed genes; Fruit; Microarray; Prunus armeniaca; Prunus mume

Indexed keywords

COMPLEMENTARY DNA; PLANT DNA;

ARTICLE; DNA MICROARRAY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; FRUIT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; PLANT GENE; PRUNUS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPECIES DIFFERENCE;

DNA, COMPLEMENTARY; DNA, PLANT; EXPRESSED SEQUENCE TAGS; FRUIT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PRUNUS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

PRUNUS; PRUNUS ARMENIACA; PRUNUS MUME;

EID: 84869086313     PISSN: 01761617     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jplph.2012.07.016     Document Type: Article

References (65)

1. Achnine L., Blancaflor E.B., Rasmussen S., Dixon R.A. Colocalization of l-phenylalanine ammonia-lyase and cinnamate 4-hydroxylase for metabolic channeling in phenylpropanoid biosynthesis. Plant Cell 2004, 16:3098-3109.
2. Aharoni A., Keizer L.C.P., Bouwmeester H.J., Sun Z., Alvarez-Huerta M., Verhoeven H.A., et al. Identification of the SAAT gene involved in strawberry flavour biogenesis by use of DNA microarrays. Plant Cell 2000, 12:647-662.
3. Aharoni A., O'Connell A. Gene expression analysis of strawberry achene and receptacle maturation using DNA microarrays. J Exp Bot 2002, 53:2073-2087.
4. Aharoni A., Vorst O. DNA microarrays for functional plant genomics. Plant Mol Biol 2002, 48:99-118.
5. Alba R., Zhang F., Payton P., Liu Y., Moore S.L., Debbie P., et al. ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant J 2004, 39:697-714.
6. Baumann K., Perez-Rodriguez M., Bradley D., Venail J., Bailey P., Jin H., et al. Control of cell and petal morphogenesis by R2R3 MYB transcription factors. Development 2007, 134(9):1691-1701.
7. Beekwilder J., Alvarez-Huerta M., Neef E., Verstappen F.W., Bouwmeester H.J., Aharoni A. Functional characterization of enzymes forming volatile esters from strawberry and banana. Plant Physiol 2004, 135:1865-1878.
8. Bomal C., Giguère I., Caron S., Boyle B., Fortin É., Duval I., et al. Competing MYB networks as switches in primary and secondary metabolism in spruce. BMC Proc 2011, 5(Suppl. 7):P63.
9. Bonghi C., Ferrarese L., Ruperti B., Tonutti P., Ramina A. Endo-β-1,4-glucanases are involved in peach fruit growth and ripening, and regulated by ethylene. Physiol Plant 1998, 102:346-352.
10. Brummell D.A. Cell wall disassembly in ripening fruit. Funct Plant Biol 2006, 33:103-119.
11. Brummell D.A., Cin V.D., Crisosto C.H., Labavitch J.M. Cell wall metabolism during maturation, ripening and senescence of peach fruit. J Exp Bot 2004, 55:2029-2039.
12. Brummell D.A., Harpster M.H. Cell wall metabolism in fruit softening and quality and its manipulation in transgenic plants. Plant Mol Biol 2001, 47:311-340.
13. Burbidge A., Grieve T., Terry C., Corlett J., Thompson A., Taylor I. Structure and expression of a cDNA encoding zeaxanthin epoxidase, isolated from a wilt-related tomato (Lycopersicon esculentum Mill.) library. J Exp Bot 1997, 48(314):1749-1750.
14. Chu M.Y. China fruit records - mei 1999, China Forestry Press, Beijing, [in Chinese].
15. Clarke J.D., Zhu T. Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives. Plant J 2006, 45:630-650.
16. Cuzin M. DNA chips: a new tool for genetic analysis and diagnostics. Transfus Clin Biol 2001, 8:291-296.
17. Defilippi B.G., Dandekar A.M., Kader A.A. Relationship of ethylene biosynthesis to volatile production, related enzymes, and precursor availability in apple peel and flesh tissues. J Agric Food Chem 2005, 53:3133-3141.
18. Degenhardt J., Nasser A., Al-Masri A.N., Kürkcüoglu S., Szankowski I., Gau A.E. Characterization by suppression subtractive hybridization of transcripts that are differentially expressed in leaves of apple scab-resistant and susceptible cultivars of Malus domestica. Mol Gen Genomics 2005, 273:326-333.
19. Duggan D.J., Bittner M., Chen Y., Meltzer P., Trent J.M. Expression profiling using cDNA microarrays. Nat Genet 1999, 21:10-14.
20. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci 1998, 95:14863-14868.
21. Fang J., Devanand P., Chao C. Practical strategy of single-nucleotide-polymorphism discovery in fruiting-mei (Prunus mume Sieb. et Zucc.) from amplified-fragment-length-polymorphism fragments. Plant Mol Bio Rep 2005, 23:227-239.
