Genomics of pear and other Rosaceae fruit trees

Breeding Science

Volumn 66, Issue 1, 2016, Pages 148-159

  Yamamoto, Toshiya ^a   Terakami, Shingo ^a  

^a NATIONAL INSTITUTE OF FRUIT TREE SCIENCE   (Japan)

Author keywords

Apple; Co linearity; Genome sequence; Peach; Pear; Reference map

Indexed keywords

EID: 84962328744     PISSN: 13447610     EISSN: 13473735     Source Type: Journal    
DOI: 10.1270/jsbbs.66.148     Document Type: Review

References (109)

1. Aranzana, M.J., J. Garcia-Mas, J. Carbo and P. Arús (2002) Development and variability analysis of microsatellite markers in peach. Plant Breed. 121: 87–92.
2. Aranzana, M.J., A. Pineda, P. Cosson, E. Dirlewanger, J. Ascasibar, G. Cipriani, C.D. Ryder, R. Testolin, A. Abbott, G.J. King et al. (2003) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theor. Appl. Genet. 106: 819–825.
3. Banno, K., H. Ishikawa, Y. Hamauzu and H. Tabira (1999) Identification of a RAPD marker linked to the susceptible gene of black spot disease in Japanese pear. J. Japan. Soc. Hort. Sci. 68: 476–481.
4. Bell, R.L., H.A. Quamme, R.E.C. Layne and R.M. Skirvin (1996) Pears. In: Janick, J. and J.N. Moore (eds.) Fruit breeding, vol I: Tree and tropical fruits. John Wiley & Sons, London, pp. 441–514.
5. Bianco, L., A. Cestaro, D.J. Sargent, E. Banchi, S. Derdak, M.D. Guardo, S. Salvi, J. Jansen, R. Viola, I. Gut et al. (2014) Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh.). PLoS ONE 9: e110377.
6. Cabrera, A., A. Kozik, W. Howad, P. Arús, A. Iezzoni and E. van der Knaap (2009) Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers. BMC Genomics 10: 562.
7. Cabrera, A., U.R. Rosyara, P. De Franceschi, A. Sebolt, S.S. Sooriyapathirana, E. Dirlewanger, J. Quero-Garcia, M. Schuster, A.F. Iezzoni and E. van der Knaap (2012) Rosaceae conserved orthologous sequences marker polymorphism in sweet cherry germplasm and construction of a SNP-based map. Tree Genet. Genomes 8: 237–247.
8. Cantini, C., A.F. Iezzoni, W.F. Lamboy, M. Bortizki and D. Struss (2001) DNA fingerprinting of tetraploid cherry germplasm using simple sequence repeats. J. Amer. Soc. Hort. Sci. 126: 205–209.
9. Celton, J.M., D.S. Tustin, D. Chagné and S.E. Gardiner (2009) Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences. Tree Genet. Genomes 5: 93–107.
10. Chagné, D., R.N. Crowhurst, M. Troggio, M.W. Davey, B. Gilmore, C. Lawley, S. Vanderzande, R.P. Hellens, S. Kumar, A. Cestaro et al. (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 7: e31745.
11. Chagné, D., R.N. Crowhurst, M. Pindo, A. Thrimawithana, C. Deng, H. Ireland, M. Fiers, H. Dzierzon, A. Cestaro, P. Fontana et al. (2014) The draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’). PLoS ONE 9: e92644.
12. Challice, J.S. (1974) Rosaceae chemotaxonomy and the origins of the Pomoideae. Bot. J. Linn. Soc. 69: 239–259.
13. Challice, J.S. (1981) Chemotaxonomic studies in the Rosaceae and the evolutionary origins of the subfamily Maloideae. Preslia 53: 289–304.
14. Chen, H., Y. Song, L.T. Li, M.A. Khan, X.G. Li, S.S. Korban, J. Wu and S.L. Zhang (2015) Construction of a high-density simple sequence repeat consensus genetic map for pear (Pyrus spp.). Plant. Mol. Biol. Rep. 33: 316–325.
