Multiple models for Rosaceae genomics

Plant Physiology

Volumn 147, Issue 3, 2008, Pages 985-1003

  Shulaev, Vladimir ^a   Korban, Schuyler S ^b   Sosinski, Bryon ^c   Abbott, Albert G ^d   Aldwinckle, Herb S ^e   Folta, Kevin M ^g   Iezzoni, Amy ^h   Main, Dorrie ⁱ   Arús, Pere ^j   Dandekar, Abhaya M ^k   Lewers, Kim ^l   Brown, Susan K ^f   Davis, Thomas M ^m   Gardiner, Susan E ⁿ   Potter, Daniel ^k   Veilleux, Richard E ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

^d CLEMSON UNIVERSITY   (United States)

^e Department of Obstetrics Gynecology   (United States)

^f New York State Agricultural Experiment Station   (United States)

^g Horticultural Sciences Department   (United States)

^h MICHIGAN STATE UNIVERSITY   (United States)

ⁱ WASHINGTON STATE UNIVERSITY   (United States)

^j CENTRE FOR RESEARCH IN AGRICULTURAL GENOMICS CRAG   (Spain)

^k UNIVERSITY OF CALIFORNIA   (United States)

^l AGRICULTURAL RESEARCH SERVICE   (United States)

^m UNIVERSITY OF NEW HAMPSHIRE   (United States)

ⁿ THE NEW ZEALAND INSTITUTE FOR PLANT AND FOOD RESEARCH LIMITED   (New Zealand)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); FRAGARIA; FRAGARIA X ANANASSA; MALUS; MALUS X DOMESTICA; PRUNUS; PRUNUS PERSICA; ROSACEAE;

APPLE; BIODIVERSITY; BIOLOGY; GENETICS; GENOMICS; HUMAN; NUTRITIONAL VALUE; PHYLOGENY; PRUNUS; REVIEW; ROSACEAE; STRAWBERRY;

BIODIVERSITY; COMPUTATIONAL BIOLOGY; FRAGARIA; GENOMICS; HUMANS; MALUS; NUTRITIVE VALUE; PHYLOGENY; PRUNUS; ROSACEAE;

EID: 51549102679     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.107.115618     Document Type: Review

References (180)

