Map-based cloning of single gene traits and quantitative traits

Genetics, Genomics and Breeding of Stone Fruits

Volumn , Issue , 2012, Pages 212-243

  Horn, Renate ^a   Sajer, Osama ^a   Esmenjaud, Daniel ^b   Claverie, Michel ^c   Dirlewanger, Elisabeth ^d  

^a UNIVERSITY OF ROSTOCK   (Germany)

^b CNRS   (France)

^c CIRAD   (France)

^d CEMAGREF   (France)

Author keywords

BAC libraries; Cloning; Genetic mapping; Molecular markers; Mutants; Peach genome sequence; Transformation

Indexed keywords

EID: 84892483118     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b13104     Document Type: Chapter

References (148)

1. Abad P, Gouzy J, Aury J-M, Castagnone-Sereno P, Danchin EGJ, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC, et al. (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol 26: 909-915.
2. Alvarez-Buylla ER, Pelaz S, Lijegren SJ, Gold SE, Burgeff C, Ditta GS, de Pouplana LR, Martinez-Castilla L, Yanfsky MF (2000) An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc Natl Acad Sci USA 97: 5328-5333.
3. Aranzana MJ, Gracia-Mas J, Carbo J, Arus P (2002) Development and variability of microsatellite markers in peach. Plant Breed 121: 87-92.
4. Aranzana MJ, Abbassi EK, Howad W, Arús P (2010) Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. BMC Genetics 11: 69.
5. Aranzana MJ, Pineda A, Cosson P, Dirlewanger E, Ascasibar J, Cipriani G, Ryder CD, Testolin R, Abbott A, King GJ, Iezzoni AF, Arús P (2003) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theor Appl Genet 106: 819-825.
6. Arora R, Rowland LJ, Tanino K (2003) Induction and release of bud dormancy in woody perennials: a science comes of age. Hort Science 38: 911-921.
7. 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 Hort Sci 119: 1312-1316.
8. Ballvora A, Pierre M, van den Ackerveken G, Schornack S, Rossier O, Ganal M, Lahaye T, Bonas U (2001) Genetic mapping and functional analysis of the tomato Bs4 locus governing recognition of the Xanthomonas campestris pv. vescatoria AvrBs4 protein. Mol Plant Microbe Interact 14: 629-638.
9. Bassi D, Dima A, Scorza R (1994) Tree structure and pruning response of six peach growth forms. J Am Soc Hort Sci 119: 378-382.
10. Besemer J, Borodovsky M (2005) Gene Mark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucl Acids Res 33: W451-W454.
11. Bielenberg DG, Wang Y, Fan S, Reighard GL, Scorza R, Abbott AG (2004) A deletion affecting several gene candidates is present in the evergrowing peach mutant. J Hered 95: 436-444.
12. Bielenberg DG, Wang Y, Li Z, Zhebentyayeva T, Fan S, Reighard GL, Scorza R, Abbott AG (2008) Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation. Tree Genet Genomes 4: 495-507.
13. Bosselut N, Van Ghelder C, Claverie M, Voisin R, Onesto JP, Rosso MN, Esmenjaud D (2011) Agrobacterium rhizogenes-mediated transformation of Prunus as an alternative for gene functional analysis in hairy-roots and composite plants. Plant Cell Rep 30: 1313-1326.
14. Boudehri K, Bendahmane A, Cardinet G, Troadec C, Moing A, Dirlewanger E (2009) Phenotypic and fine genetic characterization of the D locus controlling fruit acidity in peach. BCM Plant Biol 9: 59-72.
15. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
16. Burgos L, Ledbetter CA, Pérez-Tornero O, Ortin-Párraga F, Egea J (1997) Inheritance of sexual incompatibility in apricot. Plant Breed 116: 383-386.
17. Burke DT, Carle GF, Olson MV (1987) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236: 806-812.
18. Cambra M, Capote N, Myrta A, Llàcer G (2006) Plum pox virus and the estimated costs associated with sharka disease. EPPO Bull 36: 202-204.