15. Cipriani, G., G. Lot, W.G. Huang, M.T. Marrazzo, E. Peterlunger and R. Testolin (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.
16. Clarke, J.B., D.J. Sargent, R.I. Bošković, A. Belaj and K.R. Tobutt (2009) A cherry map from the inter-specific cross Prunus avium ‘Napoleon’ × P. nipponica based on microsatellite, gene-specific and isoenzyme markers. Tree Genet. Genomes 5: 41–51.
17. Dickson, E.E., K. Arumuganathan, S. Kresovich and J.J. Doyle (1992) Nuclear DNA content variation within the Rosaceae. Am. J. Bot. 79: 1081–1086.
18. Dirlewanger, E., P. Cosson, M. Tavaud, M.J. Aranzana, C. Poizat, A. Zanetto, P. Arús and F. Laigret (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.
19. Dirlewanger, E., P. Cosson, W. Howad, G. Capdeville, N. Bosselut, M. Claverie, R. Voisin, C. Poizat, B. Lafargue, O. Baron 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.
20. Dirlewanger, E., E. Graziano, T. Joobeur, F. Garriga-Calderé, P. Cosson, W. Howad and P. Arús (2004b) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc. Natl. Acad. Sci. USA 101: 9891–9896.
21. Dirlewanger, E., J. Claverie, A.F. Iezzoni and A. Wunsch (2009a) Sweet and Sour Cherries: Linkage Maps, QTL Detection and Marker Assisted Selection. In: Gardiner, S.E. and K.M. Folta (eds.) Plant Genetics/Genomics vol. 6: Genetics and Genomics of Rosaceae. Springer, New York, pp. 291–313.
22. Dirlewanger, E., B. Denoyes-Rothan, T. Yamamoto and D. Chagné (2009b) Genomics Tools across Rosaceae Species. In: Gardiner, S.E. and K.M. Folta (eds.) Plant Genetics/ Genomics vol 6: Genetics and Genomics of Rosaceae. Springer, New York, pp. 539–561.
23. Downey, S.L. and A.F. Iezzoni (2000) Polymorphic DNA markers in black cherry (Prunus serotina) are identified using sequences from sweet cherry, peach, and sour cherry. J. Amer. Soc. Hort. Sci. 125: 76–80.
24. Evans, R.C. and C.S. Campbell (2002) The origin of the apple subfamily (Maloideae; Rosaceae) is clarified by DNA sequence data from duplicated GBSSI genes. Am. J. Bot. 89: 1478–1484.
25. FAOSTAT (2013) http: //faostat.fao.org/
26. Fernández-Fernández, F., N.G. Harvey and C.M. James (2006) Isolation and characterization of polymorphic microsatellite markers from European pear (Pyrus communis L.). Mol. Ecol. Notes 6: 1039–1041.
27. Foulongne, M., T. Pascal, F. Pfeiffer and J. Kervella (2003) QTLs for powdery mildew resistance in peach × Prunus davidiana crosses: consistency across generations and environments. Mol. Breed. 12: 33–50.
28. Fukuda, S., K. Ishimoto, S. Sato, S. Terakami, T. Yamamoto and N. Hiehata (2014) Genetic mapping of the loquat canker resistance locus in bronze loquat (Eriobotrya deflexa). Tree Genet. Genomes 10: 875–883.
29. Gianfranceschi, L., N. Seglias, R. Tarchini, M. Komjanc and C. Gessler (1998) Simple sequence repeats for the genetic analysis of apple. Theor. Appl. Genet. 96: 1069–1076.
30. Gisbert, A.D., J. Martínez-Calvo, G. Llácer, M.L. Badenes and C. Romero (2009) Development of two loquat [Eriobotrya japonica (Thunb.) Lindl.] linkage maps based on AFLPs and SSR markers from different Rosaceae species. Mol. Breed. 23: 523–538.
31. Gonai, T., S. Terakami, C. Nishitani, T. Yamamoto and M. Kasumi (2012) Fine mapping of the scab resistance gene of Japanese pear ‘Kinchaku’ for efficient marker-assisted selection. Bull. Ibaraki Plant Biotech. Inst. 12: 27–33.
