Apple, from genome to breeding

Tree Genetics and Genomes

Volumn 8, Issue 3, 2012, Pages 509-529

  Troggio, M ^a   Gleave, A ^c   Salvi, S ^a,b   Chagne D ^c   Cestaro, A ^a   Kumar, S ^c   Crowhurst, R N ^c   Gardiner, S E ^c  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

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

Author keywords

'Omics' resources; Apple; Comparative genomics; Genetic tools; Genetic variation

Indexed keywords

MALUS; MALUS X DOMESTICA;

EID: 84862237103     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-012-0492-9     Document Type: Review

References (126)

1. Ackermann J, Fischer M, Amado R (1992) Changes in sugars, acids and amino acids during ripening and storage of apples (Cv. Glockenapfel). J Agri Food Chem 40: 1131-1134.
2. Aldasoro JJ, Aedo C, Navarro C (2005) Phylogenetic and phytogeographical relationships in Maloideae (Rosaceae) based on morphological and anatomical characters. Blumea 50(1): 3-32.
3. Allan AC, Crowhurst R, Allan AC, Crowhurst R, Gleave A, Newcomb R, Shaffer (2009) In: Folta KM, Gardiner SE (eds) Genetics and genomics of the Rosaceae. Springer, New York, USA, pp 121-142.
4. Anderson LK, Stack SM (2002) Meiotic recombination in plants. Curr Genomics 3: 507-525.
5. Awad MA, de Jager A, van Westing LM (2000) Flavonoid and chlorogenic acid levels in apple fruit: characterisation and variation. Sci Hort 83: 249-263.
6. Baldo A, Norelli JL, Farrel RE Jr, Bassett CL, Aldwinckle HS, Malnoy M (2010) Identification of genes differentially expressed during interaction of resistant and susceptible apple cultivars (Malus × domestica) with Erwinia amylovora. BMC Plant Biol 10: 1.
7. Beckmann JS, Estivill X, Antonarakis SE (2007) Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet 8: 639-646.
8. Bink MCAM, Boer MP, ter Braak CJF, Jansen J, Voorrips RE, van de Weg WE (2008) Bayesian analysis of complex traits in pedigreed plant populations. Euphytica 161: 85-96.
9. Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, Rombauts S, Vanderhaeghen R, Inzé D, Zabeau M (2003) Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol Genet Genom 269: 173-179.
10. Bus VGM, Esmenjaud D, Buck E, Laurens F (2009) Application of genetic markers in rosaceous crops. In: Folta KM, Gardiner SE (eds) Genetics and genomics of the Rosaceae. USA, Springer, New York, pp 563-600.
11. Bus VGM, Bassett HCM, Bowatte D, Chagne D, Ranatunga CA, Ulluwishewa D, Wiedow C, Gardiner SE (2010) Genome mapping of an apple scab, a powdery mildew and a woolly apple aphid resistance gene from open-pollinated Mildew Immune Selection. Tree Genet Genomes 6: 477-487.
12. Bushakra JM, Sargent DJ, Cabrera A, Crowhurst R, Girona EL, Velasco R, Symonds VV, van der Knaap E, Troggio M, Gardiner SE, Chagné D (2011) Rosaceae conserved orthologous set (RosCOS) markers as a tool to assess genome synteny between Malus and Fragaria. Tree Genet Genomes. doi: 10. 1007/s11295-011-0450-y.
13. Cabrera A, Kozik A, Howad W, Arus P, Iezzoni AF, Knaap E (2009) Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers. BMC Genom 10: 562.
14. Calenge F, Durel CE (2006) Both stable and unstable QTLs for resistance to powdery mildew are detected in apple after four years of field assessments. Mol Breed 17: 329-339.
15. Calenge F, Faure A, Goerre M, Gebhardt C, van de Weg WE, Parisi L, Durel CE (2004) Quantitative Trait Loci (QTL) analysis reveals both broad-spectrum and isolate-specific QTL for scab resistance in an apple progeny challenged with eight isolates of Venturia inaequalis. Phytopathology 94(4): 370-379.
16. Calenge F, Drouet D, Denancé C, van de Weg WE, Brisset MN, Paulin JP, Durel CE (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.