19. Cantini C, Iezzoni AF, Lamboy WF, Boritzky M, Struss D (2001) DNA fingerprinting of tetraploid cherry germplasm using simple sequence repeats. J Am Soc Hort Sci 126: 205-209.
20. 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.
21. Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellite repeats in peach (Prunus persica (L.) Batsch): isolation, characterisation and cross-species amplification in Prunus. Theor Appl Genet 99: 65-72.
22. Claverie M, Bosselut N, Lecouls AC, Voisin R, Lafargue B, Poizat C, Kleinhentz M, Laigret F, Dirlewanger E, Esmenjaud D (2004a) Location of independent root-knot nematode resistance genes in plum and peach. Theor Appl Genet 108: 765-773.
23. Claverie M, Dirlewanger E, Cosson P, Bosselut N, Lecouls AC, Voisin R, Kleinhentz M, Lafargue B, Caboche M, Chalhoub B, Esmenjaud D (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.
24. Claverie M, Dirlewanger E, Bosselut N, Van Ghelder C, Voisin R, Kleinhentz M, Lafargue B, Abad P, Rosso MN, Chalhoub B, Esmenjaud D (2011) The Ma gene for complete-spectrum resistance to Meloidogyne spp. in Prunus is a TNL with a huge repeated C-terminal post LRR region. Plant Physiol 156: 779-792.
25. Cook R, Evans K (1987) Resistance and tolerance. In: Brown RH, Kerry BR (eds) Principles and Practice of Nematode Control in Crops. Academic press, New York, pp 179-231.
26. Dangl JL, Jones JDG (2001) Plant pathogens and integrated defence responses to infection. Nature 411: 826-833.
27. Decroocq (V), Foulongne M, Lambert P, Le Gall O, Mantin C, Pascal T, Schurdi-Levraud V, Kervella J (2005) Analogues of virus resistance genes map to QTLs for resistance to sharka disease in Prunus davidiana. Mol Genet Genom 272: 680-689.
28. 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.
29. Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howad W, Arús P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 101: 9891-9896.
30. Dirlewanger E, Moing A, Rothan C, Svanella L, Pronier V, Guye A, Plomion C, Monet R (1999) Mapping QTL controlling fruit quality in peach (Prunus persica (L.) Batsch). Theor Appl Genet 98: 18-31.
31. Dirlewanger E, Pronier V, Parvery C, Rothan C, Guy A, Monet R (1998) Genetic linkage map of peach. Theor Appl Genet 97: 888-895.
32. El-kereamy A, El-sharkawy I, Ramamoorthy R, Taheri A, Errampalli D, Kumar P, Jayasankarr S (2011) Prunus domestica pathogenesis-related protein-5 activates the defense response pathway and enhances the resistance to fungal infection. Plos One Vol 6, Issue 3, e17973.
33. Entani T, Iwano M, Shiba H, Che FS, Isogai A, Takayama S (2003) Comparative analysis of the self-incompatibility (S-) locus region of Prunus mume: identification of a pollen-expressed F-box gene with allelic diversity. Genes Cells 8: 203-213.
34. Eremin VG (1978) Genetic potential of species Prunus cerasifera Ehr. and its use in breeding. Acta Hort 74: 61-65.
35. Esmenjaud D, Minot JC, Voisin R (1996) Effect of durable inoculum pressure and high temperature on root galling, nematode numbers and survival of Myrobalan plum genotypes (Prunus cerasifera Ehr.) highly resistant to Meloidogyne spp. Theor Appl Genet 92: 873-879.
36. Esmenjaud D, Minot JC, Voisin R, Pinochet J, Simard MH, Salesses G (1997) Differential response to root-knot nematodes in Prunus species and correlative genetic implications. J Nematol 29:370-380.
37. Esmenjaud D, Voisin R, Van Gelder C, Bosselut N, Larfargue B, Di Vito M, Dirlewanger E, Poessel JL, Kleinhentz M (2009) Genetic dissection of resistance to root-knot nematodes Meloidogyne spp. in plum, peach, almond, and apricot from various segregating interspecific Prunus progenies. Tree Genet Genomes 5: 279-289.