32. Grattapaglia, D. and M.D.V. Resende (2011) Genomic selection in forest tree breeding. Tree Genet. Genomes 7: 241–255.
33. Guajardo, V., S. Solís, B. Sagredo, F. Gainza, C. Muñoz, K. Gasic and P. Hinrichsen (2015) Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). PLoS ONE 10: e0127750.
34. Guilford, P., S. Prakash, J.M. Zhu, E. Rikkerink, S. Gardiner, H. Bassett and R. Forster (1997) Microsatellites in Malus × domestica (apple): abundance, polymorphism and cultivar identification. Theor. Appl. Genet. 94: 249–254.
35. Hirakawa, H., K. Shirasawa, S. Kosugi, K. Tashiro, S. Nakayama, M. Yamada, M. Kohara, A. Watanabe, Y. Kishida, T. Fujishiro et al. (2014) Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA Res. 21: 169– 181.
36. Howad, W., T. Yamamoto, E. Dirlewanger, R. Testolin, P. Cosson, G. Cipriani, A.J. Monforte, L. Georgi, A.G. Abbott and P. Arús (2005) Mapping with a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 171: 1305–1309.
37. Hummer, K.E. and J. Janick (2009) Rosaceae: Taxonomy, Economic Importance, Genomics. In: Gardiner, S.E. and K.M. Folta (eds.) Plant Genetics/ Genomics vol. 6: Genetics and Genomics of Rosaceae. Springer, New York, pp. 1–17.
38. Iketani, H., K. Abe, T. Yamamoto, K. Kotobuki, Y. Sato, T. Saito, O. Terai, N. Matsuta and T. Hayashi (2001) Mapping of disease-related genes in Japanese pear using a molecular linkage map with RAPD markers. Breed. Sci. 51: 179–184.
39. Illa, E., D.J. Sargent, E.L. Girona, J. Bushakra, A. Cestaro, R. Crowhurst, M. Pindo, A. Cabrera, E. van der Knaap, A. Iezzoni et al. (2011) Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol. Biol. 11: 9.
40. Inoue, E., M. Kasumi, F. Sakuma, H. Anzai, K. Amano and H. Hara (2006) Identification of RAPD marker linked to fruit skin color in Japanese pear (Pyrus pyrifolia Nakai). Sci. Hortic. 107: 254–258.
41. Inoue, E., Y. Matsuki, H. Anzai and K. Evans (2007) Isolation and characterization of microsatellite markers in Japanese pear (Pyrus pyrifolia Nakai). Mol. Ecol. Notes 7: 445–447.
42. Ishimizu, T., K. Inoue, M. Shimonaka, T. Saito, O. Terai and S. Norioka (1999) PCR-based method for identifying the S-genotypes of Japanese pear cultivars. Theor. Appl. Genet. 98: 961–967.
43. Itai, A., T. Kotaki, K. Tanabe, F. Tamura, D. Kawaguchi and M. Fukuda (2003) Rapid identification of 1-aminocyclopropane-1-carboxylate (ACC) synthase genotypes in cultivars of Japanese pear (Pyrus pyrifolia Nakai) using CAPS markers. Theor. Appl. Genet. 106: 1266–1272.
44. Iwata, H., T. Hayashi, S. Terakami, N. Takada, Y. Sawamura and T. Yamamoto (2013a) Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia. Breed. Sci. 63: 125–140.
45. Iwata, H., T. Hayashi, S. Terakami, N. Takada, T. Saito and T. Yamamoto (2013b) Genomic prediction of trait segregation in a progeny population: a case study of Japanese pear (Pyrus pyrifolia). BMC Genet. 14: 81.
46. Jáuregui, B., M.C. de Vicente, R. Messeguer, A. Felipe, A. Bonnet, G. Salesses and P. Arús (2001) A reciprocal translocation between ‘Garfi’ almond and ‘Nemared’ peach. Theor. Appl. Genet. 102: 1169–1176.
