Molecular genetics and genomics of the Rosoideae: State of the art and future perspectives

Horticulture Research

Volumn 1, Issue , 2014, Pages

  Longhi, Sara ^a   Giongo, Lara ^a   Buti, Matteo ^a   Surbanovski, Nada ^a   Viola, Roberto ^a   Velasco, Riccardo ^a   Award, Judson ^b   Sargent, Daniel J ^a  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b Driscoll's Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84907969352     PISSN: None     EISSN: 20527276     Source Type: Journal    
DOI: 10.1038/hortres.2014.1     Document Type: Review

References (162)

1. Hutchinson J. The genera of flowering plants, vol. 1, Dicotyledons. Oxford: Clarendon Press, 1964.
2. Schulze-Menz GK. Rosaceae. Berlin: Gebru der Borntraeger, 1964.
3. Morgan DR, Soltis DE, Robertson KR. Systematic and evolutionary implications of rbcL sequence variation in Rosaceae. Am J Bot 1994; 81: 890-903.
4. Potter D, Gao F, Bortiri PE, Oh SH, Baggett S. Phylogenetic relationships in Rosaceae inferred from chloroplast matK and trnL-TrnF nucleotide sequence data. Plant Syst Evol 2002; 231: 77-89.
5. Potter D, Eriksson T, Evans RC et al. Phylogeny and classification of Rosaceae. Plant Syst Evol 2007; 266: 5-43.
6. Staudt G. The species Fragaria, their taxonomy and geographical distribution.
7. Acta Hort 1989; 265: 23-33.
8. Rajapakse S, Byrne DH, Zhang L, Anderson N, Arumuganathan K, Ballard RE. Two genetic linkage maps of tetraploid roses. Theor Appl Genet 2001; 103: 575-583.
9. Eriksson T, Donoghue MJ, Hibbs MS. Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Syst Evol 1998; 211: 155-179.
10. Alice LA, Campbell CS. Phylogeny of Rubus (Rosaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Am J Bot 1999; 86: 81-97.
11. Njuguna W, Liston A, Cronn R, Ashman TL, Bassil N. Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing. Mol Phylogenet Evol 2013; 66: 17-29.
12. Matsumoto S, Kouchi M, Yabuki J, Kusunoki M, Ueda Y, Fukui H. Phylogenetic analyses of the genus Rosa using the matK sequence: molecular evidence for the narrow genetic background of modern roses. Sci Hort 1998; 77: 73-82.
13. Zimmermann H, Ritz CM, Hirsch H, Renison D, Wesche K, Hensen I. Highly reduced genetic diversity of Rosa rubiginosa L. populations in the invasive range. Int J Plant Sci 2010; 171: 435-446.
14. Rajapakse S, Zhang L, Ballard RE, Byrne DH. AFLP marker development in rose for genetic mapping: comparison of three restriction enzyme pairs. Acta Hort 2001; 546: 619-627.
15. Iwatsubo Y, Naruhashi N. Karyotypes of three species of Fragaria (Rosaceae). Cytologia 1989; 54: 493-497.
16. Iwatsubo Y, Naruhashi N. Cytotaxonomical studies of Rubus (Rosaceae) I. Chromosome numbers of 20 species and 2 natural hybrids. J Jpn Bot 1992; 67: 270-275.
17. Akasaka M, Ueda Y, Koba T. Karyotype analysis of wild rose species belonging to septets B, C, and D by molecular cytogenetic method. Breeding Sci 2003; 53: 177-182.
18. Nathewet P, Yanagi T, Hummer KE, Iwatsubo Y, Sone K. Karyotype analysis in wild diploid, tetraploid and hexaploid strawberries, Fragaria (Rosaceae). Cytologia 2009; 74: 355-364.
19. Potter D, Still SM, Grebenc T et al. Phylogenetic relationships in tribe Spiraeeae (Rosaceae) inferred from nucleotide sequence data. Plant Syst Evol 2007; 266: 105-118.