17. Cao S, Zhang Q, Zhu Z, Guo J, Chen Y, Xie H (2008) Preliminary proteomics analysis of the total proteins of flower bud induction of apple trees. Front Agric China 2: 467-473.
18. Cartwright DA, Troggio M, Velasco R, Gutin A (2007) Genetic mapping in the presence of genotyping errors. Genetics 176: 2521-2527.
19. Celton J-M, Husselmann LHH, Madduri M, Labuschagne IF, Rees DJG (2009b) Whole transcriptome sequencing analysis of apple leaves infected by Venturia inaequalis, using Solexa sequencing technology. In: Proceedings of the Plant & Animal Genome Conference XVII: San Diego, CA, USA: W212.
20. Celton JM, Tustin DS, Chagne D, Gardiner SE (2009b) Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences. Tree Genet Genomes 5(1): 93-107.
21. Cevik V, Ryder CD, Popovich A, Manning K, King GJ, Seymour GB (2010) A FRUITFULL-like gene is associated with genetic variation for fruit flesh firmness in apple (Malus domestica Borkh.). Tree Genet Genomes 6: 271-279.
22. Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS (2008) Development of a set of SNP markers present in expressed genes of the apple. Genomics 92: 353-358.
23. Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B et al. (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 7: e31745. doi: 10. 1371/journal. pone. 0031745.
24. Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J et al (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet 36: 1133-1137.
25. Cooper M, van Eeuwijk FA, Hammer GL, Podlich DW, Messina C (2009) Modeling QTL for complex traits: detection and context for plant breeding. Curr Opin Plant Biol 12: 231-240.
26. Crow KD, Wagner GP (2006) What is the role of genome duplication in the evolution of complexity and diversity? Mol Biol Evol 23: 887-892.
27. Crowhurst RN, Davy M, Deng C (2006) BioView-an enterprise bioinformatics system for automated analysis and annotation of non-genomic DNA sequence. In: Proceedings of the 3rd International Rosaceae Genomics Conference, 19-22 March, Napier, New Zealand.
28. Dal Cin V, Barbaro E, Danesin M, Murayama H, Velasco R, Ramina A (2009) Fruitlet abscission: A cDNA-AFLP approach to study genes differentially expressed during shedding of immature fruits reveals the involvement of a putative auxin hydrogen symporter in apple (Malus domestica L. Borkh). Gene 442: 26-36.
29. Dalrymple BP, Kirkness EF, Nefedov M et al (2007) Using comparative genomics to reorder the human genome sequence into a virtual sheep genome. Genome Biol 8: R152.
30. Davey MW, Keulemans J (2004) Determining the potential to breed for enhanced antioxidant status in Malus: mean inter- and intravarietal fruit vitamin C and glutathione content at harvest and their evolution during storage. J Agri Food Chem 52: 8031-8038.
31. Degenhardt J, Al-Masri AN, Kurkcuoglu S, Szankowski I, Gau AE (2005) Characterisation by suppression subtractive hybridization of transcripts that are differentially expressed in leaves of apple scab-resistant and susceptible cultivars of Malus domestica. Mol Genet Genom 273: 326-335.
32. Demura T, Fukuda H (2007) Transcriptional regulation in wood formation. Trends Plant Sci 12: 64-70.
33. Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howad W, Arus P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 101(26): 9891-989.
34. 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.
35. Durel CE, Laurens F, Fouillet A, Lespinasse Y (1998) Utilization of pedigree information to estimate genetic parameters from large unbalanced data sets in apple. Theor Appl Genet 96: 1077-1085.
36. Durel CE, van de Weg WE, Venisse JS, Parisi L (1999) Localisation of a major gene for apple scab resistance on the European genetic map of the Prima × Fiesta cross. 5th Workshop on Integrated Control of Pome Fruit Diseases, 24-27 August 1999, Fontevraud l'Abbaye, France. IOBC Bull 23: 245-248.