1. Aharoni A, Giri AP, Verstappen FWA, Bertea CM, Sevenier R, Sun ZK, Jongsma MA, Schwab W, Bouwmeester HJ (2004) Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species. Plant Cell 16: 3110-3131
2. Aharoni A, Keizer LCP, Bouwmeester HJ, Sun ZK, Alvarez-Huerta M, Verhoeven HA, Blaas J, van Houwelingen A, De Vos RCH, van der Voet H, et al (2000) Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell 12: 647-661
3. Aharoni A, Keizer LCP, Van den Broeck HC, Blanco-Portales R, Munoz-Blanco J, Bois G, Smit P, De Vos RCH, O'Connell AP (2002) Novel insight into vascular, stress, and auxin-dependent and -independent gene expression programs in strawberry, a non-climacteric fruit. Plant Physiol 129: 1019-1031
4. Aharoni A, O'Connell AP (2002) Gene expression analysis of strawberry achene and receptacle maturation using DNA microarrays. J Exp Bot 53: 2073-2087
5. Akiyama Y, Yamamoto Y, Ohmido N, Ohshima M, Fukui K (2001) Estimation of the nuclear DNA content of strawberries (Fragaria spp.) compared with Arabidopsis thaliana by using dual-step flow cytometry. Cytologia (Tokyo) 66: 431-436
6. Albani MC, Battey NH, Wilkinson MJ (2004) The development of ISSR-derived SCAR markers around the SEASONAL FLOWERING LOCUS (SFL) in Fragaria vesca. Theor Appl Genet 109: 571-579
7. Alsheikh MK, Suso HP, Robson M, Battey NH, Wetten A (2002) Appropriate choice of antibiotic and Agrobacterium strain improves transformation of anti biotic-sensitive Fragaria vesca and F.v. semperflorens. Plant Cell Rep 20: 1173-1180
8. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410
9. Aranzana MJ, Pineda A, Cosson P, Dirlewanger E, Ascasibar J, Cipriani G, Ryder CD, Testolin R, Abbott A, King GJ, et al (2003) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theor Appl Genet 106: 819-825
10. Arús P, Howad W, Mnejja M (2003) Marker development and marker-assisted selection in temperate fruit trees. In R Tuberosa, RL Phillips, M Gale, eds, Proceedings of an International Congress: In the Wake of the Double Helix: From the Green Revolution to the Gene Revolution. Avenue Media, Bologna, Italy, pp 309-325
11. Baird WV, Estager AS, Wells JK (1994) Estimating nuclear DNA content in peach and related diploid species using laser flow cytometry and DNA hybridization. J Am Soc Hortic Sci 119: 1312-1316
12. Baldi P, Patocchi A, Zini E, Toller C, Velasco R, Komjanc M (2004) Cloning and linkage mapping of resistance gene homologues in apple. Theor Appl Genet 109: 231-239
13. Ban Y, Honda C, Hatsuyama Y, Igarashi M, Bessho H, Moriguchi T (2007) Isolation and functional analysis of a MYB transcription factor gene that is a key regulator for the development of red coloration in apple skin. Plant Cell Physiol 48: 958-970
14. Beavis W, Gessler D, Rhee S, Rokhsar D, Main D, Mueller L, Eva Huala E, Stein L, Lawrence CJ (2005) Plant Biology Databases: A Needs Assessment - White Paper. Gramene. http://www.gramene.org/resources/plant_databases.pdf (June 2, 2008)
15. Blenda AV, Wechter WP, Reighard GL, Baird WV, Abbott AG (2006) Development and characterisation of diagnostic AFLP markers in Prunus persica for its response to peach tree short life syndrome. J Hortic Sci Biotechnol 81: 281-288
16. Bliss FA, Arulsekar S, Foolad MR, Becerra V, Gillen AM, Warburton ML, Dandekar AM, Kocsisne GM, Mydin KK (2002) An expanded genetic linkage map of Prunus based on an interspecific cross between almond and peach. Genome 45: 520-529
17. Bolar JP, Norelli JL, Harman GE, Brown SK, Aldwinckle HS (2001) Synergistic activity of endochitinase and exochitinase from Trichoderma atroviride (T. harzianum) against the pathogenic fungus (Venturia inaequalis) in transgenic apple plants. Transgenic Res 10: 533-543
18. Bolar JP, Norelli JL, Wong KW, Hayes CK, Harman GE, Aldwinckle HS (2000) Expression of endochitinase from Trichoderma harzianum in transgenic apple increases resistance to apple scab and reduces vigor. Phytopathology 90: 72-77
19. Bringhurst RS (1990) Cytogenetics and evolution in American Fragaria. HortScience 25: 879-881
20. Bus V, Ranatunga C, Gardiner S, Bassett H, Rikkerink E (2000) Marker assisted selection for pest and disease resistance in the New Zealand apple breeding programme. Acta Hortic 538: 541-547
21. Byrne DH (1990) Isozyme variability in four diploid stone fruits compared with other woody perennial plants. J Hered 81: 68-71
22. Calenge F, Van der Linden CG, Van de Weg E, Schouten HJ, Van Arkel G, Denance C, Durel CE (2005) Resistance gene analogues identified through the NBS-profiling method map close to major genes and QTL for disease resistance in apple. Theor Appl Genet 110: 660-668
23. Caragay AB (1992) Cancer-preventive foods and ingredients. Food Technol 46: 65-68
