Studies using DNA markers in Fragaria × ananassa: Genetic analysis, genome structure, and cultivar identification

Journal of the Japanese Society for Horticultural Science

Volumn 80, Issue 3, 2011, Pages 231-243

  Kunihisa, Miyuki ^a  

^a NATIONAL INSTITUTE OF VEGETABLE AND TEA SCIENCE   (Japan)

Author keywords

Disomic; DNA marker; Genome specific; Octoploid; Validation

Indexed keywords

FRAGARIA; FRAGARIA X ANANASSA;

EID: 79960883355     PISSN: 18823351     EISSN: 1882336X     Source Type: Journal    
DOI: 10.2503/jjshs1.80.231     Document Type: Review

References (70)

1. Albani, M. C., N. H. Battey and M. J. Wilkinson. 2004. The development of ISSR-derived SCAR markers around the seasonal flowering locus (SFL) in Fragaria vesca. Theor. Appl. Genet. 109: 571-579.
2. Amagai, M., K. Tasaki and Y. Kashiwaya. 2007. The method for identification of strawberry (Fragaria × ananassa Duchesne) cultivars detecting polymorphic DNA sequences by multiplex PCR. Japan Patent 2007-252318.
3. AOAC International. 2002. Guidelines for collaborative study procedures to validate characteristics of a method of analyses. http://www.aoac.org/vmeth/omamanual/omamanual.htm.
4. Arnau, G., J. Lallemand and M. Bourgoin. 2003. Fast and reliable strawberry cultivar identification using inter simple sequence repeat (ISSR) amplification. Euphytica 129: 69-79.
5. Arulsekar, S., R. S. Bringhurst and V. Voth. 1981. Inheritance of PGI and LAP isozymes in octoploid cultivated strawberries. J. Amer. Soc. Hort. Sci. 106: 679-683
6. Ashley, M. V., J. A. Wilk, S. M. N. Styan, K. J. Craft, K. L. Jones, K. A. Feldheim, K. S. Lewers and T. L. Ashman. 2003. High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae). Theor. Appl. Genet. 107: 1201-1207.
7. Bassil, N. V., M. Gunn, K. Folta and K. Lewers. 2006. Microsatellite markers for Fragaria from 'Strawberry Festival' expressed sequence tags. Mol. Ecol. Notes 6: 473-476.
8. Bringhurst, R. S. 1990. Cytogenetics and evolution in american Fragaria. HortScience 25: 879-881.
9. Bringhurst, R. S., S. Arulseker and V. Voth. 1979. Electrophoretic characterization of California strawberry cultivars. Hort-Science 14: 439 (Abstr.).
10. Bringhurst, R. S., J. F. Hancock, S. Arulseker and V. Voth. 1978. Characterizing strawberry cultivars by isozyme analysis and some applications. HortScience 13: 358 (Abstr.).
11. Brunings, A. M., C. Moyer, N. Peres and K. M. Folta. 2010. Implementation of simple sequence repeat markers to genotype Florida strawberry varieties. Euphytica 173: 63-75.
12. Byrne, D. and G. Jelenkovic. 1976. Cytological diploidization in the cultivated octoploid strawberry Fragaria × ananassa. Can. J. Genet. Cytol. 18: 653-659.
13. Cekic, C., N. H. Battey and M. J. Wilkinson. 2001. The potential of ISSR-PCR primer-pair combinations for genetic linkage analysis using the seasonal flowering locus in Fragaria as a model. Theor. Appl. Genet. 103: 540-546.
14. Congiu, L., M. Chicca, R. Cella, R. Rossi and G. Bernacchia. 2000. The use of random amplified polymorphic DNA (RAPD) markers to identify strawberry varieties: a forensic application. Mol. Ecol. 9: 229-232.
15. Da Silva, J. A. G. and B. W. S. Sobral. 1996. Genetics of polyploids. p. 3-38. In: B. W. S. Sobral (ed.). The Impact of Plant Molecular Genetics. Birkhäuser, Boston. Da Silva, J. A. G., M. E. Sorrells, W. L. Burnquist and S. D.
16. Da Silva, J. A. G., M. E. Sorrells, W. L. Burnquist and S. D. Tanksley. 1993. RFLP linkage map and genome analysis of Saccharum spontaneum. Genome 36: 782-791.
17. Davis, T. M., L. M. DiMeglio, R. Yang, S. M. N. Styan and K. S. Lewers. 2006. Assessment of SSR marker transfer from the cultivated strawberry to diploid strawberry species: functionality, linkage group assignment and use in diversity analysis. J. Amer. Soc. Hort. Sci. 131: 506-512