47. 2 progeny. Theor. Appl. Genet. 97: 1034–1041.
48. Joobeur, T., N. Periam, M.C. de Vicente, G.J. King and P. Arús (2000) Development of a second generation linkage map for almond using RAPD and SSR markers. Genome 43: 649–655.
49. Jung, S., A. Cestaro, M. Troggio, D. Main, P. Zheng, I. Cho, K.M. Folta, B. Sosinski, A. Abbott, J.M. Celton et al. (2012) Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. BMC Genomics 13: 129.
50. Klagges, C., J.A. Campoy, J. Quero-Garcıa, A. Guzman, L. Mansur, E. Gratacos, H. Silva, U.R. Rosyara, A. Iezzoni, L.A. Meisel et al. (2013) Construction and comparative analyses of highly dense linkage maps of two sweet cherry intra-specific progenies of commercial cultivars. PLoS ONE 8: e54743.
51. Korban, S.S. and S. Tartarini (2009) Apple Structural Genomics. In: Gardiner, S.E. and K.M. Folta (eds.) Plant Genetics/ Genomics vol. 6: Genetics and Genomics of Rosaceae. Springer, New York, pp. 85–119.
52. Kumar, S., D. Chagné, M.C.A.M. Bink, R.K. Volz, C. Whitworth and C. Carlisle (2012) Genomic selection for fruit quality traits in apple (Malus × domestica Borkh.). PLoS ONE 7: e36674.
53. Kumar, S., D.J. Garrick, M.C.A.M. Bink, C. Whitworth, D. Chagné and R.K. Volz (2013) Novel genomic approaches unravel genetic architecture of complex traits in apple. BMC Genomics 14: 393.
54. Lambert, P., L.S. Hagen, P. Arús and J.M. Audergon (2004) Genetic linkage maps of two apricot cultivars (Prunus armeniaca L.) compared with the almond ‘Texas’ × peach ‘Earlygold’ reference map for Prunus. Theor. Appl. Genet. 108: 1120–1130.
55. Liebhard, R., L. Gianfranceschi, B. Koller, C.D. Ryder, R. Tarchini, E. Van De Weg and C. Gessler (2002) Development and characterisation of 140 new microsatellites in apple (Malus × domestica Borkh.). Mol. Breed. 10: 217–241.
56. Liebhard, R., B. Koller, L. Gianfranceschi and C. Gessler (2003) Creating a saturated reference map for the apple (Malus × domestica Borkh.) genome. Theor. Appl. Genet. 106: 1497–1508.
57. Lopes, M.S., K.M. Sefc, M. Laimer and A. Da Camara Machado (2002) Identification of microsatellite loci in apricot. Mol. Ecol. Notes 2: 24–26.
58. Luby, J.J. and D.V. Shaw (2001) Does marker-assisted selection make dollars and sense in a fruit breeding program? HortScience 36: 872–879.
59. Maliepaard, C., F.H. Alston, G. van Arkel, L.M. Brown, E. Chevreau, F. Dunemann, K.M. Evans, S. Gardiner, P. Guilford, A.W. van Heusden et al. (1998) Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor. Appl. Genet. 97: 60–73.
60. Martínez-García, P.J., D.E. Parfitt, E.A. Ogundiwin, J. Fass, H.M. Chan, R. Ahmad, S. Lurie, A. Dandekar, T.M. Gradziel and C.H. Crisosto (2013) High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.). Tree Genet. Genomes 9: 19–36.
61. Meuwissen, T.H.E., B.J. Hayes and M.E. Goddard (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819–1829.
62. Mnejja, M., J. Garcia-Mas, J.M. Audergon and P. Arús (2010) Prunus microsatellite marker transferability across rosaceous crops. Tree Genet. Genomes 6: 689–700.
63. Montanari, S., M. Saeed, M. Knabel, Y.K. Kim, M. Troggio, M. Malnoy, R. Velasco, P. Fontana, K.H. Won, C.E. Durel et al. (2013) Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS ONE 8: e77022.