20. Thompson MM. Survey of chromosome numbers in Rubus (Rosaceae:Rosoideae). Ann Missouri Bot Garden 1997; 84: 128-164.
21. Sargent DJ, Davis TM, Tobutt KR, WilkinsonMJ, Battey NH, Simpson DW. A genetic linkagemap of microsatellite, gene-specific and morphological markers in diploid Fragaria. Theor Appl Genet 2004; 109: 1385-1391.
22. Randell RA, Howarth DG, Morden CW. Genetic analysis of natural hybrids between endemic and alien Rubus (Rosaceae) species in Hawaii. Conserv Genet 2004; 5: 217-230.
23. Bringhurst RS, Voth V. Breeding octoploid strawberries. Iowa State J Res 1984; 58: 371-381.
24. Yokoya K, Roberts AV, Mottley J, Lewis R, Brandham PE. Nuclear DNA amounts in roses. Ann Bot 2000; 85: 557-561.
25. Dickson EE, Arumuganathan K, Kresovich S, Doyle JJ. Nuclear-DNA content variation within the Rosaceae. Am J Bot 1992; 79: 1081-1086.
26. Meng RG, Finn C. Determining ploidy level and nuclear DNA content in Rubus by flow cytometry. J Am Soc Hort Sci 2002; 127: 767-775.
27. Akiyama Y, Yamamoto Y, Ohmido N, Ohshima M, Fukui K. Estimation of the nuclear DNA content of strawberries (Fragaria spp.) compared with Arabidopsis thaliana by using dual-step flow cytometry. Cytologia 2001; 66: 431-436.
28. Bennett LE, Burkhead JL, Hale KL, Terry N, Pilon M, Pilon-Smits EA. Analysis of transgenic Indian mustard plants for phytoremediation of metal-contaminated mine tailings. J Environ Qual 2003; 32: 432-440.
29. Debener T, Janakiram T, Mattiesch L. Sports and seedlings of rose varieties analysed with molecular markers. Plant Breeding 2000; 119: 71-74.
30. Congiu L, Chicca M, Cella R, Rossi R, Bernacchia G. The use of random amplified polymorphic DNA (RAPD) markers to identify strawberry varieties: A forensic application. Mol Ecol 2000; 9: 229-232.
31. Parent JG, Fortin MG, Page D. Identification of raspberry cultivars by random amplified polymorphic DNA (RAPD) analysis. Can J Plant Sci 1993; 73: 1115-1122.
32. KoopmanWJ, Wissemann V, de Cock K et al. AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae). Am J Bot 2008; 95: 353-366.
33. Degani C, Rowland LJ, Saunders JA et al. A comparison of genetic relationship measures in strawberry (Fragaria 3ananassa Duch.) based on AFLPs, RAPDs, and pedigree data. Euphytica 2001; 117: 1-12.
34. Graham J, McNicol RJ. An examination of the ability of RAPD markers to determine the relationships within and between Rubus species. Theor App Genet 1995; 90: 1128-1132.
35. Debnath SC. Inter-simple sequence repeat (ISSR)-PCR analysis to assess genetic diversity in a collection of wild cloudberry (Rubus chamaemorus L.) clones. J Hort Sci Biotech 2007; 82: 727-732.
36. Davis TM, Yu H. A linkage map of the diploid strawberry, Fragaria vesca. J Hered 1997; 88: 215-221.
37. Debener T, Mattiesch L. Construction of a genetic linkage map for roses using RAPD and AFLP markers. Theor Appl Genet 1999; 99: 891-899.
38. Graham J, Smith K, MacKenzie K, Jorgenson L, Hackett C, Powell W. 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 2004; 109: 740-749.
39. Eriksson O, Bremer B. Genet dynamics of the clonal plant Rubus-saxatilis. J Ecol 1993; 81: 533-542.
40. Harrison RE, Luby JJ, Furnier GR. Chloroplast DNA restriction fragment variation among strawberry (Fragaria spp) taxa. J Am Soc Hort Sci 1997; 122: 63-68.