24. Chagné D, Carlisle CM, Blond C, Volz RK, Whitworth CJ, Oraguzie NC, Crowhurst RN, Allan AC, Espley RV, Hellens RP, et al (2007) Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple. BMC Genomics 8: 212
25. Chaparro JX, Werner DJ, Omalley D, Sederoff RR (1994) Targeted mapping and linkage analysis of morphological isozyme, and RAPD markers in peach. Theor Appl Genet 87: 805-815
26. Cipriani G, Pinosa F, Bonoli M, Faedi W(2006) A new set of microsatellite markers for Fragaria species and their application in linkage analysis. J Hortic Sci Biotechnol 81: 668-675
27. Claverie M, Dirlewanger E, Cosson P, Bosselut N, Lecouls AC, Voisin R, Kleinhentz M, Lafargue B, Caboche M, Chalhoub B, et al (2004b) High-resolution mapping and chromosome landing at the root-knot nematode resistance locus Ma from Myrobalan plum using a large-insert BAC DNA library. Theor Appl Genet 109: 1318-1327
28. Cordenunsi BR, do Nascimento JRO, Genovese MI, Lajolo FM (2002) Influence of cultivar on quality parameters and chemical composition of strawberry fruits grown in Brazil. J Agric Food Chem 50: 2581-2586
29. Corredor E, Roman M, Garcia E, Perera E, Arús P, Naranjo T (2004) Physical mapping of rDNA genes establishes the karyotype of almond. Ann Appl Biol 144: 219-222
30. Darrow GM (1966) The strawberry: history, breeding and physiology. Holt, Rinehart and Winston, New York
31. Davis TM, Denoyes-Rothan B, Lerceteau-Kohler E (2007) Strawberry. In C Kole, ed, Genome Mapping and Molecular Breeding in Plants IV: Fruits and Nuts. Springer, Berlin, pp 189-206
32. Davis TM, Folta KM, Shields M, Zhang Q (2008) Gene pair markers: An innovative tool for comparative linkage mapping. In Proceedings of the 6th North American Strawberry Symposium. North American Strawberry Growers Association, Kemptville, Canada (in press)
33. Davis TM, Yu H (1997) A linkage map of the diploid strawberry, Fragaria vesca. J Hered 88: 215-221
34. Debener T, Mattiesch L (1999) Construction of a genetic linkage map for roses using RAPD and AFLP markers. Theor Appl Genet 99: 891-899
35. Debener T, Mattiesch L, Vosman B (2001) A molecular marker map for roses. Acta Hortic 547: 283-287
36. Defilippi BG, Dandekar AM, Kader AA (2004) Impact of suppression of ethylene action or biosynthesis on flavor metabolites in apple (Malus domestica Borkh) fruits. J Agric Food Chem 52: 5694-5701
37. Defilippi BG, Kader AA, Dandekar AM (2005) Apple aroma: alcohol acyltransferase, a rate limiting step for ester biosynthesis, is regulated by ethylene. Plant Sci 168: 1199-1210
38. Dettori MT, Quarta R, Verde I (2001) A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers. Genome 44: 783-790
39. Dirlewanger E, Cosson P, Bouderhi K, Renaud C, Capdeville G, Tauzin Y, Laigret F, Moing A (2006) Development of a second-generation genetic linkage map for peach [Prunus persica (L.) Batsch] and characterization of morphological traits affecting flower and fruit. Tree Genet Genomes 3: 1-13
40. Dirlewanger E, Cosson P, Howad W, Capdeville G, Bosselut N, Claverie M, Voisin R, Poizat C, Lafargue B, Baron O, et al (2004a) Microsatellite genetic linkage maps of myrobalan plum and an almond-peach hybrid - location of root-knot nematode resistance genes. Theor Appl Genet 109: 827-838
41. Dirlewanger E, Cosson P, Tavaud M, Aranzana MJ, Poizat C, Zanetto A, Arús P, Laigret F (2002) Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theor Appl Genet 105: 127-138
42. Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howad W, Arús P (2004b) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 101: 9891-9896
43. Dominguez I, Graziano E, Gebhardt C, Barakat A, Berry S, Arús P, Delseny M, Barnes S (2003) Plant genome archaeology: evidence for conserved ancestral chromosome segments in dicotyledonous plant species. Plant Biotechnol J 1: 91-99
44. Dondini L, Lain O, Geuna F, Banfi R, Gaiotti F, Tartarini S, Bassi D, Testolin R (2007) Development of a new SSR-based linkage map in apricot and analysis of synteny with existing Prunus maps. Tree Genet Genomes 3: 239-249
45. Dondini L, Pierantoni L, Gaiotti F, Chiondini R, Tartarini S, Bazzi C, Sansavini S (2004) Identifying QTLs for fire-blight resistance via a European pear (Pyrus communis L.) genetic linkage map. Mol Breed 14: 407-418
46. Eichholzer M, Luthy J, Gutzwiller F, Stahelin HB (2001) The role of folate, antioxidant vitamins and other constituents in fruit and vegetables in the prevention of cardiovascular disease: the epidemiological evidence. Int J Vitam Nutr Res 71: 5-17
47. El Mansouri I, Mercado JA, Valpuesta V, Lopez-Aranda JM, Pliego-Alfaro F, Quesada MA (1996) Shoot regeneration and Agrobacterium-mediated transformation of Fragaria vesca L. Plant Cell Rep 15: 642-646
48. Escobar MA, Civerolo EL, Polito VS, Pinney KA, Dandekar AM (2003) Characterization of oncogene-silenced transgenic plants: implications for Agrobacterium biology and post-transcriptional gene silencing. Mol Plant Pathol 4: 57-65