64. Moriya, S., H. Iwanami, N. Kotoda, T. Haji, K. Okada, S. Terakami, N. Mimida, T. Yamamoto and K. Abe (2012) Aligned genetic linkage maps of apple rootstock cultivar ‘JM7’ and Malus sieboldii ‘Sanashi 63’ constructed with novel EST-SSRs. Tree Genet. Genomes 8: 709–723.
65. Nashima, K., S. Terakami, S. Nishio, M. Kunihisa, C. Nishitani, T. Saito and T. Yamamoto (2015) S-genotype identification based on allele-specific PCR in Japanese pear. Breed. Sci. 65: 208–215.
66. Nishitani, C., T. Kimura, E. Ueda, W. Howad, P. Arús and T. Yamamoto (2007) Tri-/hexanucleotide microsatellite markers in peach derived from enriched genomic libraries and their application in Rosaceae. Breed. Sci. 57: 289–296.
67. Nishitani, C., S. Terakami, Y. Sawamura, N. Takada and T. Yamamoto (2009) Development of novel EST-SSR markers derived from Japanese pear (Pyrus pyrifolia). Breed. Sci. 59: 391–400.
68. sm-haplotype of Japanese pear. Plant Mol. Biol. 66: 389–400.
69. Peace, C., N. Bassil, D. Main, S. Ficklin, U.R. Rosyara, T. Stegmeir, A. Sebolt, B. Gilmore, C. Lawley, T.C. Mockler et al. (2012) Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS ONE 7: e48305.
70. Potter, D., T. Eriksson, R.C. Evans, S. Oh, J.E.E. Smedmark, D.R. Morgan, M. Kerr, K.R. Robertson, M. Arsenault, T.A. Dickinson et al. (2007) Phylogeny and classification of Rosaceae. Pl. Syst. Evol. 266: 5–43.
71. Rikkerink, E.H.A., N.C. Oraguzie and S.E. Gardiner (2007) Prospects of association mapping in perennial horticultural crops. In: Oraguzie, N.C., E.H.A. Rikkerink, S.E. Gardiner and H.N. De Silva (eds.) Association Mapping in Plants. Springer, New York, pp. 249–269.
72. Salazar, J.A., D. Ruiz, J.A. Campoy, R. Sánchez-Pérez, C.H. Crisosto, P.J. Martínez-García, A. Blenda, S. Jung, D. Main, P. Martínez-Gómez et al. (2014) Quantitative trait loci (QTL) and mendelian trait loci (MTL) analysis in Prunus: a breeding perspective and beyond. Plant Mol. Biol. Rep. 32: 1–18.
73. Sargent, D.J., A. Marchese, D.W. Simpson, W. Howad, F. Fernández-Fernández, A. Monfort, P. Arús, K.M. Evans and K.R. Tobutt (2009) Development of “universal” gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae. Tree Genet. Genomes 5: 133–145.
74. Sawamura, Y., T. Saito, N. Takada, T. Yamamoto, T. Kimura, T. Hayashi and K. Kotobuki (2004) Identification of parentage of Japanese pear ‘Housui’. J. Japan. Soc. Hort. Sci. 73: 511–518.
75. Shulaev, V., S.S. Korban, B. Sosinski, A.G. Abbott, H.S. Aldwinckle, K.M. Folta, A. Iezzoni, D. Main, P. Arús, A.M. Dandekar et al. (2008) Multiple models for Rosaceae genomics. Plant Physiol. 147: 985–1003.
76. Shulaev, V., D.J. Sargent, R.N. Crowhurst, T.C. Mockler, O. Folkerts, A.L. Delcher, P. Jaiswal, K. Mockaitis, A. Liston, S.P. Mane et al. (2011) The genome of woodland strawberry (Fragaria vesca). Nat. Genet. 43: 109–116.
77. Silfverberg-Dilworth, E., C.L. Matasci, W.E. Van de Weg, M.P.W. Van Kaauwen, M. Walser, L.P. Kodde, V. Soglio, L. Gianfranceschi, C.E. Durel, F. Costa et al. (2006) Microsatellite markers spanning the apple (Malus × domestica Borkh.) genome. Tree Genet. Genomes 2: 202–224.