41. Graham J, Smith K, Woodhead M, Russell J. Development and use of simple sequence repeat SSR markers in Rubus species. Mol Ecol Notes 2002; 2: 250-252.
42. Sargent DJ, Hadonou AM, Simpson DW. Development and characterization of polymorphic microsatellite markers from Fragaria viridis, a wild diploid strawberry. Mol Ecol Notes 2003; 3: 550-552.
43. Kimura T, Nishitani C, Iketani H, Ban Y, Yamamoto T. Development of microsatellite markers in rose. Mol Ecol Notes 2006; 6: 810-812.
44. Lewers KS, Styan SM, Hokanson SC, Bassil NV. Strawberry GenBank-derived and genomic simple sequence repeat (SSR) markers and their utility with strawberry, blackberry, and red and black raspberry. J Am Soc Hort Sci 2005; 130: 102-115.
45. Park YH, Ahn SG, Choi YM et al. Rose (Rosa hybrida L.) EST-derived microsatellite markers and their transferability to strawberry (Fragaria spp.). Sci Hort 2010; 125: 733-739.
46. Woodhead M, McCallum S, Smith K, Cardle L, Mazzitelli L, Graham J. Identification, characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs. Mol Breed 2008; 22: 555-563.
47. Shulaev V, Sargent DJ, Crowhurst RN et al. The genome of woodland strawberry (Fragaria vesca). Nat Genet 2011; 43: 109-116.
48. Sargent DJ, Passey T, Surbanovski N et al. A microsatellite linkage map for the cultivated strawberry (Fragaria 3ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection. Theor Appl Genet 2012; 124: 1229-1240.
49. Isobe SN, Hirakawa H, Sato S et al. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria x ananassa) and its applicability. DNA Res 2013; 20: 79-92.
50. Dobes C, Scheffknecht S. Isolation and characterization of microsatellite loci for the Potentilla core group (Rosaceae) using 454 sequencing. Mol Ecol Resour 2012; 12: 726-739.
51. Govan CL, Simpson DW, Johnson AW, Tobutt KR, Sargent DJ. A reliable multiplexed microsatellite set for genotyping Fragaria and its use in a survey of 60 F. x ananassa cultivars. Mol Breeding 2008; 22: 649-661.
52. Brunings AM, Moyer C, Peres N, Folta KM. Implementation of simple sequence repeatmarkers to genotype Florida strawberry varieties. Euphytica 2010; 173: 63-75.
53. Chambers A, Carle S, Njuguna W et al. A genome-enabled, high-Throughput, and multiplexed fingerprinting platform for strawberry (Fragaria L.). Mol Breeding 2013; 31: 615-629.
54. Esselink GD, Smulders MJ, Vosman B. Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theor App Genet 2003; 106: 277-286.
55. Scariot V, Akkak A, Botta R. Characterization and genetic relationships of wild species and old garden roses based on microsatellite analysis. J Am Soc Hort Sci 2006; 131: 66-73.
56. Dossett M, Bassil NV, Lewers KS, Finn CE. Genetic diversity in wild and cultivated black raspberry (Rubus occidentalis L.) evaluated by simple sequence repeat markers. Genet Resour Crop Ev 2012; 59: 1849-1865.
57. Fernandez-Fernandez F, Antanaviciute L, Govan CL, Sargent DJ. Development of a multiplexed microsatellite set for fingerprinting red raspberry (Rubus idaeus) germplasm and its transferability to other Rubus species. J Berry Res 2011, 1: 177-187.
58. Bassil NV, Nyberg A, Hummer KE, Graham J, Dossett M, Finn CE. A universal fingerprinting set for red raspberry. Acta Hort 2012; 946: 83-87.
59. Dirlewanger E, Cosson P, TavaudMet al. 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 App Genet 2002; 105: 127-138.