37. Escarpa A, Gonzalez MC (1998) High-performance liquid chromatography with diode-array detection for the determination of phenolic compounds in peel and pulp from different apple varieties. J Chromotog 823: 331-337.
38. Evans RC, Campbell CS (2002) The origin of the apple subfamily (Maloideae; Rosaceae) is clarified by DNA sequence data from duplicated GBSSI genes. Am J Bot 89(9): 1478-1484.
39. Eveland AL, McCarty DR, Koch KE (2008) Transcript profiling by 3'-untranslated region sequencing resolves expression of gene families. Plant Physiol 146: 32-44.
40. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C (2006) Copy number variation: new insights in genome diversity. Genome Res 16: 949-961.
41. Fuleki T, Pelayo E, Palabay RB (1994) Sugar composition of varietal juices produced from fresh and stored apples. J Agri Food Chem 42: 1266-1275.
42. Gardiner SE, Bus VGM, Rushholme RL, Chagné D, Rikkerink E (2007) Apple. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol 4. Springer, Berlin, Heidelberg, Gemany pp 1-62.
43. Garkava-Gustavsson L, Brantestam AK, Sehic J, Nybom H (2008) Molecular characterisation of indigenous Swedish apple cultivars based on SSR and S-allele analysis. Hereditas 145: 99-112.
44. Gasic K, Gonzalez DO, Thimmapuram J, Liu L, Malnoy M, Gong G, Han YP, Vodkin LO, Aldwinckle HS, Carroll NJ, Orvis KS, Goldsbrough P, Clifton S, Pape D, Fulton L, Martin J, Theising B, Wisniewski ME, Fazio G, Feltus FA, Korban SS (2009) Comparative analysis and functional annotation of a large expressed sequence tag collection of apple. Plant Genome 2(1): 23-38.
45. Goffinet B, Gerber S (2000) Quantitative trait loci: a meta-analysis. Genetics 155: 463-473.
46. Guarino C, Arena S, De Simone L, D'Ambrosio C, Santoro S, Rocco M, Scaloni A, Marra M (2007) Proteomic analysis of the major soluble components in Annurca apple flesh. Mol Nutr Food Res 51: 2550262.
47. Guyot S, Marnet N, Sanoner P, Drilleau J-F (2003) Variability of the polyphenolic composition of cider apple (Malus domestica) fruit and juices. J Agri Food Chem 51: 6240-6247.
48. Han Y, Gasic K, Marron B, Beever JE, Korban SS (2007) A BAC-based physical map of the apple genome. Genomics 89: 630-637.
49. Hanada K, Takakashi K, Myouga F, Toyada T, Li W-H, Shinozaki K (2009) Evolutionary Persistence of functional compensation by duplicate genes in Arabidopsis. Genome Biol Evol 1: 409-414.
50. Harris SA, Robinson JP, Juniper BE (2002) Genetic clues to the origin of the apple. Trends Genet 18: 426-430.
51. Hokanson SC, Szewc-McFadden AK, Lamboy WF, McFerson JR (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus × domestica Borkh. core subset collection. Theor Appl Genet 97: 671-683.
52. Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10: 156-161.
53. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19: 1068-1076.
54. Hummer KE, Janick J (2009) Rosaceae: taxonomy, economic importance, genomics. In: Folta K, Gardiner S (eds) Genetics and genomics of Rosaceae. Springer, New York, pp 1-17.
55. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
56. Illa E, Sargent DJ, Lopez Girona E, Bushakra J, Cestaro A, Crowhurst R, Pindo M, Cabrera A, van der Knaap E, Iezzoni A, Gardiner S, Velasco R, Arús P, Chagné D, Troggio M (2011) Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol Biol 11: 9. doi: 101186/1471-2148-11-9.
57. Jaillon O, Aury JM, Noel B et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161): 463-U465.
58. Janick J, Cummins JV, Brown SK, Hemmat M (1996) Apples. In: Janick J, Moore JN (eds) Fruit breeding, vol I-tree and tropical fruits. Wiley, New York, pp 1-66.