78. Soriano, J.M., C. Romero, S. Vilanova, G. Llacer and M.L. Badenes (2005) Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb.) Lindl.) assessed by SSR markers. Genome 48: 108–114.
79. Sosinski, B., M. Gannavarapu, L.D. Hager, L.E. Beck, G.J. King, C.D. Ryder, S. Rajapakse, W.V. Baird, R.E. Ballard and A.G. Abbott (2000) Characterization of microsatellite markers in peach [Prunus persica (L.) Batsch]. Theor. Appl. Genet. 101: 421–428.
80. Staton, M., T. Zhebentyayeva, B. Olukolu, G.C. Fang, D. Nelson, J.E. Carlson and A.G. Abbott (2015) Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics 16: 744.
81. Struss, D., M. Boritzki, R. Karle and A.F. Iezzoni (2002) Microsatellite markers differentiate eight Giessen cherry rootstocks. HortScience 37: 191–193.
82. Terakami, S., M. Shoda, Y. Adachi, T. Gonai, M. Kasumi, Y. Sawamura, H. Iketani, K. Kotobuki, A. Patocchi, C. Gessler et al. (2006) Genetic mapping of the pear scab resistance gene Vnk of Japanese pear cultivar Kinchaku. Theor. Appl. Genet. 113: 743–752.
83. Terakami, S., Y. Adachi, H. Iketani, Y. Sato, Y. Sawamura, N. Takada, C. Nishitani and T. Yamamoto (2007) Genetic mapping of genes for susceptibility to black spot disease in Japanese pears. Genome 50: 735–741.
84. Terakami, S., T. Kimura, C. Nishitani, Y. Sawamura, T. Saito, T. Hirabayashi and T. Yamamoto (2009) Genetic linkage map of the Japanese pear ‘Housui’ identifying three homozygous genomic regions. J. Japan. Soc. Hort. Sci. 78: 417–424.
85. Terakami, S., C. Nishitani and T. Yamamoto (2013) Development of SNP markers for marker-assisted selection in pear. Acta Hortic. 976: 463–469.
86. Terakami, S., C. Nishitani, M. Kunihisa, K. Shirasawa, S. Sato, S. Tabata, K. Kurita, H. Kanamori, Y. Katayose, N. Takada et al. (2014) Transcriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai). Tree Genet. Genomes 10: 853–863.
87. Testolin, R., T. Marrazzo, G. Cipriani, R. Quarta, I. Verde, M.T. Dettori, M. Pancaldi and S. Sansavini (2000) Microsatellite DNA in peach [Prunus persica (L.) Batsch] and its use in fingerprinting and testing the genetic origin of cultivars. Genome 43: 512–520.
88. van Dyk, M.M., M.K. Soeker, I.F. Labuschagne and D.J.G. Rees (2010) Identification of a major QTL for time of initial vegetative bud-break in apple (Malus × domestica Borkh.). Tree Genet. Genomes 6: 489–502.
89. Velasco, R., A. Zharkikh, J. Affourtit, A. Dhingra, A. Cestaro, A. Kalyanaraman, P. Fontana, S.K. Bhatnagar, M. Troggio, D. Pruss et al. (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat. Genet. 42: 833–839.
90. Verde, I., N. Bassil, S. Scalabrin, B. Gilmore, C.T. Lawley, K. Gasic, D. Micheletti, U.R. Rosyara, F. Cattonaro, E. Vendramin et al. (2012) Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS ONE 7: e35668.
91. Verde, I., A.G. Abbott, S. Scalabrin, S. Jung, S. Shu, F. Marroni, T. Zhebentyayeva, M.T. Dettori, J. Grimwood, F. Cattonaro et al. (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat. Genet. 45: 487–494.
92. Vilanova, S., D.J. Sargent, P. Arús and A. Monfort (2008) Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC Plant Biol. 8: 67.