60. Gasic K, Han Y, Kertbundit S et al. Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Mol Breed 2009; 23: 397-411.
61. Davis TM, DiMeglio LM, Yang R, Styan SM, Lewers KS. Assessment of SSR marker transfer from the cultivated strawberry to diploid strawberry species: functionality, linkage group assignment, and use in diversity analysis. J Am Soc Hort Sci 2006; 131: 506-512.
62. Zorrilla-Fontanesi Y, Cabeza A, Torres AM et al. Development and bin mapping of strawberry genic-SSRs in diploid Fragaria and their transferability across the Rosoideae subfamily. Mol Breed 2011; 27: 137-156.
63. Zorrilla-Fontanesi Y, Cabeza A, Dominguez P et al. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria 3ananassa). Theor App Genet 2011; 123: 755-778.
64. Marulanda M, Lopez AM, Uribe M. Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers. Genet Mol Res 2012; 11: 322-331.
65. Rousseau-Gueutin M, Richard L, Le Dantec L, Caron H, Denoyes-Rothan B.t Development, mapping and transferability of Fragaria EST-SSRs within the Rosodae supertribe. Plant Breed 2011; 130: 248-255.
66. Koning-Boucoiran CF, Gitonga VW, Yan Z et al. The mode of inheritance in tetraploid cut roses. Theor Appl Genet 2012; 125: 591-607.
67. Vilanova S, Sargent DJ, Arus P, Monfort A. Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC Plant Biol 2008; 8: 67.
68. Bushakra JM, Stephens MJ, Atmadjaja AN et al. Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Theor Appl Genet 2012; 125: 311-327.
69. Hubbard M, Kelly J, Rajapakse S, Abbott A, Ballard R. Restriction-fragment-lengthpolymorphisms in rose and their use for cultivar identification. Hortscience 1992; 27: 172-173.
70. Fulton TM, van der Hoeven R, Eannetta NT, Tanksley SD. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 2002; 14: 1457-1467.
71. Cabrera A, Kozik A, Howad W, Arus P, Iezzoni AF, van der Knaap E. Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers. BMC Genomics 2009; 10: 562.
72. Yan Z, Denneboom C, Hattendorf A et al. Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Theor Appl Genet 2005; 110: 766-777.
73. Folta KM, Staton M, Stewart PJ et al. Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria 3 ananassa). BMC Plant Biol 2005; 5: 12.
74. Ge AJ, Han J, Li XD et al. Characterization of SNPs in strawberry cultivars in China. Genet Mol Res 2013; 12: 639-645.
75. Zhang J, Esselink GD, Che D, Fougere-Danezan M, Arens P, Smulders MJ. The diploid origins of allopolyploid rose species studied using single nucleotide polymorphism haplotypes flanking a microsatellite repeat. J Hort Sci Biotechnol 2013; 88: 85-92.
76. Illa E, Sargent DJ, Girona EL et al. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol Biol 2011; 11: 9.
77. Ruiz-Rojas JJ, Sargent DJ, Shulaev V et al. SNP discovery and genetic mapping of TDNA insertional mutants in Fragaria vesca L. Theor App Genet 2010; 121: 449-463.
78. Kunihisa M, Fukino N, Matsumoto S. Development of cleavage amplified polymorphic sequence (CAPS) markers for identification of strawberry cultivars. Euphytica 2003; 134: 209-215.
79. Celton JM, Christoffels A, Sargent DJ, Xu X, Rees DJ, Xu XM. Genome-wide SNP identification by high-Throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map. BMC Biol 2010, 8: 155.
80. Ward JA, Bhangoo J, Fernandez-Fernandez F et al. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genomeindependent imputation. BMC Genomics 2013; 14: 2.
81. Koning-Boucoiran CF, Smulders MJ, Krens FA, Esselink GD, Maliepaard C. SNP genotyping in tetraploid cut roses. Acta Hort 2012; 953: 351-356.