59. Janssen BJ, Thodey K, Schaffer RJ, Alba R, Balakrishnan L, Bishop R, Boweb 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.
60. Jensen PJ, Rytter J, Detwiler EA, Travis JW, McNellis TW (2003) Rootstock effects on gene expression patterns in apple tree scions. Plant Mol Biol 493: 493-511.
61. Jensen PJ, Makalowska I, Altman N, Fazio G, Praul C, Maximova SN, Crassweller RM, Travis JW, McNellis TW (2010) Rootstock-regulated gene expression patterns in apple scions. Tree Genet Genomes 6: 57-72.
62. Kenis K, Keulemans J, Davey MW (2008) Identification and stability of QTLs for fruit quality traits in apple. Tree Genet Genomes 4: 647-661.
63. Khan MA, Durel CE, Duffy B, Drouet D, Kellerhals M, Gessler C, Patocchi A (2007) Development of molecular markers linked to the 'Fiesta' linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection. Genome 50: 568-577.
64. King GJ, Maliepaard C, Lynn JR, Alston FH, Durel CE, Evans KM, Griffon B, Laurens F, Manganaris AG, Chrevens T, 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.
65. 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.
66. Knee M, Hatfield SGS (1981) The metabolism of alcohols by apple fruit tissue. J Sci Food Agri 32: 593-600.
67. Kumar SK, Volz RK, Alspach PA, Bus VGM (2010) Development of a recurrent apple breeding programme in New Zealand: a synthesis of results, and a proposed revised breeding strategy. Euphytica 173: 207-222.
68. Kumar S, Volz R, Weskett R (2011) Genetic architecture of fruit quality traits in Malus x domestica (Borkh.) compared between own-rooted seedlings and vegetative propagules on 'M. 9' rootstock. Tree Genet Genomes 7: 1079-1088. doi: 10. 1007/s11295-011-0396-0.
69. Kumar S, Chagné D, Bink MCAM, Volz RK, Whitworth C, Carlisle C (2012) Genomic selection for fruit quality traits in apple (Malus × domestica Borkh.) PLoS ONE 7: e36674. doi: 10. 1371/journal. pone. 0036674.
70. Kurkcuoglu S, Piotrowski M, Gau AE (2004) Up-regulation of pathogenesis-related proteins in the apoplast of Malus domestica after application of a non-pathogenic bacterium. J Biosci 59(843-848): 7.
71. 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: 917-926.
72. Lespinasse Y, Bouvier L, Djulbic M, Chevreau E (1999) Haploidy in apple and pear. Acta Hort 484: 49-54.
73. Liebhard R, Kellerhals M, Pfammatter W, Jertmini M, Gessler C (2003) Mapping quantitative physiological traits in apple (Malus × domestica Borkh.). Plant Mol Biol 52: 511-526.
74. Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E, Wittwer C (2004) Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin Chem 50: 1156-1164.
75. Liu Y, Zhang S (2004) Phosphorylation of 1-aminocyclopropane-1-carboxylic acid synthase by MPK6, a stress-responsive mitogen-activated protein kinase, induces ethylene biosynthesis in Arabidopsis. Plant Cell 16: 3386-3399.
76. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
77. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
78. Micheletti D, Troggio M, Baldi P, Costa F, Pindo M, Komjanc M, Malnoy M, Zharkikh A, Magnago P, Velasco R, Salvi S (2010) LD estimation and analysis of diversity in apple. In: Proceedings of Plant & Animal Genomes XVIII Conference, San Diego, CA, USA W255.
79. Myles S, Chia JM, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D (2010) Rapid genomic characterization of the genus Vitis. PLoS One 5(1): e8219.
80. 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-K (2006) Analyses of expressed sequence tags from apple. Plant Physiol 141: 147-166.
81. Noiton DAM, Alspach PA (1996) Founding clones, inbreeding, coancestry, and status number of modern apple cultivars. J Am Soc Hort Sci 121: 773-782.