38. Etienne C, Moing A, Dirlewanger E, Raymond P, Monet R, Rothan C (2002a) Isolation and characterization of six peach cDNAs encoding key proteins in organic acid metabolism and solute accumulation: involvement in regulating peach fruit acidity. Physiol Plant 114: 259-270.
39. Etienne C, Rothan C, Moing A, Plomion C, Bodenes C, Svanella-Dumas L, Cosson P, Pronier V, Monet R, Dirlewanger E (2002b) Candidate genes and QTLs for sugar and organic acid content in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 105: 145-159.
40. Fan S, Bielenberg DG, Zhebentyayeva TN, Reighard GL, Okie WR, Holland D, Abbott AG (2010) Mapping quantitative trait loci associated with chilling requirement and bloom date in peach (Prunus persica). New Phytol 185: 917-930.
41. Foulonge 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.
42. Gassmann W, Hinsch ME, Staskawicz BJ (1999) The Arabidopsis RPS24 bacterial-resistance gene is a member of the TIR-NBS-LRR family of the disease resistance genes. Plant J 20: 265-277.
43. 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.
44. 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.
45. Gonzalez-Padilla IM, Webb K, Scorza R (2003) Early antibiotic selection and efficient rooting and acclimatization improve the production of transgenic plum plants (Prunus domestica L.). Plant Cell Rep 22: 38-45.
46. Hamilton CM, Frary A, Lewis C, Tanksley SD (1996) Stable transfer of intact high-molecularweight DNA into plant chromosomes. Proc Natl Acad Sci USA 93: 9975-9979.
47. Horn R, Lecouls AC, 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 TN, Yeisoo Y, Hye Ran K, Jesudurai C, Sosinski B, Arús P, Baird V, Parfitt D, Reighard GL, 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.
48. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arús P (2005) Mapping a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 171: 1305-1309.
49. Hoyerová K, Perry L, Hand P, Laňková M, Kocábek T, May S, Kottová J, Pačes J, Napier R, Zažímalová E (2008) Functional Characterization of PaLAX1, a Putative Auxin Permease, in Heterologous Plant Systems. Plant Physiol 146: 1128-1141.
50. Ion-Nagy L, Lansac M, Eyquard JP, Salvador B, Garia JA, Le Gall O, Hernould M, Schurdi-Levraud V, Decroocq V (2006) PPV long-distance movement is occasionally permitted in resistant apricot hosts. Virus Res 120: 70-78.
51. Jiménez S, Reighard GL, Bielenberg DG (2010) Gene expression of DAM5 and DAM6 is suppressed by chilling temperatures and inversely correlated with bud break rate. Plant Mol Biol 73: 157-167.
52. Jiménez S, Lawton-Rauh AL, Reighard GL, Abbott AG, Bielenberg DG (2009) Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from peach. BMC Plant Biol 9: 81-93.
53. 2 progeny. Theor Appl Genet 97: 1034-1041.
54. Kerr ID, Bennett MJ (2007) New insight into the biochemical mechanisms regulating auxin transport in plants. Biochem J 401: 613-622.
55. Khallouk S, Voisin R, Van Ghelder C, Engler G, Amiri S, Esmenjaud D (2011) Histological mechanism of the resistance conferred by the Ma gene against Meloidogyne incognita in Prunus. Phytopathology 101: 945-951.
56. Krysan PJ, Young JC, Sussman MR (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11: 2283-2290.
57. Lalli D, Abbott A, Zhebentyayeva T, Badenes M, Damsteegt V, Polák J, Krska B, Salava J (2008) A genetic linkage map for an apricot (Prunus armeniaca L.) BC1 population mapping plum pox virus resistance. Tree Genet Genomes 4: 481-493.