22. Fang J., Tao J., Chao C. The genetic diversity of mei, apricot, plum, and peach revealed by AFLP. J Hortic Sci Biotechnol 2006, 81:898-902.
23. Fang J., Twito T., Zhang Z., Chao C. Genetic relationships among fruiting-mei (Prunus mume Sieb. et Zucc.) cultivars evaluated with AFLP and SNP markers. Genome 2006, 40:1256-1264.
24. Frick U.B., Schaller A. cDNA microarray analysis of fusicoccin-induced changes in gene expression in tomato plants. Planta 2002, 216:83-94.
25. Fonseca S., Hackler L., Zvara A., Ferreira S., Balde A., Dudits D., et al. Monitoring gene expression along pear fruit development, ripening and senescence using cDNA microarrays. Plant Sci 2005, 167:457-469.
26. Grimplet J., Romieu C., Audergon J.M., Marty I., Albagnac G., Lambert P., et al. Transcriptomic study of apricot fruit (Prunus armeniaca) ripening among 13,006 expressed sequence tags. Physiol Plant 2005, 125:281-292.
27. Gross K.C., Sams C.E. Changes in cell wall neutral sugar composition during fruit ripening: a species survey. Phytochemistry 1984, 23:2457-2461.
28. Hayama H., Shimada T., Fujii H., Ito A., Kashimura Y. Ethylene regulation of softening and softening-related genes in peach. J Exp Bot 2006, 57:4071-4077.
29. Hormaza J.I. Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. Theor Appl Genet 2002, 104:321-328.
30. Hovav R., Udall J.A., Hovav E., Rapp R.F.L., Wendel J.F. A majority of cotton genes are expressed in single-celled fiJ F. Planta 2008, 227:319-329.
31. Jung C., Seo J.S., Han S.W., Koo Y.J., Kim C.H., Song S.I., et al. Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic arabidopsis. Plant Physiol 2008, 146:623-635.
32. Keller B., Emrich K., Hoecker N., Sauer M., Hochholdinger F., Piepho H.P. Designing a microarray experiment to estimate dominance in maize (Zea mays L.). Theor Appl Genet 2005, 111:57-64.
33. Laitinen R.A.E., Pöllänen E., Teeri T.H., Elomaa P., Kotilainen M. Transcriptional analysis of petal organogenesis in Gerbera hybrid. Planta 2007, 226:347-360.
34. Lee D.H., Kang S.G., Suh S.G., Byun J.K. Purification and characterization of a β-galactosidase from peach (Prunus persica). Mol Cells 2003, 15:68-74.
35. Lee Y., Yu G., Seo Y.S., Han S.E., Choi Y., Kim D., et al. Microarray analysis of apple gene expression engaged in early fruit development. Plant Cell Rep 2007, 26:917-926.
36. Li X., Wang Y., Wang B., Wang C., Shangguan L., Huang Z., et al. Genetic relationships between fruiting and flowering mei (Prunus mume) cultivars using SNP markers. J Hortic Sci Biotechnol 2010, 85:329-334.
37. Liu C.J., Dixon R.A. Elicitor-induced association of isoflavone O-methyltransferase with endomembranes prevents the formation and 7-O-methylation of daidzein during isoflavonoid phytoalexin biosynthesis. Plant Cell 2001, 13:2643-2658.
38. Lu Y. Discussion on translation of Prunus mume name into English. J Beijing Forestry Univ 2000, 17-18. [The International Symposium on Mei and Wintersweets' Culture Special Issue].
39. Ludwików A., Kierzek D., Gallois P., Zeef L., Sadowski J. Gene expression proWling of ozone-treated arabidopsis abi1td insertional mutant: protein phosphatase 2C ABI1 modulates biosynthesis ratio of ABA and ethylene. Planta 2009, 230:1003-1017.
40. Luo M., Liang X.Q., Dang P., Holbrook C.C., Bausher M.G., Lee R.D., et al. Microarray-based screening of differentially expressed genes in peanut in response to Aspergillus parasiticus infection and drought stress. Plant Sci 2005, 169:695-703.
41. Manrique-Trujillo S.M., Ramírez-López A.C., Ibarra-Laclette E., Gómez-Lim M.A. Identification of genes differentially expressed during ripening of banana. J Plant Physiol 2007, 164(8):1037-1050.
42. Moore S., Vrebalov J., Payton P., Giovannoni J. Use of genomics tools to isolate key ripening genes and analyse fruit maturation in tomato. J Exp Bot 2002, 53:2023-2030.
43. Nobile P.M., Wattebled F., Quecini V., Girardi C.L., Lormeau M., Laurens F. Identification of a novel α-l-arabinofuranosidase gene associated with mealiness in apple. J Exp Bot 2011, 62(12):4309-4321.