82. Elshire RJ, Glaubitz JC, Sun Q et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. Plos ONE 2011; 6: e19379.
83. Cronn R, Knaus BJ, Liston A et al. Targeted enrichment strategies for nextgeneration plant biology. Am J Bot 2012; 99: 291-311.
84. Tennessen JA, Govindarajulu R, Liston A, Ashman TL. Targeted sequence capture provides insight into genome structure and genetics of male sterility in a gynodioecious diploid strawberry, Fragaria vesca subsp. bracteata (Rosaceae). G3 2013; 3: 1341-1351.
85. Bassil NH. Development and preliminary evaluation of the IStraw90 AxiomH array in cultivated strawberry (Fragaria 3ananassa). In: Proceedings of American Society for Horticultural Science Annual Conference; 22-25 July; Palm Desert, CA, USA. ASHS: Alexandria, VA, USA, 2013; 17.
86. Antanaviciute L, Fernandez-Fernandez F, Jansen J et al. Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC Genom 2012; 13: 203.
87. Verde I, Bassil N, Scalabrin S et al. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. Plos ONE 2012; 7: e35668.
88. Peace C, Bassil N, Main D et al. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. Plos ONE 2012; 7: e48305.
89. Deng C, Davis TM. Molecular identification of the yellow fruit color (c) locus in diploid strawberry: A candidate gene approach. Theor Appl Genet 2001; 103: 316-322.
90. Sargent DJ, Clarke J, Simpson DW et al. An enhanced microsatellite map of diploid Fragaria. Theor Appl Genet 2006; 112: 1349-1359.
91. Sargent DJ, Rys A, Nier S, Simpson DW, Tobutt KR. The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera. Theor Appl Genet 2007; 114: 373-384.
92. Sargent DJ, Cipriani G, Vilanova S et al. The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map. Genome 2008; 51: 120-127.
93. Illa E, Sargent DJ, Girona EL et al. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol Biol 2011, 11: 9.
94. Sargent DJ, Kuchta P, Girona EL et al. Simple sequence repeat marker development and mapping targeted to previously unmapped regions of the strawberry genome sequence. Plant Genome 2011; 4: 165-177.
95. Darrow GM. The strawberry: history, breeding and physiology. New York: Holt, Rinehart and Winston, 1966.
96. Bringhurst RS. Cytogenetics and evolution in american Fragaria. Hortscience 1990; 25: 879-881.
97. Lerceteau-Kohler E, Guerin G, Laigret F, Denoyes-Rothan B. Characterization of mixed disomic and polysomic inheritance in the octoploid strawberry (Fragaria3 ananassa) using AFLP mapping. Theor Appl Genet 2003; 107: 619-628.
98. Spigler RB, Lewers KS, Main DS, Ashman TL. Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome. Heredity 2008; 101: 507-517.
99. van Dijk T, Noordijk Y, Dubos T et al. Microsatellite allele dose and configuration establishment (MADCE): An integrated approach for genetic studies in allopolyploids. BMC Plant Biol 2012; 12: 25.
100. Rousseau-Gueutin M, Lerceteau-Kohler E, Barrot L et al. Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics 2008; 179: 2045-2060.
101. Spigler RB, Lewers KS, Johnson AL, Ashman TL. Comparative mapping reveals autosomal origin of sex chromosome in octoploid Fragaria virginiana. J Hered 2010; 101: S107-S117.
102. Sargent DJ, Fernandez-Fernandez F, Ruiz-Roja JJ et al. A genetic linkage map of the cultivated strawberry (Fragaria 3ananassa) and its comparison to the diploid Fragaria reference map. Mol Breed 2009; 24: 293-303.
103. Zorrilla-Fontanesi Y, Rambla JL, Cabeza A et al. Genetic analysis of strawberry fruit aroma and identification of O-methyltransferase FaOMT as the locus controlling natural variation in mesifurane content. Plant Physiol 2012; 159: 851-870.