58. Le Dantec L, Cardinet G, Bonet J, Fouché M, Boudehri K, Monfort A, Poëssel JL, Moing A, Dirlewanger E (2010) Development and mapping of peach candidate genes involved in fruit quality and their transferability and potential use in other Rosaceae species. Tree Genet Genomes 6: 995-1012.
59. Llácer G, Cambra M, Laviña A (1985) Detection of plum pox virus in Spain. EPPO Bull 15: 325-329.
60. Lambert P, Dicenta F, Rubio M, Audergon JM (2007) QTL analysis of resistance to sharka disease in apricot (Prunus armeniaca L.) ‘Polonais’ x ‘Stark Early Orange’ F1 progeny. Tree Genet Genomes 3: 299-309.
61. Lander ES, Green P, Abrahamson J, Barlow A, Daley MJ, Lincoln SE, Newburg L (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.
62. Lecouls AC, Rubio-Cabetas MJ, Minot JC, Voisin R, Bonnet A, Salesses G, Dirlewanger E, Esmenjaud D (1999) RAPD and SCAR markers linked to the Ma1 root-knot nematode resistance gene in Myrobalan plum (Prunus cerasifera Ehr.). Theor Appl Genet 99: 328-336.
63. Lecouls AC, Bergougnoux V, Rubio-Cabetas MJ, Bosselut N, Voisin R, Poessel JL, Faurobert M, Bonnet A, Salesses G, Dirlewanger E, Esmenjaud D (2004) Marker-assisted selection for the wide-spectrum resistance to root-knot nematodes conferred by the Ma gene from Myrobalan plum (Prunus cerasifera) in interspecific Prunus material. Mol Breed 13: 113-124.
64. Li Z, Reighard GL, Abbott AG, Bielenberg DG (2009) Dormancy-associated MADS genes from the EVG locus of peach [Prunus persica (L.) Batsch] have distinct seasonal and photoperiodic expression patterns. J Exp Bot 60: 3521-3530.
65. Liang FS, Zhang KC, Yu ZW, Yang JL, Zhang XM, Jin D, Wang B (2004) Construction, characterization, and screening of a transformation-competent artificial chromosome library of peach. Plant Mol Biol Rep 22: 37-48.
66. Liu YG, Chen Y (2007) High-efficiency thermal asymmetric interlaced PCR for amplification of unknown flanking sequences. Bio/Techniques 43: 649-656.
67. Liu YG, Mitsukawa N, Oosumi T, Whittier RF (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J 8: 457-463.
68. Majoros WH, Pertea M, Salzberg SL (2004) Tigr Scan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20: 2878-2879.
69. Mante S, Morgens PH, Scorza R, Cordts JM, Callahan AM (1991) Agrobacterium-mediated transformation of plum (Prunus domestica L.) hypocotyl slices and regeneration of transgenic plants. Bio/Technology 9: 853-857.
70. Marandel G, Pascal T, Candresse T, Decroocq V (2009a) Quantitative resistance to plum pox virus in Prunus davidiana P1908 linked to components of the eukaryotic translation initiation complex. Plant Pathol 58: 425-435.
71. Marandel G, Slava J, Abbott A, Candresse T, Decroocq V (2009b) Quantitative trait loci metaanalysis of plum pox virus resistance in apricot (Prunus armeniaca L.): new insights on the organization and identification of genomic resistance factors. Mol Plant Pathol 10: 347-360.
72. Martin GB, Bagdanove AJ, Sess G (2003) Understanding the functions of plant disease resistance proteins. Annu Rev Plant Biol 54: 23-61.
73. Martinez-Gomez P, Dicenta F (2000) Evaluation of resistance of apricot cultivars to a Spanish isolate of plum pox virus (PPV). Plant Breed 199: 179-181.
74. McCubbin AG, Wang X, Kao TH (2000) Identification of self-incompatibility (S) locus linked pollen cDNA markers in Petunia inflata. Genome 43: 619-627.
75. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88: 9828-9832.
76. Miller S, Scorza R (2010) Response of two novel peach tree growth habits to in-row tree spacing, training system, and pruning: Effect on growth and pruning. J Am Pomol Soc 64: 199-217.