18. Degani, C., L. J. Rowland, A. Levi, J. A. Hortynski and G. J. Galletta. 1998. DNA fingerprinting of strawberry (Fragaria × ananassa) cultivars using randomly amplified polymorphic DNA (RAPD) markers. Euphytica 102: 247-253.
19. Degani, C., L. J. Rowland, J. A. Saunders, S. C. Hokanson, E. L. Ogden, A. Golan-Goldhirsh and G. J. Galletta. 2001. A comparison of genetic relationship measures in strawberry (Fragaria × ananassa Duch.) based on AFLPs, RAPDs, and pedigree data. Euphytica 117: 1-12.
20. Federova, N. 1946. Crossability and phylogenetic relations in the main European species of Fragaria. Comp. Rend. Acad. Sci. USSR 53: 545-547.
21. Feldsine, P. T., A. H. Lienau, R. L. Forgey and R. D. Calhoon. 1997. Visual immunoprecipitate assay (VIP) for Listeria monocytogenes and related Listeria species detection in selected foods: collaborative study. J. AOAC Int. 80: 791-805.
22. Feldsine, P. T., A. H. Lienau, S. C. Leung, L. A. Mui, F. Humbert, M. Bohnert, K. Mooijman, S. Schulten, P. I. Veld, P. Rollier, R. Leuschner and K. Capps. 2003. Detection of Salmonella in fresh cheese, poultry products, and dried egg products by the ISO 6579 Salmonella culture procedure and the AOAC official method: collaborative study. J. AOAC Int. 86: 275-295.
23. Gidoni, D., M. Rom, T. Kunik, M. Zur, E. Izsak, S. Izhar and N. Firon. 1994. Strawberry cultivar identification using random amplified polymorphic DNA (RAPD) markers. Plant Breed. 113: 339-342.
24. Govan, C. L., D. W. Simpson, A. W. Johnson, K. R. Tobutt and D. J. Sargent. 2008. A reliable multiplexed microsatellite set for genotyping Fragaria and its use in a survey of 60 F. × ananassa cultivars. Mol. Breeding 22: 649-661.
25. Grattapaglia, D. and R. Sederoff. 1994. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudotestcross: mapping strategy and RAPD markers. Genetics 137: 1121-1137.
26. Halldén, C., M. Hansen, N. O. Nilsson, A. Hjerdin and T. Säll. 1996. Competition as a source of errors in RAPD analysis. Theor. Appl. Genet. 93: 1185-1192.
27. Harrison, R. E., J. J. Luby and G. R. Furnier. 1997. Chloroplast DNA restriction fragment variation among strawberry (Fragaria spp.) taxa. J. Amer. Soc. Hort. Sci. 122: 63-68.
28. Haymes, K. M., B. Henken, T. M. Davis and W. E. Weg. 1997. Identification of RAPD markers linked to a Phytophthora fragariae resistance gene (Rpf1) in the cultivated strawberry. Theor. Appl. Genet. 94: 1097-1101.
29. Ibrahim, A. M. F., K. Sadanaga and E. L. Denisen. 1981. Chromosomal behavior in octoploid strawberry progenies and their parental clones during meiosis. J. Amer. Soc. Hort. Sci. 106: 522-526.
30. Ichijima, K. 1926. Cytological and genetic studies on Fragaria. Genetics 11: 590-604.
31. Kunihisa, M. 2008. Development of genome-specific DNA markers in F. × ananassa and their application to cultivar identification (In Japanese with English summary). Ph.D. Thesis, University of Tsukuba, Tsukuba.
32. Kunihisa, M., N. Fukino and S. Matsumoto. 2005a. CAPS markers improved by cluster-specific amplification for identification of octoploid strawberry (Fragaria × ananassa Duch.) cultivars, and their disomic inheritance. Theor. Appl. Genet. 110: 1410-1418.
33. Kunihisa, M., S. Matsumoto and N. Fukino. 2003. Development of cleavage amplified polymorphic sequence (CAPS) markers for identification of strawberry cultivars. Euphytica 134: 209-215.
34. Kunihisa, M., S. Matsumoto and N. Fukino. 2005b. Cultivar identification of strawberry fruits imported from Korea by use of DNA markers. Bull. Natl. Inst. Veg. Tea Sci. 4: 71-76 (In Japanese with English abstract).
35. Kunihisa, M., H. Ueda, N. Fukino and S. Matsumoto. 2009a. DNA markers for identification of strawberry (Fragaria × ananassa Duch.) cultivars based on probability theory. J. Japan. Soc. Hort. Sci. 78: 211-217.