104. Haymes KM, Henken B, Davis TM, van de Weg WE. Identification of RAPD markers linked to a Phytophthora fragariae resistance gene (Rpf1) in the cultivated strawberry. Theor Appl Genet 1997, 94: 1097-1101.
105. Haymes KM, van de Weg WE, Arens P, Maas JL, Vosman B, den Nijs AP. Development of SCAR markers linked to a Phytophthora fragariae resistance gene and their assessment in European and North American strawberry genotypes. J Am Soc Hort Sci 2000; 125: 330-339.
106. Whitaker VM. Applications of molecular markers in strawberry. J Berry Res 2011; 1: 115-127.
107. Lerceteau-Köhler E, Moing A, Guerin G et al. QTL analysis for fruit quality traits and resistance to Colletotrichum acutatum and Phytophthora cactorum in octoploid strawberry (Fragaria 3 ananassa). Acta Hort 2004; 649: 93-97.
108. Lerceteau-Kohler E, Guerin G, Denoyes-Rothan B. Identification of SCAR markers linked to Rca2 anthracnose resistance gene and their assessment in strawberry germplasm. Theor Appl Genet 2005; 111: 862-870.
109. Sugimoto T, Tamaki K, Matsumoto J, Yamamoto Y, Shiwaku K, Watanabe K. Detection of RAPD markers linked to the everbearing gene in Japanese cultivated strawberry. Plant Breed 2005; 124: 498-501.
110. Weebadde CK, Wang D, Finn CE et al. Using a linkage mapping approach to identify QTL for day-neutrality in the octoploid strawberry. Plant Breed 2008; 127: 94-101.
111. Gaston A, Perrotte J, Lerceteau-Kohler E et al. PFRU, a single dominant locus regulates the balance between sexual and asexual plant reproduction in cultivated strawberry. J Exp Bot 2013; 64: 1837-1848.
112. Lerceteau-Köhler E, Moing A, Guerin G et al. Genetic dissection of fruit quality traits in the octoploid cultivated strawberry highlights the role of homoeo-QTL in their control. Theor Appl Genet 2012; 124: 1059-1077.
113. Graham J, Smith K, Tierney I, MacKenzie K, Hackett CA. Mapping gene H controlling cane pubescence in raspberry and its association with resistance to cane botrytis and spur blight, rust and cane spot. Theor Appl Genet 2006; 112: 818-831.
114. Jennings DL. Balanced lethals and polymorphism in Rubus idaeus. Heredity 1967; 22: 465-479.
115. Jennings DL. Resistance to Didymella-Applanata in red raspberry and some related species. Ann Appl Biol 1982; 101: 331-333.
116. Jennings DL, Brydon E. Further-studies on resistance to Leptosphaeriaconiothyrium in the red raspberry and related species. Ann Appl Biol 1989; 115: 499-506.
117. Jennings DL. Some evidence on the influence of the morphology of raspberry canes upon their ability to be attacked by certain fungi. Hort Res 1962; 1: 100-111.
118. Jennings DL, McGregor GR. Resistance to cane spot (Elsinoe-veneta) in the red raspberry and its relationship to resistance to yellow rust (Phragmidium-rubiidaei). Euphytica 1988; 37: 173-180.
119. Anthony VM, Williamson B, Jennings DL, Shattock RC. Inheritance of resistance to yellow rust (Phragmidium-rubi-idaei) in red raspberry. Ann Appl Biol 1986; 109: 365-374.
120. Graham J, Hackett CA, Smith K, Woodhead M, Hein I, McCallum S. Mapping QTLs for developmental traits in raspberry from bud break to ripe fruit. Theor Appl Genet 2009; 118: 1143-1155.
121. McCallum S, Woodhead M, Hackett CA, Kassim A, Paterson A, Graham J. Genetic and environmental effects influencing fruit colour and QTL analysis in raspberry. Theor Appl Genet 2010; 121: 611-627.