44. Ortega-García F., Peragón J. Phenylalanine ammonia-lyase, polyphenol oxidase, and phenol concentration in fruits of Olea europaea L. cv. Picual, Verdial, Arbequina, and Frantoio during ripening. J Agric Food Chem 2009, 57(21):10331-10340.
45. Pressey R., Avants J.K. Separation and characterization of endopolygalacturonase and exopolygalacturonase from peaches. Plant Physiol 1973, 52:252-256.
46. Ramakers C., Ruijtera J.M., Lekane Depreza R.H., Moorman A.F.M. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 2003, 339:62-66.
47. Robles P., Pelaz S. Flower and fruit development in arabidopsis thaliana. Int J Dev Biol 2005, 49:633-643.
48. Salentijn E.M.J., Aharoni A., Schaart J.G., Boone M.J., Krens F.A. Differential gene expression analysis of strawberry cultivars that differ in fruit-firmness. Physiol Plant 2003, 118:571-578.
49. Santo M., Carolina D., Pagano E.A., Sozzi G.O. Differential expression of α-l-arabinofuranosidase and α-l-arabinofuranosidase/β-d-xylosidase genes during peach growth and ripening. Plant Physiol Biochem 2009, 47(7):562-569.
50. Seki M., Narusaka M., Abe H., Kasuga M., Yamaguchi-Shinozaki K., Carninci P., et al. Monitoring the expression pattern of 1300 arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 2001, 13:61-72.
51. Sekine D., Munemura I., Gao M., Mitsuhashi W., Toyomasu T., Murayama H. Cloning of cDNAs encoding cell-wall hydrolases from pear (Pyrus communis) fruit and their involvement in fruit softening and development of melting texture. Physiol Plant 2006, 126:163-174.
52. Shimada T., Fuiii H., Endo T., Yazaki J., Kishimoto N., Shimbo K., et al. Toward comprehensive expression profiling by microarray analysis in citrus: monitoring the expression profiles of 2213 genes during fruit development. Plant Sci 2005, 168:1383-1385.
53. Stutte G.W., Monje O., Hatfield R.D., Ferl A., Simone C.G. Microgravity effects on leaf morphology, cell structure, carbon metabolism and mRNA expression of dwarf wheat. Planta 2006, 224:1038-1049.
54. Tateishi A., Mori H., Watari J., Nagashima K., Yamaki S., Inoue H. Isolation, characterization, and cloning of α-l-arabinofuranosidase expressed during fruit ripening of Japanese pear. Plant Physiol 2005, 138:1653-1664.
55. Terrier N., Glissant D., Grimplet J., Barrieu F., Abbal P., Couture C., et al. Isogene specific oligo arrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.) development. Planta 2005, 222:832-847.
56. Tian L., Kong W.F., Pan Q.H., Zhan J.C., Wen P.F., Chen J.Y., et al. Expression of the chalcone synthase gene from grape and preparation of an anti-CHS antibody. Protein Express Purif 2006, 50(2):223-228.
57. Tuskan G.A., Difazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313(5793):1596-1604.
58. Tuteja N. Abscisic acid and abiotic stress signaling. Plant Signal Behav 2007, 2(3):135-138.
59. Waters D.L.E., Holton T.A., Ablett E.M., Lee L.S., Henry R.J. cDNA microarrays analysis of developing grape (Vitis vinifera cv. Shiraz) berry skin. Funct Integr Genomics 2005, 5:40-58.
60. Wheeler S., Loveys B., Ford C., Davies C. The relationship between the expression of abscisic acid biosynthesis genes, accumulation of abscisic acid and the promotion of Vitis vinifera L. berry ripening by abscisic acid. Aust J Grape Wine Res 2009, 15:195-204.
61. Xu B.Y., Su W., Liu J.H., Wang J.B., Jin Z.Q. Differentially expressed cDNAs at the early stage of banana ripening identified by suppression subtractive hybridization and cDNA microarray. Planta 2007, 226(2):529-539.
62. Zhao J., Wang J., An L., Doerge W., Chen Z.J., Grau C.R., et al. Analysis of gene expression profiles in response to Sclerotinia sclerotiorum in Brassica napus. Planta 2007, 227:13-24.
63. Zheng J., Zhao J., Tao Y., Wang J., Liu Y., Fu J., et al. Isolation and analysis of water stress induced genes in maize seedlings by subtractive PCR and cDNA macroarray. Plant Mol Biol 2004, 55:807-823.
64. Zhuang J.P., Su J., Li X.P., Chen W.X. Changes in α-l-arabinofIuranosidase activity in peel and pulp of banana (Musa sp.) fruits during ripening and softening. J Plant Physiol Mol Biol 2007, 33(2):13l-16l.
65. Ziliotto F., Begheldo M., Rasori A., Bonghi C., Tonutti P. Transcriptome profiling of ripening nectarine (Prunus persica L. Batsch) fruit treated with 1-MCP. J Exp Bot 2008, 59(10):2781-2791.