36. Kunihisa, M., H. Ueda, N. Fukino and S. Matsumoto. 2009b. Genotyping of strawberry (Fragaria × ananassa Duch.) cultivars by DNA markers: Interlaboratory study. J. AOAC Int. 92: 896-906.
37. Lerceteau-Köhler, E., G. Guérin, F. Laigret and B. Denoyes-Rothan. 2003. Characterization of mixed disomic and polysomic inheritance in the octoploid strawberry (Fragaria × ananassa) using AFLP mapping. Theor. Appl. Genet. 107: 619-628.
38. Lewers, K. S., S. M. N. Styan and S. C. Hokanson. 2005. Strawberry GenBank-derived and genomic simple sequence repeat (SSR) markers and their utility with strawberry, blackberry, and red and black raspberry. J. Amer. Soc. Hort. Sci. 130: 102-115.
39. Longley, A. E. 1926. Chromosomes and their significance in strawberry classification. J. Agr. Res. 15: 559-568.
40. MacKey, J. 1970. Significance of mating systems for chromosomes and gametes in polyploids. Hereditas 66: 165-176.
41. MacKey, J. 1987. Implications of polyploidy breeding. Biol. Zent. Bl. 106: 257-266.
42. Martinez-Zapater, J. M. and J. L. Oliver. 1984. Genetic analysis of isozyme loci in tetraploid potatoes (Solanum tuberosum L.). Genetics 108: 669-679.
43. McClure, F. D. 1990. Design and analysis of qualitative collaborative studies: minimum collaborative program. J. AOAC Int. 73: 953-960.
44. Mok, D. W. S. and W. D. Evans. 1971. Chromosome associations at diakinesis in the cultivated strawberry. Can. J. Genet. Cytol. 13: 231-236.
45. Monma, S., S. Okitsu and K. Takada. 1990. Inheritance of everbearing in cultivated strawberry. Bull. Natl. Res. Inst. Veg. Ornam. Plants Tea Jpn. Ser. C1: 21-29 (In Japanese with English abstract).
46. Morishita, M., O. Yamakawa and T. Mochizuki. 1996. Studies on interspecific hybrids of strawberry. Bull. Natl. Res. Inst. Veg. Ornam. Plants Tea Jpn. Ser. A11: 69-95 (In Japanese with English abstract).
47. Noguchi, Y., T. Mochizuki and K. Sone. 2002. Breeding of a new aromatic strawberry by interspecific hybridization, Fragaria × ananassa × F. nilgerrensis. J. Japan. Soc. Hort. Sci. 71: 208-213.
48. Potter, D. 2000. Phylogenetic relationships among species of Fragaria (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. Systematic Botany 25: 337-348.
49. Powers, L. 1944. Meiotic studies of crosses between Fragaria ovalis and F. × ananassa. J. Agr. Res. 69: 435-448.
50. Risch, N. J. and B. Devlin. 1992. On the probability of matching DNA fingerprints. Science 255: 717-720.
51. Rousseau-Gueutin, M., A. Gaston, A. Aïnouche, M. L. Aïnouche, K. Olbricht, G. Staudt, L. Richard and B. Denoyes-Rothan. 2009. Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): New insights from phylogenetic analyses of low-copy nuclear genes. Mol. Phylogen. Evol. 51: 515-530.
52. Rousseau-Gueutin, M., E. Lerceteau-Köhler, L. Barrot, D. J. Sargent, A. Monfort, D. Simpson, P. Arus, G. Guérin and B. Denoyes-Rothan. 2008. 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 179: 2045-2060.
53. Sargent, D. J., J. Clarke, D. W. Simpson, K. R. Tobutt, P. Arus, A. Monfort, S. Vilanova, B. Denoyes-Rothan, M. Rousseau, K. M. Folta, N. V. Bassil and N. H. Battey. 2006. An enhanced microsatellite map of diploid Fragaria. Theor. Appl. Genet. 112: 1349-1359.
54. Sargent, D. J., T. M. Davis, K. R. Tobutt, M. J. Wilkinson, N. H. Battey and D. W. Simpson. 2004a. A genetic linkage map of microsatellite, gene-specific and morphological markers in diploid Fragaria. Theor. Appl. Genet. 109: 1385-1391.
55. Sargent, D. J., F. Fernandéz-Fernandéz, J. J. Ruiz-Roja, B. G. Sutherland, A. Passey, A. B. Whitehouse and D. W. Simpson. 2009. A genetic linkage map of the cultivated strawberry (Fragaria × ananassa) and its comparison to the diploid Fragaria reference map. Mol. Breeding 24: 293-303.