77. Milligan SB, Bodeau J, Yaghoobi J, Kaloshian I, Zabel P, Williamson VM (1998) The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes. Plant Cell 10: 1307-1319.
78. Mnejja M, Gracia-Mas J, Howad W, Badenes ML, Arús P (2004) Simple-sequence repeat (SSR) markers of Japanese plum (Prunus salicina Lindl) are highly polymorphic and transferable to peach and almond. Mol Ecol Notes 4: 163-166.
79. Mnejja M, Gracia-Mas J, Howad W, Arús P (2005) Development and transportability across Prunus species of 42 polymorphic almond microsatellites. Mol Ecol Notes 5: 531-535.
80. Mnejja M, Garcia-Mas J, Audergon JM, Arús P (2010) Prunus microsatellite marker transferability across rosaceous crops. Tree Genet Genomes 6: 689-700.
81. Monet R (1979) Genetic transmission of the ʼnon-acid’ character. Incidence on selection for quality. In: (INRA ed) Eucarpia Symposium Tree Fruit Breeding, Angers, France, pp 273-276.
82. Ogundiwin EA, Marti C, Forment J, Pons C, Granell A, Gradziel TM, Peace CP, Crisoto CH (2008) Development of Chill Peach genomic tools and identification of cold-responsive genes in peach fruit. Plant Mol Biol 68: 379-397.
83. Olukolu, BA, Trainin T, Fan S, Kole C, Bielenberg DG, Reighard GL, Abbott AG, Holland D (2009) Genetic linkage mapping for molecular dissection of chilling requirement and bud-break in apricot (Prunus armeniaca L.). Genome 52: 819-828.
84. 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.
85. Oosumi T, Ruiz-Rojas JJ, Veilleux RE, Dickerman A, Shulaev V (2010) Implementing reverse genetics in Rosaceae: analysis of T-DNA flanking sequences of insertional mutant lines in the diploid strawberry, Fragaria vesca. Physiol Plant 140: 1-9.
86. Paal J, Henselewski H, Muth J, Kesem K, Menéndez CM, Salamini F, Ballvora A, Gebhardt C (2004) Molecular cloning of the potato Gro1-4 gene conferring resistance to pathotype Ro1 of the root cyst nematode Globodera rostochiensis, based on a candidate gene approach. Plant J 38: 285-297.
87. Peters JL, Cnudde F, Gerats T (2003) Forward genetics and map-based cloning approaches. Trends Plant Sci 8: 484-491.
88. Petri C, Lopez-Noguera S, Alburquerque N, Egea J, Burgos L (2008a) An antibiotic-based selection strategy to regenerate transformed plants from apricot leaves with high efficiency. Plant Sci 175: 777-783.
89. Petri C, Wang H, Alburquerque N, Faize M, Burgos L (2008b) Agrobacterium-mediated transformation of apricot (Prunus armeniaca L.) leaf explants. Plant Cell Rep 27: 1317-1324.
90. Petri C, Webb K, Hily JM, Dardick C, Scorza R (2008c) High transformation efficiency in plum (Prunus domestica L.): a new tool for functional genomics studies in Prunus spp. Mol Breed 22: 581-591.
91. Pilarova P, Marandel G, Decroocq V, Salava J, Krska B, Abbott AG (2010) Quantitative trait analyses of resistance to plum pox virus in the apricot F1 progeny ‘Harlayne’ x ‘Vestar’. Tree Genet Genomics 6: 467-475.
92. Ravelonandro M, Scorza R, Bachelier JC, Labonne G, Levy L, Damsteegt V, Callahan AM, Dunez J (1997) Resistance of transgenic Prunus domestica to plum pox virus infection. Plant Dis 81: 1231.
93. Ravelonandro M, Scorza R, Callahan A, Levy L, Jacquet C, Monsion M, Damsteegt V (2000) The use of transgenic fruit trees as a resistance strategy for virus epidemics: the plum pox (sharka) model. Virus Res 71: 63-69.