49. 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
50. Etienne C, Rothan C, Moing A, Plomion C, Bodénès C, Svanella-Dumas L, Cosson P, Pronier V, Monet R, Dirlewanger E (2002) Candidate genes and QTLs for sugar and organic acid content in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 105: 145-159
51. Folta KM, Davis TM (2006) Strawberry genes and genomics. Crit Rev Plant Sci 25: 399-415
52. Folta KM, Dhingra A (2006) Transformation of strawberry: the basis for translational genomics in Rosaceae. In Vitro Cell Dev Biol Plant 42: 482-490
53. Foolad MR, Arulsekar S, Becerra V, Bliss FA (1995) A genetic map of Prunus based on an interspecific cross between peach and almond. Theor Appl Genet 91: 262-269
54. Foulongne M, Pascal T, Arús P, Kervella J (2003) The potential of Prunus davidiana for introgression into peach [Prunus persica (L.) Batsch] assessed by comparative mapping. Theor Appl Genet 107: 227-238
55. Gardiner S, Bus V, Rusholme R, Chagné D, Rikkerink E (2007) Apple. In C Kole, ed, Genome Mapping and Molecular Breeding, Vol 4. Springer-Verlag, Heidelberg, pp 1-62
56. Georgi LL, Wang Y, Reighard GL, Mao L, Wing RA, Abbott AG (2003) Comparison of peach and Arabidopsis genomic sequences: fragmentary conservation of gene neighborhoods. Genome 46: 268-276
57. Georgi LL, Wang Y, Yvergniaux D, Ormsbee T, Inigo M, Reighard G, Abbott AG (2002) Construction of a BAC library and its application to the identification of simple sequence repeats in peach. Prunus persica (L.) Batsch. Theor Appl Genet 105: 1151-1158
58. Gleave AP, Ampomah-Dwamena C, Berthold S, Dejnoprat S, Karunairetnam S, Nain B, Wang YY, Crowhurst RN, MacDiarmid RM (2008) Identification and characterisation of primary microRNAs from apple (Malus domestica cv. Royal Gala) expressed sequence tags. Tree Genet Genomes 4: 343-358
59. Gonzales MD, Archuleta E, Farmer A, Gajendran K, Grant D, Shoemaker R, Beavis WD, Waugh ME (2005) The Legume Information System (LIS): an integrated information resource for comparative legume biology. Nucleic Acids Res 33: D660-D665
60. Graham J, Smith K, MacKenzie K, Jorgenson L, Hackett C, Powell W (2004) The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers. Theor Appl Genet 109: 740-749
61. Guterman I, Shalit M, Menda N, Piestun D, Dafny-Yelin M, Shalev G, Bar E, Davydov O, Ovadis M, Emanuel M, et al (2002) Rose scent: genomics approach to discovering novel floral fragrance-related genes. Plant Cell 14: 2325-2338
62. Habu T, Kishida H, Morikita M, Kitajima A, Yamada T, Tao R (2006) A simple and rapid procedure for the detection of self-compatible individuals in Japanese apricot (Prunus mume Sieb. et Zucc.) using the loop-mediated isothermal amplification (LAMP) method. HortScience 41: 1156-1158
63. Haffner K, Vestrheim S (1997) Fruit quality of strawberry cultivars. Acta Hortic 439: 325-332
64. Häkkinen SH, Kärenlampi SO, Heinonen IM, Mykkänen HM, Törrönen AR (1998) HPLC method for screening of flavonoids and phenolic acids in berries. J Sci Food Agric 77: 543-551
65. Häkkinen SH, Törrönen AR (2000) Content of flavonols and selected phenolic acids in strawberries and Vaccinium species: influence of cultivar, cultivation site and technique. Food Res Int 33: 517-524
66. Han Y, Gasic K, Marron B, Beever JE, Korban SS (2007) A BAC-based physical map of the apple genome. Genomics 89: 630-637
67. Harris GK, Gupta A, Nines RG, Kresty LA, Habib SG, Frankel WL, LaPerle K, Gallaher DD, Schwartz SJ, Stoner GD (2001) Effects of lyophilized black raspberries on azoxymethane-induced colon cancer and 8-hydroxy-2′- deoxyguanosine levels in the Fischer 344 rat. Nutr Cancer 40: 125-133
68. 1 progeny. Plant Cell Rep 17: 279-283
69. Haymes KM, Van de Weg WE, Arens P, Maas JL, Vosman B, Den Nijs APM (2000) Development of SCAR markers linked to a Phytophthora fragariae resistance gene and their assessment in European and North American strawberry genotypes. J Am Soc Hortic Sci 125: 330-339
70. Hemmat M, Weeden NF, Brown SK (2003) Mapping and evaluation of Malus x domestica microsatellites in apple and pear. J Am Soc Hortic Sci 128: 515-520
71. Hemmat M, Weeden NF, Manganaris AG, Lawson DM (1994) Molecular marker linkage map for apple. J Hered 85: 4-11
72. Hokanson SC (2001) SNiPs, chips, BACs, and YACs: Are small fruits part of the party mix? HortScience 36: 859-871
73. Horn R, Lecouls AC, Callahan A, Dandekar A, Garay L, McCord P, Howad W, Chan H, Verde I, Main D, et al (2005) Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110: 1419-1428
74. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arús P (2005) Mapping with a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 171: 1305-1309
75. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9: 868-877
76. Huaracha E, Xu M, Korban SS (2004) Narrowing down the region of the Vf locus for scab resistance in apple using AFLP-derived SCARs. Theor Appl Genet 108: 274-279
77. Hurtado MA, Romero C, Vilanova S, Abbott AG, Llacer G, Badenes ML (2002) Genetic linkage maps of two apricot cultivars (Prunus armeniaca L.), and mapping of PPV (sharka) resistance. Theor Appl Genet 105: 182-191
78. Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, et al (2006) Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res 34: D717-723
79. Janick J, Cummins JN, Brown SK, Hemmat M (1996) Apples. In J Janick, JN Moore, eds, Fruit Breeding, Vol I: Tree and Tropical Fruits. John Wiley and Sons, New York, pp 1-77
80. Jauregui B, de Vicente MC, Messeguer R, Felipe A, Bonnet A, Salesses G, Arús P (2001) A reciprocal translocation between 'Garfi' almond and 'Nemared' peach. Theor Appl Genet 102: 1169-1176
81. Jelenkovic G, Harrington E (1972) Morphology of the pachytene chromosomes in Prunus persica. Can J Genet Cytol 14: 317-324
82. Joobeur T, Periam N, Vicente MC, King GJ, Arús P (2000) Development of a second generation linkage map for almond using RAPD and SSR markers. Genome 43: 649-655
83. 2 progeny. Theor Appl Genet 97: 1034-1041
84. Jung S, Jesudurai C, Staton M, Du ZD, Ficklin S, Cho IH, Abbott A, Tomkins J, Main D (2004) GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. BMC Bioinformatics 5: 130
85. Jung S, Main D, Staton M, Cho I, Zhebentyayeva T, Arús P, Abbott A (2006) Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes. BMC Genomics 7: 81
86. Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36: D1034-D1040
87. Kardailsky I, Shukla VK, Ahn JH, Dagenais N, Christensen SK, Nguyen JT, Chory J, Harrison MJ, Weigel D (1999) Activation tagging of the floral inducer FT. Science 286: 1962-1965
88. Kaufmann H, Mattiesch L, Lorz H, Debener T (2003) Construction of a BAC library of Rosa rugosa Thunb. and assembly of a contig spanning Rdr1, a gene that confers resistance to blackspot. Mol Genet Genomics 268: 666-674
89. Kenis K, Keulemans J (2005) Genetic linkage maps of two apple cultivars (Malus x domestica Borkh.) based on AFLP and microsatellite markers. Mol Breed 15: 205-219
90. Kishore GM, Shewmaker C (1999) Biotechnology: enhancing human nutrition in developing and developed worlds. Proc Natl Acad Sci USA 96: 5968-5972
91. Ko K, Brown SK, Norelli JL, Aldwinckle HS (1998) Alterations in nptII and gus expression following micropropagation of transgenic M7 apple rootstock lines. J Am Soc Hortic Sci 123: 11-18
92. Ko KS, Norelli JL, Reynoird JP, Boresjza-Wysocka E, Brown SK, Aldwinckle HS (2000) Effect of untranslated leader sequence of AMV RNA 4 and signal peptide of pathogenesis-related protein 1b on attacin gene expression, and resistance to fire blight in transgenic apple. Biotechnol Lett 22: 373-381
93. Korban SS, Chen H (1992) Apples. In F Hammerschlag, R Litz, eds, Biotechnology of Fruit Tree Crops. CAB International, Oxnard, CA, pp 203-227
94. Krysan PJ, Young JC, Sussman MR (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11: 2283-2290
95. Kurata N, Yamazaki Y (2006) Oryzabase. An integrated biological and genome information database for rice. Plant Physiol 140: 12-17
96. Lalli DA, Decroocq V, Blenda AV, Schurdi-Levraud V, Garay L, Le Gall O, Damsteegt V, Reighard GL, Abbott AG (2005) Identification and mapping of resistance gene analogs (RGAs) in Prunus: a resistance map for Prunus. Theor Appl Genet 111: 1504-1513
97. Lambert P, Hagen LS, Arús P, Audergon JM (2004) Genetic linkage maps of two apricot cultivars (Prunus armeniaca L.) compared with the almond Texas x peach Earlygold reference map for Prunus. Theor Appl Genet 108: 1120-1130
98. Lavid N, Wang JH, Shalit M, Guterman I, Bar E, Beuerle T, Menda N, Shafir S, Zamir D, Adam Z, et al (2002) O-Methyltransferases involved in the biosynthesis of volatile phenolic derivatives in rose petals. Plant Physiol 129: 1899-1907
99. Lawrence CJ, Schaeffer ML, Seigfried TE, Campbell DA, Harper LC (2007) MaizeGDB's new data types, resources and activities. Nucleic Acids Res 35: D895-900
100. Lazzari B, Caprera A, Vecchietti A, Stella A, Milanesi L, Pozzi C (2005) ESTree db: a tool for peach functional genomics. BMC Bioinformatics (Suppl 4) 6: S16
101. Lee YP, Yu GH, Seo YS, Han SE, Choi YO, Kim D, Mok IG, Kim WT, Sung SK (2007) Microarray analysis of apple gene expression engaged in early fruit development. Plant Cell Rep 26: 917-926
102. Lerceteau-Kohler E, Guerin G, Laigret F, Denoyes-Rothan B (2003) Characterization of mixed disomic and polysomic inheritance in the octoploid strawberry (Fragaria x ananassa) using AFLP mapping. Theor Appl Genet 107: 619-628
103. Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van de Weg E, Gessler C (2002) Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.). Mol Breed 10: 217-241
104. Liebhard R, Kellerhals M, Pfammatter W, Jertmini M, Gessler C (2003a) Mapping quantitative physiological traits in apple (Malus x domestica Borkh.). Plant Mol Biol 52: 511-526
105. Liebhard R, Koller B, Gianfranceschi L, Gessler C (2003c) Creating a saturated reference map for the apple (Malus x domestica Borkh.) genome. Theor Appl Genet 106: 1497-1508
106. Liebhard R, Koller B, Patocchi A, Kellerhals M, Pfammatter W, Jermini M, Gessler C (2003b) Mapping quantitative field resistance against apple scab in a 'Fiesta' x 'Discovery' progeny. Phytopathology 93: 493-501
107. López M, Vargas FJ, Batlle I (2006) Self-(in)compatibility almond genotypes: a review. Euphytica 150: 1-16
108. Lu ZX, Sosinski B, Reighard GL, Baird WV, Abbott AG (1998) Construction of a genetic linkage map and identification of AFLP markers for resistance to root-knot nematodes in peach rootstocks. Genome 41: 199-207
109. Macheix JJ, Sapis JC, Fleuriet A (1991) Phenolic compounds and polyphenoloxidase in relation to browning in grapes and wines. Crit Rev Food Sci Nutr 30: 441-486
110. Maliepaard C, Alston FH, van Arkel G, Brown LM, Chevreau E, Dunemann F, Evans KM, Gardiner S, Guilford P, van Heusden AW, et al (1998) Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor Appl Genet 97: 60-73
111. Mandal S, Stoner GD (1990) Inhibition of N- nitrosobenzylmethylamine-induced esophageal tumorigenesis in rats by ellagic acid. Carcinogenesis 11: 55-61
112. Marshall RE (1954) Cherries and Cherry Products, Vol 5. Interscience Publishers Ltd., New York
113. Masuda T, Yonemori S, Oyama Y, Takeda Y, Tanaka T, Andoh T, Shinohara A, Nakata M (1999) Evaluation of the antioxidant activity of environmental plants: activity of the leaf extracts from seashore plants. J Agric Food Chem 47: 1749-1754
114. Mazur WM, Uehara M, Wahala K, Adlercreutz H (2000) Phyto-oestrogen content of berries, and plasma concentrations and urinary excretion of enterolactone after asingle strawberry-meal in human subjects. Br J Nutr 83: 381-387
115. Mezzetti B, Costantini E (2006) Strawberry (Fragaria x ananassa). Methods Mol Biol 344: 287-295
116. Miller PJ, Parfitt DE, Weinbaum SA (1989) Outcrossing in peach. HortScience 24: 359-360
117. Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, et al (2005) The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 138: 1310-1317
118. Nagaraj SH, Gasser RB, Ranganathan S (2007) A hitchhiker's guide to expressed sequence tag (EST) analysis. Brief. Bioinformatics 8: 6-21
119. Naik S, Hampson C, Gasic K, Bakkeren G, Korban SS (2006) Development and linkage mapping of E-STS and RGA markers for functional gene homologues in apple. Genome 49: 959-968
120. Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EHA, Allan AC, Beuning LL, Bowen JH, Gera E, Jamieson KR, Janssen BJ, et al (2006) Analyses of expressed sequence tags from apple. Plant Physiol 141: 147-166
121. 1 mapping population and its comparison with the Fragaria reference map (FV X FN). J Hortic Sci Biotechnol 81: 645-650
122. Norelli JL, Borejsza-Wysocka E, Baldo AM, Aldwinckle HS, Bassett CL, Farrell RE, Malnoy M, Lalli DA, Korban SS, Gasic K, et al (2007) Functional genomic analysis of apple (Malus) ESTs associated with fire blight (Erwinia amylovora). Phytopathology 97: S185-S185
123. Oosumi T, Gruszewski HA, Blischak LA, Baxter AJ, Wadl PA, Shuman JL, Veilleux RE, Shulaev V (2006) High-efficiency transformation of the diploid strawberry (Fragaria vesca) for functional genomics. Planta 223: 1219-1230
124. 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
125. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85: 2444-2448
126. Pedreschi R, Vanstreels E, Carpentier S, Hertog M, Lammertyn J, Robben J, Noben JP, Swennen R, Vanderleyden J, Nicolai BM (2007) Proteomic analysis of core breakdown disorder in Conference pears (Pyrus communis L.). Proteomics 7: 2083-2099
127. Pichler FB, Walton EF, Davy M, Triggs C, Janssen B, Wunsche JN, Putterill J, Schaffer RJ (2007) Relative developmental, environmental, and tree-to-tree variability in buds from field-grown apple trees. Tree Genet Genomes 3: 329-339
128. 1 populations. Theor Appl Genet 109: 1519-1524
129. Pooler MR, Scorza R (1997) Irradiation and heat affect peach pollen germination and fertility. HortScience 32: 290-291
130. Potter D, Eriksson T, Evans RC, Oh S, Smedmark JEE, Morgan DR, Kerr M, Robertson KR, Arsenault M, Dickinson TA, et al (2007) Phylogeny and classification of Rosaceae. Plant Syst Evol 266: 5-43
131. Potter D, Gao F, Bortiri PE, Oh SH, Baggett S (2002) Phylogenetic relationships in Rosaceae inferred from chloroplast matK and trnL-trnF nucleotide sequence data. Plant Syst Evol 231: 77-89