82. Norelli JL, Farrell RE Jr, Basset CL, Baldo AM, Lalli DA, Aldwinckle HS, Wisniewski ME (2009) Rapid transcriptional response of apple to fire blight disease revealed by cDNA suppression subtractive hybridisation analysis. Tree Genet Genomes 5: 27-40.
83. Olmstead JW, Sebolt AM, Cabrera A, Sooriyapathirana SS, Hammar S, Iriarte G, Wang D, Chen CY, van der Knaap E, Iezzoni AF (2008) Construction of an intra-specific sweet cherry (Prunus avium L.) genetic linkage map and synteny analysis with the Prunus reference map. Tree Genet Genom 4: 897-910.
84. Olsen AN, Ernst HA, Leggio LL, Skriver K (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci 10: 79-87.
85. Paris R, Dondini L, Tartarini S, Bastia D, Mantovani V, Sansavini S (2009a) An optimized cDNA-AFLP protocol for the identification of TDFs Involved in the Malus-Venturia inaequalis interaction. Acta Hort 814: 841-844.
86. Paris R, Dondini L, Tartarini S, Sansavini S (2009b) First evidence of d-HPLC efficiency for and automated cDNA-AFLP in the apple scab resistance model. Acta Hort 839: 457-462.
87. 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.
88. Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229): 551-556.
89. Patocchi A, Frei A, Frey JE, Kellerhals M (2009) Towards improvement of marker assisted selection of apple scab resistant cultivars: Venturia inaequalis virulence surveys and standardization of molecular marker alleles associated with resistance genes. Mol Breed 24: 337-347.
90. Pichler FB, Walton EF, Davey M, Triggs C, Janssen B, Wunsche JN, Putterill J, Schaffer RJ (2007) Relative developmental, environmental and tree-to-tree variability in buds from fieldgrown apple trees. Tree Genet Genomes 3: 329-339.
91. Proost S, van Bel M, Sterck L, Billiau K, van Parys T, van de Peer Y, Vandepoele K (2009) PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell 21(12): 3718-31.
92. Rafalski JA (2010) Association genetics in crop improvement. Curr Opin Plant Biol 13: 174-180.
93. Rowan DD, Allen JM, Fielder S, Hunt MB (1999) Biosynthesis of straightchain ester volatiles in red delicious and granny smith apples using deuterium-labelled precursors. J Agric Food Chem 47: 2553-2562.
94. Rowan DD, Hunt MB, Dimouro A, Alspach PA, Weskett R, Volz RK, Gardiner SE, Change D (2009) Profiling fruit volatiles in the progeny of a 'Royal Gala' × 'Granny Smith' apple (Malus × domestica) cross. J Agri Food Chem 57: 7953-7961.
95. Rudell DR, Mattheis JP (2009) Superficial scald development and related metabolism is modified by postharvest light irradiation. Postharvest Biol Technol 51: 174-182.
96. Rudell DR, Mattheis JP, Curry EA (2008) Prestorage ultraviolet-white light irradiation alters apple peel metabolome. J Agri Food Chem 56: 1138-1147.
97. Ruiz R, Garca-Luis A, Monerri C, Guardiola JL (2001) Carbohydrate availability in relation to fruitlet abscission in citrus. Ann Bot 87: 805-812.
98. 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.
99. Schaffer RJ, Friel EN, Souleyre EJF, Bolitho K, Thodey K, Ledger S, Bowen JH, Ma JH, Nain B, Cohen D, Gleave AP, Crowhurst RN, Janssen BJ, Yao J-L, 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.
100. Schaffer SM, Krishnan V, Kalyanaraman A, Dhingra (2010) A comparative transcriptomics in apple using quantitative 3' untranslated region (UTR) pyrosequencing. In: Proceedings of the Plant & Animal Genome Conference XVIII, San Diego, CA USA P087.
101. Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183.
102. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi MY, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
103. Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimaki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M (2007) Strong association of de novo copy number mutations with autism. Science 316: 445-449.