94. Remington DL, Unger MC, Purugganan MD (2001) Map-based cloning of quantitative trait loci: progress and prospects. Genet Res 78: 213-218.
95. Robaglia C, Caranta C (2006) Translation initiation factors: a weak link in plant RNA virus infection. Trends Plant Sci 11: 40-45.
96. Roberts PA (1992) Current status of the availability, development, and use of host plantresistance to nematodes. J Nematol 24: 213-227.
97. Rodriguez J, Sherman WB, Scorza R, Wisniewski M, Okie WR (1994) Evergreen peach, its inheritance and dormant behavior. J Am Soc Hort Sci 119: 789-792.
98. Rohde A, Ruttnik T, Hostyn V, Sterck L, Van Driessche K, Boerjan W (2007) Gene epression during induction, maintenance, and release of dormancy in apical buds of poplar. J Exp Bot 58: 4047-4060.
99. Romero C, Vilanova S, Burgos L, Martínez-Calvo J, Vicente M, Llácer G, Badenes ML (2004). Analysis of the S-locus structure in Prunus armeniaca L. Identification of S-haplotype specific S-RNase and F-Box genes. Plant Mol Biol 56: 145-157.
100. Ruiz EMV, Soriano JM, Romeo C, Zhentyayeva T, Terol J, Zuraiga E, Llacer G, Abbott AG, Badenes ML (2011) Narrowing down the apricot plum pox virus resistance locus and comparative analysis within the peach genome syntenic region. Mol Plant Pathol 12: 535-547.
101. Sajer O, Scorza R, Dardick C, Zhebentyayeva T, Abbott A, Horn R (2012) Development of sequence-tagged site markers linked to the pillar growth type in peach [Prunus persica L. (Batsch)]. Plant Breed 131: 186-192.
102. Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 516-522.
103. Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D (2006) Highly specific gene silencing by artificial MicroRNAs in Arabidopsis. Plant Cell 18: 1121-1133.
104. Scorza R (1984) Characterization of four distinct peach tree growth types. J Am Soc Hort Sci 109: 455-457.
105. Scorza R, Ravelonandro M, Callahan AM, Cordts JM, Fuchs M, Dunez J, Gonsalves D (1994) Transgenic plums (Prunus domestica L.) express the plum pox virus coat protein gene. Plant Cell Rep 14: 18-22.
106. Scorza R (2005) Theory and practice of genetically manipulating peach tree architecture. NY Fruit Quarterly 3: 27-31.
107. Scorza R, Callahan A, Levy L, Damsteegt V, Webb K, Ravelonandro M (2001) Post-transcriptional gene silencing in plum pox virus resistant transgenic European plum containig the plum pox potyvirus coat protein gene. Transgen Res 10: 201-209.
108. Scorza R, Miller S, Glenn DM, Okie WR, Tworkoski T (2006) Developing peach cultivars with novel tree growth habits. In: Infante R (ed) Proc 6th Intl Peach Symposium. Acta Hort (ISHS) 713: 61-64.
109. Sicard O, Marandel G, Soriano JM, Lalli DA, Lambert P, Salava J, Badenes ML, Abbott AG, Decroocq V (2008) Flanking the major plum pox virus resistance locus in apricot with co-dominant markers (SSRs) derived from candidate resistance genes. Tree Genet Genomes 4: 359-365.
110. Sijacic P, Wang X, Skirpan AL, Wang Y, Dowd PE, McCubbin AG, Huang S, Kao T (2004) Identification of the pollen determinant of S-RNase-mediated self-incompatibility. Nature 429: 302-305.
111. SharafiY, Motallebi-Azar AR (2011) Gamma irradiation influences on some biological traits in two almond (Prunus amygdalus L.) cultivars. J Med Plants Res 5: 255-258.
112. Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and maintenance of 300-kilobasepair fragments of human DNA in Escherichia coli using an F-factor based vector. Proc Natl Acad Sci USA 89: 8794-8797.