132. Quilot B, Wu BH, Kervella J, Genard M, Foulongne M, Moreau K (2004) QTL analysis of quality traits in an advanced backcross between Prunus persica cultivars and the wild relative species P. davidiana. Theor Appl Genet 109: 884-897
133. Rajapakse S, Byrne DH, Zhang L, Anderson N, Arumuganathan K, Ballard RE (2001) Two genetic linkage maps of tetraploid roses. Theor Appl Genet 103: 575-583
134. Renaut J, Hausman JF, Bassett C, Artlip T, Cauchie HM, Witters E, Wisniewski M (2008) Quantitative proteomic analysis of short photo-period and low-temperature responses in bark tissues of peach (Prunus persica L. Batsch). Tree Genet Genomes (in press)
135. Renaut J, Hausman JF, Wisniewski ME (2006) Proteomics and lowtemperature studies: bridging the gap between gene expression and metabolism. Physiol Plant 126: 97-109
136. Reuter A, Fortunato D, Garoffo LP, Napolitano L, Scheurer S, Giuffrida MG, Vieths S, Conti AD (2005) Novel isoforms of Pru av 1 with diverging immunoglobulin E binding properties identified by a synergistic combination of molecular biology and proteomics. Proteomics 5: 282-289
137. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, et al (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228
138. Rudell DR, Mattheis JP, Curry FA (2008) Prestorage ultraviolet-white light irradation alters apple peel metabolome. J Agric Food Chem 56: 1138-1147
139. Salesses G, Mouras A (1977) Use of protoplasts for the study of Prunus chromosomes. Ann Amélior Plant 27: 363-368
140. Sargent DJ, Clarke J, Simpson DW, Tobutt KR, Arús P, Monfort A, Vilanova S, Denoyes-Rothan B, Rousseau M, Folta KM, et al (2006) An enhanced microsatellite map of diploid Fragaria. Theor Appl Genet 112: 1349-1359
141. Sargent DJ, Davis TM, Tobutt KR, Wilkinson MJ, Battey NH, Simpson DW (2004) A genetic linkage map of microsatellite, gene-specific and morphological markers in diploid Fragaria. Theor Appl Genet 109: 1385-1391
142. Sargent DJ, Rys A, Nier S, Simpson DW, Tobutt KR (2007) The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera. Theor Appl Genet 114: 373-384
143. Scalliet G, Lionnet C, Le Bechec M, Dutron L, Magnard JL, Baudino S, Bergougnoux V, Jullien F, Chambrier P, Vergne P, et al (2006) Role of petal-specific orcinol O-methyltransferases in the evolution of rose scent. Plant Physiol 140: 18-29
144. Schaffer RJ, Friel EN, Souleyre EJF, Bolitho K, Thodey K, Ledger S, Bowen JH, Ma JH, Nain B, Cohen D, et al (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
145. Schieber A, Stintzing FC, Carle R (2001) By-products of plant food processing as a source of functional compounds: recent developments. Trends Food Sci Technol 12: 401-413
146. Schwab W, Aharoni A, Raab T, Perez AG, Sanz C (2001) Cytosolic aldolase is a ripening related enzyme in strawberry fruits (Fragaria x ananassa). Phytochemistry 56: 407-415
147. Scorza R, Mehlenbacher SA, Lightner GW (1985) Inbreeding and coancestry of freestone peach cultivars of the eastern United States and implications for peach germplasm improvement. J Am Soc Hortic Sci 110: 547-552
148. Scorza R, Sherman WB (1996) Peaches. In J Janick, JN Moore, eds, Fruit Breeding, Vol 1. Tree and Tropical Fruits. John Wiley and Sons, New York, pp 325-440
149. Selmar D (1999) Cyanide in foods: biology of cyanogenic glucosides and related nutritional problems. In JT Romeo, ed, Phytochemicals in Human Health Protection, Nutrition, and Plant Defense, Vol 33. Kluwer Academic, New York, pp 369-392
150. Silfverberg-Dilworth E, Matasci CL, Van de Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, et al (2006) Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome. Tree Genet Genomes 2: 202-224
151. Smartt J, Simmonds NW (1995) Evolution of Crop Plants, Ed 2. Longman Scientific and Technical, Harlow, UK
152. Sugimoto T, Tamaki K, Matsumoto J, Yamamoto Y, Shiwaku K, Watanabe K (2005) Detection of RAPD markers linked to the everbearing gene in Japanese cultivated strawberry. Plant Breed 124: 498-501
153. Sung SK, Jeong DH, Nam JM, Kim SH, Kim SR, An G (1998) Expressed sequence tags of fruits, peels, and carpels and analysis of mRNA expression levels of the tagged cDNAs of fruits from the Fuji apple. Mol Cells 8: 565-577
154. Swanson CA (1998) Vegetables, fruits, and cancer risk: the role of phytochemicals. In WR Bidlack, ST Omaye, MS Meskin, DKW Topham, eds, Phytochemicals. A New Paradigm. CRC Press L.L.C., Boca Raton, FL, pp 1-12
155. Tahmatsidou V, O'Sullivan J, Cassells AC, Voyiatzis D, Paroussi G (2006) Comparison of AMF and PGPR inoculants for the suppression of Verticillium wilt of strawberry (Fragaria x ananassa cv. Selva). Appl Soil Ecol 32: 316-324
156. Tartarini S, Sansavini S, Vinatzer B, Gennari FCD (2000) Efficiency of marker assisted selection (MAS) for the Vf scab resistance gene.