104. Stoeckli S, Mody K, Patocchi A, Kellerhals M, Dorn S (2009) Rust mite resistance in apple assessed by quantitative trait loci analysis. Tree Genet Genomes 5: 257-267.
105. Tang HB, Wang XY, Bowers JE, Ming R, Alam M, Paterson AH (2008) Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res 18(12): 1944-1954.
106. Tanksley SD, Ganal MW, Prince JP, de-Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Roder MS, Wing RA, Wu W, Young ND (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160.
107. Taylor JE, Whitelaw CA (2001) Signals in abscission. New Phytol 151: 323-339.
108. Tsao R, Yang R, Young JC, Honghui Zhu H (2003) Polyphenolic profiles in eight apple cultivars using high-performance liquid chromatography (HPLC). J Agric Food Chem 51: 6347-6353.
109. van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K (2009) The flowering world: a tale of duplications. Trends Plant Sci 14(12): 680-688.
110. Vandepoele K, Saeys Y, Simillion C, Raes J, van de Peer Y (2002) The Automatic Detection of Homologous Regions (ADHoRe) and its application to microcolinearity between Arabidopsis and Rice. Genome Res 12: 1792-801.
111. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A et al (2007) High quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One 2: e1326.
112. Velasco R, Zharkikh A, Affourtit J et al (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42: 833-839.
113. Veyrieras JB, Goffinet B, Charcosset A (2007) MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BMC Bioinformatics 8: 49.
114. Vilanova S, Sargent DJ, Arús P, Monfort A (2008) Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC Plant Biol 8: 67.
115. Volz RK, Rikkerink E, Austin P, Lawrence T, Bus VGM (2009) "Fast Breeding" in apple: a strategy to accelerate introgression of new traits into elite germplasm. Acta Hort 814: 163-168.
116. Wang W, Tai F, Chen S (2008) Optimizing Protein extraction from plant tissues for enhanced preoteomics analysis. J Sep Sci 31: 2032-2039.
117. Wang L, Li P, Brutnell TP (2010) Exploring plant transcriptomes using ultra high-throughput sequencing. Briefings Functional Genom 9: 118-128.
118. Weigel D, Mott R (2009) The 1001 genomes project for Arabidopsis thaliana. Genome Biol 10(5): 107.
119. Wiedow C, Chagné D, Souleyre E, Rowan D, Hunt M, Lambert C, Cestaro A, Velasco R, Volz R, Gardiner SE (2010) QTL and candidate gene mapping of 'Ripe Apple' aroma. In: Proceedings of Plant & Animal Genome XVIII Conference, January 9-13, 2010 San Diego, CA USA P476.
120. Wisniewski M, Bassett C, Macarisin D, Norelli J, Artlip T (2009) Transcriptomic and proteomic response of fruit trees to abiotic stress. Acta Hort 839: 681-688.
121. Wolfe J, Wehr WJA (1988) Rosaceous Chamaebatiaria-like foliage from the Paleogene of western North America. Aliso 12: 177-200.
122. Youens-Clark K, Faga B, Stein L, Ware D (2009) CMap 1. 01: a comparative mapping application for the Internet. Bioinformatics 25(22): 3040-3042.
123. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.
124. Zhang H, Cha S, Yeung ES (2007) Colloidal graphite-assisted laser desorption/ionization MS and MSn of small molecules. 2. Direct profiling and MS imaging of small metabolites from fruit. Anal Chem 79: 6575-6584.
125. Zharkikh A, Troggio M, Pruss D, Cestaro A, Eldrdge G, Pindo M, Mitchell JT, Vezzulli S, Bhatnagar S, Fontana P, Viola R, Gutin A, Salamini F, Skolnick M, Velasco R (2008) Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: Problems and solutions. J Biotechnol 136(1-2): 38-43.
126. Zhong R, Lee C, Zhou J, McCarthy RL, Ye Z-H (2008) A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell 20: 2763-2782.