113. Smith NA, Singh SP, Wang MB, Stoutjesdijk PA, Green AG, Waterhouse PM (2000) Total silencing by intron-spliced hairpin RNAs. Nature 407: 319-320.
114. Soderlund C, Humphrey S, Dunhum A, French L (2000) Contigs built with fingerprints, markers and FPC 4.7. Genome Res 10: 1772-1787.
115. Soriano JM, Vera-Ruiz EM, Vilanova S, Martínez-Calvo J, Llácer G, Badenes ML, Romero C (2008) Identification and mapping of a locus conferring plum pox virus resistance in two apricot-improved linkage maps. Tree Genet Genomes 4: 391-402.
116. Sosinski B, Gannavarapu M, Hager LD, Beck LE, King GJ, Ryder CD, Rajapakse S, Baird WV, Ballard RE, Abbott AG (2000) Characterization of microsatellite markers in peach (Prunus persica L Batsch). Theor Appl Genet 101: 421-428.
117. Speulman E, Metz PLJ, van Arkel G, te Lintel Hekkert B, Stiekema WJ, Pereira A (1999) A twocomponent enhancer-inhibitor transposon mutagenesis system for functional analysis of the Arabidopsis genome. Plant Cell 11: 1853-1866.
118. Srinivasan C, Liu Z, Scorza R (2011) Ectopic expression of class 1 KNOX genes induce adventitious shoot regeneration and alter growth and development of tobacco (Nicotiana tabacum L) and European plum (Prunus domestica L). Plant Cell Rep 30: 655-664.
119. Tanksley SD, Ganal MW, Martin GB (1995) Chromosomal landing: a paradigm for map-based cloning in plants with large genomes. Trends Genet 11: 63-68.
120. Tao R, Yamane H, Sugiura A (1999) Molecular typing of S-alleles through identification, characterization and cDNA cloning for S-RNAses in sweet cherry. J Am Soc Hort Sci 124: 224-233.
121. Tattersall DB, van Heeswijck R, Hoj PB (1997) Identification and characterization of a fruit-specific, thaumatin-like protein that accumulates at very high levels in conjunction with the onset of sugar accumulation and berry softening in grapes. Plant Physiol 114: 759-769.
122. Testolin R, Messina R, Lain O, Marrazzo MT, Huang WG, Cipriani G (2004) Microsatellites isolated in almond from an AC-repeat enriched library. Mol Ecol Notes 4: 459-461.
123. Urtubia C, Devia J, Castro A, Zamora P, Aguirre C, Tapia E, Barba P, Dell’Orto, Moynhihan MR, Petri C, Scorza R, Prieto H (2008) Agrobacterium-mediated genetic transformation of Prunus salicina. Plant Cell Rep 27: 1333-1340.
124. Ushijima K, Sassa H, Dandekar AM, Gradziel TM, Tao R (2003) Structural and transcriptional analysis of the self-incompatibility locus of almond: identification of a pollen-expressed F-box gene with haplotype-specific polymorphism. Plant Cell 15: 771-781.
125. Ushijima K, Sassa H, Tao R, Yamane H, Dandekar AM, Gradziel TM, Hirano H (1998) Cloning and characterization of cDNAs encoding S-RNases from almond (Prunus dulcis). Primary structural features and sequence diversity of the S-RNases in Rosaceae. Mol Gen Gent 260: 261-268.
126. Utz HF, Melchinger AE (1996) PLABQTL: A program for composite interval mapping of QTL. J Agri Genom 2: 1-5.
127. Van der Biezen EA, Jones JD (1998) Plant disease-resistance proteins and the gene-for-gene concept. Trends Biochem Sci 23: 454-456.
128. Van der Hoorn RA, Kamoun S (2008) From Guard to Decoy: a new model for perception of plant pathogen effectors. Plant Cell 20: 2009-2017.
129. Verde I, Lauria M, Dettori MT, Vendramin E, Balconi C, Micali S, Wang Y, Marrazzo MT, Cipriani G, Hartings H, Testolin R, Abbott AG, Motto M, Quarta R (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.