122. Woodhead M, Williamson S, Smith K et al. Identification of quantitative trait loci for cane splitting in red raspberry (Rubus idaeus). Mol Breed 2013; 31: 111-122.
123. Woodhead M, Weir A, Smith K, McCallum S, MacKenzie K, Graham J. Functional markers for red raspberry. J Am Soc Hort Sci 2010; 135: 418-427.
124. Keep E. Dwarfing in the raspberry, Rubus idaeus L. Euphytica 1968; 18: 256-276.
125. Pattison JA, Samuelian SK, Weber CA. Inheritance of Phytophthora root rot resistance in red raspberry determined by generation means and molecular linkage analysis. Theor Appl Genet 2007; 115: 225-236.
126. Bushakra JM, Krieger C, Deng D et al. QTL involved in the modification of cyanidin compounds in black and red raspberry fruit. Theor Appl Genet 2013; 126: 847-865.
127. Kassim A, Poette J, Paterson A et al. Environmental and seasonal influences on red raspberry anthocyanin antioxidant contents and identification of quantitative traits loci (QTL). Mol Nutr Food Res 2009; 53: 625-634.
128. Castro P, Stafne ET, Clark JR, Lewers KS. Genetic map of the primocane?fruiting and thornless traits of tetraploid blackberry. Theor Appl Genet 2013; 126: 2521-2532.
129. Crespel L, Zhang D, Meynet J, Gudin S. Estimation of heterozygosity in two botanic rose species using AFLP markers. Acta Hort 2001; 546: 187-191.
130. Hibrand-Saint Oyant L, Crespel L, Rajapakse S, Zhang L, Foucher F. Genetic linkage maps of rose constructed with new microsatellite markers and locating QTL controlling flowering traits. Tree Genet Genomes 2008; 4: 11-23.
131. Linde M, Hattendorf A, Kaufmann H, Debener T. Powdery mildew resistance in roses: QTL mapping in different environments using selective genotyping. Theor Appl Genet 2006; 113: 1081-1092.
132. Shupert DA, Byrne DH, Pemberton HB. Inheritance of flower traits, leaflet number and prickles in roses. Acta Hort 2007; 751: 331-335.
133. Spiller M, Linde M, Hibrand-Saint Oyant L et al. Towards a unified genetic map for diploid roses. Theor Appl Genet 2011; 122: 489-500.
134. Ma Y, Crane CF, Byrne DH. Meiotic behavior in a tetraploid rose and its hybrid progeny. Hortscience 2000; 35: 1127-1131.
135. Gar O, Sargent DJ, Tsai CJ et al. An autotetraploid linkage map of rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence. Plos ONE 2011, 6: e20463.
136. Bonet R, Girona EL, Sargent DJ et al. The development and characterisation og a bacterial artificial chromosome library for Fragaria vesca. BMC Res Notes 2009; 2: 188.
137. Pontaroli AC, Rogers RL, Zhang Q et al. Gene content and distribution in the nuclear genome of Fragaria vesca. Plant Genome 2009; 2: 93-101.
138. Kaufmann H, Mattiesch L, Lorz H, Debener T. 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 Genom 2003; 268: 666-674.
139. Hein I, Williamson S, Russell J, Powell W. Isolation of high molecular weight DNA suitable for BAC library construction from woody perennial soft-fruit species. Biotechniques 2005; 38: 69-71.
140. Graham J, Hackett CA, Smith K et al. Towards an understanding of the nature of resistance to Phytophthora root rot in red raspberry. Theor Appl Genet 2011; 123: 585-601.
141. Biber A, Kaufmann H, Linde M, Spiller M, Terefe D, Debener T. Molecular markers from a BAC contig spanning the Rdr1 locus: A tool for marker-Assisted selection in roses. Theor Appl Genet 2010; 120: 765-773.
142. Terefe-Ayana D, Kaufmann H, Linde M, Debener T. Evolution of the Rdr1 TNLcluster in roses and other Rosaceous species. BMC Genomics 2012; 13: 409.