157. Tatum TC, Stepanovic S, Biradar DP, Rayburn AL, Korban SS (2005) Variation in nuclear DNA content in Malus species and cultivated apples. Genome 48: 924-930
158. Teo G, Suziki Y, Uratsu SL, Lampinen B, Ormonde N, Hu WK, DeJong TM, Dandekar AM (2006) Silencing leaf sorbitol synthesis alters long-distance partitioning and apple fruit quality. Proc Natl Acad Sci USA 103: 18842-18847
159. Vavilov NI (1951) The origin, variation, immunity and breeding of cultivated plants. Selected writings of N.I. Vavilov, translated from Russian by K. Starr Chester. Chron Bot 13: 1-366
160. Verde I, Lauria M, Dettori M, Vendramin E, Balconi C, Micali S, Wang Y, Marrazzo MT, Cipriani G, Hartings H, et al (2005) Microsatellite and AFLP markers in the Prunus persica [L. (Batsch)] x P. ferganensis BC1 linkage map: saturation and coverage improvement. Theor Appl Genet 111: 1013-1021
161. Vilanova S, Romero C, Abernathy D, Abbott AG, Burgos L, Llacer G, Badenes ML (2003) Construction and application of a bacterial artificial chromosome (BAC) library of Prunus armeniaca L. for the identification of clones linked to the self-incompatibility locus. Mol Genet Genomics 269: 685-691
162. Vinatzer BA, Patocchi A, Gianfranceschi L, Tartarini S, Zhang HB, Gessler C, Sansavini S (2001) Apple contains receptor-like genes homologous to the Cladosporium fulvum resistance gene family of tomato with a cluster of genes cosegregating with Vf apple scab resistance. Mol Plant Microbe Interact 14: 508-515
163. Vinatzer BA, Zhang HB, Sansavini S (1998) Construction and characterization of a bacterial artificial chromosome library of apple. Theor Appl Genet 97: 1183-1190
164. Viruel MA, Messeguer R, Devicente MC, Garciamas J, Puigdomenech P, Vargas F, Arús P (1995) A linkage map with RFLP and isozyme markers for almond. Theor Appl Genet 91: 964-971
165. Wang D, Fan J, Ranu RS (2004) Cloning and expression of 1-amino-cyclopropane-1-carboxylate synthase cDNA from rosa (Rosa x hybrida). Plant Cell Rep 22: 422-429
166. Wang D, Karle R, Brettin TS, Iezzoni AF (1998) Genetic linkage map in sour cherry using RFLP markers. Theor Appl Genet 97: 1217-1224
167. Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, et al (2002) Gramene, a tool for grass genomics. Plant Physiol 130: 1606-1613
168. Weebadde CK, Wang D, Finn CE, Lewers KS, Luby JJ, Bushakra J, Sjulin TM, Hancock JF (2008) Using a linkage mapping approach to identify QTL for day-neutrality in the octoploid strawberry. Plant Breed 127: 94-101
169. Weigel D, Ahn JH, Blazquez MA, Borevitz JO, Christensen SK, Fankhauser C, Ferrandiz C, Kardailsky I, Malancharuvil EJ, Neff MM, et al (2000) Activation tagging in Arabidopsis. Plant Physiol 122: 1003-1013
170. Wisniewski M, Bassett C, Norelli J, Macarisin D, Artlip T, Gasic K, Korban S (2008) Expressed sequence tag analysis of the response of apple (Malus x domestica 'Royal Gala') to low temperature and water deficit. Physiol Plant 133: 298-317
171. Xu M, Song J, Cheng Z, Jiang J, Korban SS (2001) A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction for positional cloning of the apple scab resistance gene Vf. Genome 44: 1104-1113
172. Xu ML, Korban SS (2002a) A cluster of four receptor-like genes resides in the Vf locus that confers resistance to apple scab disease. Genetics 162: 1995-2006
173. Xu ML, Korban SS (2002b) AFLP-derived SCARs facilitate construction of a 1.1 Mb sequence-ready map of a region that spans the Vf locus in the apple genome. Plant Mol Biol 50: 803-818
174. Yamamoto T, Kimura T, Saito T, Kotobuki K, Matsuta N, Liebhard R, Gessler C, van de Weg WE, Hayashi T (2004) Genetic linkage maps of Japanese and European pears aligned to the apple consensus map. Acta Hortic 663: 51-56
175. Yamamoto T, Kimura T, Shoda M, Imai T, Saito T, Sawamura Y, Kotobuki K, Hayashi T, Matsuta N (2002) Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor Appl Genet 106: 9-18
176. Yamamoto T, Yamaguchi M, Hayashi T (2005) An integrated genetic linkage map of peach by SSR, STS, AFLP and RAPD. J Jpn Soc Hort Sci 74: 204-213
177. Yan Z, Denneboom C, Hattendorf A, Dolstra O, Debener T, Stam P, Visser PB (2005) Construction of an integratedmap of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Theor Appl Genet 110: 766-777
178. Yau MH, Che CT, Liang SM, Kong YC, Fong WP (2002) An aqueous extract of Rubus chingii fruits protects primary rat hepatocytes against tert-butyl hydroperoxide induced oxidative stress. Life Sci 72: 329-338
179. Zhebentyayeva TN, Horn R, Mook J, Lecouls A, Georgi L, Abbott AG, Reighard GL, Swire-Clark G, Baird WV (2006) A physical framework for the peach genome. Acta Hortic 713: 83-88
180. Ziegler RG, Mayne ST, Swanson CA (1996) Nutrition and lung cancer. Cancer Causes Control 7: 157-177