130. Veyrieras JB, Goffinet B, Charcosset A (2007) MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BCM Bioinformat 8: 49.
131. Vigers AJ, Wiedermann S, Roberts WK, Legrand M, Selitrennikoff CP, et al. (1992) Thaumatinlike pathogenesis-related proteins are antifungal. Plant Sci 83: 155-161.
132. 2 progeny linkage map based on SSR and AFLP markers, mapping plum pox virus resistance and self-incompatibility traits. Theor Appl Genet 107: 239-247.
133. Vilanova S, Romero C, Abernathy D, Abbott AG, Burgos L, Llacer G, Badenes ML (2003b) 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 Genom 269: 685-691.
134. Voisin R, Minot JC, Esmenjaud D (1999) Penetration, development and emigration of juveniles of the nematode Meloidogyne arenaria in Myrobalan plum (Prunus cerasifera) clones bearing the Ma resistance genes. Eur J Plant Pathol 105: 103-108.
135. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23: 4407-4414.
136. Wang Q, Zhang K, Qu X, Jia J, Shi J, Jin D, Wang B (2001) Construction and characterization of a bacterial artificial chromosome library of peach. Theor Appl Genet 103: 1174-1179.
137. Wang Y, Garay L, Georgi LL, Reighard GL, Scorza R, Abbott AG (2002a) Development of bacterial artificial chromosome contigs in the evergrowing gene region in peach [Prunus persica (L.) Batsch]. Acta Hort 592: 183-189.
138. Wang Y, Georgi LL, Reighard GL, Scorza R, Abbott AG (2002b) Genetic mapping of the evergrowing gene in peach [Prunus persica (L.) Batsch]. J Hered 93: 352-358.
139. Wang Y, Georgi LL, Zhebentyayeva TN, Reighard GL, Scorza R, Abbott AG (2002c) Highthroughput targeted SSR marker development in peach (Prunus persica). Genome 45: 319-328.
140. Waterhouse PM, Grahm MW, Wang MB (1998) Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci USA 95: 1359-13964.
141. Whitham S, Dinesh-Kumar SP, Choi D, Hehl R, Corr C, Baker B (1994) The product of the tobacco mosaic virus resistance gene N: similarity to Toll and Interleukin-1 receptor. Cell 78: 1101-1115.
142. Yaegaki H, Shimada T, Moriguchi T, Hayma H, Haji T, Yamaguchi M (2001) Molecular characterization of S-RNase genes and S-genotypes in Japanese apricot (Prunus mume Sieb. Et Zucc.) Sex Plant Reprod 13: 251-257.
143. Yamazaki K, Okabe M, Takahashi E (1987) New broomy flowering peach cultivars ‘Terutebeni’, ‘Terutemomo’ and ‘Teruteshiro’. Bull Kanagawa Hort Exp Sta 34: 54-56.
144. Yamane H, Ikeda K, Ushijima K, Sassa H, Tao R (2003) A pollen-expressed gene for a novel protein with an F-box motif that is very tightly linked to gene for S-RNase of two species of cherry, Prunus cerasus and P. avium. Plant Cell Physiol 44: 764-769.
145. Yamane H, Tao R, Sugiura A, Hauck NR, Iezzoni AF (2001) Identification and characterization of S-RNases in tetraploid sour cherry (Prunus cerasus). J Am Soc Hort Sci 126: 661-667.
146. Yoshida M: Genetical studies on the fruit quality of peach varieties. I. Acidity (1970) Bull Hort Res Stn Jpn Ser A 9: 1-15.
147. Zhebentyayeva TN, Swire-Clark G, Georgi LL, Garay L, Jung S, Forrest S, Blenda AV, Blackmon B, Mook J, Horn R, Howad W, Arús P, Main D, Tomkins JP, Sosinski B, Baird WV, Reighard GL, Abbott AG (2008) A framework physical map for peach, a model Rosaceae species. Tree Genet Genomics 4: 745-756.
148. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.