143. Potter D, Luby JJ, Harrison RE. Phylogenetic relationships among species of Fragaria (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. Syst Bot 2000; 25: 337-348.
144. Salamone I, Govindarajulu R, Falk S, Parks M, Liston A, Ashman TL. Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries. Am J Bot 2013; 100: 939-950.
145. Ferrarini M, Moretto M, Ward JA et al. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. BMC Genom 2013; 14: 670.
146. Hamilton JP, Buell CR. Advances in plant genome sequencing. Plant J 2012; 70: 177-190.
147. Jung S, Cestaro A, TroggioMet al. Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. BMC Genom 2012; 13: 129.
148. Koskela EA, Mouhu K, Albani MC et al. Mutation in TERMINAL FLOWER1 reverses the photoperiodic requirement for flowering in the wild strawberry Fragaria vesca. Plant Physiol 2012; 159: 1043-1054.
149. Ward JA, Price J, Clement MJ et al. Draft assembly and analysis of the highly heterozygous diploid red raspberry genome. In: Proceedings of Plant and Animal Genome XX Conference; 14-18 January 2012; San Diego, CA, USA. Sherago International, NJ, USA, 2012; 315.
150. Bassil N, Gilmore B, Dossett M et al. Developing genomics resources in black raspberry. In: Rosaceous Genomics Conference 6; 30 September-4 October 2012; Mezzocorona (Trento), Italy. Fondazione Edmund Mach: San Michele all'Adige, Italy, 2012; 48.
151. Geoff W, Michael K, Dmitry P, Tim B, John L. Production of long (1.5kb-15.0kb), accurate, DNA sequencing reads using an Illumina HiSeq2000 to support de novo assembly of the blue catfish genome. In: Proceedings of Plant and Animal Genome XXI Conference; 12-16 January 2013; San Diego, CA, USA. Sherago International, NJ, USA, 2013; 487.
152. Iwata H, Gaston A, Remay A et al. The TFL1 homologue KSN is a regulator of continuous flowering in rose and strawberry. Plant J 2012; 69: 116-125.
153. Albani MC, Battey NH, Wilkinson MJ. The development of ISSR-derived SCAR markers around the SEASONAL FLOWERING LOCUS (SFL) in Fragaria vesca. Theor Appl Genet 2004; 109: 571-579.
154. Nier S, Simpson DW, Tobutt KR, Sargent DJ. A genetic linkage map of an interspecific diploid Fragaria BC1 mapping population and its comparison with the Fragaria reference map (FV3FN). J Hort Sci Biotechnol 2006; 81: 645-650.
155. Brown T, Wareing PF. The genetical control of the everbearing habit and three other characters in varieties of Fragaria vesca. Euphytica 1965; 14: 97-112.
156. Remay A, Lalanne D, Thouroude T, Le Couviour F, Hibrand-Saint Oyant L, Foucher F. A survey of flowering genes reveals the role of gibberellins in floral control in rose. Theor Appl Genet 2009; 119: 767-781.
157. Kawamura K, Oyant LH, Crespel L, Thouroude T, LalanneD, Foucher F. Quantitative trait loci for flowering time and inflorescence architecture in rose. Theor Appl Genet 2011; 122: 661-675.
158. Folta KM, Clancy MA, Chamala S et al. A transcript accounting from diverse tissues of a cultivated strawberry. Plant Genome 2010; 3: 90-105.
159. Ward JA, Ponnala L, Weber CA. Strategies for transcriptome analysis in nonmodel plants. Am J Bot 2012; 99: 267-276.
160. Dubois A, Carrere S, Raymond O et al. Transcriptome database resource and gene expression atlas for the rose. BMC Genom 2012; 13: 11.
161. Kim J, Park JH, Lim CJ et al. Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. BMC Genom 2012; 13: 18.
162. Kang CY, Darwish O, Geretz A, Shahan R, Alkharouf N, Liu ZC. Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. Plant Cell 2013; 25: 1960-1978.