93. Weber, J.L. and P.E. May (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44: 388–396.
94. Wu, J., Z. Wang, Z. Shi, S. Zhang, R. Ming, S. Zhu, M.A. Khan, S. Tao, S.S. Korban, H. Wang et al. (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 23: 396–408.
95. Wu, J., L.T. Li, M. Li, M.A. Khan, X.G. Li, H. Chen, H. Yin and S.L. Zhang (2014) High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. J. Exp. Bot. 65: 5771–5781.
96. Yamamoto, T., T. Kimura, Y. Sawamura, K. Kotobuki, Y. Ban, T. Hayashi and N. Matsuta (2001) SSRs isolated from apple can identify polymorphism and genetic diversity in pear. Theor. Appl. Genet. 102: 865–870.
97. Yamamoto, T., T. Kimura, M. Shoda, Y. Ban, T. Hayashi and N. Matsuta (2002a) Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). Mol. Ecol. Notes 2: 14–16.
98. Yamamoto, T., T. Kimura, Y. Sawamura, T. Manabe, K. Kotobuki, T. Hayashi, Y. Ban and N. Matsuta (2002b) Simple sequence repeats for genetic analysis in pear. Euphytica 124: 129–137.
99. Yamamoto, T., T. Kimura, M. Shoda, T. Imai, T. Saito, Y. Sawamura, K. Kotobuki, T. Hayashi and N. Matsuta (2002c) Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor. Appl. Genet. 106: 9–18.
100. Yamamoto, T., K. Mochida, T. Imai, Y.Z. Shi, I. Ogihara and T. Hayashi (2002d) Microsatellite markers in peach (Prunus persica (L.) Batsch) derived from an enriched genomic and cDNA libraries. Mol. Ecol. Notes 2: 298–301.
101. Yamamoto, T., K. Mochida and T. Hayashi (2003) Shanhai Suimitsuto, one of the origins of Japanese peach cultivars. J. Japan. Soc. Hort. Sci. 72: 116–121.
102. Yamamoto, T., T. Kimura, T. Saito, K. Kotobuki, N. Matsuta, R. Liebhard, C. Gessler, W.E. van de Weg and T. Hayashi (2004a) Genetic linkage maps of Japanese and European pears aligned to the apple consensus map. Acta Hortic. 663: 51–56.
103. Yamamoto, T., T. Kimura, J. Soejima, T. Sanada, Y. Ban and T. Hayashi (2004b) Identification of quince varieties using SSR markers developed from pear and apple. Breed. Sci. 54: 239–244.
104. Yamamoto, T., M. Yamaguchi and T. Hayashi (2005) An integrated genetic linkage map of peach by SSR, STS, AFLP and RAPD. J. Japan. Soc. Hort. Sci. 74: 204–213.
105. Yamamoto, T., T. Kimura, S. Terakami, C. Nishitani, Y. Sawamura, T. Saito, K. Kotobuki and T. Hayashi (2007) Integrated reference genetic linkage maps of pear based on SSR and AFLP markers. Breed. Sci. 57: 321–329.
106. Yamamoto, T., S. Terakami, S. Moriya, F. Hosaka, K. Kurita, H. Kanamori, Y. Katayose, T. Saito and C. Nishitani (2013) DNA markers developed from genome sequencing analysis in Japanese pear (Pyrus pyrifolia). Acta Hortic. 976: 477–483.
107. Yamamoto, T., S. Terakami, N. Takada, S. Nishio, N. Onoue, C. Nishitani, M. Kunihisa, E. Inoue, H. Iwata, T. Hayashi et al. (2014) Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai). Breed. Sci. 64: 351–361.
108. Zhang, M.Y., L. Fan, Q.Z. Liu, Y. Song, S.W. Wei, S.L. Zhang and J. Wu (2014) A novel set of EST-derived SSR markers for pear and cross-species transferability in Rosaceae. Plant Mol. Biol. Rep. 32: 290–302.
109. Zhang, Q., W. Chen, L. Sun, F. Zhao, B. Huang, W. Yang, Y. Tao, J. Wang, Z. Yuan, G. Fan et al. (2012) The genome of Prunus mume. Nat. Commun. 3: 1318.