56. Sargent, D. J., A. M. Hadnou, M. J. Wilkinson, N. H. Battey and J. A. Hawkins. 2004b. Cross-species amplification and phylogenetic reconstruction using Fragaria microsatellite primers. Acta Hort. 649: 87-92.
57. Senanayake, Y. D. A. and R. S. Bringhurst. 1967. Origin of Fragaria polyploids. I. Cytological analysis. Am. J. Bot. 54: 221-228.
58. Shimomura, K. and K. Hirashima. 2006. Development and characterization of simple sequence repeats (SSR) as markers to identify strawberry cultivars (Fragaria × ananassa Duch.). J. Japan. Soc. Hort. Sci. 75: 399-402.
59. 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, P. Burns, T. M. Davis, J. P. Slovin, N. Bassil, R. P. Hellens, C. Evans, T. Harkins, C. Kodira, B. Desany, O. R. Crasta, R. V. Jensen, A. C. Allan, T. P. Michael, J. C. Setubal, J. M. Celton, D. J. Rees, K. P. Williams, S. H. Holt, J. J. Ruiz Rojas, M. Chatterjee, B. Liu, H. Silva, L. Meisel, A. Adato, S. A. Filichkin, M. Troggio, R. Viola, T. L. Ashman, H. Wang, P. Dharmawardhana, J. Elser, R. Raja, H. D. Priest, D. W. Jr. Bryant, S. E. Fox, S. A. Givan, L. J. Wilhelm, S. Naithani, A. Christoffels, D. Y. Salama, J. Carter, E. Lopez Girona, A. Zdepski, W. Wang, R. A. Kerstetter, W. Schwab, S. S. Korban, J. Davik, A. Monfort, B. Denoyes-Rothan, P. Arus, R. Mittler, B. Flinn, A. Aharoni, J. L. Bennetzen, S. L. Salzberg, A. W. Dickerman, R. Velasco, M. Borodovsky, R. E. Veilleux and K. M. Folta. 2011. The genome of woodland strawberry (Fragaria vesca). Nat. Genet. 43: 109-116.
60. Spigler, R. B., K. S. Lewers, D. S. Malin and T-L. Ashman. 2008. Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome. Heredity 101: 507-517.
61. Stebbins, G. L. 1971. Chromosomal evolution in higher plants. Edward Arnold Ltd., London.
62. Sugimoto, T., K. Tamaki, J. Matsumoto, Y. Yamamoto, K. Shiwaku and K. Watanabe. 2005. Detection of RAPD markers linked to the everbearing gene in Japanese cultivated strawberry. Plant Breed. 124: 498-501.
63. This, P., A. Jung, P. Boccacci, J. Borrego, R. Botta, L. Costantini, M. Crespan, G. S. Dangl, C. Eisenheld, F. Ferreira-Monteiro, S. Grando, J. Ibaňez, T. Lacombe, V. Laucou, R. Magalhães, C. P. Meredith, N. Milani, E. Peterlunger, F. Regner, L. Zulini and E. Maul. 2004. Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor. Appl. Genet. 109: 1448-1458.
64. Truong, C., A. E. Palme, F. Felber and Y. Naciri-Graven. 2005. Isolation and characterization of microsatellite markers in the tetraploid birch, Betula pubescens ssp. tortuosa. Mol. Ecol. Notes 5: 96-98.
65. Tyrka, M., P. Dziadczyk and J. A. Hortyňski. 2002. Simplified AFLP procedure as a tool for identification of strawberry cultivars and advanced breeding lines. Euphytica 125: 273-280.
66. Ukai, Y. 2004. Theory of cultivar identification. Agric. Hortic. (Nogyo-oyobi-engei) 79: 194-198 (In Japanese).
67. Wall, A. M., R. Riley and M. D. Gale. 1971. Position of a locus on chromosome 5B of Triticum-Aestivum affecting homoeologous meiotic pairing. Genet. Res. 18: 329-339.
68. Weebadde, C. K., D. Wang, C. E. Finn, K. S. Lewers, J. J. Luby, J. Bushakra, T. M. Sjulin and J. F. Hancock. 2008. Using a linkage mapping approach to identify QTL for day-neutrality in the octoploid strawberry. Plant Breed. 127: 94-101.
69. Wu, K. K., W. Burnquist, M. E. Sorrells, T. L. Tew, P. H. Moore and S. D. Tanksley. 1992. The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor. Appl. Genet. 83: 294-300.
70. Yanagi, T., K. E. Hummer, T. Iwata, K. Sone, P. Nathewet and T. Takamura. 2010. Aneuploid strawberry (2n = 8x + 2 = 58) was developed from homozygous unreduced gamete (8x) produced by second division restitution in pollen. Sci. Hortic. 125: 123-128.